diff --git a/main/404.html b/main/404.html
index cbaca5770..3c4518486 100644
--- a/main/404.html
+++ b/main/404.html
@@ -42,6 +42,17 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/teal.modules.clinical/news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="https://insightsengineering.github.io/teal.modules.clinical/coverage-report/">Coverage report</a></li>
diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html
index f6031bd2d..23598b019 100644
--- a/main/CODE_OF_CONDUCT.html
+++ b/main/CODE_OF_CONDUCT.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index f6d2a0f9f..b37340db6 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html
index 37613676d..85c755bed 100644
--- a/main/LICENSE-text.html
+++ b/main/LICENSE-text.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/SECURITY.html b/main/SECURITY.html
index 05e0fe1e8..bf2919277 100644
--- a/main/SECURITY.html
+++ b/main/SECURITY.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/articles/generate_tmc_test_data.html b/main/articles/generate_tmc_test_data.html
index 950c97eae..7a7287d08 100644
--- a/main/articles/generate_tmc_test_data.html
+++ b/main/articles/generate_tmc_test_data.html
@@ -42,6 +42,17 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/articles/index.html b/main/articles/index.html
index 0502a26d4..30cea7c5e 100644
--- a/main/articles/index.html
+++ b/main/articles/index.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/articles/quickstart_substitute.html b/main/articles/quickstart_substitute.html
index 34f1cc668..eb3ddfcd2 100644
--- a/main/articles/quickstart_substitute.html
+++ b/main/articles/quickstart_substitute.html
@@ -42,6 +42,17 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/articles/teal-modules-clinical.html b/main/articles/teal-modules-clinical.html
index ff0cb23cb..3cce95eac 100644
--- a/main/articles/teal-modules-clinical.html
+++ b/main/articles/teal-modules-clinical.html
@@ -42,6 +42,17 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/authors.html b/main/authors.html
index 0f1ebdec7..7ba257f56 100644
--- a/main/authors.html
+++ b/main/authors.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/index.html b/main/index.html
index b451f99ec..0695ceaca 100644
--- a/main/index.html
+++ b/main/index.html
@@ -44,6 +44,17 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
diff --git a/main/news/index.html b/main/news/index.html
index 54c84ab55..4116c3361 100644
--- a/main/news/index.html
+++ b/main/news/index.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/add_expr.html b/main/reference/add_expr.html
index 696202016..a5207b52b 100644
--- a/main/reference/add_expr.html
+++ b/main/reference/add_expr.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/arm_ref_comp_observer.html b/main/reference/arm_ref_comp_observer.html
index 086af9333..df1bc0a29 100644
--- a/main/reference/arm_ref_comp_observer.html
+++ b/main/reference/arm_ref_comp_observer.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/as_num.html b/main/reference/as_num.html
index c52a54eef..10f2822f0 100644
--- a/main/reference/as_num.html
+++ b/main/reference/as_num.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/bracket_expr.html b/main/reference/bracket_expr.html
index 2328930ec..2d61481a6 100644
--- a/main/reference/bracket_expr.html
+++ b/main/reference/bracket_expr.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/call_concatenate.html b/main/reference/call_concatenate.html
index cc6737b22..247bde625 100644
--- a/main/reference/call_concatenate.html
+++ b/main/reference/call_concatenate.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/check_arm_ref_comp.html b/main/reference/check_arm_ref_comp.html
index 7d2635e44..f1d0154d9 100644
--- a/main/reference/check_arm_ref_comp.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/clean_description.html b/main/reference/clean_description.html
index 1eaf38dce..2d97e5381 100644
--- a/main/reference/clean_description.html
+++ b/main/reference/clean_description.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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index 5f70fcb4b..2a8d2add0 100644
--- a/main/reference/color_lab_values.html
+++ b/main/reference/color_lab_values.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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index 7680ecd05..fd2e83c93 100644
--- a/main/reference/column_annotation_label.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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index 8f0f84506..496ef36c4 100644
--- a/main/reference/control_tte.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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index 7dd66d561..c6f5ea782 100644
--- a/main/reference/cs_to_des_filter.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/cs_to_des_select.html b/main/reference/cs_to_des_select.html
index 6b6999c87..c3fddc98f 100644
--- a/main/reference/cs_to_des_select.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/cs_to_filter_spec.html b/main/reference/cs_to_filter_spec.html
index 83e213d0a..2fd9d3dc2 100644
--- a/main/reference/cs_to_filter_spec.html
+++ b/main/reference/cs_to_filter_spec.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/cs_to_select_spec.html b/main/reference/cs_to_select_spec.html
index e38c66646..c932b5d11 100644
--- a/main/reference/cs_to_select_spec.html
+++ b/main/reference/cs_to_select_spec.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/default_total_label.html b/main/reference/default_total_label.html
index 7f860b218..8a6062fc1 100644
--- a/main/reference/default_total_label.html
+++ b/main/reference/default_total_label.html
@@ -32,6 +32,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/ex_data.html b/main/reference/ex_data.html
index 0632a7239..1db10a2e6 100644
--- a/main/reference/ex_data.html
+++ b/main/reference/ex_data.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/extract_input.html b/main/reference/extract_input.html
index 63829d773..6eb055d9f 100644
--- a/main/reference/extract_input.html
+++ b/main/reference/extract_input.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/facet_grid_formula.html b/main/reference/facet_grid_formula.html
index f892eb46e..08e6f1c6d 100644
--- a/main/reference/facet_grid_formula.html
+++ b/main/reference/facet_grid_formula.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/get_g_forest_obj_var_name.html b/main/reference/get_g_forest_obj_var_name.html
index f23540677..c4cf65458 100644
--- a/main/reference/get_g_forest_obj_var_name.html
+++ b/main/reference/get_g_forest_obj_var_name.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/get_paramcd_label.html b/main/reference/get_paramcd_label.html
index f7deea3e1..af8f9b101 100644
--- a/main/reference/get_paramcd_label.html
+++ b/main/reference/get_paramcd_label.html
@@ -30,6 +30,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/get_var_labels.html b/main/reference/get_var_labels.html
index a0f4f8b82..521ec7608 100644
--- a/main/reference/get_var_labels.html
+++ b/main/reference/get_var_labels.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/h_concat_expr.html b/main/reference/h_concat_expr.html
index 96d7d1268..ee35bd2c0 100644
--- a/main/reference/h_concat_expr.html
+++ b/main/reference/h_concat_expr.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/index.html b/main/reference/index.html
index de57b5682..06f51edee 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/is.cs_or_des.html b/main/reference/is.cs_or_des.html
index d9c5a7ab0..f957c4764 100644
--- a/main/reference/is.cs_or_des.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/make_barchart_simple_call.html b/main/reference/make_barchart_simple_call.html
index 81e013900..4b6a03955 100644
--- a/main/reference/make_barchart_simple_call.html
+++ b/main/reference/make_barchart_simple_call.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/module_arguments.html b/main/reference/module_arguments.html
index 39d5caee7..f713259ae 100644
--- a/main/reference/module_arguments.html
+++ b/main/reference/module_arguments.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/pipe_expr.html b/main/reference/pipe_expr.html
index 3470d80fc..d71de6f77 100644
--- a/main/reference/pipe_expr.html
+++ b/main/reference/pipe_expr.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/prepare_arm.html b/main/reference/prepare_arm.html
index 8a7579aba..211b8951a 100644
--- a/main/reference/prepare_arm.html
+++ b/main/reference/prepare_arm.html
@@ -30,6 +30,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/prepare_arm_levels.html b/main/reference/prepare_arm_levels.html
index db6f99211..546e25766 100644
--- a/main/reference/prepare_arm_levels.html
+++ b/main/reference/prepare_arm_levels.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/split_choices.html b/main/reference/split_choices.html
index d7f7d5f5a..6ea8c530d 100644
--- a/main/reference/split_choices.html
+++ b/main/reference/split_choices.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/split_col_expr.html b/main/reference/split_col_expr.html
index 277602222..634071a2c 100644
--- a/main/reference/split_col_expr.html
+++ b/main/reference/split_col_expr.html
@@ -32,6 +32,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/split_interactions.html b/main/reference/split_interactions.html
index b25e67974..f8e27ef04 100644
--- a/main/reference/split_interactions.html
+++ b/main/reference/split_interactions.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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index 77f61a3c7..d6955e5a6 100644
--- a/main/reference/substitute_names.html
+++ b/main/reference/substitute_names.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/substitute_q.html b/main/reference/substitute_q.html
index b4cd06091..99519797f 100644
--- a/main/reference/substitute_q.html
+++ b/main/reference/substitute_q.html
@@ -28,6 +28,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/teal.modules.clinical-package.html b/main/reference/teal.modules.clinical-package.html
index 17f65bbc2..cef75aefe 100644
--- a/main/reference/teal.modules.clinical-package.html
+++ b/main/reference/teal.modules.clinical-package.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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index 70f257853..b26d898f6 100644
--- a/main/reference/template_a_gee.html
+++ b/main/reference/template_a_gee.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_abnormality.html b/main/reference/template_abnormality.html
index 43a951b23..a8fa734d9 100644
--- a/main/reference/template_abnormality.html
+++ b/main/reference/template_abnormality.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_abnormality_by_worst_grade.html b/main/reference/template_abnormality_by_worst_grade.html
index 0a59f4706..24bd8cb96 100644
--- a/main/reference/template_abnormality_by_worst_grade.html
+++ b/main/reference/template_abnormality_by_worst_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_adverse_events.html b/main/reference/template_adverse_events.html
index feacaf2a1..21f5e6bd4 100644
--- a/main/reference/template_adverse_events.html
+++ b/main/reference/template_adverse_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_ancova.html b/main/reference/template_ancova.html
index 1a3fb4413..108cab957 100644
--- a/main/reference/template_ancova.html
+++ b/main/reference/template_ancova.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_arguments.html b/main/reference/template_arguments.html
index 688a4163a..0e9a1b29d 100644
--- a/main/reference/template_arguments.html
+++ b/main/reference/template_arguments.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/template_basic_info.html b/main/reference/template_basic_info.html
index 10c7a8e09..dc993bb10 100644
--- a/main/reference/template_basic_info.html
+++ b/main/reference/template_basic_info.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_binary_outcome.html b/main/reference/template_binary_outcome.html
index e5c07869d..e361b61c2 100644
--- a/main/reference/template_binary_outcome.html
+++ b/main/reference/template_binary_outcome.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_coxreg_m.html b/main/reference/template_coxreg_m.html
index 27064be8f..ee1e532d6 100644
--- a/main/reference/template_coxreg_m.html
+++ b/main/reference/template_coxreg_m.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_coxreg_u.html b/main/reference/template_coxreg_u.html
index 19a17c96f..7e5069088 100644
--- a/main/reference/template_coxreg_u.html
+++ b/main/reference/template_coxreg_u.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_events.html b/main/reference/template_events.html
index 4e5fe0b21..bf6d08176 100644
--- a/main/reference/template_events.html
+++ b/main/reference/template_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_events_by_grade.html b/main/reference/template_events_by_grade.html
index efc94b849..fa4b10b4d 100644
--- a/main/reference/template_events_by_grade.html
+++ b/main/reference/template_events_by_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/template_events_col_by_grade.html b/main/reference/template_events_col_by_grade.html
index 4dd26be98..2f206600c 100644
--- a/main/reference/template_events_col_by_grade.html
+++ b/main/reference/template_events_col_by_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_events_patyear.html b/main/reference/template_events_patyear.html
index b885cb46a..d9c3f4969 100644
--- a/main/reference/template_events_patyear.html
+++ b/main/reference/template_events_patyear.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_events_summary.html b/main/reference/template_events_summary.html
index f25855d43..91ab283d7 100644
--- a/main/reference/template_events_summary.html
+++ b/main/reference/template_events_summary.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_exposure.html b/main/reference/template_exposure.html
index 2306e95b4..04ca2e531 100644
--- a/main/reference/template_exposure.html
+++ b/main/reference/template_exposure.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_fit_mmrm.html b/main/reference/template_fit_mmrm.html
index 17ebbaf77..a491550a3 100644
--- a/main/reference/template_fit_mmrm.html
+++ b/main/reference/template_fit_mmrm.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/template_forest_rsp.html b/main/reference/template_forest_rsp.html
index 9ae48178a..3d9005ef1 100644
--- a/main/reference/template_forest_rsp.html
+++ b/main/reference/template_forest_rsp.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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index 1b87e6ab1..fc9fd34ab 100644
--- a/main/reference/template_forest_tte.html
+++ b/main/reference/template_forest_tte.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_g_ci.html b/main/reference/template_g_ci.html
index a790e582b..12dd7e69e 100644
--- a/main/reference/template_g_ci.html
+++ b/main/reference/template_g_ci.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_g_ipp.html b/main/reference/template_g_ipp.html
index 55175da2a..268290cba 100644
--- a/main/reference/template_g_ipp.html
+++ b/main/reference/template_g_ipp.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_g_km.html b/main/reference/template_g_km.html
index 1e730bb12..23b2e4dbb 100644
--- a/main/reference/template_g_km.html
+++ b/main/reference/template_g_km.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_g_lineplot.html b/main/reference/template_g_lineplot.html
index 037432fc5..939588e9e 100644
--- a/main/reference/template_g_lineplot.html
+++ b/main/reference/template_g_lineplot.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_laboratory.html b/main/reference/template_laboratory.html
index 03301cc28..acc2f04ca 100644
--- a/main/reference/template_laboratory.html
+++ b/main/reference/template_laboratory.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_logistic.html b/main/reference/template_logistic.html
index 4461880d8..c2a3e8c8c 100644
--- a/main/reference/template_logistic.html
+++ b/main/reference/template_logistic.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_medical_history.html b/main/reference/template_medical_history.html
index 704694344..3f5d6ed0d 100644
--- a/main/reference/template_medical_history.html
+++ b/main/reference/template_medical_history.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_mult_events.html b/main/reference/template_mult_events.html
index c9da6406d..b1d8d34d7 100644
--- a/main/reference/template_mult_events.html
+++ b/main/reference/template_mult_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_patient_timeline.html b/main/reference/template_patient_timeline.html
index f133ce3f1..266b1888f 100644
--- a/main/reference/template_patient_timeline.html
+++ b/main/reference/template_patient_timeline.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_prior_medication.html b/main/reference/template_prior_medication.html
index 97d6c9b85..29f12c8c6 100644
--- a/main/reference/template_prior_medication.html
+++ b/main/reference/template_prior_medication.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_shift_by_arm.html b/main/reference/template_shift_by_arm.html
index 114a256d0..dd65017c6 100644
--- a/main/reference/template_shift_by_arm.html
+++ b/main/reference/template_shift_by_arm.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_shift_by_arm_by_worst.html b/main/reference/template_shift_by_arm_by_worst.html
index b96cd9876..7764d9ce6 100644
--- a/main/reference/template_shift_by_arm_by_worst.html
+++ b/main/reference/template_shift_by_arm_by_worst.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/template_shift_by_grade.html b/main/reference/template_shift_by_grade.html
index 26c1924da..a42182909 100644
--- a/main/reference/template_shift_by_grade.html
+++ b/main/reference/template_shift_by_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_smq.html b/main/reference/template_smq.html
index e55ed4968..cba56291a 100644
--- a/main/reference/template_smq.html
+++ b/main/reference/template_smq.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_summary.html b/main/reference/template_summary.html
index 20a5632e3..fd7b98f4e 100644
--- a/main/reference/template_summary.html
+++ b/main/reference/template_summary.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/template_summary_by.html b/main/reference/template_summary_by.html
index 6fdff8400..0c87c436e 100644
--- a/main/reference/template_summary_by.html
+++ b/main/reference/template_summary_by.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/template_therapy.html b/main/reference/template_therapy.html
index 324aa5358..1fbd5e8f0 100644
--- a/main/reference/template_therapy.html
+++ b/main/reference/template_therapy.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/template_tte.html b/main/reference/template_tte.html
index 6ec35d57d..2b3cdf731 100644
--- a/main/reference/template_tte.html
+++ b/main/reference/template_tte.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/template_vitals.html b/main/reference/template_vitals.html
index abbe6b522..caf7018ee 100644
--- a/main/reference/template_vitals.html
+++ b/main/reference/template_vitals.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_a_gee.html b/main/reference/tm_a_gee.html
index d061118c7..84eaa5f9a 100644
--- a/main/reference/tm_a_gee.html
+++ b/main/reference/tm_a_gee.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_a_mmrm.html b/main/reference/tm_a_mmrm.html
index 90e3d7037..e2395e9b5 100644
--- a/main/reference/tm_a_mmrm.html
+++ b/main/reference/tm_a_mmrm.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_barchart_simple.html b/main/reference/tm_g_barchart_simple.html
index 8ef66a540..65870b161 100644
--- a/main/reference/tm_g_barchart_simple.html
+++ b/main/reference/tm_g_barchart_simple.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_g_ci.html b/main/reference/tm_g_ci.html
index 8229ab75f..b0fd4bb40 100644
--- a/main/reference/tm_g_ci.html
+++ b/main/reference/tm_g_ci.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_forest_rsp.html b/main/reference/tm_g_forest_rsp.html
index 576f987a9..751cd0fde 100644
--- a/main/reference/tm_g_forest_rsp.html
+++ b/main/reference/tm_g_forest_rsp.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_forest_tte.html b/main/reference/tm_g_forest_tte.html
index 91ab25ab8..4565c3911 100644
--- a/main/reference/tm_g_forest_tte.html
+++ b/main/reference/tm_g_forest_tte.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_ipp.html b/main/reference/tm_g_ipp.html
index 6c4093f37..83b4cf4f9 100644
--- a/main/reference/tm_g_ipp.html
+++ b/main/reference/tm_g_ipp.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_km.html b/main/reference/tm_g_km.html
index 59b02bdf7..91b9ab04e 100644
--- a/main/reference/tm_g_km.html
+++ b/main/reference/tm_g_km.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_lineplot.html b/main/reference/tm_g_lineplot.html
index 7bc0f9061..4afe94828 100644
--- a/main/reference/tm_g_lineplot.html
+++ b/main/reference/tm_g_lineplot.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_pp_adverse_events.html b/main/reference/tm_g_pp_adverse_events.html
index beb8639c5..b1de520c7 100644
--- a/main/reference/tm_g_pp_adverse_events.html
+++ b/main/reference/tm_g_pp_adverse_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_pp_patient_timeline.html b/main/reference/tm_g_pp_patient_timeline.html
index a991607d9..f382a2802 100644
--- a/main/reference/tm_g_pp_patient_timeline.html
+++ b/main/reference/tm_g_pp_patient_timeline.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_pp_therapy.html b/main/reference/tm_g_pp_therapy.html
index 73dcfca4c..792e9283d 100644
--- a/main/reference/tm_g_pp_therapy.html
+++ b/main/reference/tm_g_pp_therapy.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_g_pp_vitals.html b/main/reference/tm_g_pp_vitals.html
index 70e39af8c..af9cbf39c 100644
--- a/main/reference/tm_g_pp_vitals.html
+++ b/main/reference/tm_g_pp_vitals.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_abnormality.html b/main/reference/tm_t_abnormality.html
index a1791fe90..8cb4e68a0 100644
--- a/main/reference/tm_t_abnormality.html
+++ b/main/reference/tm_t_abnormality.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_abnormality_by_worst_grade.html b/main/reference/tm_t_abnormality_by_worst_grade.html
index 1af0775d7..81f475a47 100644
--- a/main/reference/tm_t_abnormality_by_worst_grade.html
+++ b/main/reference/tm_t_abnormality_by_worst_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_ancova.html b/main/reference/tm_t_ancova.html
index b913bedb4..77e151f4c 100644
--- a/main/reference/tm_t_ancova.html
+++ b/main/reference/tm_t_ancova.html
@@ -28,6 +28,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_binary_outcome.html b/main/reference/tm_t_binary_outcome.html
index 4b82af90e..f8879720d 100644
--- a/main/reference/tm_t_binary_outcome.html
+++ b/main/reference/tm_t_binary_outcome.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_coxreg.html b/main/reference/tm_t_coxreg.html
index 1e4abd6c4..47bbe500c 100644
--- a/main/reference/tm_t_coxreg.html
+++ b/main/reference/tm_t_coxreg.html
@@ -30,6 +30,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_events.html b/main/reference/tm_t_events.html
index dc5a0b251..742f2e8ec 100644
--- a/main/reference/tm_t_events.html
+++ b/main/reference/tm_t_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_events_by_grade.html b/main/reference/tm_t_events_by_grade.html
index 437f3b194..39b773acb 100644
--- a/main/reference/tm_t_events_by_grade.html
+++ b/main/reference/tm_t_events_by_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_events_patyear.html b/main/reference/tm_t_events_patyear.html
index 4c2450086..632ba4c42 100644
--- a/main/reference/tm_t_events_patyear.html
+++ b/main/reference/tm_t_events_patyear.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_events_summary.html b/main/reference/tm_t_events_summary.html
index 575cf0063..e80cac8e7 100644
--- a/main/reference/tm_t_events_summary.html
+++ b/main/reference/tm_t_events_summary.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_exposure.html b/main/reference/tm_t_exposure.html
index 4627c9690..7da1eedf4 100644
--- a/main/reference/tm_t_exposure.html
+++ b/main/reference/tm_t_exposure.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_logistic.html b/main/reference/tm_t_logistic.html
index 1d36c2fe2..dfe7b8537 100644
--- a/main/reference/tm_t_logistic.html
+++ b/main/reference/tm_t_logistic.html
@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_mult_events.html b/main/reference/tm_t_mult_events.html
index 956693aa5..314f575b7 100644
--- a/main/reference/tm_t_mult_events.html
+++ b/main/reference/tm_t_mult_events.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_pp_basic_info.html b/main/reference/tm_t_pp_basic_info.html
index 4d1a23490..e3cbf0f3b 100644
--- a/main/reference/tm_t_pp_basic_info.html
+++ b/main/reference/tm_t_pp_basic_info.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_pp_laboratory.html b/main/reference/tm_t_pp_laboratory.html
index bf7c8218b..c2e33ef3e 100644
--- a/main/reference/tm_t_pp_laboratory.html
+++ b/main/reference/tm_t_pp_laboratory.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_pp_medical_history.html b/main/reference/tm_t_pp_medical_history.html
index 637dc7ee4..d6ccb66ac 100644
--- a/main/reference/tm_t_pp_medical_history.html
+++ b/main/reference/tm_t_pp_medical_history.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_pp_prior_medication.html b/main/reference/tm_t_pp_prior_medication.html
index bf920fe10..aad598470 100644
--- a/main/reference/tm_t_pp_prior_medication.html
+++ b/main/reference/tm_t_pp_prior_medication.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_shift_by_arm.html b/main/reference/tm_t_shift_by_arm.html
index 603060175..ec7f84da7 100644
--- a/main/reference/tm_t_shift_by_arm.html
+++ b/main/reference/tm_t_shift_by_arm.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_shift_by_arm_by_worst.html b/main/reference/tm_t_shift_by_arm_by_worst.html
index 438978543..2ac216d1b 100644
--- a/main/reference/tm_t_shift_by_arm_by_worst.html
+++ b/main/reference/tm_t_shift_by_arm_by_worst.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tm_t_shift_by_grade.html b/main/reference/tm_t_shift_by_grade.html
index c7468488c..b2d7cea20 100644
--- a/main/reference/tm_t_shift_by_grade.html
+++ b/main/reference/tm_t_shift_by_grade.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_smq.html b/main/reference/tm_t_smq.html
index 17a7182e8..84696b6e9 100644
--- a/main/reference/tm_t_smq.html
+++ b/main/reference/tm_t_smq.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_summary.html b/main/reference/tm_t_summary.html
index c90f100a7..e5ab8443d 100644
--- a/main/reference/tm_t_summary.html
+++ b/main/reference/tm_t_summary.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_summary_by.html b/main/reference/tm_t_summary_by.html
index 49ae534c8..694027a02 100644
--- a/main/reference/tm_t_summary_by.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/tm_t_tte.html b/main/reference/tm_t_tte.html
index 1a2b42fe0..15afcd24e 100644
--- a/main/reference/tm_t_tte.html
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@@ -26,6 +26,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/validate_arm.html b/main/reference/validate_arm.html
index 06c59ff9a..827369d82 100644
--- a/main/reference/validate_arm.html
+++ b/main/reference/validate_arm.html
@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/validate_standard_inputs.html b/main/reference/validate_standard_inputs.html
index 6915d0731..8ebbe3750 100644
--- a/main/reference/validate_standard_inputs.html
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@@ -24,6 +24,17 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
+<!-- start dropdown for versions --> <li class="nav-item dropdown">
+        <a href="#" class="nav-link dropdown-toggle"
+          data-bs-toggle="dropdown" role="button"
+          aria-expanded="false" aria-haspopup="true"
+          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/main">main</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/latest-tag">latest-tag</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.16">v0.8.16</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.15">v0.8.15</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.8.14">v0.8.14</a>
+<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.clinical/v0.9.0">v0.9.0</a> </div></li>
+<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/search.json b/main/search.json
index 5a55ceec3..fb9f0a2b0 100644
--- a/main/search.json
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Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"generating-minimal-data-to-test-teal-modules-clinical","dir":"Articles","previous_headings":"","what":"Generating minimal data to test teal.modules.clinical","title":"Example Data Generation","text":"following script used create save cached synthetic CDISC data data/ directory use examples tests teal.modules.clinical package. script/vignette initialized Emily de la Rua tern. Disclaimer: vignette concerns mainly development minimal stable test data kept internal feature tracking.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"setup-helper-functions","dir":"Articles","previous_headings":"","what":"Setup & Helper Functions","title":"Example Data Generation","text":"","code":"library(dplyr) library(teal.data)  study_duration_secs <- lubridate::seconds(lubridate::years(2))  sample_fct <- function(x, N, ...) {    checkmate::assert_number(N)   factor(sample(x, N, replace = TRUE, ...), levels = if (is.factor(x)) levels(x) else x) }  retain <- function(df, value_var, event, outside = NA) {   indices <- c(1, which(event == TRUE), nrow(df) + 1)   values <- c(outside, value_var[event == TRUE])   rep(values, diff(indices)) }  relvar_init <- function(relvar1, relvar2) {   if (length(relvar1) != length(relvar2)) {     message(simpleError(       \"The argument value length of relvar1 and relvar2 differ. They must contain the same number of elements.\"     ))     return(NA)   }   return(list(\"relvar1\" = relvar1, \"relvar2\" = relvar2)) }  rel_var <- function(df = NULL, var_name = NULL, var_values = NULL, related_var = NULL) {   if (is.null(df)) {     message(\"Missing data frame argument value.\")     return(NA)   } else {     n_relvar1 <- length(unique(df[, related_var, drop = TRUE]))     n_relvar2 <- length(var_values)     if (n_relvar1 != n_relvar2) {       message(paste(\"Unequal vector lengths for\", related_var, \"and\", var_name))       return(NA)     } else {       relvar1 <- unique(df[, related_var, drop = TRUE])       relvar2_values <- rep(NA, nrow(df))       for (r in seq_len(length(relvar1))) {         matched <- which(df[, related_var, drop = TRUE] == relvar1[r])         relvar2_values[matched] <- var_values[r]       }       return(relvar2_values)     }   } }  visit_schedule <- function(visit_format = \"WEEK\",                            n_assessments = 10L,                            n_days = 5L) {   if (!(toupper(visit_format) %in% c(\"WEEK\", \"CYCLE\"))) {     message(\"Visit format value must either be: WEEK or CYCLE\")     return(NA)   }   if (toupper(visit_format) == \"WEEK\") {     assessments <- 1:n_assessments     assessments_ord <- -1:n_assessments     visit_values <- c(\"SCREENING\", \"BASELINE\", paste(toupper(visit_format), assessments, \"DAY\", (assessments * 7) + 1))   } else if (toupper(visit_format) == \"CYCLE\") {     cycles <- sort(rep(1:n_assessments, times = 1, each = n_days))     days <- rep(seq(1:n_days), times = n_assessments, each = 1)     assessments_ord <- 0:(n_assessments * n_days)     visit_values <- c(\"SCREENING\", paste(toupper(visit_format), cycles, \"DAY\", days))   }   visit_values <- stats::reorder(factor(visit_values), assessments_ord) }  rtpois <- function(n, lambda) stats::qpois(stats::runif(n, stats::dpois(0, lambda), 1), lambda)  rtexp <- function(n, rate, l = NULL, r = NULL) {   if (!is.null(l)) {     l - log(1 - stats::runif(n)) / rate   } else if (!is.null(r)) {     -log(1 - stats::runif(n) * (1 - exp(-r * rate))) / rate   } else {     stats::rexp(n, rate)   } }  str_extract <- function(string, pattern) regmatches(string, gregexpr(pattern, string))  with_label <- function(x, label) {   attr(x, \"label\") <- as.vector(label)   x }  common_var_labels <- c(   USUBJID = \"Unique Subject Identifier\",   STUDYID = \"Study Identifier\",   PARAM = \"Parameter\",   PARAMCD = \"Parameter Code\",   AVISIT = \"Analysis Visit\",   AVISITN = \"Analysis Visit (N)\",   AVAL = \"Analysis Value\",   AVALU = \"Analysis Value Unit\",   AVALC = \"Character Result/Finding\",   BASE = \"Baseline Value\",   BASE2 = \"Screening Value\",   ABLFL = \"Baseline Record Flag\",   ABLFL2 = \"Screening Record Flag\",   CHG = \"Absolute Change from Baseline\",   PCHG = \"Percentage Change from Baseline\",   ANRIND = \"Analysis Reference Range Indicator\",   BNRIND = \"Baseline Reference Range Indicator\",   ANRLO = \"Analysis Normal Range Lower Limit\",   ANRHI = \"Analysis Normal Range Upper Limit\",   CNSR = \"Censor\",   ADTM = \"Analysis Datetime\",   ADY = \"Analysis Relative Day\",   ASTDY = \"Analysis Start Relative Day\",   AENDY = \"Analysis End Relative Day\",   ASTDTM = \"Analysis Start Datetime\",   AENDTM = \"Analysis End Datetime\",   VISITDY = \"Planned Study Day of Visit\",   EVNTDESC = \"Event or Censoring Description\",   CNSDTDSC = \"Censor Date Description\",   BASETYPE = \"Baseline Type\",   DTYPE = \"Derivation Type\",   ONTRTFL = \"On Treatment Record Flag\",   WORS01FL = \"Worst Observation in Window Flag 01\",   WORS02FL = \"Worst Post-Baseline Observation\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adsl","dir":"Articles","previous_headings":"","what":"ADSL","title":"Example Data Generation","text":"","code":"generate_adsl <- function(N = 200) {    set.seed(1)   sys_dtm <- lubridate::fast_strptime(\"20/2/2019 11:16:16.683\", \"%d/%m/%Y %H:%M:%OS\", tz = \"UTC\")   country_site_prob <- c(.5, .121, .077, .077, .075, .052, .046, .025, .014, .003)    adsl <- tibble::tibble(     STUDYID = rep(\"AB12345\", N) %>% with_label(\"Study Identifier\"),     COUNTRY = sample_fct(       c(\"CHN\", \"USA\", \"BRA\", \"PAK\", \"NGA\", \"RUS\", \"JPN\", \"GBR\", \"CAN\", \"CHE\"),       N,       prob = country_site_prob     ) %>% with_label(\"Country\"),     SITEID = sample_fct(1:20, N, prob = rep(country_site_prob, times = 2)),     SUBJID = paste(\"id\", seq_len(N), sep = \"-\") %>% with_label(\"Subject Identifier for the Study\"),     AGE = (sapply(stats::rchisq(N, df = 5, ncp = 10), max, 0) + 20) %>% with_label(\"Age\"),     SEX = c(\"F\", \"M\") %>% sample_fct(N, prob = c(.52, .48)) %>% with_label(\"Sex\"),     ARMCD = c(\"ARM A\", \"ARM B\", \"ARM C\") %>% sample_fct(N) %>% with_label(\"Planned Arm Code\"),     ARM = dplyr::recode(       .data$ARMCD,       \"ARM A\" = \"A: Drug X\", \"ARM B\" = \"B: Placebo\", \"ARM C\" = \"C: Combination\"     ) %>% with_label(\"Description of Planned Arm\"),     ACTARMCD = .data$ARMCD %>% with_label(\"Actual Arm Code\"),     ACTARM = .data$ARM %>% with_label(\"Description of Actual Arm\"),     RACE = c(       \"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\", \"AMERICAN INDIAN OR ALASKA NATIVE\",       \"MULTIPLE\", \"NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER\", \"OTHER\", \"UNKNOWN\"     ) %>%       sample_fct(N, prob = c(.55, .23, .16, .05, .004, .003, .002, .002)) %>%       with_label(\"Race\"),     TRTSDTM = sys_dtm + sample(seq(0, study_duration_secs), size = N, replace = TRUE) %>%       with_label(\"Datetime of First Exposure to Treatment\"),     TRTEDTM = c(TRTSDTM + study_duration_secs) %>%       with_label(\"Datetime of Last Exposure to Treatment\"),     EOSDY = ceiling(as.numeric(difftime(TRTEDTM, TRTSDTM, units = \"days\"))) %>%       with_label(\"End of Study Relative Day\"),     EOSDT = lubridate::date(TRTEDTM) %>% with_label(\"End of Study Date\"),     STRATA1 = c(\"A\", \"B\", \"C\") %>% sample_fct(N) %>% with_label(\"Stratification Factor 1\"),     STRATA2 = c(\"S1\", \"S2\") %>% sample_fct(N) %>% with_label(\"Stratification Factor 2\"),     BMRKR1 = stats::rchisq(N, 6) %>% with_label(\"Continuous Level Biomarker 1\"),     BMRKR2 = sample_fct(c(\"LOW\", \"MEDIUM\", \"HIGH\"), N) %>% with_label(\"Continuous Level Biomarker 2\")   )    # associate sites with countries and regions   adsl <- adsl %>%     dplyr::mutate(       SITEID = paste0(.data$COUNTRY, \"-\", .data$SITEID) %>% with_label(\"Study Site Identifier\"),       REGION1 = factor(dplyr::case_when(         COUNTRY %in% c(\"NGA\") ~ \"Africa\",         COUNTRY %in% c(\"CHN\", \"JPN\", \"PAK\") ~ \"Asia\",         COUNTRY %in% c(\"RUS\") ~ \"Eurasia\",         COUNTRY %in% c(\"GBR\") ~ \"Europe\",         COUNTRY %in% c(\"CAN\", \"USA\") ~ \"North America\",         COUNTRY %in% c(\"BRA\") ~ \"South America\",         TRUE ~ as.character(NA)       )) %>% with_label(\"Geographic Region 1\"),       SAFFL = factor(\"Y\") %>% with_label(\"Safety Population Flag\")     ) %>%     dplyr::mutate(       USUBJID = paste(.data$STUDYID, .data$SITEID, .data$SUBJID, sep = \"-\") %>%         with_label(\"Unique Subject Identifier\")     )    # disposition related variables   # using probability of 1 for the \"DEATH\" level to ensure at least one death record exists   l_dcsreas <- list(     choices = c(       \"ADVERSE EVENT\", \"DEATH\", \"LACK OF EFFICACY\", \"PHYSICIAN DECISION\",       \"PROTOCOL VIOLATION\", \"WITHDRAWAL BY PARENT/GUARDIAN\", \"WITHDRAWAL BY SUBJECT\"     ),     prob = c(.2, 1, .1, .1, .2, .1, .1)   )   l_dthcat_other <- list(     choices = c(       \"Post-study reporting of death\", \"LOST TO FOLLOW UP\", \"MISSING\", \"SUICIDE\", \"UNKNOWN\"     ),     prob = c(.1, .3, .3, .2, .1)   )    adsl <- adsl %>%     dplyr::mutate(       EOSSTT = dplyr::case_when(         EOSDY == max(EOSDY, na.rm = TRUE) ~ \"COMPLETED\",         EOSDY < max(EOSDY, na.rm = TRUE) ~ \"DISCONTINUED\",         is.na(TRTEDTM) ~ \"ONGOING\"       ) %>% with_label(\"End of Study Status\")     ) %>%     dplyr::mutate(       EOTSTT = .data$EOSSTT %>% with_label(\"End of Treatment Status\")     ) %>%     dplyr::mutate(       DCSREAS = ifelse(         .data$EOSSTT == \"DISCONTINUED\",         sample(x = l_dcsreas$choices, size = N, replace = TRUE, prob = l_dcsreas$prob),         as.character(NA)       ) %>% with_label(\"Reason for Discontinuation from Study\")     )    tmc_ex_adsl <- adsl %>%     dplyr::mutate(DTHDT = dplyr::case_when(       DCSREAS == \"DEATH\" ~ lubridate::date(TRTEDTM + lubridate::days(sample(0:50, size = N, replace = TRUE)))     ) %>% with_label(\"Date of Death\"))    save(tmc_ex_adsl, file = \"data/tmc_ex_adsl.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adae","dir":"Articles","previous_headings":"","what":"ADAE","title":"Example Data Generation","text":"","code":"generate_adae <- function(adsl = tmc_ex_adsl,                           max_n_aes = 5) {   set.seed(1)   lookup_ae <- tibble::tribble(     ~AEBODSYS, ~AELLT, ~AEDECOD, ~AEHLT, ~AEHLGT, ~AETOXGR, ~AESOC, ~AESER, ~AEREL,     \"cl A.1\", \"llt A.1.1.1.1\", \"dcd A.1.1.1.1\", \"hlt A.1.1.1\", \"hlgt A.1.1\", \"1\", \"cl A\", \"N\", \"N\",     \"cl A.1\", \"llt A.1.1.1.2\", \"dcd A.1.1.1.2\", \"hlt A.1.1.1\", \"hlgt A.1.1\", \"2\", \"cl A\", \"Y\", \"N\",     \"cl B.1\", \"llt B.1.1.1.1\", \"dcd B.1.1.1.1\", \"hlt B.1.1.1\", \"hlgt B.1.1\", \"5\", \"cl B\", \"Y\", \"Y\",     \"cl B.2\", \"llt B.2.1.2.1\", \"dcd B.2.1.2.1\", \"hlt B.2.1.2\", \"hlgt B.2.1\", \"3\", \"cl B\", \"N\", \"N\",     \"cl B.2\", \"llt B.2.2.3.1\", \"dcd B.2.2.3.1\", \"hlt B.2.2.3\", \"hlgt B.2.2\", \"1\", \"cl B\", \"Y\", \"N\",     \"cl C.1\", \"llt C.1.1.1.3\", \"dcd C.1.1.1.3\", \"hlt C.1.1.1\", \"hlgt C.1.1\", \"4\", \"cl C\", \"N\", \"Y\",     \"cl C.2\", \"llt C.2.1.2.1\", \"dcd C.2.1.2.1\", \"hlt C.2.1.2\", \"hlgt C.2.1\", \"2\", \"cl C\", \"N\", \"Y\",     \"cl D.1\", \"llt D.1.1.1.1\", \"dcd D.1.1.1.1\", \"hlt D.1.1.1\", \"hlgt D.1.1\", \"5\", \"cl D\", \"Y\", \"Y\",     \"cl D.1\", \"llt D.1.1.4.2\", \"dcd D.1.1.4.2\", \"hlt D.1.1.4\", \"hlgt D.1.1\", \"3\", \"cl D\", \"N\", \"N\",     \"cl D.2\", \"llt D.2.1.5.3\", \"dcd D.2.1.5.3\", \"hlt D.2.1.5\", \"hlgt D.2.1\", \"1\", \"cl D\", \"N\", \"Y\"   )    aag <- utils::read.table(     sep = \",\", header = TRUE,     text = paste(       \"NAMVAR,SRCVAR,GRPTYPE,REFNAME,REFTERM,SCOPE\",       \"CQ01NAM,AEDECOD,CUSTOM,D.2.1.5.3/A.1.1.1.1 aesi,dcd D.2.1.5.3,\",       \"CQ01NAM,AEDECOD,CUSTOM,D.2.1.5.3/A.1.1.1.1 aesi,dcd A.1.1.1.1,\",       \"SMQ01NAM,AEDECOD,SMQ,C.1.1.1.3/B.2.2.3.1 aesi,dcd C.1.1.1.3,BROAD\",       \"SMQ01NAM,AEDECOD,SMQ,C.1.1.1.3/B.2.2.3.1 aesi,dcd B.2.2.3.1,BROAD\",       \"SMQ02NAM,AEDECOD,SMQ,Y.9.9.9.9/Z.9.9.9.9 aesi,dcd Y.9.9.9.9,NARROW\",       \"SMQ02NAM,AEDECOD,SMQ,Y.9.9.9.9/Z.9.9.9.9 aesi,dcd Z.9.9.9.9,NARROW\",       sep = \"\\n\"     ), stringsAsFactors = FALSE   )    adae <- Map(     function(id, sid) {       n_aes <- sample(c(0, seq_len(max_n_aes)), 1)       i <- sample(seq_len(nrow(lookup_ae)), n_aes, TRUE)       dplyr::mutate(         lookup_ae[i, ],         USUBJID = id,         STUDYID = sid       )     },     adsl$USUBJID,     adsl$STUDYID   ) %>%     Reduce(rbind, .) %>%     `[`(c(10, 11, 1, 2, 3, 4, 5, 6, 7, 8, 9)) %>%     dplyr::mutate(       AETERM = gsub(\"dcd\", \"trm\", .data$AEDECOD) %>% with_label(\"Reported Term for the Adverse Event\"),       AESEV = dplyr::case_when(         AETOXGR == 1 ~ \"MILD\",         AETOXGR %in% c(2, 3) ~ \"MODERATE\",         AETOXGR %in% c(4, 5) ~ \"SEVERE\"       ) %>% with_label(\"Severity/Intensity\")     )    # merge adsl to be able to add AE date and study day variables   adae <- dplyr::inner_join(adae, adsl, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ASTDY = ceiling(difftime(ASTDTM, TRTSDTM, units = \"days\"))) %>%     # add 1 to end of range incase both values passed to sample() are the same     dplyr::mutate(AENDTM = sample(       seq(lubridate::as_datetime(ASTDTM), lubridate::as_datetime(TRTENDT + 1), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(AENDY = ceiling(difftime(AENDTM, TRTSDTM, units = \"days\"))) %>%     dplyr::mutate(LDOSEDTM = dplyr::case_when(       TRTSDTM < ASTDTM ~ lubridate::as_datetime(stats::runif(1, TRTSDTM, ASTDTM)),       TRUE ~ ASTDTM     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$AETERM)    adae <- adae %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(AESEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$ASTDTM,       .data$AETERM,       .data$AESEQ     )    outcomes <- c(     \"UNKNOWN\",     \"NOT RECOVERED/NOT RESOLVED\",     \"RECOVERED/RESOLVED WITH SEQUELAE\",     \"RECOVERING/RESOLVING\",     \"RECOVERED/RESOLVED\"   )    adae <- adae %>%     dplyr::mutate(       AEOUT = factor(ifelse(         .data$AETOXGR == \"5\",         \"FATAL\",         as.character(sample_fct(outcomes, nrow(adae), prob = c(0.1, 0.2, 0.1, 0.3, 0.3)))       )) %>% with_label(\"Outcome of Adverse Event\"),       TRTEMFL = ifelse(.data$ASTDTM >= .data$TRTSDTM, \"Y\", \"\") %>%         with_label(\"Treatment Emergent Analysis Flag\")     )    l_aag <- split(aag, interaction(aag$NAMVAR, aag$SRCVAR, aag$GRPTYPE, drop = TRUE))    # Create aesi flags   l_aesi <- lapply(l_aag, function(d_adag, d_adae) {     names(d_adag)[names(d_adag) == \"REFTERM\"] <- d_adag$SRCVAR[1]     names(d_adag)[names(d_adag) == \"REFNAME\"] <- d_adag$NAMVAR[1]      if (d_adag$GRPTYPE[1] == \"CUSTOM\") {       d_adag <- d_adag[-which(names(d_adag) == \"SCOPE\")]     } else if (d_adag$GRPTYPE[1] == \"SMQ\") {       names(d_adag)[names(d_adag) == \"SCOPE\"] <- paste0(substr(d_adag$NAMVAR[1], 1, 5), \"SC\")     }      d_adag <- d_adag[-which(names(d_adag) %in% c(\"NAMVAR\", \"SRCVAR\", \"GRPTYPE\"))]     d_new <- dplyr::left_join(x = d_adae, y = d_adag, by = intersect(names(d_adae), names(d_adag)))     d_new[, dplyr::setdiff(names(d_new), names(d_adae)), drop = FALSE]   }, adae)   adae <- dplyr::bind_cols(adae, l_aesi)    actions <- c(     \"DOSE RATE REDUCED\",     \"UNKNOWN\",     \"NOT APPLICABLE\",     \"DRUG INTERRUPTED\",     \"DRUG WITHDRAWN\",     \"DOSE INCREASED\",     \"DOSE NOT CHANGED\",     \"DOSE REDUCED\",     \"NOT EVALUABLE\"   )    tmc_ex_adae <- adae %>%     dplyr::mutate(       AEACN = factor(ifelse(         .data$AETOXGR == \"5\",         \"NOT EVALUABLE\",         as.character(sample_fct(actions, nrow(adae), prob = c(0.05, 0.05, 0.05, 0.01, 0.05, 0.1, 0.45, 0.1, 0.05)))       )) %>% with_label(\"Action Taken With Study Treatment\")     ) %>%     col_relabel(       AEBODSYS = \"Body System or Organ Class\",       AELLT = \"Lowest Level Term\",       AEDECOD = \"Dictionary-Derived Term\",       AEHLT = \"High Level Term\",       AEHLGT = \"High Level Group Term\",       AETOXGR = \"Analysis Toxicity Grade\",       AESOC = \"Primary System Organ Class\",       AESER = \"Serious Event\",       AEREL = \"Analysis Causality\",       AESEQ = \"Sponsor-Defined Identifier\",       LDOSEDTM = \"End Time/Time of Last Dose\",       CQ01NAM = \"CQ 01 Reference Name\",       SMQ01NAM = \"SMQ 01 Reference Name\",       SMQ01SC = \"SMQ 01 Scope\",       SMQ02NAM = \"SMQ 02 Reference Name\",       SMQ02SC = \"SMQ 02 Scope\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adae)[is.na(col_labels(tmc_ex_adae))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adae[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adae, file = \"data/tmc_ex_adae.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adaette","dir":"Articles","previous_headings":"","what":"ADAETTE","title":"Example Data Generation","text":"","code":"generate_adaette <- function(adsl = tmc_ex_adsl) {   set.seed(1)   lookup_adaette <- tibble::tribble(     ~ARM, ~CATCD, ~CAT, ~LAMBDA, ~CNSR_P,     \"ARM A\", \"1\", \"any adverse event\", 1 / 80, 0.4,     \"ARM B\", \"1\", \"any adverse event\", 1 / 100, 0.2,     \"ARM C\", \"1\", \"any adverse event\", 1 / 60, 0.42,     \"ARM A\", \"2\", \"any serious adverse event\", 1 / 100, 0.3,     \"ARM B\", \"2\", \"any serious adverse event\", 1 / 150, 0.1,     \"ARM C\", \"2\", \"any serious adverse event\", 1 / 80, 0.32,     \"ARM A\", \"3\", \"a grade 3-5 adverse event\", 1 / 80, 0.2,     \"ARM B\", \"3\", \"a grade 3-5 adverse event\", 1 / 100, 0.08,     \"ARM C\", \"3\", \"a grade 3-5 adverse event\", 1 / 60, 0.23   )   evntdescr_sel <- \"Preferred Term\"   cnsdtdscr_sel <- c(     \"Clinical Cut Off\",     \"Completion or Discontinuation\",     \"End of AE Reporting Period\"   )    random_patient_data <- function(patient_info) {     startdt <- lubridate::date(patient_info$TRTSDTM)     trtedtm <- lubridate::floor_date(dplyr::case_when(       is.na(patient_info$TRTEDTM) ~ lubridate::date(patient_info$TRTSDTM) + study_duration_secs,       TRUE ~ lubridate::date(patient_info$TRTEDTM)     ), unit = \"day\")     enddts <- c(patient_info$EOSDT, lubridate::date(trtedtm))     enddts_min_index <- which.min(enddts)     adt <- enddts[enddts_min_index]     adtm <- lubridate::as_datetime(adt)     ady <- as.numeric(adt - startdt + 1)     data.frame(       ARM = patient_info$ARM,       STUDYID = patient_info$STUDYID,       SITEID = patient_info$SITEID,       USUBJID = patient_info$USUBJID,       PARAMCD = \"AEREPTTE\",       PARAM = \"Time to end of AE reporting period\",       CNSR = 0,       AVAL = lubridate::days(ady) / lubridate::years(1),       AVALU = \"YEARS\",       EVNTDESC = ifelse(enddts_min_index == 1, \"Completion or Discontinuation\", \"End of AE Reporting Period\"),       CNSDTDSC = NA,       ADTM = adtm,       ADY = ady,       stringsAsFactors = FALSE     )   }    paramcd_hy <- c(\"HYSTTEUL\", \"HYSTTEBL\")   param_hy <- c(\"Time to Hy's Law Elevation in relation to ULN\", \"Time to Hy's Law Elevation in relation to Baseline\")   param_init_list <- relvar_init(param_hy, paramcd_hy)   adsl_hy <- dplyr::select(adsl, \"STUDYID\", \"USUBJID\", \"TRTSDTM\", \"SITEID\", \"ARM\")   adaette_hy <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     stringsAsFactors = FALSE   )    adaette_hy <- dplyr::left_join(adaette_hy, adsl_hy, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::mutate(       PARAMCD = factor(rel_var(         df = as.data.frame(adaette_hy),         var_values = param_init_list$relvar2,         related_var = \"PARAM\"       ))     ) %>%     dplyr::mutate(       CNSR = sample(c(0, 1), prob = c(0.1, 0.9), size = dplyr::n(), replace = TRUE),       EVNTDESC = dplyr::if_else(         .data$CNSR == 0,         \"First Post-Baseline Raised ALT or AST Elevation Result\",         NA_character_       ),       CNSDTDSC = dplyr::if_else(.data$CNSR == 0, NA_character_,         sample(c(\"Last Post-Baseline ALT or AST Result\", \"Treatment Start\"),           prob = c(0.9, 0.1),           size = dplyr::n(), replace = TRUE         )       )     ) %>%     dplyr::rowwise() %>%     dplyr::mutate(ADTM = dplyr::case_when(       CNSDTDSC == \"Treatment Start\" ~ TRTSDTM,       TRUE ~ TRTSDTM + sample(seq(0, study_duration_secs), size = dplyr::n(), replace = TRUE)     )) %>%     dplyr::mutate(       ADY_int = lubridate::date(ADTM) - lubridate::date(TRTSDTM) + 1,       ADY = as.numeric(ADY_int),       AVAL = lubridate::days(ADY_int) / lubridate::weeks(1),       AVALU = \"WEEKS\"     ) %>%     dplyr::select(-TRTSDTM, -ADY_int)    random_ae_data <- function(lookup_info, patient_info, patient_data) {     cnsr <- sample(c(0, 1), 1, prob = c(1 - lookup_info$CNSR_P, lookup_info$CNSR_P))     ae_rep_tte <- patient_data$AVAL[patient_data$PARAMCD == \"AEREPTTE\"]     data.frame(       ARM = rep(patient_data$ARM, 2),       STUDYID = rep(patient_data$STUDYID, 2),       SITEID = rep(patient_data$SITEID, 2),       USUBJID = rep(patient_data$USUBJID, 2),       PARAMCD = c(         paste0(\"AETTE\", lookup_info$CATCD),         paste0(\"AETOT\", lookup_info$CATCD)       ),       PARAM = c(         paste(\"Time to first occurrence of\", lookup_info$CAT),         paste(\"Number of occurrences of\", lookup_info$CAT)       ),       CNSR = c(cnsr, NA),       AVAL = c(         ifelse(cnsr == 1, ae_rep_tte, rtexp(1, lookup_info$LAMBDA * 365.25, r = ae_rep_tte)),         ifelse(cnsr == 1, 0, rtpois(1, lookup_info$LAMBDA * 365.25))       ),       AVALU = c(\"YEARS\", NA),       EVNTDESC = c(ifelse(cnsr == 0, sample(evntdescr_sel, 1), \"\"), NA),       CNSDTDSC = c(ifelse(cnsr == 1, sample(cnsdtdscr_sel, 1), \"\"), NA),       stringsAsFactors = FALSE     ) %>% dplyr::mutate(       ADY = dplyr::if_else(is.na(AVALU), NA_real_, ceiling(as.numeric(lubridate::dyears(AVAL), \"days\"))),       ADTM = dplyr::if_else(         is.na(AVALU),         lubridate::as_datetime(NA),         patient_info$TRTSDTM + lubridate::days(ADY)       )     )   }    adaette <- split(adsl, adsl$USUBJID) %>%     lapply(function(patient_info) {       patient_data <- random_patient_data(patient_info)       lookup_arm <- lookup_adaette %>%         dplyr::filter(.data$ARM == as.character(patient_info$ARMCD))       ae_data <- split(lookup_arm, lookup_arm$CATCD) %>%         lapply(random_ae_data, patient_data = patient_data, patient_info = patient_info) %>%         Reduce(rbind, .)       dplyr::bind_rows(patient_data, ae_data)     }) %>%     Reduce(rbind, .)   adaette <- rbind(adaette, adaette_hy)    tmc_ex_adaette <- adsl %>%     dplyr::inner_join(       dplyr::select(adaette, -\"SITEID\", -\"ARM\"),       by = c(\"STUDYID\", \"USUBJID\"),       multiple = \"all\"     ) %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::arrange(.data$ADTM) %>%     dplyr::mutate(PARAM = as.factor(.data$PARAM)) %>%     dplyr::mutate(PARAMCD = as.factor(.data$PARAMCD)) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adaette)[is.na(col_labels(tmc_ex_adaette))]),     function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adaette[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adaette, file = \"data/tmc_ex_adaette.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adcm","dir":"Articles","previous_headings":"","what":"ADCM","title":"Example Data Generation","text":"","code":"generate_adcm <- function(adsl = tmc_ex_adsl,                           max_n_cms = 5L) {   set.seed(1)   lookup_cm <- tibble::tribble(     ~CMCLAS, ~CMDECOD, ~ATIREL,     \"medcl A\", \"medname A_1/3\", \"PRIOR\",     \"medcl A\", \"medname A_2/3\", \"CONCOMITANT\",     \"medcl A\", \"medname A_3/3\", \"CONCOMITANT\",     \"medcl B\", \"medname B_1/4\", \"CONCOMITANT\",     \"medcl B\", \"medname B_2/4\", \"PRIOR\",     \"medcl B\", \"medname B_3/4\", \"PRIOR\",     \"medcl B\", \"medname B_4/4\", \"CONCOMITANT\",     \"medcl C\", \"medname C_1/2\", \"CONCOMITANT\",     \"medcl C\", \"medname C_2/2\", \"CONCOMITANT\"   )    adcm <- Map(function(id, sid) {     n_cms <- sample(c(0, seq_len(max_n_cms)), 1)     i <- sample(seq_len(nrow(lookup_cm)), n_cms, TRUE)     dplyr::mutate(       lookup_cm[i, ],       USUBJID = id,       STUDYID = sid     )   }, adsl$USUBJID, adsl$STUDYID) %>%     Reduce(rbind, .) %>%     `[`(c(4, 5, 1, 2, 3)) %>%     dplyr::mutate(CMCAT = .data$CMCLAS %>% with_label(\"Category for Medication\"))    # merge adsl to be able to add CM date and study day variables   adcm <- dplyr::inner_join(     adcm,     adsl,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ASTDY = ceiling(difftime(ASTDTM, TRTSDTM, units = \"days\"))) %>%     # add 1 to end of range incase both values passed to sample() are the same     dplyr::mutate(AENDTM = sample(       seq(lubridate::as_datetime(ASTDTM), lubridate::as_datetime(TRTENDT + 1), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(AENDY = ceiling(difftime(AENDTM, TRTSDTM, units = \"days\"))) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(STUDYID, USUBJID, ASTDTM)    tmc_ex_adcm <- adcm %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(CMSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$CMSEQ) %>%     dplyr::mutate(       ATC1 = paste(\"ATCCLAS1\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 1 Text\"),       ATC2 = paste(\"ATCCLAS2\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 2 Text\"),       ATC3 = paste(\"ATCCLAS3\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 3 Text\"),       ATC4 = paste(\"ATCCLAS4\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 4 Text\")     ) %>%     dplyr::mutate(       CMINDC = sample(c(         \"Nausea\", \"Hypertension\", \"Urticaria\", \"Fever\",         \"Asthma\", \"Infection\", \"Diabete\", \"Diarrhea\", \"Pneumonia\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Indication\"),       CMDOSE = sample(1:99, dplyr::n(), replace = TRUE) %>% with_label(\"Dose per Administration\"),       CMTRT = substr(.data$CMDECOD, 9, 13) %>% with_label(\"Reported Name of Drug, Med, or Therapy\"),       CMDOSU = sample(c(         \"ug/mL\", \"ug/kg/day\", \"%\", \"uL\", \"DROP\",         \"umol/L\", \"mg\", \"mg/breath\", \"ug\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Dose Units\")     ) %>%     dplyr::mutate(       CMROUTE = sample(c(         \"INTRAVENOUS\", \"ORAL\", \"NASAL\",         \"INTRAMUSCULAR\", \"SUBCUTANEOUS\", \"INHALED\", \"RECTAL\", \"UNKNOWN\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Route of Administration\"),       CMDOSFRQ = sample(c(         \"Q4W\", \"QN\", \"Q4H\", \"UNKNOWN\", \"TWICE\",         \"Q4H\", \"QD\", \"TID\", \"4 TIMES PER MONTH\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Dosing Frequency per Interval\")     ) %>%     col_relabel(       CMCLAS = \"Medication Class\",       CMDECOD = \"Standardized Medication Name\",       ATIREL = \"Time Relation of Medication\",       CMSEQ = \"Sponsor-Defined Identifier\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adcm)[is.na(col_labels(tmc_ex_adcm))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adcm[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adcm, file = \"data/tmc_ex_adcm.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adeg","dir":"Articles","previous_headings":"","what":"ADEG","title":"Example Data Generation","text":"","code":"generate_adeg <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_eg = 3L) {   set.seed(1)   param <- c(\"QT Duration\", \"RR Duration\", \"Heart Rate\", \"ECG Interpretation\")   paramcd <- c(\"QT\", \"RR\", \"HR\", \"ECGINTP\")   paramu <- c(\"msec\", \"msec\", \"beats/min\", \"\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adeg <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    adeg$PARAMCD <- as.factor(rel_var(     df = adeg,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adeg <- adeg %>% dplyr::mutate(AVAL = dplyr::case_when(     .data$PARAMCD == \"QT\" ~ stats::rnorm(nrow(adeg), mean = 350, sd = 100),     .data$PARAMCD == \"RR\" ~ stats::rnorm(nrow(adeg), mean = 1050, sd = 300),     .data$PARAMCD == \"HR\" ~ stats::rnorm(nrow(adeg), mean = 70, sd = 20),     .data$PARAMCD == \"ECGINTP\" ~ NA_real_   ))    adeg <- adeg %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ NA_real_   ))    adeg$AVALU <- as.factor(rel_var(     df = adeg,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adeg <- adeg[order(adeg$STUDYID, adeg$USUBJID, adeg$PARAMCD, adeg$AVISITN), ]   adeg <- Reduce(rbind, lapply(split(adeg, adeg$USUBJID), function(x) {     x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]     x$ABLFL <- ifelse(toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",       \"Y\",       ifelse(toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\", \"Y\", \"\")     )     x   }))    adeg$BASE <- ifelse(adeg$AVISITN >= 0, retain(adeg, adeg$AVAL, adeg$ABLFL == \"Y\"), adeg$AVAL)   adeg <- adeg %>%     dplyr::mutate(ANRLO = dplyr::case_when(       .data$PARAMCD == \"QT\" ~ 200,       .data$PARAMCD == \"RR\" ~ 600,       .data$PARAMCD == \"HR\" ~ 40,       .data$PARAMCD == \"ECGINTP\" ~ NA_real_     )) %>%     dplyr::mutate(ANRHI = dplyr::case_when(       .data$PARAMCD == \"QT\" ~ 500,       .data$PARAMCD == \"RR\" ~ 1500,       .data$PARAMCD == \"HR\" ~ 100,       .data$PARAMCD == \"ECGINTP\" ~ NA_real_     )) %>%     dplyr::mutate(ANRIND = factor(dplyr::case_when(       .data$AVAL < .data$ANRLO ~ \"LOW\",       .data$AVAL >= .data$ANRLO & .data$AVAL <= .data$ANRHI ~ \"NORMAL\",       .data$AVAL > .data$ANRHI ~ \"HIGH\"     )))    adeg <- adeg %>%     dplyr::mutate(CHG = ifelse(.data$AVISITN > 0, .data$AVAL - .data$BASE, NA)) %>%     dplyr::mutate(PCHG = ifelse(.data$AVISITN > 0, 100 * (.data$CHG / .data$BASE), NA)) %>%     dplyr::mutate(BASETYPE = \"LAST\") %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BNRIND = .data$ANRIND[.data$ABLFL == \"Y\"]) %>%     dplyr::ungroup() %>%     dplyr::mutate(DTYPE = NA)    adeg$ANRIND <- factor(adeg$ANRIND, levels = c(\"LOW\", \"NORMAL\", \"HIGH\"))   adeg$BNRIND <- factor(adeg$BNRIND, levels = c(\"LOW\", \"NORMAL\", \"HIGH\"))    adeg <- dplyr::inner_join(     adsl,     adeg,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::ungroup() %>%     dplyr::group_by(USUBJID) %>%     dplyr::arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adeg <- adeg %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$BASETYPE,       .data$AVISITN,       .data$DTYPE,       .data$ADTM     )    adeg <- adeg %>%     dplyr::mutate(ONTRTFL = factor(dplyr::case_when(       is.na(.data$TRTSDTM) ~ \"\",       is.na(.data$ADTM) ~ \"Y\",       (.data$ADTM < .data$TRTSDTM) ~ \"\",       (.data$ADTM > .data$TRTEDTM) ~ \"\",       TRUE ~ \"Y\"     ))) %>%     dplyr::mutate(AVALC = ifelse(       .data$PARAMCD == \"ECGINTP\",       as.character(sample_fct(c(\"ABNORMAL\", \"NORMAL\"), nrow(adeg), prob = c(0.25, 0.75))),       as.character(.data$AVAL)     ))    adeg <- adeg %>% dplyr::mutate(row_check = seq_len(nrow(adeg)))   get_groups <- function(data, minimum) {     data <- data %>%       dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%       dplyr::arrange(.data$ADTM) %>%       dplyr::filter(         (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &           (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)       ) %>%       {         if (minimum == TRUE) {           dplyr::filter(., .data$AVAL == min(.data$AVAL)) %>%             dplyr::mutate(., DTYPE = \"MINIMUM\", AVISIT = \"POST-BASELINE MINIMUM\")         } else {           dplyr::filter(., .data$AVAL == max(.data$AVAL)) %>%             dplyr::mutate(., DTYPE = \"MAXIMUM\", AVISIT = \"POST-BASELINE MAXIMUM\")         }       } %>%       dplyr::slice(1) %>%       dplyr::ungroup()     return(data)   }    lbls <- col_labels(adeg)   adeg <- rbind(adeg, get_groups(adeg, TRUE), get_groups(adeg, FALSE)) %>%     dplyr::arrange(.data$row_check) %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::arrange(.data$AVISIT, .by_group = TRUE) %>%     dplyr::ungroup()   col_labels(adeg) <- lbls    adeg <- adeg[, -which(names(adeg) %in% c(\"row_check\"))]   flag_variables <- function(data, worst_obs) {     data_compare <- data %>%       dplyr::mutate(row_check = seq_len(nrow(data)))     data <- data_compare %>%       {         if (worst_obs == FALSE) {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE, .data$AVISIT) %>%             dplyr::arrange(., .data$ADTM)         } else {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE)         }       } %>%       dplyr::filter(         .data$AVISITN > 0 & (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM) &           is.na(.data$DTYPE)       ) %>%       {         if (worst_obs == TRUE) {           dplyr::arrange(., .data$AVALC) %>% dplyr::filter(., ifelse(             .data$PARAMCD == \"ECGINTP\",             ifelse(.data$AVALC == \"ABNORMAL\", .data$AVALC == \"ABNORMAL\", .data$AVALC == \"NORMAL\"),             .data$AVAL == min(.data$AVAL)           ))         } else {           dplyr::filter(., ifelse(             .data$PARAMCD == \"ECGINTP\",             .data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\",             .data$AVAL == min(.data$AVAL)           ))         }       } %>%       dplyr::slice(1) %>%       {         if (worst_obs == TRUE) {           dplyr::mutate(., new_var = dplyr::case_when(             (.data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\") ~ \"Y\",             (!is.na(.data$AVAL) & is.na(.data$DTYPE)) ~ \"Y\",             TRUE ~ \"\"           ))         } else {           dplyr::mutate(., new_var = dplyr::case_when(             (.data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\") ~ \"Y\",             (!is.na(.data$AVAL) & is.na(.data$DTYPE)) ~ \"Y\",             TRUE ~ \"\"           ))         }       } %>%       dplyr::ungroup()      data_compare$new_var <- ifelse(data_compare$row_check %in% data$row_check, \"Y\", \"\")     data_compare <- data_compare[, -which(names(data_compare) %in% c(\"row_check\"))]      return(data_compare)   }   adeg <- flag_variables(adeg, FALSE) %>% dplyr::rename(WORS01FL = \"new_var\")   adeg <- flag_variables(adeg, TRUE) %>% dplyr::rename(WORS02FL = \"new_var\")    tmc_ex_adeg <- adeg %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BASEC = ifelse(       .data$PARAMCD == \"ECGINTP\",       .data$AVALC[.data$AVISIT == \"BASELINE\"],       as.character(.data$BASE)     )) %>%     dplyr::ungroup() %>%     col_relabel(BASEC = \"Baseline Character Value\")    i_lbls <- sapply(     names(col_labels(tmc_ex_adeg)[is.na(col_labels(tmc_ex_adeg))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adeg[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adeg, file = \"data/tmc_ex_adeg.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adex","dir":"Articles","previous_headings":"","what":"ADEX","title":"Example Data Generation","text":"","code":"generate_adex <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_exs = 3L) {   set.seed(1)   param <- c(     \"Dose administered during constant dosing interval\",     \"Number of doses administered during constant dosing interval\",     \"Total dose administered\",     \"Total number of doses administered\"   )   paramcd <- c(\"DOSE\", \"NDOSE\", \"TDOSE\", \"TNDOSE\")   paramu <- c(\"mg\", \" \", \"mg\", \" \")   parcat1 <- c(\"INDIVIDUAL\", \"OVERALL\")   parcat2 <- c(\"Drug A\", \"Drug B\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adex <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = c(       rep(         param_init_list$relvar1[1],         length(levels(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days)))       ),       rep(         param_init_list$relvar1[2],         length(levels(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days)))       ),       param_init_list$relvar1[3:4]     ),     stringsAsFactors = FALSE   )    adex$PARAMCD <- as.factor(rel_var(     df = adex,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adex$AVALU <- as.factor(rel_var(     df = adex,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adex <- adex %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(PARCAT_ind = sample(c(1, 2), size = 1)) %>%     dplyr::mutate(PARCAT2 = ifelse(.data$PARCAT_ind == 1, parcat2[1], parcat2[2])) %>%     dplyr::select(-\"PARCAT_ind\")    adex <- adex %>% dplyr::mutate(PARCAT1 = dplyr::case_when(     (.data$PARAMCD == \"TNDOSE\" | .data$PARAMCD == \"TDOSE\") ~ \"OVERALL\",     .data$PARAMCD == \"DOSE\" | .data$PARAMCD == \"NDOSE\" ~ \"INDIVIDUAL\"   ))    adex_visit <- adex %>%     dplyr::filter(.data$PARAMCD == \"DOSE\" | .data$PARAMCD == \"NDOSE\") %>%     dplyr::mutate(       AVISIT = rep(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days), 2)     )    adex <- dplyr::left_join(     adex %>%       dplyr::group_by(         .data$USUBJID,         .data$STUDYID,         .data$PARAM,         .data$PARAMCD,         .data$AVALU,         .data$PARCAT1,         .data$PARCAT2       ) %>%       dplyr::mutate(id = dplyr::row_number()),     adex_visit %>%       dplyr::group_by(         .data$USUBJID,         .data$STUDYID,         .data$PARAM,         .data$PARAMCD,         .data$AVALU,         .data$PARCAT1,         .data$PARCAT2       ) %>%       dplyr::mutate(id = dplyr::row_number()),     by = c(\"USUBJID\", \"STUDYID\", \"PARCAT1\", \"PARCAT2\", \"id\", \"PARAMCD\", \"PARAM\", \"AVALU\")   ) %>%     dplyr::select(-\"id\")    adex <- adex %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ 999000   ))    adex2 <- split(adex, adex$USUBJID) %>%     lapply(function(pinfo) {       pinfo %>%         dplyr::filter(.data$PARAMCD == \"DOSE\") %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2, .data$AVISIT) %>%         dplyr::mutate(changeind = dplyr::case_when(           .data$AVISIT == \"SCREENING\" ~ 0,           .data$AVISIT != \"SCREENING\" ~ sample(c(-1, 0, 1),             size = 1,             prob = c(0.25, 0.5, 0.25),             replace = TRUE           )         )) %>%         dplyr::ungroup() %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2) %>%         dplyr::mutate(           csum = cumsum(.data$changeind),           changeind = dplyr::case_when(             .data$csum <= -3 ~ sample(c(0, 1), size = 1, prob = c(0.5, 0.5)),             .data$csum >= 3 ~ sample(c(0, -1), size = 1, prob = c(0.5, 0.5)),             TRUE ~ .data$changeind           )         ) %>%         dplyr::mutate(csum = cumsum(.data$changeind)) %>%         dplyr::ungroup() %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2, .data$AVISIT) %>%         dplyr::mutate(AVAL = dplyr::case_when(           .data$csum == -2 ~ 480,           .data$csum == -1 ~ 720,           .data$csum == 0 ~ 960,           .data$csum == 1 ~ 1200,           .data$csum == 2 ~ 1440         )) %>%         dplyr::select(-c(\"csum\", \"changeind\")) %>%         dplyr::ungroup()     }) %>%     Reduce(rbind, .)    adextmp <- dplyr::full_join(adex2, adex, by = names(adex))   adex <- adextmp %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(AVAL = ifelse(.data$PARAMCD == \"NDOSE\", 1, .data$AVAL)) %>%     dplyr::mutate(AVAL = ifelse(       .data$PARAMCD == \"TNDOSE\",       sum(.data$AVAL[.data$PARAMCD == \"NDOSE\"]),       .data$AVAL     )) %>%     dplyr::ungroup() %>%     dplyr::group_by(.data$USUBJID, .data$STUDYID, .data$PARCAT2) %>%     dplyr::mutate(AVAL = ifelse(       .data$PARAMCD == \"TDOSE\",       sum(.data$AVAL[.data$PARAMCD == \"DOSE\"]),       .data$AVAL     ))    adex <- dplyr::inner_join(adsl, adex, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM)    adex <- adex %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(EXSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ASTDTM,       .data$AVISITN     ) %>%     col_relabel(       PARCAT1 = \"Parameter Category (Individual/Overall)\",       PARCAT2 = \"Parameter Category (Drug A/Drug B)\",       EXSEQ = \"Analysis Sequence Number\"     )    visit_levels <- str_extract(levels(adex$AVISIT), pattern = \"[0-9]+\")   vl_extracted <- vapply(visit_levels, function(x) as.numeric(x[2]), numeric(1))   vl_extracted <- c(-1, 1, vl_extracted[!is.na(vl_extracted)])    tmc_ex_adex <- adex %>%     dplyr::mutate(VISITDY = as.numeric(as.character(factor(AVISIT, labels = vl_extracted)))) %>%     dplyr::mutate(ASTDTM = lubridate::as_datetime(TRTSDTM) + lubridate::days(VISITDY)) %>%     dplyr::distinct(USUBJID, .keep_all = TRUE)    i_lbls <- sapply(     names(col_labels(tmc_ex_adex)[is.na(col_labels(tmc_ex_adex))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adex[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adex, file = \"data/tmc_ex_adex.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adlb","dir":"Articles","previous_headings":"","what":"ADLB","title":"Example Data Generation","text":"","code":"generate_adlb <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_lbs = 3L) {   set.seed(1)   lbcat <- c(\"CHEMISTRY\", \"CHEMISTRY\", \"IMMUNOLOGY\")   param <- c(     \"Alanine Aminotransferase Measurement\",     \"C-Reactive Protein Measurement\",     \"Immunoglobulin A Measurement\"   )   paramcd <- c(\"ALT\", \"CRP\", \"IGA\")   paramu <- c(\"U/L\", \"mg/L\", \"g/L\")   aval_mean <- c(20, 1, 2)   visit_format <- \"WEEK\"    # validate and initialize related variables   lbcat_init_list <- relvar_init(param, lbcat)   param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adlb <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    # assign AVAL based on different test   adlb <- adlb %>%     dplyr::mutate(AVAL = stats::rnorm(nrow(adlb), mean = 1, sd = 0.2)) %>%     dplyr::left_join(data.frame(PARAM = param, ADJUST = aval_mean), by = \"PARAM\") %>%     dplyr::mutate(AVAL = .data$AVAL * .data$ADJUST) %>%     dplyr::select(-\"ADJUST\")    # assign related variable values: PARAMxLBCAT are related   adlb$LBCAT <- as.factor(rel_var(     df = adlb,     var_name = \"LBCAT\",     var_values = lbcat_init_list$relvar2,     related_var = \"PARAM\"   ))    # assign related variable values: PARAMxPARAMCD are related   adlb$PARAMCD <- as.factor(rel_var(     df = adlb,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adlb$AVALU <- as.factor(rel_var(     df = adlb,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adlb <- adlb %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ NA_real_   ))    adlb <- adlb %>%     dplyr::mutate(AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     ))    # order to prepare for change from screening and baseline values   adlb <- adlb[order(adlb$STUDYID, adlb$USUBJID, adlb$PARAMCD, adlb$AVISITN), ]    adlb <- Reduce(rbind, lapply(split(adlb, adlb$USUBJID), function(x) {     x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]     x$ABLFL2 <- ifelse(x$AVISIT == \"SCREENING\", \"Y\", \"\")     x$ABLFL <- ifelse(toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",       \"Y\",       ifelse(toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\", \"Y\", \"\")     )     x   }))    adlb$BASE <- ifelse(adlb$ABLFL2 != \"Y\", retain(adlb, adlb$AVAL, adlb$ABLFL == \"Y\"), NA)   anrind_choices <- c(\"HIGH\", \"LOW\", \"NORMAL\")   adlb <- adlb %>%     dplyr::mutate(BASETYPE = \"LAST\") %>%     dplyr::mutate(ANRIND = sample_fct(anrind_choices, nrow(adlb), prob = c(0.1, 0.1, 0.8))) %>%     dplyr::mutate(ANRLO = dplyr::case_when(       .data$PARAMCD == \"ALT\" ~ 7,       .data$PARAMCD == \"CRP\" ~ 8,       .data$PARAMCD == \"IGA\" ~ 0.8     )) %>%     dplyr::mutate(ANRHI = dplyr::case_when(       .data$PARAMCD == \"ALT\" ~ 55,       .data$PARAMCD == \"CRP\" ~ 10,       .data$PARAMCD == \"IGA\" ~ 3     )) %>%     dplyr::mutate(DTYPE = NA) %>%     dplyr::mutate(       ATOXGR = factor(dplyr::case_when(         .data$ANRIND == \"LOW\" ~ sample(           c(\"-1\", \"-2\", \"-3\", \"-4\", \"-5\"),           nrow(adlb),           replace = TRUE,           prob = c(0.30, 0.25, 0.20, 0.15, 0)         ),         .data$ANRIND == \"HIGH\" ~ sample(           c(\"1\", \"2\", \"3\", \"4\", \"5\"),           nrow(adlb),           replace = TRUE,           prob = c(0.30, 0.25, 0.20, 0.15, 0)         ),         .data$ANRIND == \"NORMAL\" ~ \"0\"       )) %>% with_label(\"Analysis Toxicity Grade\")     ) %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BTOXGR = .data$ATOXGR[.data$ABLFL == \"Y\"]) %>%     dplyr::ungroup() %>%     col_relabel(BTOXGR = \"Baseline Toxicity Grade\")    # High and low descriptions of the different PARAMCD values   # This is currently hard coded as the GDSR does not have these descriptions yet   grade_lookup <- tibble::tribble(     ~PARAMCD, ~ATOXDSCL, ~ATOXDSCH,     \"ALB\", \"Hypoalbuminemia\", NA_character_,     \"ALKPH\", NA_character_, \"Alkaline phosphatase increased\",     \"ALT\", NA_character_, \"Alanine aminotransferase increased\",     \"AST\", NA_character_, \"Aspartate aminotransferase increased\",     \"BILI\", NA_character_, \"Blood bilirubin increased\",     \"CA\", \"Hypocalcemia\", \"Hypercalcemia\",     \"CHOLES\", NA_character_, \"Cholesterol high\",     \"CK\", NA_character_, \"CPK increased\",     \"CREAT\", NA_character_, \"Creatinine increased\",     \"CRP\", NA_character_, \"C reactive protein increased\",     \"GGT\", NA_character_, \"GGT increased\",     \"GLUC\", \"Hypoglycemia\", \"Hyperglycemia\",     \"HGB\", \"Anemia\", \"Hemoglobin increased\",     \"IGA\", NA_character_, \"Immunoglobulin A increased\",     \"POTAS\", \"Hypokalemia\", \"Hyperkalemia\",     \"LYMPH\", \"CD4 lymphocytes decreased\", NA_character_,     \"PHOS\", \"Hypophosphatemia\", NA_character_,     \"PLAT\", \"Platelet count decreased\", NA_character_,     \"SODIUM\", \"Hyponatremia\", \"Hypernatremia\",     \"WBC\", \"White blood cell decreased\", \"Leukocytosis\",   )    # merge grade_lookup onto adlb   adlb <- dplyr::left_join(adlb, grade_lookup, by = \"PARAMCD\")    # merge adsl to be able to add LB date and study day variables   adlb <- dplyr::inner_join(     adsl,     adlb,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::ungroup() %>%     dplyr::group_by(USUBJID) %>%     dplyr::arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adlb <- adlb %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(LBSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$BASETYPE,       .data$AVISITN,       .data$DTYPE,       .data$ADTM,       .data$LBSEQ     ) %>%     col_relabel(LBSEQ = \"Lab Test or Examination Sequence Number\")    adlb <- adlb %>% dplyr::mutate(ONTRTFL = factor(dplyr::case_when(     is.na(.data$TRTSDTM) ~ \"\",     is.na(.data$ADTM) ~ \"Y\",     (.data$ADTM < .data$TRTSDTM) ~ \"\",     (.data$ADTM > .data$TRTEDTM) ~ \"\",     TRUE ~ \"Y\"   )))    flag_variables <- function(data,                              apply_grouping,                              apply_filter,                              apply_mutate) {     data_compare <- data %>% dplyr::mutate(row_check = seq_len(nrow(data)))     data <- data_compare %>%       {         if (apply_grouping == TRUE) {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE, .data$AVISIT)         } else {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE)         }       } %>%       dplyr::arrange(.data$ADTM, .data$LBSEQ) %>%       {         if (apply_filter == TRUE) {           dplyr::filter(             .,             (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           ) %>%             dplyr::filter(.data$ATOXGR == max(as.numeric(as.character(.data$ATOXGR))))         } else if (apply_filter == FALSE) {           dplyr::filter(             .,             (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           ) %>%             dplyr::filter(.data$ATOXGR == min(as.numeric(as.character(.data$ATOXGR))))         } else {           dplyr::filter(             .,             .data$AVAL == min(.data$AVAL) &               (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           )         }       } %>%       dplyr::slice(1) %>%       {         if (apply_mutate == TRUE) {           dplyr::mutate(., new_var = ifelse(is.na(.data$DTYPE), \"Y\", \"\"))         } else {           dplyr::mutate(., new_var = ifelse(is.na(.data$AVAL) == FALSE & is.na(.data$DTYPE), \"Y\", \"\"))         }       } %>%       dplyr::ungroup()      data_compare$new_var <- ifelse(data_compare$row_check %in% data$row_check, \"Y\", \"\")     data_compare <- data_compare[, -which(names(data_compare) %in% c(\"row_check\"))]     return(data_compare)   }   adlb <- flag_variables(adlb, TRUE, \"ELSE\", FALSE) %>% dplyr::rename(WORS01FL = \"new_var\")   adlb <- flag_variables(adlb, FALSE, TRUE, TRUE) %>% dplyr::rename(WGRHIFL = \"new_var\")   adlb <- flag_variables(adlb, FALSE, FALSE, TRUE) %>% dplyr::rename(WGRLOFL = \"new_var\")   adlb <- flag_variables(adlb, TRUE, TRUE, TRUE) %>% dplyr::rename(WGRHIVFL = \"new_var\")   adlb <- flag_variables(adlb, TRUE, FALSE, TRUE) %>% dplyr::rename(WGRLOVFL = \"new_var\")    tmc_ex_adlb <- adlb %>% dplyr::mutate(     ANL01FL = ifelse(       (.data$ABLFL == \"Y\" | (.data$WORS01FL == \"Y\" & is.na(.data$DTYPE))) &         (.data$AVISIT != \"SCREENING\"),       \"Y\",       \"\"     ) %>% with_label(\"Analysis Flag 01 Baseline Post-Baseline\"),     PARAM = as.factor(.data$PARAM)   )    tmc_ex_adlb <- tmc_ex_adlb %>%     group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     mutate(BNRIND = .data$ANRIND[.data$ABLFL == \"Y\"]) %>%     ungroup() %>%     dplyr::mutate(ADY = ceiling(as.numeric(difftime(.data$ADTM, .data$TRTSDTM, units = \"days\"))))    tmc_ex_adlb$PARAMCD <- as.factor(tmc_ex_adlb$PARAMCD)   tmc_ex_adlb <- tmc_ex_adlb %>%     dplyr::mutate(CHG = .data$AVAL - .data$BASE) %>%     dplyr::mutate(PCHG = 100 * (.data$CHG / .data$BASE)) %>%     col_relabel(       LBCAT = \"Category for Lab Test\",       ATOXDSCL = \"Analysis Toxicity Description Low\",       ATOXDSCH = \"Analysis Toxicity Description High\",       WGRHIFL = \"Worst High Grade per Patient\",       WGRLOFL = \"Worst Low Grade per Patient\",       WGRHIVFL = \"Worst High Grade per Patient per Visit\",       WGRLOVFL = \"Worst Low Grade per Patient per Visit\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adlb)[is.na(col_labels(tmc_ex_adlb))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adlb[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adlb, file = \"data/tmc_ex_adlb.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"admh","dir":"Articles","previous_headings":"","what":"ADMH","title":"Example Data Generation","text":"","code":"generate_admh <- function(adsl = tmc_ex_adsl,                           max_n_mhs = 10L) {   set.seed(1)   lookup_mh <- tibble::tribble(     ~MHBODSYS, ~MHDECOD, ~MHSOC,     \"cl A\", \"trm A_1/2\", \"cl A\",     \"cl A\", \"trm A_2/2\", \"cl A\",     \"cl B\", \"trm B_1/3\", \"cl B\",     \"cl B\", \"trm B_2/3\", \"cl B\",     \"cl B\", \"trm B_3/3\", \"cl B\",     \"cl C\", \"trm C_1/2\", \"cl C\",     \"cl C\", \"trm C_2/2\", \"cl C\",     \"cl D\", \"trm D_1/3\", \"cl D\",     \"cl D\", \"trm D_2/3\", \"cl D\",     \"cl D\", \"trm D_3/3\", \"cl D\"   )    admh <- Map(     function(id, sid) {       n_mhs <- sample(0:max_n_mhs, 1)       i <- sample(seq_len(nrow(lookup_mh)), n_mhs, TRUE)       dplyr::mutate(         lookup_mh[i, ],         USUBJID = id,         STUDYID = sid       )     },     adsl$USUBJID,     adsl$STUDYID   ) %>%     Reduce(rbind, .) %>%     `[`(c(4, 5, 1, 2, 3)) %>%     dplyr::mutate(MHTERM = .data$MHDECOD %>% with_label(\"Reported Term for the Medical History\"))    admh <- dplyr::inner_join(     adsl,     admh,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$MHTERM) %>%     dplyr::mutate(MHDISTAT = sample(       x = c(\"Resolved\", \"Ongoing with treatment\", \"Ongoing without treatment\"),       prob = c(0.6, 0.2, 0.2),       size = dplyr::n(),       replace = TRUE     ) %>% with_label(\"Status of Disease\"))    tmc_ex_admh <- admh %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(MHSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM) %>%     col_relabel(       MHBODSYS = \"Body System or Organ Class\",       MHDECOD = \"Dictionary-Derived Term\",       MHSOC = \"Primary System Organ Class\",       MHSEQ = \"Sponsor-Defined Identifier\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_admh)[is.na(col_labels(tmc_ex_admh))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_admh[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_admh, file = \"data/tmc_ex_admh.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adqs","dir":"Articles","previous_headings":"","what":"ADQS","title":"Example Data Generation","text":"","code":"generate_adqs <- function(adsl = tmc_ex_adsl,                           n_assessments = 5L,                           n_days = 5L) {   set.seed(1)   param <- c(     \"BFI All Questions\",     \"Fatigue Interference\",     \"Function/Well-Being (GF1,GF3,GF7)\",     \"Treatment Side Effects (GP2,C5,GP5)\",     \"FKSI-19 All Questions\"   )   paramcd <- c(\"BFIALL\", \"FATIGI\", \"FKSI-FWB\", \"FKSI-TSE\", \"FKSIALL\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)    adqs <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = param_init_list$relvar1,     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    adqs <- dplyr::mutate(     adqs,     AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     )   )    adqs$PARAMCD <- rel_var(df = adqs, var_name = \"PARAMCD\", var_values = param_init_list$relvar2, related_var = \"PARAM\")   adqs$AVAL <- stats::rnorm(nrow(adqs), mean = 50, sd = 8) + adqs$AVISITN * stats::rnorm(nrow(adqs), mean = 5, sd = 2)   adqs <- adqs[order(adqs$STUDYID, adqs$USUBJID, adqs$PARAMCD, adqs$AVISITN), ]    adqs <- Reduce(     rbind,     lapply(       split(adqs, adqs$USUBJID),       function(x) {         x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]         x$ABLFL2 <- ifelse(x$AVISIT == \"SCREENING\", \"Y\", \"\")         x$ABLFL <- ifelse(           toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",           \"Y\",           ifelse(             toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\",             \"Y\",             \"\"           )         )         x       }     )   )    adqs$BASE <- ifelse(adqs$ABLFL2 != \"Y\", retain(adqs, adqs$AVAL, adqs$ABLFL == \"Y\"), NA)   adqs <- adqs %>% dplyr::mutate(CHG = .data$AVAL - .data$BASE)    adqs <- dplyr::inner_join(     adsl,     adqs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     ungroup() %>%     group_by(USUBJID) %>%     arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    tmc_ex_adqs <- adqs %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adqs)[is.na(col_labels(tmc_ex_adqs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adqs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adqs, file = \"data/tmc_ex_adqs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adrs","dir":"Articles","previous_headings":"","what":"ADRS","title":"Example Data Generation","text":"","code":"generate_adrs <- function(adsl = tmc_ex_adsl) {   set.seed(1)   param_codes <- stats::setNames(1:5, c(\"CR\", \"PR\", \"SD\", \"PD\", \"NE\"))    lookup_ars <- expand.grid(     ARM = c(\"A: Drug X\", \"B: Placebo\", \"C: Combination\"),     AVALC = names(param_codes)   ) %>% dplyr::mutate(     AVAL = param_codes[.data$AVALC],     p_scr = c(rep(0, 3), rep(0, 3), c(1, 1, 1), c(0, 0, 0), c(0, 0, 0)),     p_bsl = c(rep(0, 3), rep(0, 3), c(1, 1, 1), c(0, 0, 0), c(0, 0, 0)),     p_cycle = c(c(.35, .25, .4), c(.30, .20, .20), c(.2, .25, .3), c(.14, 0.20, 0.18), c(.01, 0.1, 0.02)),     p_eoi = c(c(.35, .25, .4), c(.30, .20, .20), c(.2, .25, .3), c(.14, 0.20, 0.18), c(.01, 0.1, 0.02)),     p_fu = c(c(.25, .15, .3), c(.15, .05, .25), c(.3, .25, .3), c(.3, .55, .25), rep(0, 3))   )    adrs <- split(adsl, adsl$USUBJID) %>%     lapply(function(pinfo) {       probs <- dplyr::filter(lookup_ars, .data$ARM == as.character(pinfo$ACTARM))       # screening       rsp_screen <- sample(probs$AVALC, 1, prob = probs$p_scr) %>% as.character()       # baseline       rsp_bsl <- sample(probs$AVALC, 1, prob = probs$p_bsl) %>% as.character()       # cycle       rsp_c2d1 <- sample(probs$AVALC, 1, prob = probs$p_cycle) %>% as.character()       rsp_c4d1 <- sample(probs$AVALC, 1, prob = probs$p_cycle) %>% as.character()       # end of induction       rsp_eoi <- sample(probs$AVALC, 1, prob = probs$p_eoi) %>% as.character()       # follow up       rsp_fu <- sample(probs$AVALC, 1, prob = probs$p_fu) %>% as.character()        best_rsp <- min(param_codes[c(rsp_screen, rsp_bsl, rsp_eoi, rsp_fu, rsp_c2d1, rsp_c4d1)])       best_rsp_i <- which.min(param_codes[c(rsp_screen, rsp_bsl, rsp_eoi, rsp_fu, rsp_c2d1, rsp_c4d1)])        avisit <- c(\"SCREENING\", \"BASELINE\", \"CYCLE 2 DAY 1\", \"CYCLE 4 DAY 1\", \"END OF INDUCTION\", \"FOLLOW UP\")        # meaningful date information       TRTSTDT <- lubridate::date(pinfo$TRTSDTM)        TRTENDT <- lubridate::date(dplyr::if_else(          !is.na(pinfo$TRTEDTM), pinfo$TRTEDTM,         lubridate::floor_date(TRTSTDT + study_duration_secs, unit = \"day\")       ))       scr_date <- TRTSTDT - lubridate::days(100)       bs_date <- TRTSTDT       flu_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       eoi_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       c2d1_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       c4d1_date <- min(lubridate::date(c2d1_date + lubridate::days(60)), TRTENDT)        tibble::tibble(         STUDYID = pinfo$STUDYID,         USUBJID = pinfo$USUBJID,         PARAMCD = as.factor(c(rep(\"OVRINV\", 6), \"BESRSPI\", \"INVET\")),         PARAM = as.factor(dplyr::recode(           .data$PARAMCD,           OVRINV = \"Overall Response by Investigator - by visit\",           OVRSPI = \"Best Overall Response by Investigator (no confirmation required)\",           BESRSPI = \"Best Confirmed Overall Response by Investigator\",           INVET = \"Investigator End Of Induction Response\"         )),         AVALC = c(           rsp_screen, rsp_bsl, rsp_c2d1, rsp_c4d1, rsp_eoi, rsp_fu,           names(param_codes)[best_rsp],           rsp_eoi         ),         AVAL = param_codes[.data$AVALC],         AVISIT = factor(c(avisit, avisit[best_rsp_i], avisit[5]), levels = avisit)       ) %>%         merge(           tibble::tibble(             AVISIT = avisit,             ADTM = c(scr_date, bs_date, c2d1_date, c4d1_date, eoi_date, flu_date),             AVISITN = c(-1, 0, 2, 4, 999, 999),             TRTSDTM = pinfo$TRTSDTM           ) %>%             dplyr::select(-\"TRTSDTM\"),           by = \"AVISIT\"         )     }) %>%     Reduce(rbind, .) %>%     dplyr::mutate(       AVALC = factor(.data$AVALC, levels = names(param_codes)),       DTHFL = factor(sample(c(\"Y\", \"N\"), nrow(.), replace = TRUE, prob = c(1, 0.8))) %>%         with_label(\"Death Flag\")     )    # merge ADSL to be able to add RS date and study day variables   adrs <- dplyr::inner_join(     adsl,     adrs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   )    tmc_ex_adrs <- adrs %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adrs)[is.na(col_labels(tmc_ex_adrs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adrs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adrs, file = \"data/tmc_ex_adrs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"adtte","dir":"Articles","previous_headings":"","what":"ADTTE","title":"Example Data Generation","text":"","code":"generate_adtte <- function(adsl = tmc_ex_adsl) {   set.seed(1)   lookup_tte <- tibble::tribble(     ~ARM, ~PARAMCD, ~PARAM, ~LAMBDA, ~CNSR_P,     \"ARM A\", \"OS\", \"Overall Survival\", log(2) / 610, 0.4,     \"ARM B\", \"OS\", \"Overall Survival\", log(2) / 490, 0.3,     \"ARM C\", \"OS\", \"Overall Survival\", log(2) / 365, 0.2,     \"ARM A\", \"PFS\", \"Progression Free Survival\", log(2) / 365, 0.4,     \"ARM B\", \"PFS\", \"Progression Free Survival\", log(2) / 305, 0.3,     \"ARM C\", \"PFS\", \"Progression Free Survival\", log(2) / 243, 0.2,     \"ARM A\", \"EFS\", \"Event Free Survival\", log(2) / 365, 0.4,     \"ARM B\", \"EFS\", \"Event Free Survival\", log(2) / 305, 0.3,     \"ARM C\", \"EFS\", \"Event Free Survival\", log(2) / 243, 0.2,     \"ARM A\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 305, 0.4,     \"ARM B\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 243, 0.3,     \"ARM C\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 182, 0.2   )    evntdescr_sel <- c(     \"Death\",     \"Disease Progression\",     \"Last Tumor Assessment\",     \"Adverse Event\",     \"Last Date Known To Be Alive\"   )    cnsdtdscr_sel <- c(     \"Preferred Term\",     \"Clinical Cut Off\",     \"Completion or Discontinuation\",     \"End of AE Reporting Period\"   )    adtte <- split(adsl, adsl$USUBJID) %>%     lapply(FUN = function(pinfo) {       lookup_tte %>%         dplyr::filter(.data$ARM == as.character(pinfo$ACTARMCD)) %>%         dplyr::rowwise() %>%         dplyr::mutate(           STUDYID = pinfo$STUDYID,           USUBJID = pinfo$USUBJID,           CNSR = sample(c(0, 1), 1, prob = c(1 - .data$CNSR_P, .data$CNSR_P)),           AVAL = stats::rexp(1, .data$LAMBDA),           AVALU = \"DAYS\",           EVNTDESC = if (.data$CNSR == 1) {             sample(evntdescr_sel[-c(1:2)], 1)           } else {             ifelse(.data$PARAMCD == \"OS\",               sample(evntdescr_sel[1], 1),               sample(evntdescr_sel[c(1:2)], 1)             )           }         ) %>%         dplyr::select(-\"LAMBDA\", -\"CNSR_P\")     }) %>%     Reduce(rbind, .)    # merge ADSL to be able to add TTE date and study day variables   adtte <- dplyr::inner_join(     adsl,     dplyr::select(adtte, -\"ARM\"),     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ADTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adtte <- adtte %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(PARAM = as.factor(.data$PARAM)) %>%     dplyr::mutate(PARAMCD = as.factor(.data$PARAMCD)) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )   lbls <- col_labels(adtte)    # adding adverse event counts and log follow-up time   tmc_ex_adtte <- dplyr::bind_rows(     adtte,     data.frame(adtte %>%       dplyr::group_by(.data$USUBJID) %>%       dplyr::slice_head(n = 1) %>%       dplyr::mutate(         PARAMCD = \"TNE\",         PARAM = \"Total Number of Exacerbations\",         AVAL = stats::rpois(1, 3),         AVALU = \"COUNT\",         lgTMATRSK = log(stats::rexp(1, rate = 3)),         dplyr::across(c(\"ADTM\", \"EVNTDESC\"), ~NA)       ))   ) %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )   col_labels(tmc_ex_adtte) <- c(lbls, lgTMATRSK = \"Log Time At Risk\")    i_lbls <- sapply(     names(col_labels(tmc_ex_adtte)[is.na(col_labels(tmc_ex_adtte))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adtte[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adtte, file = \"data/tmc_ex_adtte.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"advs","dir":"Articles","previous_headings":"","what":"ADVS","title":"Example Data Generation","text":"","code":"generate_advs <- function(adsl = tmc_ex_adsl,                           n_assessments = 5L,                           n_days = 5L) {   set.seed(1)   param <- c(     \"Diastolic Blood Pressure\",     \"Pulse Rate\",     \"Respiratory Rate\",     \"Systolic Blood Pressure\",     \"Temperature\", \"Weight\"   )   paramcd <- c(\"DIABP\", \"PULSE\", \"RESP\", \"SYSBP\", \"TEMP\", \"WEIGHT\")   paramu <- c(\"Pa\", \"beats/min\", \"breaths/min\", \"Pa\", \"C\", \"Kg\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    advs <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments),     stringsAsFactors = FALSE   )    advs <- dplyr::mutate(     advs,     AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     )   )    advs$PARAMCD <- as.factor(rel_var(     df = advs,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))   advs$AVALU <- as.factor(rel_var(     df = advs,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    advs$AVAL <- stats::rnorm(nrow(advs), mean = 50, sd = 8)   advs <- advs[order(advs$STUDYID, advs$USUBJID, advs$PARAMCD, advs$AVISITN), ]    advs <- dplyr::inner_join(     adsl,     advs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ADTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ADY = ceiling(difftime(ADTM, TRTSDTM, units = \"days\"))) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    tmc_ex_advs <- advs %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_advs)[is.na(col_labels(tmc_ex_advs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_advs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_advs, file = \"data/tmc_ex_advs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/generate_tmc_test_data.html","id":"generate-data","dir":"Articles","previous_headings":"","what":"Generate Data","title":"Example Data Generation","text":"","code":"# Generate & load adsl tmp_fol <- getwd() setwd(dirname(tmp_fol)) generate_adsl() load(\"data/tmc_ex_adsl.rda\")  # Generate other datasets generate_adae() generate_adaette() generate_adcm() generate_adeg() generate_adex() generate_adlb() generate_admh() generate_adqs() generate_adrs() generate_adtte() generate_advs()  setwd(tmp_fol)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"section","dir":"Articles","previous_headings":"","what":"Quick start: `substitute` for NSE","title":"Quick start: `substitute` for NSE","text":"Considering expression, R usually evaluates returns value. Instead focusing value, also possible work code generated value. non standard evaluation, NSE, starts. function substitute important element non-standard evaluation. instance, consider defined <- 5, expression returns 5, substitute() returns code obtain value: . principle teal relies : generate expressions. return result expression result panel app. return corresponding code (expression) Show R Code. expression returning displayed value must reactive. information encoding one hand, filtering panel hand modify expression displayed value. , teal needs work expressions values relies heavily NSE. NSE advanced notion mixing Shiny app development source difficulties : hindered coding efficiency Shiny app must run order check correct execution code. limited possibilities testing. alternative, possible focus first NSE aspects plain R, ready, integrate Shiny App. following practical examples demonstrating NSE works. choice made focus substitute.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"nse-principle","dir":"Articles","previous_headings":"The Basics","what":"NSE Principle","title":"Quick start: `substitute` for NSE","text":"happened? substitute returns code value, attempt run code, therefore possible return expression make sense (yet), instance involving two non defined objects. values b exist, expression can run without error: Now, function name substitute reason. returning expression, also operates substitutions terms within given expression. happened? objects b exist function environment substitute called. terms expression within substitute replaced values b. Indeed, returning expression, substitute verifies b don’t value existing evaluation environment. , values b used expression. also possible use second argument substitute, env, environment (list) containing objects. expression submitted substitute corresponding objects env, terms within expression substituted provided values: happened? environment values b taken directly declared within substitute expression (argument expr) values substituted (argument env). substitute returned non-evaluated expression, use eval() evaluate . slightly elaborate expression:  Note : x argument name plot preserved, x object replaced.","code":"non_evaluated_expression <- substitute(expr = a + b) non_evaluated_expression ## a + b eval(non_evaluated_expression) ## Error in eval(non_evaluated_expression): object 'b' not found non_evaluated_expression <- substitute(expr = a + b) a <- 1 b <- 5 eval(non_evaluated_expression) ## [1] 6 fun <- function(a, b) {   substitute(expr = a + b) } non_evaluated_expression <- fun(5, -2) non_evaluated_expression ## 5 + -2 eval(non_evaluated_expression) ## [1] 3 non_evaluated_expression <- substitute(   expr = a + b,   env = list(a = 5, b = 5) ) non_evaluated_expression ## 5 + 5 eval(non_evaluated_expression) ## [1] 10 non_evaluated_expression <- substitute(   expr = plot(x = x, y = exp(x), main = text),   env = list(x = 0:10, text = \"A graph\") ) non_evaluated_expression ## plot(x = 0:10, y = exp(0:10), main = \"A graph\") eval(non_evaluated_expression)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"replace-an-object-name","dir":"Articles","previous_headings":"The Basics","what":"Replace an object name","title":"Quick start: `substitute` for NSE","text":"formulas, character strings accepted, execute substitution? object names specific class (name); .names coerces character string object name (alternatively, .symbol provides identical result):","code":"# Error expected: plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = Sepal.Length,     y = Sepal.Width,     text = \"Iris, again ...\"   ) ) ## Error in eval(expr, envir, enclos): object 'Sepal.Length' not found # Error expected: plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = \"Sepal.Length\",     y = \"Sepal.Width\",     text = \"Iris, again ...\"   ) ) plot_expr ## plot(\"Sepal.Width\" ~ \"Sepal.Length\", data = iris, main = \"Iris, again ...\") eval(plot_expr) ## Error in terms.formula(formula, data = data): invalid term in model formula plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) plot_expr ## plot(Sepal.Width ~ Sepal.Length, data = iris, main = \"Iris, again ...\") eval(plot_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"what-about-dataframe-names","dir":"Articles","previous_headings":"The Basics","what":"What about dataframe names?","title":"Quick start: `substitute` for NSE","text":"Lets imagine pipe-flavored expression, df term corresponding dataframe substituted: df %>% plot(y ~ x, data = ., main = text). principle exposed can work directly without addition. However, df expression replaced directly value object provided expression generating dataframe: pipeline working humanly readable.  can replace value expression generating value? pretty much topic vignette: substitute.","code":"library(dplyr) ##  ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ##  ##     filter, lag ## The following objects are masked from 'package:base': ##  ##     intersect, setdiff, setequal, union  short_iris <- head(iris) plot_expr <- substitute(   expr = df %>% plot(y ~ x, data = ., main = text),   env = list(     df = short_iris,     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) eval(plot_expr) plot_expr ## list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4), Sepal.Width = c(3.5,  ## 3, 3.2, 3.1, 3.6, 3.9), Petal.Length = c(1.4, 1.4, 1.3, 1.5,  ## 1.4, 1.7), Petal.Width = c(0.2, 0.2, 0.2, 0.2, 0.2, 0.4), Species = c(1L,  ## 1L, 1L, 1L, 1L, 1L)) %>% plot(Sepal.Width ~ Sepal.Length, data = .,  ##     main = \"Iris, again ...\") plot_expr <- substitute(   expr = df %>% plot(y ~ x, data = ., main = text),   env = list(     df = substitute(iris),     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) plot_expr ## iris %>% plot(Sepal.Width ~ Sepal.Length, data = ., main = \"Iris, again ...\") eval(plot_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"in-a-nutshell","dir":"Articles","previous_headings":"The Basics","what":"In a nutshell","title":"Quick start: `substitute` for NSE","text":"expr expression (eventually) substituted. env environment potential replacement value might needed. object name (like formulas e.g. y ~ x) , use .name .symbol. data frame name (like iris) , use substitute.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"direct-use-of-substitute","dir":"Articles","previous_headings":"rtables","what":"Direct use of substitute","title":"Quick start: `substitute` for NSE","text":"substitute approach can used rtables pipelines. Lets prepare example reporting data LB domain. example based template LBT01; target report columns lab test result per study arm, values (AVAL) changes baseline (CHG), per analysis visit rows. data can prepared follows: rtables expression obtained : expression valid … : … easily readable …: … can arranged:","code":"library(teal.modules.clinical) library(dplyr)  adlb <- tmc_ex_adlb adlb_f <- adlb %>%   filter(     PARAM == \"Alanine Aminotransferase Measurement\" &       ARMCD %in% c(\"ARM A\", \"ARM B\") & AVISIT == \"WEEK 1 DAY 8\"   ) rtables_expr <- substitute(   expr = basic_table() %>%     split_cols_by(arm, split_fun = drop_split_levels) %>%     split_rows_by(visit, split_fun = drop_split_levels) %>%     split_cols_by_multivar(       vars = c(\"AVAL\", \"CHG\"),       varlabels = c(\"Value\", \"Change\")     ) %>%     summarize_colvars() %>%     build_table(df = df),   env = list(     df = substitute(adlb_f),     arm = \"ARM\",     visit = \"AVISIT\"   ) ) eval(rtables_expr) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 rtables_expr ## basic_table() %>% split_cols_by(\"ARM\", split_fun = drop_split_levels) %>%  ##     split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>%  ##     split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c(\"Value\",  ##         \"Change\")) %>% summarize_colvars() %>% build_table(df = adlb_f) library(teal) library(styler)  #' Stylish code #' #' Deparse an expression and display the code following NEST conventions. #' #' @param expr (`call`)\\cr or possibly understood as so. #' styled_expr <- function(expr) {   print(     styler::style_text(text = deparse(expr)),     colored = FALSE   ) } #' #' @examples styled_expr(rtables_expr) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"substitute-in-a-function","dir":"Articles","previous_headings":"rtables","what":"substitute in a function","title":"Quick start: `substitute` for NSE","text":"Moving , substitute can actually wrapped function, way rtables pipelines programmatically obtained: results obtained … , fine tuning easier. instance, variable designating study arm visit can changed, expected feature teal module encoding panel.","code":"rtables_expr <- function(df,                          arm,                          visit) {   substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ) %>%       summarize_colvars() %>%       build_table(df = df),     env = list(       df = substitute(df),       arm = arm,       visit = visit     )   ) } result <- rtables_expr(df = adlb_f, arm = \"ARM\", visit = \"AVISIT\") styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f) eval(result) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 result <- rtables_expr(df = adlb_f, arm = \"ARMCD\", visit = \"AVISITN\") eval(result) ## Split var [AVISITN] was not character or factor. Converting to factor ##                         ARM A                        ARM B            ##                  Value         Change         Value         Change    ## ————————————————————————————————————————————————————————————————————— ## 1                                                                     ##   n               69             69            73             73      ##   Mean (SD)   20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median         20.4           2.4           20.0           -0.2     ##   Min - Max   12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARMCD\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISITN\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"chain-expressions-in-a-pipeline","dir":"Articles","previous_headings":"rtables","what":"Chain expressions in a pipeline","title":"Quick start: `substitute` for NSE","text":"also possible manipulate expressions, instance, expressions might chained pipeline. Expressions can arranged list, way, possible conditional editing expressions. context rtables, layers enclosing analyze call handle .stats option. lean expression include .stats option, default value changed. expected feature teal module rendering code Show R Code: First application standard statistics: statistics specifications:","code":"#' Expressions as a pipeline #' #' Accepts expressions to be chained using the `magrittr` pipeline-flavor. #' @param ... (`call`)\\cr or object which can be interpreted as so. #'    (e.g. `name`) #' pipe_expr <- function(...) {   exprs <- unlist(list(...))   exprs <- lapply(     exprs,     function(x) {       x <- deparse(x)       paste(x, collapse = \" \")     }   )   exprs <- unlist(exprs)   exprs <- paste(exprs, collapse = \" %>% \")   str2lang(exprs) }  #' @examples result <- pipe_expr(   expr1 = substitute(df),   expr2 = substitute(head) ) result ## df %>% head rtables_expr <- function(df,                          arm,                          visit,                          .stats = NULL) {   # The rtables layout is decomposed into a list of expressions.   lyt <- list()   # 1. First the columns and rows:   lyt$structure <- substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ),     env = list(       arm = arm,       visit = visit     )   )   # 2. The analyze layer which depends on the use of .stats.   lyt$analyze <- if (is.null(.stats)) {     substitute(       summarize_colvars()     )   } else {     substitute(       summarize_colvars(.stats = .stats),       list(.stats = .stats)     )   }   # 3. And finishing with rtables::build_table.   lyt$build <- substitute(     build_table(df = df),     list(df = substitute(df))   )   # As previously demonstrated, expressions can be manipulated and   # chained in a pipeline.   pipe_expr(lyt) } result <- rtables_expr(df = adlb_f, arm = \"ARM\", visit = \"AVISIT\") styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f) eval(result) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 result <- rtables_expr(   df = adlb_f, arm = \"ARM\", visit = \"AVISIT\",   .stats = c(\"n\", \"mean_sd\") ) styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars(.stats = c(\"n\", \"mean_sd\")) %>% ##   build_table(df = adlb_f) eval(result) ##                      A: Drug X                B: Placebo        ##                  Value       Change       Value        Change   ## ——————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                    ##   n                69          69           73           73     ##   Mean (SD)    20.8 (4.1)   1.6 (6.1)   20.2 (4.1)   -0.2 (5.6)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"including-pre-processing","dir":"Articles","previous_headings":"rtables","what":"Including pre-processing","title":"Quick start: `substitute` for NSE","text":"Finally, also possible wrap several expressions single function. instance, teal module generally includes pre-processing section: now possible modify studied parameter (PARAMCD) addition study arm visit variables names. two expressions consistent: two expressions can executed return rtables:","code":"rtables_expr <- function(df,                          paramcd,                          arm,                          visit,                          .stats = NULL) {   # y is a list which will collect two expressions:   # 1. y$data with the preprocessing steps.   # 2. y$rtables the table layout and build.   y <- list()   # 1. Preprocessing ---   y$data <- substitute(     df <- df %>%       filter(         PARAMCD == paramcd &           ARMCD %in% c(\"ARM A\", \"ARM B\") & AVISIT == \"WEEK 1 DAY 8\"       ),     list(       df = substitute(df),       paramcd = paramcd     )   )   # 2. rtables layout ---   lyt <- list()   lyt$structure <- substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ),     env = list(       arm = arm,       visit = visit     )   )   lyt$analyze <- if (is.null(.stats)) {     substitute(       summarize_colvars()     )   } else {     substitute(       summarize_colvars(.stats = .stats),       list(.stats = .stats)     )   }   lyt$build <- substitute(     build_table(df = df),     list(df = substitute(df))   )   y$rtables <- pipe_expr(lyt)   # Finally returns y as a list with two expressions.   y } adlb <- tmc_ex_adlb result <- rtables_expr(   df = adlb, paramcd = \"CRP\", arm = \"ARM\", visit = \"AVISIT\",   .stats = c(\"n\", \"mean_sd\") ) styled_expr(result$data) ## adlb <- adlb %>% filter(PARAMCD == \"CRP\" & ARMCD %in% c( ##   \"ARM A\", ##   \"ARM B\" ## ) & AVISIT == \"WEEK 1 DAY 8\") styled_expr(result$rtables) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars(.stats = c(\"n\", \"mean_sd\")) %>% ##   build_table(df = adlb) result_exec <- mapply(eval, result) result_exec$rtables ##                      A: Drug X              B: Placebo       ##                  Value      Change       Value      Change   ## ———————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                 ##   n               69          69          73          73     ##   Mean (SD)    1.0 (0.2)   0.0 (0.3)   1.0 (0.2)   0.0 (0.3)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/quickstart_substitute.html","id":"in-a-nutshell-1","dir":"Articles","previous_headings":"rtables","what":"In a nutshell","title":"Quick start: `substitute` for NSE","text":"point, possible : generate rtables pipelines. chain expressions pipeline (e.g. pipe_expr) decompose rtables pipeline add conditional layers (e.g. .stats). group expressions single list control pre-processing rtables pipeline.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/teal-modules-clinical.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started with {teal.modules.clinical}","text":"teal.modules.clinical package implementing number teal modules helpful exploring clinical trials data, specifically targeted towards data following ADaM standards. teal.modules.clinical modules can used data ADaM standard clinical data, features package tailored towards data type. concepts presented require knowledge core features teal, specifically launch teal application pass data . Therefore, highly recommended refer home page introductory vignette teal package.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/teal-modules-clinical.html","id":"main-features","dir":"Articles","previous_headings":"","what":"Main Features","title":"Getting Started with {teal.modules.clinical}","text":"package provides ready--use teal modules can embed teal application. modules generate highly customizable tables, plots, outputs often used exploratory data analysis, including: ANCOVA - tm_t_ancova() Cox regression - tm_t_coxreg() Kaplan-Meier plot - tm_g_km() Logistic regression - tm_t_logistic() Bar chart - tm_g_barchart_simple() Confidence interval plot - tm_g_ci() Binary outcome response table - tm_t_binary_outcome() Summary adverse events table - tm_t_events_summary() SMQ table - tm_t_smq() Time--event table - tm_t_tte() library also offers group patient profile modules targeted clinical statisticians physicians want review data per patient basis. modules present data patient’s adverse events, severity, current therapy, laboratory results . See full index package functions & modules .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/articles/teal-modules-clinical.html","id":"a-simple-application","dir":"Articles","previous_headings":"","what":"A Simple Application","title":"Getting Started with {teal.modules.clinical}","text":"teal.modules.clinical module needs embedded inside shiny/teal application interact . simple application including bar chart module look like : Consider consulting documentation examples module (e.g. ?tm_g_barchart_simple). many, can also find useful links TLG Catalog additional example apps can found. teal.modules.clinical exports modules needs support libraries run teal app flesh functionality. example , tm_g_barchart_simple() function teal.modules.clinical whereas init() teal function, data_extract_spec(), select_spec(), variable_choices() teal.transform functions, cdisc_data() teal.data function. Let’s break app pieces: lines load libraries used example. use example data provided teal.modules.clinical package: nestcolor optional package can loaded apply standardized NEST color palette module plots. need load teal teal.modules.clinical already depends . next step, use teal create shiny UI server functions can launch using shiny. data argument tells teal input data - ADaM datasets ADSL ADAE - modules argument indicates modules included application. , include one module: tm_g_barchart_simple(). Finally, use shiny launch application: teal.modules.clinical modules allow specification arguments using teal.transform::choices_selected(), tm_t_summary() module following example. Please refer API reference specific modules examples information customization options available.","code":"library(teal.modules.clinical) library(nestcolor)  ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = list(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADAE\",         select = select_spec(           choices = variable_choices(             ADAE,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       )     )   ) )  if (interactive()) shinyApp(app$ui, app$server) library(teal.modules.clinical) library(nestcolor) ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = list(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADAE\",         select = select_spec(           choices = variable_choices(             ADAE,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       )     )   ) ) if (interactive()) shinyApp(app$ui, app$server) ADSL <- tmc_ex_adsl  app <- init(   data = cdisc_data(ADSL = ADSL, code = \"ADSL <- tmc_ex_adsl\"),   modules = list(     tm_t_summary(       label = \"Demographic Table\",       dataname = \"ADSL\",       arm_var = choices_selected(choices = c(\"ARM\", \"ARMCD\"), selected = \"ARM\"),       summarize_vars = choices_selected(         choices = c(\"SEX\", \"RACE\", \"BMRKR2\", \"EOSDY\", \"DCSREAS\", \"AGE\"),         selected = c(\"SEX\", \"RACE\")       )     )   ) )  if (interactive()) shinyApp(app$ui, app$server)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Mahmoud Hallal. Author. Dawid Kaledkowski. Author. Rosemary Li. Author. Heng Wang. Author. Pawel Rucki. Author. Nikolas Burkoff. Author. Konrad Pagacz. Author. Vaakesan Sundrelingam. Contributor. Francois Collin. Contributor. Imanol Zubizarreta. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Hallal M, Kaledkowski D, Li R, Wang H, Rucki P, Burkoff N, Pagacz K (2024). teal.modules.clinical: 'teal' Modules Standard Clinical Outputs. R package version 0.9.1.9023, https://github.com/insightsengineering/teal.modules.clinical/, https://insightsengineering.github.io/teal.modules.clinical/.","code":"@Manual{,   title = {teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs},   author = {Joe Zhu and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Mahmoud Hallal and Dawid Kaledkowski and Rosemary Li and Heng Wang and Pawel Rucki and Nikolas Burkoff and Konrad Pagacz},   year = {2024},   note = {R package version 0.9.1.9023,     https://github.com/insightsengineering/teal.modules.clinical/},   url = {https://insightsengineering.github.io/teal.modules.clinical/}, }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/index.html","id":"tealmodulesclinical","dir":"","previous_headings":"","what":"teal Modules for Standard Clinical Outputs","title":"teal Modules for Standard Clinical Outputs","text":"package contains set standard teal modules used CDISC data order generate many standard outputs used clinical trials. modules include, limited : Forest plots (tm_g_forest_rsp()/tm_g_forest_tte()) Line plots (tm_g_lineplot()) Kaplan-Meier plots (tm_g_km()) … MMRM (tm_a_mmrm()) Logistic regression (tm_t_logistic()) Cox regression (tm_t_coxreg()) … Unique patients (tm_t_summary()) Exposure across patients (tm_t_exposure()) Change baseline parameters (tm_t_summary_by()) … Table basic information chosen patient (tm_t_pp_basic_info()) Plot patient vitals time (tm_g_pp_vitals()) General timeline individual patients (tm_g_pp_patient_timeline()) … modules package implemented using functions R package tern order produce output. Please see Teal Gallery TLG Catalog examples shiny apps created using modules package.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"teal Modules for Standard Clinical Outputs","text":"Alternatively, might want use development version.","code":"install.packages('teal.modules.clinical') # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.modules.clinical\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"teal Modules for Standard Clinical Outputs","text":"understand use package, please refer Getting Started article, provides multiple examples code implementation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"teal Modules for Standard Clinical Outputs","text":"encounter bug feature request, please file issue. questions, discussions, staying date, please use teal channel pharmaverse slack workspace.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"teal Modules for Standard Clinical Outputs","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression List — add_expr","title":"Expression List — add_expr","text":"Add new expression list (expressions).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression List — add_expr","text":"","code":"add_expr(expr_ls, new_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression List — add_expr","text":"expr_ls (list call) list new expression added. new_expr (call) new expression add.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression List — add_expr","text":"list call.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Expression List — add_expr","text":"Offers stricter control add new expressions existing list. list expressions can later used generate pipeline, instance pipe_expr.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/add_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression List — add_expr","text":"","code":"library(rtables)  lyt <- list() lyt <- add_expr(lyt, substitute(basic_table())) lyt <- add_expr(   lyt, substitute(split_cols_by(var = arm), env = list(armcd = \"ARMCD\")) ) lyt <- add_expr(   lyt,   substitute(     test_proportion_diff(       vars = \"rsp\", method = \"cmh\", variables = list(strata = \"strata\")     )   ) ) lyt <- add_expr(lyt, quote(build_table(df = dta))) pipe_expr(lyt) #> basic_table() %>% split_cols_by(var = arm) %>% test_proportion_diff(vars = \"rsp\",  #>     method = \"cmh\", variables = list(strata = \"strata\")) %>%  #>     build_table(df = dta)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/arm_ref_comp_observer.html","id":null,"dir":"Reference","previous_headings":"","what":"Observer for Treatment reference variable — arm_ref_comp_observer","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"Updates reference comparison Treatments selected Treatment variable changes","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/arm_ref_comp_observer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"","code":"arm_ref_comp_observer(   session,   input,   output,   id_ref = \"Ref\",   id_comp = \"Comp\",   id_arm_var,   data,   arm_ref_comp,   module,   on_off = reactive(TRUE),   input_id = \"buckets\",   output_id = \"arms_buckets\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/arm_ref_comp_observer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"session (environment) shiny session input (character) shiny input output (character) shiny input id_ref (character) id reference Treatment input UI element id_comp (character) id comparison group input UI element id_arm_var (character) id Treatment variable input UI element data (reactive data.frame) dataset used validate Treatment reference inputs set id_ref input. arm_ref_comp (unknown) Treatment reference compare variables provided nested list Treatment variable corresponds list specifying default levels reference comparison treatments. module (character) name module called (used produce informative error messages) on_off (logical) reactive can used stop whole observer FALSE. input_id (character) unique id buckets referenced . output_id (character) name UI id output written .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/arm_ref_comp_observer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"Returns shinyvalidate::InputValidator checks least one reference comparison arm","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse text input to numeric vector — as_num","title":"Parse text input to numeric vector — as_num","text":"Generic parse text numeric vectors. initially designed robust interpretation text input teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse text input to numeric vector — as_num","text":"","code":"as_num(str)  # Default S3 method as_num(str)  # S3 method for class 'character' as_num(str)  # S3 method for class 'numeric' as_num(str)  # S3 method for class 'factor' as_num(str)  # S3 method for class 'logical' as_num(str)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse text input to numeric vector — as_num","text":"str (vector) extract numeric .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse text input to numeric vector — as_num","text":"vector numeric directly parsed numeric boolean. list numeric parsed character string, character string associated list item.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse text input to numeric vector — as_num","text":"function intended extract numeric character string, factor levels, boolean return vector numeric.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/as_num.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse text input to numeric vector — as_num","text":"","code":"dta <- list(   character = c(\"text10,20.5letter30.!\", \"!-.40$$-50e5[\", NA),   factor    = factor(c(\"]+60e-6, 7.7%%8L\", \"%90sep.100\\\"1L\", NA_character_)),   numeric   = c(1, -5e+2, NA),   logical   = c(TRUE, FALSE, NA) ) lapply(dta, as_num) #> $character #> $character[[1]] #> [1] 10.0 20.5 30.0 #>  #> $character[[2]] #> [1] -4e-01 -5e+06 #>  #> $character[[3]] #> [1] NA #>  #>  #> $factor #> $factor[[1]] #> [1] 0.00006 7.70000 8.00000 #>  #> $factor[[2]] #> [1] 90.0  0.1  1.0 #>  #> $factor[[3]] #> [1] NA #>  #>  #> $numeric #> [1]    1 -500   NA #>  #> $logical #> [1]  1  0 NA #>"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/bracket_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expressions in Brackets — bracket_expr","title":"Expressions in Brackets — bracket_expr","text":"Groups several expressions single bracketed expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/bracket_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expressions in Brackets — bracket_expr","text":"","code":"bracket_expr(exprs)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/bracket_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expressions in Brackets — bracket_expr","text":"exprs (list call) expressions concatenate single bracketed expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/bracket_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expressions in Brackets — bracket_expr","text":"{ object. See base::Paren() details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/bracket_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expressions in Brackets — bracket_expr","text":"","code":"adsl <- tmc_ex_adsl adrs <- tmc_ex_adrs  expr1 <- substitute(   expr = anl <- subset(df, PARAMCD == param),   env = list(df = as.name(\"adrs\"), param = \"INVET\") ) expr2 <- substitute(expr = anl$rsp_lab <- d_onco_rsp_label(anl$AVALC)) expr3 <- substitute(   expr = {     anl$is_rsp <- anl$rsp_lab %in%       c(\"Complete Response (CR)\", \"Partial Response (PR)\")   } )  res <- bracket_expr(list(expr1, expr2, expr3)) eval(res) table(anl$rsp_lab, anl$is_rsp) #>                            #>                            FALSE TRUE #>   Complete Response (CR)       0   60 #>   Partial Response (PR)        0   45 #>   Stable Disease (SD)         50    0 #>   Progressive Disease (PD)    39    0 #>   Not Evaluable (NE)           6    0"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/call_concatenate.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate expressions via a binary operator — call_concatenate","title":"Concatenate expressions via a binary operator — call_concatenate","text":"e.g. combine + ggplot without introducing parentheses due associativity","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/call_concatenate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate expressions via a binary operator — call_concatenate","text":"","code":"call_concatenate(args, bin_op = \"+\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/call_concatenate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate expressions via a binary operator — call_concatenate","text":"args arguments concatenate operator bin_op binary operator concatenate ","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/call_concatenate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate expressions via a binary operator — call_concatenate","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/call_concatenate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Concatenate expressions via a binary operator — call_concatenate","text":"","code":"library(ggplot2)  # What we want to achieve call(\"+\", quote(f), quote(g)) #> f + g call(\"+\", quote(f), call(\"+\", quote(g), quote(h))) # parentheses not wanted #> f + (g + h) call(\"+\", call(\"+\", quote(f), quote(g)), quote(h)) # as expected without unnecessary parentheses #> f + g + h Reduce(function(existing, new) call(\"+\", existing, new), list(quote(f), quote(g), quote(h))) #> f + g + h  # how we do it call_concatenate(list(quote(f), quote(g), quote(h))) #> f + g + h call_concatenate(list(quote(f))) #> f call_concatenate(list()) #> NULL call_concatenate(   list(quote(ggplot(mtcars)), quote(geom_point(aes(wt, mpg)))) ) #> ggplot(mtcars) + geom_point(aes(wt, mpg))  eval(   call_concatenate(     list(quote(ggplot(mtcars)), quote(geom_point(aes(wt, mpg))))   ) )"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/check_arm_ref_comp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"","code":"check_arm_ref_comp(x, df_to_check, module)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/check_arm_ref_comp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"x (character) Name variable df_to_check (data.frame) table check module (character) teal module ref comp called ","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/check_arm_ref_comp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"TRUE FALSE whether variable ref comp","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/clean_description.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up categorical variable description — clean_description","title":"Clean up categorical variable description — clean_description","text":"Cleaning categorical variable descriptions presenting.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/clean_description.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up categorical variable description — clean_description","text":"","code":"clean_description(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/clean_description.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up categorical variable description — clean_description","text":"x (character) vector categories descriptions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/clean_description.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up categorical variable description — clean_description","text":"string","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/clean_description.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up categorical variable description — clean_description","text":"","code":"clean_description(\"Level A (other text)\") #> [1] \"Level A\" clean_description(\"A long string that should be shortened\") #> [1] \"A long string tha...\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/color_lab_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Mapping function for Laboratory Table — color_lab_values","title":"Mapping function for Laboratory Table — color_lab_values","text":"Map value level characters values proper html tags, colors icons.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/color_lab_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mapping function for Laboratory Table — color_lab_values","text":"","code":"color_lab_values(   x,   classes = c(\"HIGH\", \"NORMAL\", \"LOW\"),   colors = list(HIGH = \"red\", NORMAL = \"grey\", LOW = \"blue\"),   default_color = \"black\",   icons = list(HIGH = \"glyphicon glyphicon-arrow-up\", LOW =     \"glyphicon glyphicon-arrow-down\") )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/color_lab_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mapping function for Laboratory Table — color_lab_values","text":"x (character) vector elements format (value level). classes (character) classes vector. colors (list) color per class. default_color (character) default color. icons (list) certain icons per level.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/color_lab_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mapping function for Laboratory Table — color_lab_values","text":"character vector element formatted HTML tag corresponding value x.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/color_lab_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mapping function for Laboratory Table — color_lab_values","text":"","code":"color_lab_values(c(\"LOW\", \"LOW\", \"HIGH\", \"NORMAL\", \"HIGH\")) #>                                                                                           LOW  #> \"<span style='color:blue!important'>LOW<i class='glyphicon glyphicon-arrow-down'><\/i><\/span>\"  #>                                                                                           LOW  #> \"<span style='color:blue!important'>LOW<i class='glyphicon glyphicon-arrow-down'><\/i><\/span>\"  #>                                                                                          HIGH  #>   \"<span style='color:red!important'>HIGH<i class='glyphicon glyphicon-arrow-up'><\/i><\/span>\"  #>                                                                                        NORMAL  #>                        \"<span style='color:grey!important'>NORMAL<i class='NULL'><\/i><\/span>\"  #>                                                                                          HIGH  #>   \"<span style='color:red!important'>HIGH<i class='glyphicon glyphicon-arrow-up'><\/i><\/span>\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/column_annotation_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Get full label, useful for annotating plots — column_annotation_label","title":"Get full label, useful for annotating plots — column_annotation_label","text":"Get full label, useful annotating plots","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/column_annotation_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get full label, useful for annotating plots — column_annotation_label","text":"","code":"column_annotation_label(dataset, column, omit_raw_name = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/column_annotation_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get full label, useful for annotating plots — column_annotation_label","text":"dataset (data.frame) dataset column (character) column get label omit_raw_name (logical) omits raw name square brackets label found","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/column_annotation_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get full label, useful for annotating plots — column_annotation_label","text":"\"Label [Column name]\" label exists, otherwise \"Column name\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/column_annotation_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get full label, useful for annotating plots — column_annotation_label","text":"","code":"data <- mtcars column_annotation_label(data, \"cyl\") #> [1] \"cyl\" attr(data[[\"cyl\"]], \"label\") <- \"Cylinder\" column_annotation_label(data, \"cyl\") #> [1] \"Cylinder [cyl]\" column_annotation_label(data, \"cyl\", omit_raw_name = TRUE) #> [1] \"Cylinder\" column_annotation_label(tmc_ex_adsl, \"ACTARM\") #> [1] \"Description of Actual Arm [ACTARM]\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/control_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Control Function for Time-To-Event teal Module — control_tte","title":"Control Function for Time-To-Event teal Module — control_tte","text":"Controls arguments Cox regression survival analysis results.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/control_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control Function for Time-To-Event teal Module — control_tte","text":"","code":"control_tte(   surv_time = list(conf_level = 0.95, conf_type = \"plain\", quantiles = c(0.25, 0.75)),   coxph = list(pval_method = \"log-rank\", ties = \"efron\", conf_level = 0.95),   surv_timepoint = control_surv_timepoint(conf_level = 0.95, conf_type = c(\"plain\",     \"none\", \"log\", \"log-log\")) )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/control_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control Function for Time-To-Event teal Module — control_tte","text":"surv_time (list) control parameters survfit model. See tern::control_surv_time() details. coxph (list) control parameters Cox-PH model. See tern::control_coxph() details. surv_timepoint (list) control parameters survfit model time point. See tern::control_surv_timepoint() details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"Convert choices_selected data_extract_spec filter_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"","code":"cs_to_des_filter(   cs,   dataname,   multiple = FALSE,   include_vars = FALSE,   label = \"Filter by\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. dataname (character) name data multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). include_vars (flag) whether include filter variables fixed selection result. can useful preserving reuse rtables code e.g. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"(teal.transform::data_extract_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_select.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"Convert choices_selected data_extract_spec select_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_select.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"","code":"cs_to_des_select(   cs,   dataname,   multiple = FALSE,   ordered = FALSE,   label = \"Select\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_select.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. dataname (character) name data multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). ordered (logical(1)) Flags whether selection order tracked. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_des_select.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"(teal.transform::data_extract_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_filter_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to filter_spec — cs_to_filter_spec","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"Convert choices_selected filter_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_filter_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"","code":"cs_to_filter_spec(cs, multiple = FALSE, label = \"Filter by\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_filter_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_filter_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"(teal.transform::filter_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_select_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to select_spec — cs_to_select_spec","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"Convert choices_selected select_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_select_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"","code":"cs_to_select_spec(cs, multiple = FALSE, ordered = FALSE, label = \"Select\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_select_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). ordered (logical(1)) Flags whether selection order tracked. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/cs_to_select_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"(select_spec)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string for total column label — default_total_label","title":"Default string for total column label — default_total_label","text":"default string used label \"total\" column. value used default value total_label argument throughout teal.modules.clinical package. specified module user via total_label argument, R environment options via set_default_total_label(), \"Patients\" used.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string for total column label — default_total_label","text":"","code":"default_total_label()  set_default_total_label(total_label)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string for total column label — default_total_label","text":"total_label (string) Single string value set R environment options default label use \"total\" column. Use getOption(\"tmc_default_total_label\") check current value set R environment (defaults \"Patients\" set).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string for total column label — default_total_label","text":"default_total_label returns current value R environment option set \"tmc_default_total_label\", \"Patients\" otherwise. set_default_total_label return value.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string for total column label — default_total_label","text":"default_total_label(): Getter default total column label. set_default_total_label(): Setter default total column label. Sets option \"tmc_default_total_label\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/default_total_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string for total column label — default_total_label","text":"","code":"# Default settings default_total_label() #> [1] \"All Patients\" getOption(\"tmc_default_total_label\") #> NULL  # Set custom value set_default_total_label(\"All Patients\")  # Settings after value has been set default_total_label() #> [1] \"All Patients\" getOption(\"tmc_default_total_label\") #> [1] \"All Patients\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC Data for Examples — ex_data","title":"Simulated CDISC Data for Examples — ex_data","text":"Simulated CDISC Data Examples","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC Data for Examples — ex_data","text":"","code":"tmc_ex_adsl  tmc_ex_adae  tmc_ex_adaette  tmc_ex_adcm  tmc_ex_adeg  tmc_ex_adex  tmc_ex_adlb  tmc_ex_admh  tmc_ex_adqs  tmc_ex_adrs  tmc_ex_adtte  tmc_ex_advs"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC Data for Examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 26 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 51 columns. object class tbl_df (inherits tbl, data.frame) 1800 rows 35 columns. object class tbl_df (inherits tbl, data.frame) 512 rows 45 columns. object class tbl_df (inherits tbl, data.frame) 5200 rows 48 columns. object class tbl_df (inherits tbl, data.frame) 200 rows 37 columns. object class tbl_df (inherits tbl, data.frame) 3000 rows 58 columns. object class tbl_df (inherits tbl, data.frame) 1077 rows 33 columns. object class tbl_df (inherits tbl, data.frame) 7000 rows 36 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 34 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 34 columns. object class tbl_df (inherits tbl, data.frame) 8400 rows 34 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC Data for Examples — ex_data","text":"tmc_ex_adsl: ADSL data tmc_ex_adae: ADAE data tmc_ex_adaette: ADAETTE data tmc_ex_adcm: ADCM data tmc_ex_adeg: ADEG data tmc_ex_adex: ADEX data tmc_ex_adlb: ADLB data tmc_ex_admh: ADMH data tmc_ex_adqs: ADQS data tmc_ex_adrs: ADRS data tmc_ex_adtte: ADTTE data tmc_ex_advs: ADVS data","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/extract_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracts html id for data_extract_ui — extract_input","title":"Extracts html id for data_extract_ui — extract_input","text":"data_extract_ui located extended html id. use ns(\"original id\") reference, extended specific suffixes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/extract_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts html id for data_extract_ui — extract_input","text":"","code":"extract_input(varname, dataname, filter = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/extract_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts html id for data_extract_ui — extract_input","text":"varname (character) original html id.  retrieved ns(\"original id\") UI function session$ns(\"original id\")/\"original id\" server function. dataname (character)dataname data_extract input. might retrieved like data_extract_spec(...)[[1]]$dataname. filter (logical) optional, connected extract_data_spec objects passed filter argument","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/extract_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts html id for data_extract_ui — extract_input","text":"string","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/extract_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracts html id for data_extract_ui — extract_input","text":"","code":"extract_input(\"ARM\", \"ADSL\") #> [1] \"ARM-dataset_ADSL_singleextract-select\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/facet_grid_formula.html","id":null,"dir":"Reference","previous_headings":"","what":"Facetting formula x_facet ~ y_facet — facet_grid_formula","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"Replaces x_facet y_facet . empty character","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/facet_grid_formula.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"","code":"facet_grid_formula(x_facet, y_facet)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/facet_grid_formula.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"x_facet (character(1)) name x facet, empty, facet along x. y_facet (character(1)) name y facet, empty, facet along y.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/facet_grid_formula.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"facet grid formula formula(x_facet ~ y_facet)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_g_forest_obj_var_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"Utility function extracting paramcd forest plots","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_g_forest_obj_var_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"","code":"get_g_forest_obj_var_name(paramcd, input, filter_idx = 1)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_g_forest_obj_var_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"paramcd teal.transform::data_extract_spec() variable value designating studied parameter. input shiny app input filter_idx filter section index (default 1)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_paramcd_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the associated parameter value for paramcd — get_paramcd_label","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"Utility function extracting parameter value associated paramcd value label. parameter value paramcd label, paramcd value returned. used generating title.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_paramcd_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"","code":"get_paramcd_label(anl, paramcd)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_paramcd_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"anl Analysis dataset paramcd teal.transform::data_extract_spec() variable value designating studied parameter.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_var_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get variable labels — get_var_labels","text":"","code":"get_var_labels(datasets, dataname, vars)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_var_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get variable labels — get_var_labels","text":"datasets (teal::FilteredData) Data built teal dataname (character) name dataset vars (character) Column names data","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/get_var_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get variable labels — get_var_labels","text":"character variable labels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/h_concat_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression Deparsing — h_concat_expr","title":"Expression Deparsing — h_concat_expr","text":"Deparse expression string.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/h_concat_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression Deparsing — h_concat_expr","text":"","code":"h_concat_expr(expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/h_concat_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression Deparsing — h_concat_expr","text":"expr (call) object can used .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/h_concat_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression Deparsing — h_concat_expr","text":"string.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/h_concat_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression Deparsing — h_concat_expr","text":"","code":"expr <- quote({   library(rtables)   basic_table() %>%     split_cols_by(var = \"ARMCD\") %>%     test_proportion_diff(       vars = \"rsp\", method = \"cmh\", variables = list(strata = \"strata\")     ) %>%     build_table(df = dta) })  h_concat_expr(expr) #> [1] \"{\\n    library(rtables)\\n    basic_table() %>% split_cols_by(var = \\\"ARMCD\\\") %>% test_proportion_diff(vars = \\\"rsp\\\", \\n        method = \\\"cmh\\\", variables = list(strata = \\\"strata\\\")) %>% \\n        build_table(df = dta)\\n}\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/is.cs_or_des.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"Whether object class teal.transform::choices_selected()","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/is.cs_or_des.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"","code":"is.cs_or_des(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/is.cs_or_des.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"x object checked","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/is.cs_or_des.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"(logical)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/make_barchart_simple_call.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"ggplot2 call generate simple bar chart","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/make_barchart_simple_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"","code":"make_barchart_simple_call(   y_name,   x_name = NULL,   fill_name = NULL,   x_facet_name = NULL,   y_facet_name = NULL,   label_bars = TRUE,   barlayout = c(\"side_by_side\", \"stacked\"),   flip_axis = FALSE,   rotate_bar_labels = FALSE,   rotate_x_label = FALSE,   rotate_y_label = FALSE,   expand_y_range = 0,   facet_scales = \"free_x\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/make_barchart_simple_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"y_name (character NULL) name y-axis variable. x_name (character NULL) name x-axis variable. Defaults NULL dependent extract input can empty. fill_name (character NULL) name variable determine bar fill color. x_facet_name (character NULL) name variable use horizontal plot faceting. y_facet_name (character NULL) name variable use vertical plot faceting. label_bars (logical NULL) whether bars labeled. TRUE, label bar numbers also drawn text. barlayout (character NULL) type bar layout. Options \"stacked\" (default) \"side_by_side\". flip_axis (character NULL) whether flip plot axis. rotate_bar_labels (logical NULL) whether bar labels rotated 45 degrees. rotate_x_label (logical NULL) whether x-axis labels rotated 45 degrees. rotate_y_label (logical NULL) whether y-axis labels rotated 45 degrees. expand_y_range (numeric NULL) fraction y-axis range expand . facet_scales (character) value passed scales argument ggplot2::facet_grid(). Options fixed, free_x, free_y, free. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/make_barchart_simple_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"call produce ggplot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists arguments teal modules used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. avisit (teal.transform::choices_selected()) value analysis visit AVISIT interest. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. dataname (character) analysis data used teal module. default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. hlt (teal.transform::choices_selected()) name variable high level term events. id_var (teal.transform::choices_selected()) object specifying variable name subject id. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results interact_var discrete. interaction needed, default option FALSE. label (character) menu item label module teal app. llt (teal.transform::choices_selected()) name variable low level term events. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. pre_output (shiny.tag) optional, text placed output put output context. example title. strata_var (teal.transform::choices_selected()) names variables stratified analysis. summarize_vars (teal.transform::choices_selected()) names variables summarized. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. time_points (teal.transform::choices_selected()) object available choices preselected option time points can used tern::surv_timepoint(). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. useNA (character) whether missing data (NA) displayed level. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/module_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Module Arguments — module_arguments","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/module_arguments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Module Arguments — module_arguments","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams module_arguments Parameters identical descriptions & input types Standard Template Arguments section excluded reduce duplication module function inherits parameters corresponding template function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/pipe_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expressions as a Pipeline — pipe_expr","title":"Expressions as a Pipeline — pipe_expr","text":"Concatenate expressions single pipeline-flavor expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/pipe_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expressions as a Pipeline — pipe_expr","text":"","code":"pipe_expr(exprs, pipe_str = \"%>%\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/pipe_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expressions as a Pipeline — pipe_expr","text":"exprs (list call) expressions concatenate pipeline (%>%). pipe_str (character) character separates expressions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/pipe_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expressions as a Pipeline — pipe_expr","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/pipe_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expressions as a Pipeline — pipe_expr","text":"","code":"pipe_expr(   list(     expr1 = substitute(df),     expr2 = substitute(head)   ) ) #> df %>% head"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression: Arm Preparation — prepare_arm","title":"Expression: Arm Preparation — prepare_arm","text":"function generate standard expression pre-processing dataset teal module applications. especially interest preprocessing steps needs applied similarly several datasets (e.g. ADSL ADRS).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression: Arm Preparation — prepare_arm","text":"","code":"prepare_arm(   dataname,   arm_var,   ref_arm,   comp_arm,   compare_arm = !is.null(ref_arm),   ref_arm_val = paste(ref_arm, collapse = \"/\"),   drop = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression: Arm Preparation — prepare_arm","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. ref_arm_val (character) replacement name reference level. drop (logical) drop unused variable levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression: Arm Preparation — prepare_arm","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Expression: Arm Preparation — prepare_arm","text":"teal.modules.clinical, user interface includes manipulation study arms. Classically: arm variable (e.g. ARM, ACTARM), reference arm (0 ), comparison arm (1 ) possibility combine comparison arms. Note arms compared , produced expression reduced optionally dropping non-represented levels arm. comparing arms, pre-processing includes three steps: Filtering dataset retain arms interest (reference comparison). Optional, one arm designated reference combined single level. reference explicitly reassigned non-represented levels arm dropped.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression: Arm Preparation — prepare_arm","text":"","code":"prepare_arm(   dataname = \"adrs\",   arm_var = \"ARMCD\",   ref_arm = \"ARM A\",   comp_arm = c(\"ARM B\", \"ARM C\") ) #> adrs %>% dplyr::filter(ARMCD %in% c(\"ARM A\", \"ARM B\", \"ARM C\")) %>%  #>     dplyr::mutate(ARMCD = stats::relevel(ARMCD, ref = \"ARM A\")) %>%  #>     dplyr::mutate(ARMCD = droplevels(ARMCD))  prepare_arm(   dataname = \"adsl\",   arm_var = \"ARMCD\",   ref_arm = c(\"ARM B\", \"ARM C\"),   comp_arm = \"ARM A\" ) #> adsl %>% dplyr::filter(ARMCD %in% c(\"ARM B\", \"ARM C\", \"ARM A\")) %>%  #>     dplyr::mutate(ARMCD = combine_levels(ARMCD, levels = c(\"ARM B\",  #>         \"ARM C\"), new_level = \"ARM B/ARM C\")) %>% dplyr::mutate(ARMCD = stats::relevel(ARMCD,  #>     ref = \"ARM B/ARM C\")) %>% dplyr::mutate(ARMCD = droplevels(ARMCD))"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression: Prepare Arm Levels — prepare_arm_levels","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"function generates standard expression pre-processing dataset arm levels used apply steps safety teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"","code":"prepare_arm_levels(dataname, parentname, arm_var, drop_arm_levels = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"{ object. See base::Paren() details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/prepare_arm_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"","code":"prepare_arm_levels(   dataname = \"adae\",   parentname = \"adsl\",   arm_var = \"ARMCD\",   drop_arm_levels = TRUE ) #> { #>     adae <- adae %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #>     arm_levels <- levels(adae[[\"ARMCD\"]]) #>     adsl <- adsl %>% dplyr::filter(ARMCD %in% arm_levels) #>     adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #> }  prepare_arm_levels(   dataname = \"adae\",   parentname = \"adsl\",   arm_var = \"ARMCD\",   drop_arm_levels = FALSE ) #> { #>     adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #>     arm_levels <- levels(adsl[[\"ARMCD\"]]) #>     adae <- adae %>% dplyr::mutate(ARMCD = factor(ARMCD, levels = arm_levels)) #> }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":null,"dir":"Reference","previous_headings":"","what":"Split choices_selected objects with interactions into their component variables — split_choices","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"Split choices_selected objects interactions component variables","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"","code":"split_choices(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"x (choices_selected) object interaction terms","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"choices_selected() object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"uses regex \\\\*|: perform split.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_choices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"","code":"split_choices(choices_selected(choices = c(\"x:y\", \"a*b\"), selected = all_choices())) #> $choices #> [1] \"x\" \"y\" \"a\" \"b\" #>  #> $selected #> [1] \"x\" \"y\" \"a\" \"b\" #>  #> $fixed #> [1] FALSE #>  #> attr(,\"class\") #> [1] \"choices_selected\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_col_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Split-Column Expression — split_col_expr","title":"Split-Column Expression — split_col_expr","text":"Renders expression column split rtables depending : expected arm comparison expected arm combination","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_col_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split-Column Expression — split_col_expr","text":"","code":"split_col_expr(compare, combine, ref, arm_var)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_col_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split-Column Expression — split_col_expr","text":"compare (logical) TRUE reference level included. combine (logical) TRUE group combination included. ref (character) reference level (used combine = TRUE). arm_var (character) arm grouping variable name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_col_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split-Column Expression — split_col_expr","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_col_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split-Column Expression — split_col_expr","text":"","code":"split_col_expr(   compare = TRUE,   combine = FALSE,   ref = \"ARM A\",   arm_var = \"ARMCD\" ) #> rtables::split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_interactions.html","id":null,"dir":"Reference","previous_headings":"","what":"Split interaction terms into their component variables — split_interactions","title":"Split interaction terms into their component variables — split_interactions","text":"Split interaction terms component variables","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_interactions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split interaction terms into their component variables — split_interactions","text":"","code":"split_interactions(x, by = \"\\\\*|:\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_interactions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split interaction terms into their component variables — split_interactions","text":"x (character) string representing interaction usually form x:y x*y. (character) regex split interaction term .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_interactions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split interaction terms into their component variables — split_interactions","text":"vector strings element component variable extracted interaction term x.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/split_interactions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split interaction terms into their component variables — split_interactions","text":"","code":"split_interactions(\"x:y\") #> [1] \"x\" \"y\" split_interactions(\"x*y\") #> [1] \"x\" \"y\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitute Names in a Quoted Expression — substitute_names","title":"Substitute Names in a Quoted Expression — substitute_names","text":"function substitutes names left- right-hand sides quoted expression. addition can also standard substitutions right-hand side.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitute Names in a Quoted Expression — substitute_names","text":"","code":"substitute_names(expr, names, others = list())  h_subst_lhs_names(qexpr, names)  substitute_lhs_names(qexpr, names)  substitute_rhs(qexpr, env)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitute Names in a Quoted Expression — substitute_names","text":"expr (language) expression. names (named list name) requested name substitutions. others (named list) requested substitutions happen right-hand side. qexpr (language) quoted expression. env (environment list) requested variable substitutions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitute Names in a Quoted Expression — substitute_names","text":"modified expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_names.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Substitute Names in a Quoted Expression — substitute_names","text":"h_subst_lhs_names(): Helper function just substitute top-level names left-hand side quoted expression. substitute_lhs_names(): recursively substitutes names left-hand sides quoted expression. substitute_rhs(): substitutes right-hand side quoted expression. Note just synonym substitute_q().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_q.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitute in Quoted Expressions — substitute_q","title":"Substitute in Quoted Expressions — substitute_q","text":"version substitute needed substitute() evaluate first argument, often useful able modify quoted expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_q.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitute in Quoted Expressions — substitute_q","text":"","code":"substitute_q(qexpr, env)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_q.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitute in Quoted Expressions — substitute_q","text":"qexpr (language) quoted expression. env (environment list) requested variable substitutions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_q.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitute in Quoted Expressions — substitute_q","text":"modified expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/substitute_q.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Substitute in Quoted Expressions — substitute_q","text":"simplified package pryr avoid another dependency.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/teal.modules.clinical-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","title":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","text":"Provides teal modules standard clinical trials outputs. teal modules add encoding panel interactively change encodings within teal.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/teal.modules.clinical-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Mahmoud Hallal mahmoud.hallal@roche.com Dawid Kaledkowski dawid.kaledkowski@roche.com Rosemary Li li.yaqiong@gene.com Heng Wang wang.heng@gene.com Pawel Rucki pawel.rucki@roche.com Nikolas Burkoff Konrad Pagacz contributors: Vaakesan Sundrelingam [contributor] Francois Collin [contributor] Imanol Zubizarreta [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_a_gee.html","id":null,"dir":"Reference","previous_headings":"","what":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"Creates valid expression generate analysis table using Generalized Estimating Equations (GEE).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_a_gee.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"","code":"template_a_gee(   output_table,   data_model_fit = \"ANL\",   dataname_lsmeans = \"ANL_ADSL\",   input_arm_var = \"ARM\",   ref_group = \"A: Drug X\",   aval_var,   id_var,   arm_var,   visit_var,   split_covariates,   cor_struct,   conf_level = 0.95,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_a_gee.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"output_table (character) type output table (\"t_gee_cov\", \"t_gee_coef\", \"t_gee_lsmeans\"). data_model_fit (character) dataset used fit model tern.gee::fit_gee(). dataname_lsmeans (character) dataset used alt_counts_df argument rtables::build_table(). aval_var (character) name analysis value variable. id_var (character) variable name subject id. arm_var (character) variable names can used arm_var. visit_var (character) variable names can used visit variable. Must factor dataname. split_covariates (character) vector names variables use covariates tern.gee::vars_gee(). cor_struct (character) assumed correlation structure tern.gee::fit_gee. conf_level (numeric) value confidence level within range (0, 1). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_a_gee.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Abnormality Summary Table — template_abnormality","title":"Template: Abnormality Summary Table — template_abnormality","text":"Creates valid expression generate table summarize abnormality.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Abnormality Summary Table — template_abnormality","text":"","code":"template_abnormality(   parentname,   dataname,   arm_var,   id_var = \"USUBJID\",   by_vars,   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   grade = \"ANRIND\",   baseline_var = \"BNRIND\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   add_total = FALSE,   total_label = default_total_label(),   exclude_base_abn = FALSE,   drop_arm_levels = TRUE,   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args(),   tbl_title )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Abnormality Summary Table — template_abnormality","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. by_vars (character) variable names used split summary rows. abnormal (named list) indicating abnormality direction grades. grade (character) name variable used specify abnormality grade. Variable must factor. baseline_var (character) name variable specifying baseline abnormality grade. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). exclude_base_abn (logical) whether exclude patients abnormal values baseline. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (character) NA level input dataset, defaults \"<Missing>\". basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). tbl_title (character) Title label variables bars","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Abnormality Summary Table — template_abnormality","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"Creates valid expression generate table summarize abnormality grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"","code":"template_abnormality_by_worst_grade(   parentname,   dataname,   arm_var,   id_var = \"USUBJID\",   paramcd = \"PARAMCD\",   atoxgr_var = \"ATOXGR\",   worst_high_flag_var = \"WGRHIFL\",   worst_low_flag_var = \"WGRLOFL\",   worst_flag_indicator = \"Y\",   add_total = FALSE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. paramcd (character) name parameter code variable. atoxgr_var (character) name variable indicating Analysis Toxicity Grade. worst_high_flag_var (character) name variable indicating Worst High Grade flag worst_low_flag_var (character) name variable indicating Worst Low Grade flag worst_flag_indicator (character) flag value indicating worst grade. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_abnormality_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_adverse_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"Creates valid expression generate adverse events table ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_adverse_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"","code":"template_adverse_events(   dataname = \"ANL\",   aeterm = \"AETERM\",   tox_grade = \"AETOXGR\",   causality = \"AEREL\",   outcome = \"AEOUT\",   action = \"AEACN\",   time = \"ASTDY\",   decod = NULL,   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_adverse_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"dataname (character) analysis data used teal module. aeterm (character) name reported term adverse event variable. tox_grade (character) name standard toxicity grade variable. causality (character) name causality variable. outcome (character) name outcome adverse event variable. action (character) name action taken study treatment variable. time (character) name study day start adverse event variable. decod (character) name dictionary derived term variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_adverse_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: ANCOVA Summary — template_ancova","title":"Template: ANCOVA Summary — template_ancova","text":"Creates valid expression generate analysis variance summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: ANCOVA Summary — template_ancova","text":"","code":"template_ancova(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   combine_comp_arms = FALSE,   aval_var,   label_aval = NULL,   cov_var,   include_interact = FALSE,   interact_var = NULL,   interact_y = FALSE,   paramcd_levels = \"\",   paramcd_var = \"PARAMCD\",   label_paramcd = NULL,   visit_levels = \"\",   visit_var = \"AVISIT\",   conf_level = 0.95,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: ANCOVA Summary — template_ancova","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. label_aval (character) label value variable used title rendering. cov_var (character) names covariates variables. include_interact (logical) whether interaction term included model. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results. interaction needed, default option FALSE. paramcd_levels (character) variable levels studied parameter. paramcd_var (character) variable name studied parameter. label_paramcd (character) variable label used title rendering. visit_levels (character) variable levels studied visits. visit_var (character) variable names can used visit variable. Must factor dataname. conf_level (numeric) value confidence level within range (0, 1). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: ANCOVA Summary — template_ancova","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Template Arguments — template_arguments","title":"Standard Template Arguments — template_arguments","text":"documentation function lists arguments teal module templates used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Template Arguments — template_arguments","text":"add_total (logical) whether include column total number patients. anl_name (character) analysis data used teal module. arm_var (character) variable names can used arm_var. atirel (character) name time relation medication variable. aval Please use aval_var argument instead. avalu Please use avalu_var argument instead. avalu_var (character) name analysis value unit variable. aval_var (character) name analysis value variable. baseline_var (character) name variable baseline values analysis variable. base_var Please use baseline_var argument instead. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). by_vars (character) variable names used split summary rows. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmstdy (character) name study relative day start medication variable. cnsr_var (character) name censoring variable. combine_comp_arms (logical) triggers combination comparison arms. compare_arm (logical) triggers comparison study arms. comp_arm (character) level comparison arm case arm comparison. conf_level (numeric) value confidence level within range (0, 1). control (list) list settings analysis. cov_var (character) names covariates variables. dataname (character) analysis data used teal module. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\"). hlt (character) name variable high level term events. id_var (character) variable name subject id. include_interact (logical) whether interaction term included model. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. llt (character) name variable low level term events. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). na.rm (logical) whether NA values removed prior analysis. numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. paramcd (character) name parameter code variable. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_id (character) patient ID. prune_diff (number) threshold use trimming table using criteria difference rates two columns. prune_freq (number) threshold use trimming table using event incidence rate column. ref_arm (character) level reference arm case arm comparison. sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. strata_var (character) names variables stratified analysis. subgroup_var (character) variable names can used subgroups. sum_vars (character) names variables summarized. time_points (character) time points can used tern::surv_timepoint(). time_unit_var (character) name variable representing time units. title (character) title output. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). treatment_flag (character) name value indicating treatment records treatment_flag_var. treatment_flag_var (character) name treatment flag variable. useNA (character) whether missing data (NA) displayed level. var_labels (named character) optional variable labels relabeling analysis variables. visit_var (character) variable names can used visit variable. Must factor dataname. worst_flag_indicator (character) value indicating worst grade. worst_flag_var (character) name worst flag variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Template Arguments — template_arguments","text":"list expressions generate table plot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_arguments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Template Arguments — template_arguments","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams template_arguments","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_basic_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Basic Info — template_basic_info","title":"Template: Patient Profile Basic Info — template_basic_info","text":"Creates valid expression generate patient profile basic info report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_basic_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Basic Info — template_basic_info","text":"","code":"template_basic_info(dataname = \"ANL\", vars, patient_id = NULL)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_basic_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Basic Info — template_basic_info","text":"dataname (character) analysis data used teal module. vars (character) names variables shown table. patient_id (character) patient ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_basic_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Basic Info — template_basic_info","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_binary_outcome.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Binary Outcome — template_binary_outcome","title":"Template: Binary Outcome — template_binary_outcome","text":"Creates valid expression generate binary outcome analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_binary_outcome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Binary Outcome — template_binary_outcome","text":"","code":"template_binary_outcome(   dataname,   parentname,   arm_var,   paramcd,   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVALC\",   show_rsp_cat = TRUE,   responder_val = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),   responder_val_levels = responder_val,   control = list(global = list(method = \"waldcc\", conf_level = 0.95), unstrat =     list(method_ci = \"waldcc\", method_test = \"schouten\", odds = TRUE), strat =     list(method_ci = \"cmh\", method_test = \"cmh\", strat = NULL)),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_binary_outcome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Binary Outcome — template_binary_outcome","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) response parameter value use table title. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. show_rsp_cat (logical) display multinomial response estimations. responder_val (character) short label observations translate AVALC responder/non-responder. responder_val_levels (character) levels responses shown multinomial response estimations. control (list) list settings analysis. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_binary_outcome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Binary Outcome — template_binary_outcome","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_m.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Multi-Variable Cox Regression — template_coxreg_m","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"Creates valid expression generate multi-variable Cox regression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_m.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"","code":"template_coxreg_m(   dataname,   cov_var,   arm_var,   cnsr_var,   aval_var,   ref_arm,   comp_arm,   paramcd,   at = list(),   strata_var = NULL,   combine_comp_arms = FALSE,   control = control_coxreg(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_m.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"dataname (character) analysis data used teal module. cov_var (character) names covariates variables. arm_var (character) variable names can used arm_var. cnsr_var (character) name censoring variable. aval_var (character) name analysis value variable. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. paramcd (character) name parameter code variable. (list numeric) candidate covariate numeric type variable, use specify value covariate effect estimated. strata_var (character) names variables stratified analysis. combine_comp_arms (logical) triggers combination comparison arms. control (list) list settings analysis (see control_coxreg()). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_m.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_u.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Univariable Cox Regression — template_coxreg_u","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"Creates valid expression generate univariable Cox regression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_u.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"","code":"template_coxreg_u(   dataname,   cov_var,   arm_var,   cnsr_var,   aval_var,   ref_arm,   comp_arm,   paramcd,   at = list(),   strata_var = NULL,   combine_comp_arms = FALSE,   control = control_coxreg(),   na_level = default_na_str(),   append = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_u.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"dataname (character) analysis data used teal module. cov_var (character) names covariates variables. arm_var (character) variable names can used arm_var. cnsr_var (character) name censoring variable. aval_var (character) name analysis value variable. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. paramcd (character) name parameter code variable. (list numeric) candidate covariate numeric type variable, use specify value covariate effect estimated. strata_var (character) names variables stratified analysis. combine_comp_arms (logical) triggers combination comparison arms. control (list) list settings analysis (see control_coxreg()). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). append (logical) whether result appended previous one. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_coxreg_u.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Events by Term — template_events","title":"Template: Events by Term — template_events","text":"Creates valid expression generate table events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Events by Term — template_events","text":"","code":"template_events(   dataname,   parentname,   arm_var,   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   sort_criteria = c(\"freq_desc\", \"alpha\"),   sort_freq_col = total_label,   prune_freq = 0,   prune_diff = 0,   drop_arm_levels = TRUE,   incl_overall_sum = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Events by Term — template_events","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. sort_freq_col (character) column sort frequency sort_criteria set freq_desc. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. incl_overall_sum (flag)  whether two rows summarize overall number adverse events included top table. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Events by Term — template_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Events by Grade — template_events_by_grade","title":"Template: Events by Grade — template_events_by_grade","text":"Creates valid expression generate table summarize events grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Events by Grade — template_events_by_grade","text":"","code":"template_events_by_grade(   dataname,   parentname,   arm_var,   id = \"\",   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   grade,   label_grade = NULL,   prune_freq = 0,   prune_diff = 0,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Events by Grade — template_events_by_grade","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. id (character) unique identifier patients datasets, default \"USUBJID\". hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. grade (character) name severity level variable. label_grade (string) label grade variable dataname. label extracted module. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Events by Grade — template_events_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_col_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"Creates valid expression generate table summarize adverse events grouped grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_col_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"","code":"template_events_col_by_grade(   dataname,   parentname,   arm_var,   grading_groups = list(`Any Grade (%)` = c(\"1\", \"2\", \"3\", \"4\", \"5\"), `Grade 1-2 (%)` =     c(\"1\", \"2\"), `Grade 3-4 (%)` = c(\"3\", \"4\"), `Grade 5 (%)` = \"5\"),   add_total = TRUE,   total_label = default_total_label(),   id = \"USUBJID\",   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   grade = \"AETOXGR\",   label_grade = NULL,   prune_freq = 0.1,   prune_diff = 0,   na_level = default_na_str(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_col_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. grading_groups (list) named list grading groups. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). id (character) name variable uniquely identify patients datasets. hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. grade (character) name grade variable base grading_groups . label_grade (character) label grade variable dataname. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_col_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_patyear.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"Creates valid expression generate table event rates adjusted patient-years.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_patyear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"","code":"template_events_patyear(   dataname,   parentname,   arm_var,   events_var,   label_paramcd,   aval_var = \"AVAL\",   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   control = control_incidence_rate(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_patyear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. events_var (character) name variable number observed events. label_paramcd (character)paramcd variable text use table title. aval_var (character) name analysis value variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). control (list) list settings analysis. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_patyear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Summary — template_events_summary","title":"Template: Adverse Events Summary — template_events_summary","text":"Creates valid expression generate adverse events summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Summary — template_events_summary","text":"","code":"template_events_summary(   anl_name,   parentname,   arm_var,   dthfl_var = \"DTHFL\",   dcsreas_var = \"DCSREAS\",   flag_var_anl = NULL,   flag_var_aesi = NULL,   aeseq_var = \"AESEQ\",   llt = \"AEDECOD\",   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   count_dth = TRUE,   count_wd = TRUE,   count_subj = TRUE,   count_pt = TRUE,   count_events = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Summary — template_events_summary","text":"anl_name (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. dthfl_var (character) name variable subject death flag parentname. Records \"Y\" summarized table row \"Total number deaths\". dcsreas_var (character) name variable study discontinuation reason parentname. Records \"ADVERSE EVENTS\" summarized table row \"Total number patients withdrawn study due AE\". flag_var_anl (character) name flag variable dataset used count adverse event sub-groups (e.g. Serious events, Related events, etc.). Variable labels used table row names exist. flag_var_aesi (character) name flag variable dataset used count adverse event special interest groups. flag variables must type logical. Variable labels used table row names exist. aeseq_var (character) name variable adverse events sequence number dataset. Used counting total number events. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). count_dth (logical) whether show count total deaths (based dthfl_var). Defaults TRUE. count_wd (logical) whether show count patients withdrawn study due adverse event (based dcsreas_var). Defaults TRUE. count_subj (logical) whether show count unique subjects (based USUBJID). applies event flag variables provided. count_pt (logical) whether show count unique preferred terms (based llt). applies event flag variables provided. count_events (logical) whether show count events (based aeseq_var). applies event flag variables provided.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_events_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Summary — template_events_summary","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Exposure Table for Risk management plan — template_exposure","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"Creates valid expression generate exposure table risk management plan.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"","code":"template_exposure(   parentname,   dataname,   id_var,   paramcd,   paramcd_label = NULL,   row_by_var,   col_by_var = NULL,   add_total = FALSE,   total_label = \"Total\",   add_total_row = TRUE,   total_row_label = \"Total number of patients and patient time*\",   drop_levels = TRUE,   na_level = default_na_str(),   aval_var,   avalu_var,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. id_var (character) variable name subject id. paramcd (character) name parameter code variable. paramcd_label (character) column dataname dataset value used label argument paramcd. row_by_var (character) variable name used split values rows. col_by_var (character) variable name used split values columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). add_total_row (flag) whether \"total\" level added others includes levels constitute split. custom label can set level via total_row_label argument. total_row_label (character) string display total row label row enabled (see add_total_row). drop_levels (flag) whether empty rows removed table. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). aval_var (character) name analysis value variable. avalu_var (character) name analysis value unit variable. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_fit_mmrm.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"Creates valid expression generate analysis tables plots Mixed Model Repeated Measurements.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_fit_mmrm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"","code":"template_fit_mmrm(   parentname,   dataname,   aval_var,   arm_var,   ref_arm,   comp_arm = NULL,   combine_comp_arms = FALSE,   id_var,   visit_var,   cov_var,   conf_level = 0.95,   method = \"Satterthwaite\",   cor_struct = \"unstructured\",   weights_emmeans = \"proportional\",   parallel = FALSE )  template_mmrm_tables(   parentname,   dataname,   fit_name,   arm_var,   ref_arm,   visit_var,   paramcd,   show_relative = c(\"increase\", \"reduction\", \"none\"),   table_type = \"t_mmrm_cov\",   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )  template_mmrm_plots(   fit_name,   lsmeans_plot = list(select = c(\"estimates\", \"contrasts\"), width = 0.6, show_pval =     FALSE),   diagnostic_plot = list(type = \"fit-residual\", z_threshold = NULL),   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_fit_mmrm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. aval_var (character) name analysis value variable. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. combine_comp_arms (logical) triggers combination comparison arms. id_var (character) variable name subject id. visit_var (character) variable names can used visit variable. Must factor dataname. cov_var (character) names covariates variables. conf_level (numeric) value confidence level within range (0, 1). method (string) string specifying adjustment method. cor_struct (string) string specifying correlation structure, defaults \"unstructured\". See tern.mmrm::build_formula() options. weights_emmeans argument emmeans::emmeans(), \"proportional\" default. parallel (flag) flag controls whether optimizer search can use available free cores machine (default). fit_name (string) name fitted MMRM object. paramcd (character) name parameter code variable. show_relative (string) \"reduction\" (control - treatment, default) \"increase\" (treatment - control) shown relative change baseline. table_type (string) type table output. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). lsmeans_plot (named list) list controls LS means plot. See tern.mmrm::g_mmrm_lsmeans(). diagnostic_plot (named list) list controls diagnostic_plot. See tern.mmrm::g_mmrm_diagnostic(). ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_fit_mmrm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"list expressions generate table plot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_fit_mmrm.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"template_mmrm_tables(): Creates valid expressions generate MMRM LS means, covariance matrix, fixed effects, diagnostic tables. template_mmrm_plots(): Creates valid expressions generate MMRM LS means diagnostic plots.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Response Forest Plot — template_forest_rsp","title":"Template: Response Forest Plot — template_forest_rsp","text":"Creates valid expression generate response forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Response Forest Plot — template_forest_rsp","text":"","code":"template_forest_rsp(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   obj_var_name = \"\",   aval_var = \"AVALC\",   responders = c(\"CR\", \"PR\"),   subgroup_var,   strata_var = NULL,   stats = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\"),   riskdiff = NULL,   conf_level = 0.95,   col_symbol_size = NULL,   rel_width_forest = 0.25,   font_size = 15,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Response Forest Plot — template_forest_rsp","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. obj_var_name (character) additional text append table title. aval_var (character) name analysis value variable. responders (character) values aval_var considered responders. subgroup_var (character) variable names can used subgroups. strata_var (character) names variables stratified analysis. stats (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (numeric) value confidence level within range (0, 1). col_symbol_size (integer NULL) column index used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, caption. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Response Forest Plot — template_forest_rsp","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Survival Forest Plot — template_forest_tte","title":"Template: Survival Forest Plot — template_forest_tte","text":"Creates valid expression generate survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Survival Forest Plot — template_forest_tte","text":"","code":"template_forest_tte(   dataname = \"ANL\",   parentname = \"ANL_ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   obj_var_name = \"\",   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   subgroup_var,   strata_var = NULL,   stats = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   riskdiff = NULL,   conf_level = 0.95,   col_symbol_size = NULL,   time_unit_var = \"AVALU\",   rel_width_forest = 0.25,   font_size = 15,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Survival Forest Plot — template_forest_tte","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. obj_var_name (character) additional text append table title. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. subgroup_var (character) variable names can used subgroups. strata_var (character) names variables stratified analysis. stats (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (numeric) value confidence level within range (0, 1). col_symbol_size (integer NULL) column index used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. time_unit_var (character) name variable representing time units. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Survival Forest Plot — template_forest_tte","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Confidence Interval Plot — template_g_ci","title":"Template: Confidence Interval Plot — template_g_ci","text":"Creates valid expression generate ggplot2::ggplot() confidence interval plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Confidence Interval Plot — template_g_ci","text":"","code":"template_g_ci(   dataname,   x_var,   y_var,   grp_var = NULL,   stat = c(\"mean\", \"median\"),   conf_level = 0.95,   unit_var = \"AVALU\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Confidence Interval Plot — template_g_ci","text":"dataname (character) analysis data used teal module. x_var (character) name treatment variable put x-axis. y_var (character) name response variable put y-axis. grp_var (character) name group variable used determine plot colors, point shapes, line types. stat (character) statistic plot. Options \"mean\" \"median\". conf_level (numeric) value confidence level within range (0, 1). unit_var (character) name unit variable. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Confidence Interval Plot — template_g_ci","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Individual Patient Plots — template_g_ipp","title":"Template: Individual Patient Plots — template_g_ipp","text":"Creates valid expression generate ggplot2::ggplot() plots individual patients.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Individual Patient Plots — template_g_ipp","text":"","code":"template_g_ipp(   dataname = \"ANL\",   paramcd,   arm_var,   arm_levels,   avalu_first,   paramcd_first,   aval_var = \"AVAL\",   avalu_var = \"AVALU\",   id_var = \"USUBJID\",   visit_var = \"AVISIT\",   base_var = lifecycle::deprecated(),   baseline_var = \"BASE\",   add_baseline_hline = FALSE,   separate_by_obs = FALSE,   ggplot2_args = teal.widgets::ggplot2_args(),   suppress_legend = FALSE,   add_avalu = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Individual Patient Plots — template_g_ipp","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. arm_var (character) variable names can used arm_var. arm_levels (character) vector levels arm_var. avalu_first (character)avalu_var text append plot title y-axis label add_avalu TRUE. paramcd_first (character)paramcd text append plot title y-axis label. aval_var (character) name analysis value variable. avalu_var (character) name analysis value unit variable. id_var (character) variable name subject id. visit_var (character) name variable visit timepoints. base_var Please use baseline_var argument instead. baseline_var (character) name variable baseline values analysis variable. add_baseline_hline (logical) whether horizontal line added plot baseline y-value. separate_by_obs (logical) whether create multi-panel plots. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, x, y. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\"). suppress_legend (logical) whether suppress plot legend. add_avalu (logical) whether avalu_first text appended plot title y-axis label.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Individual Patient Plots — template_g_ipp","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Kaplan-Meier Plot — template_g_km","title":"Template: Kaplan-Meier Plot — template_g_km","text":"Creates valid expression generate Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Kaplan-Meier Plot — template_g_km","text":"","code":"template_g_km(   dataname = \"ANL\",   arm_var = \"ARM\",   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   xticks = NULL,   strata_var = NULL,   time_points = NULL,   facet_var = \"SEX\",   font_size = 11,   conf_level = 0.95,   ties = \"efron\",   xlab = \"Survival time\",   time_unit_var = \"AVALU\",   yval = \"Survival\",   ylim = NULL,   pval_method = \"log-rank\",   annot_surv_med = TRUE,   annot_coxph = TRUE,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),   legend_pos = NULL,   position_coxph = lifecycle::deprecated(),   width_annots = lifecycle::deprecated(),   rel_height_plot = 0.8,   ci_ribbon = FALSE,   title = \"KM Plot\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Kaplan-Meier Plot — template_g_km","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. strata_var (character) names variables stratified analysis. time_points (character) time points can used tern::surv_timepoint(). facet_var (character) name variable use facet plot. font_size (numeric) font size value. conf_level (numeric) value confidence level within range (0, 1). ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. xlab (string) x-axis label. time_unit_var (character) name variable representing time units. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. pval_method (string) method used estimation p.values; wald (default) likelihood. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. position_coxph Please use x y elements control_annot_coxph instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\" rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. title (character) title output.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Kaplan-Meier Plot — template_g_km","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Line Plot — template_g_lineplot","title":"Template: Line Plot — template_g_lineplot","text":"Creates valid expression generate ggplot2::ggplot() line plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Line Plot — template_g_lineplot","text":"","code":"template_g_lineplot(   dataname = \"ANL\",   strata = \"ARM\",   x = \"AVISIT\",   y = \"AVAL\",   y_unit = \"AVALU\",   paramcd = \"PARAMCD\",   param = \"ALT\",   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = c(\"n\", \"mean_sd\", \"median\", \"range\"),   mid_type = \"pl\",   conf_level = 0.95,   incl_screen = TRUE,   mid_point_size = 2,   table_font_size = 4,   title = \"Line Plot\",   y_lab = \"\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Line Plot — template_g_lineplot","text":"dataname (character) analysis data used teal module. strata (string NA) group variable name. x (string) x-variable name. y (string) y-variable name. y_unit (string NA) y-axis unit variable name. paramcd (string NA) parameter code variable name. param (character) parameter filter data . mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). conf_level (numeric) value confidence level within range (0, 1). incl_screen (logical) whether screening visit included. mid_point_size (numeric(1)) font size mid plot points. table_font_size (numeric(1)) font size text table. title (string) plot title. y_lab (string NULL) y-axis label. NULL label added. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, caption, y, lty. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Line Plot — template_g_lineplot","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_laboratory.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Laboratory Table — template_laboratory","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"Creates valid expression generate patient profile laboratory table using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_laboratory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"","code":"template_laboratory(   dataname = \"ANL\",   paramcd = \"PARAMCD\",   param = \"PARAM\",   anrind = \"ANRIND\",   timepoints = \"ADY\",   aval = lifecycle::deprecated(),   aval_var = \"AVAL\",   avalu = lifecycle::deprecated(),   avalu_var = \"AVALU\",   patient_id = NULL,   round_value = 0L )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_laboratory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. param (character) name parameter variable. anrind (character) name analysis reference range indicator variable. timepoints (character) name time variable. aval Please use aval_var argument instead. aval_var (character) name analysis value variable. avalu Please use avalu_var argument instead. avalu_var (character) name analysis value unit variable. patient_id (character) patient ID. round_value (numeric) number decimal places round .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_laboratory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Logistic Regression — template_logistic","title":"Template: Logistic Regression — template_logistic","text":"Creates valid expression generate logistic regression table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Logistic Regression — template_logistic","text":"","code":"template_logistic(   dataname,   arm_var,   aval_var,   paramcd = lifecycle::deprecated(),   label_paramcd,   cov_var,   interaction_var,   ref_arm,   comp_arm,   topleft = \"Logistic Regression\",   conf_level = 0.95,   combine_comp_arms = FALSE,   responder_val = c(\"CR\", \"PR\"),   at = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Logistic Regression — template_logistic","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. fit logistic model arm/treatment variable, set NULL. aval_var (character) name analysis value variable. paramcd paramcd argument used function. label_paramcd (character) label response parameter value print table title. cov_var (character) names covariates variables. interaction_var (character) names variables can used interaction variable selection. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. topleft (character) text use top-left annotation table. conf_level (numeric) value confidence level within range (0, 1). combine_comp_arms (logical) triggers combination comparison arms. responder_val (character) values responder variable corresponding successful response. (numeric NULL) optional values interaction variable. Otherwise median used. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Logistic Regression — template_logistic","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_medical_history.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Medical History — template_medical_history","title":"Template: Patient Profile Medical History — template_medical_history","text":"Creates valid expression generate patient profile medical history report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_medical_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Medical History — template_medical_history","text":"","code":"template_medical_history(   dataname = \"ANL\",   mhterm = \"MHTERM\",   mhbodsys = \"MHBODSYS\",   mhdistat = \"MHDISTAT\",   patient_id = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_medical_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Medical History — template_medical_history","text":"dataname (character) analysis data used teal module. mhterm (character) name reported term medical history variable. mhbodsys (character) name body system organ class variable. mhdistat (character) name status disease variable. patient_id (character) patient ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_medical_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Medical History — template_medical_history","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_mult_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Multiple Events by Term — template_mult_events","title":"Template: Multiple Events by Term — template_mult_events","text":"Creates valid expression generate table multiple events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_mult_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Multiple Events by Term — template_mult_events","text":"","code":"template_mult_events(   dataname,   parentname,   arm_var,   seq_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_mult_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Multiple Events by Term — template_mult_events","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. seq_var (character) name analysis sequence number variable. Used counting unique number events. hlt (character) name variable high level term events. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_mult_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Multiple Events by Term — template_mult_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_patient_timeline.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Timeline Plot — template_patient_timeline","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"Creates valid expression generate patient profile timeline ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_patient_timeline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"","code":"template_patient_timeline(   dataname = \"ANL\",   aeterm = \"AETERM\",   aetime_start = \"ASTDTM\",   aetime_end = \"AENDTM\",   dstime_start = \"CMASTDTM\",   dstime_end = \"CMAENDTM\",   cmdecod = \"CMDECOD\",   aerelday_start = NULL,   aerelday_end = NULL,   dsrelday_start = NULL,   dsrelday_end = NULL,   relative_day = FALSE,   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_patient_timeline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"dataname (character) analysis data used teal module. aeterm (character) name reported term adverse event variable. aetime_start (character) name start date/time adverse event variable. aetime_end (character) name end date/time adverse event variable. dstime_start (character) name date/time first exposure treatment variable. dstime_end (character) name date/time last exposure treatment variable. cmdecod (character) name standardized medication name variable. aerelday_start (character) name adverse event study start day variable. aerelday_end (character) name adverse event study end day variable. dsrelday_start (character) name concomitant medications study start day variable. dsrelday_end (character) name concomitant medications study day start variable. relative_day (logical) whether use relative days (TRUE) absolute dates (FALSE). patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_patient_timeline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_prior_medication.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Prior Medication — template_prior_medication","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"Creates valid expression generate patient profile prior medication report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_prior_medication.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"","code":"template_prior_medication(   dataname = \"ANL\",   atirel = \"ATIREL\",   cmdecod = \"CMDECOD\",   cmindc = \"CMINDC\",   cmstdy = \"CMSTDY\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_prior_medication.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"dataname (character) analysis data used teal module. atirel (character) name time relation medication variable. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmstdy (character) name study relative day start medication variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_prior_medication.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Shift by Arm — template_shift_by_arm","title":"Template: Shift by Arm — template_shift_by_arm","text":"Creates valid expression generate summary table analysis indicator levels arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Shift by Arm — template_shift_by_arm","text":"","code":"template_shift_by_arm(   dataname,   parentname,   arm_var = \"ARM\",   paramcd = \"PARAMCD\",   visit_var = \"AVISIT\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   aval_var = \"ANRIND\",   base_var = lifecycle::deprecated(),   baseline_var = \"BNRIND\",   na.rm = FALSE,   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Shift by Arm — template_shift_by_arm","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) name parameter code variable. visit_var (character) variable names can used visit variable. Must factor dataname. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. aval_var (character) name analysis reference range indicator variable. base_var Please use baseline_var argument instead. baseline_var (character) name baseline reference range indicator variable. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Shift by Arm — template_shift_by_arm","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm_by_worst.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"Creates valid expression generate summary table worst analysis indicator variable level per subject arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm_by_worst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"","code":"template_shift_by_arm_by_worst(   dataname,   parentname,   arm_var = \"ARM\",   paramcd = \"PARAMCD\",   worst_flag_var = \"WORS02FL\",   worst_flag = \"Y\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   aval_var = \"ANRIND\",   base_var = lifecycle::deprecated(),   baseline_var = \"BNRIND\",   na.rm = FALSE,   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm_by_worst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) name parameter code variable. worst_flag_var (character) name worst flag variable. worst_flag (character) value indicating worst analysis indicator level. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. aval_var (character) name analysis reference range indicator variable. base_var Please use baseline_var argument instead. baseline_var (character) name baseline reference range indicator variable. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_arm_by_worst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Grade Summary Table — template_shift_by_grade","title":"Template: Grade Summary Table — template_shift_by_grade","text":"Creates valid expression generate grade summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Grade Summary Table — template_shift_by_grade","text":"","code":"template_shift_by_grade(   parentname,   dataname,   arm_var = \"ARM\",   id_var = \"USUBJID\",   visit_var = \"AVISIT\",   worst_flag_var = c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\"),   worst_flag_indicator = \"Y\",   anl_toxgrade_var = \"ATOXGR\",   base_toxgrade_var = \"BTOXGR\",   paramcd = \"PARAMCD\",   drop_arm_levels = TRUE,   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   code_missing_baseline = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Grade Summary Table — template_shift_by_grade","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. visit_var (character) variable names can used visit variable. Must factor dataname. worst_flag_var (character) name worst flag variable. worst_flag_indicator (character) value indicating worst grade. anl_toxgrade_var (character) name variable indicating analysis toxicity grade. base_toxgrade_var (character) name variable indicating baseline toxicity grade. paramcd (character) name parameter code variable. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). code_missing_baseline (logical) whether missing baseline grades counted grade 0. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_shift_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Grade Summary Table — template_shift_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_smq.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"Creates valid expression generate adverse events table Standardized MedDRA Query.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_smq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"","code":"template_smq(   dataname,   parentname,   arm_var,   llt = \"AEDECOD\",   add_total = TRUE,   total_label = default_total_label(),   sort_criteria = c(\"freq_desc\", \"alpha\"),   drop_arm_levels = TRUE,   na_level = default_na_str(),   smq_varlabel = \"Standardized MedDRA Query\",   baskets = c(\"SMQ01NAM\", \"SMQ02NAM\", \"CQ01NAM\"),   id_var = \"USUBJID\",   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_smq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). smq_varlabel (character) label use new column SMQ created tern::h_stack_by_baskets(). baskets (character) names selected standardized/customized queries variables. id_var (character) variable name subject id. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_smq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Summary of Variables — template_summary","title":"Template: Summary of Variables — template_summary","text":"Creates valid expression generate table summarize variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Summary of Variables — template_summary","text":"","code":"template_summary(   dataname,   parentname,   arm_var,   sum_vars,   show_labels = lifecycle::deprecated(),   add_total = TRUE,   total_label = default_total_label(),   var_labels = character(),   arm_var_labels = NULL,   na.rm = FALSE,   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\", \"geom_mean\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Summary of Variables — template_summary","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. sum_vars (character) names variables summarized. show_labels  add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). var_labels (named character) optional variable labels relabeling analysis variables. arm_var_labels (character NULL) vector column variable labels display, length arm_var. NULL, labels displayed. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Summary of Variables — template_summary","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary_by.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Summarize Variables by Row Groups Module — template_summary_by","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"Creates valid expression generate table summarize variables row groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"","code":"template_summary_by(   parentname,   dataname,   arm_var,   id_var,   sum_vars,   by_vars,   var_labels = character(),   add_total = TRUE,   total_label = default_total_label(),   parallel_vars = FALSE,   row_groups = FALSE,   na.rm = FALSE,   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   drop_zero_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. sum_vars (character) names variables summarized. by_vars (character) variable names used split summary rows. var_labels (named character) optional variable labels relabeling analysis variables. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). parallel_vars (logical) whether summarized variables arranged columns. Can set TRUE chosen analysis variables numeric. row_groups (logical) whether summarized variables arranged row groups. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. drop_zero_levels (logical) whether rows zero counts columns removed table. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_summary_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_therapy.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Therapy Table and Plot — template_therapy","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"Creates valid expression generate patient profile therapy table ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_therapy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"","code":"template_therapy(   dataname = \"ANL\",   atirel = \"ATIREL\",   cmdecod = \"CMDECOD\",   cmindc = \"CMINDC\",   cmdose = \"CMDOSE\",   cmtrt = \"CMTRT\",   cmdosu = \"CMDOSU\",   cmroute = \"CMROUTE\",   cmdosfrq = \"CMDOSFRQ\",   cmstdy = \"CMSTDY\",   cmendy = \"CMENDY\",   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_therapy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"dataname (character) analysis data used teal module. atirel (character) name time relation medication variable. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmdose (character) name dose per administration variable. cmtrt (character) name reported name drug, med, therapy variable. cmdosu (character) name dose units variable. cmroute (character) name route administration variable. cmdosfrq (character) name dosing frequency per interval variable. cmstdy (character) name study relative day start medication variable. cmendy (character) name study day end medication variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_therapy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Time-To-Event — template_tte","title":"Template: Time-To-Event — template_tte","text":"Creates valid expression generate time--event analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Time-To-Event — template_tte","text":"","code":"template_tte(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var = \"ARM\",   paramcd,   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   strata_var = NULL,   time_points = NULL,   time_unit_var = \"AVALU\",   event_desc_var = \"EVNTDESC\",   control = control_tte(),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Time-To-Event — template_tte","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) endpoint parameter value use table title. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. strata_var (character) names variables stratified analysis. time_points (character) time points can used tern::surv_timepoint(). time_unit_var (character) name variable representing time units. event_desc_var (character) name variable events description. control (list) list settings analysis. See control_tte() details. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Time-To-Event — template_tte","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_vitals.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Vitals Plot — template_vitals","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"Creates valid expression generate patient profile vitals ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_vitals.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"","code":"template_vitals(   dataname = \"ANL\",   paramcd = \"PARAMCD\",   paramcd_levels = c(\"SYSBP\", \"DIABP\", \"PUL\", \"RESP\", \"OXYSAT\", \"WGHT\", \"TEMP\"),   xaxis = \"ADY\",   aval = lifecycle::deprecated(),   aval_var = \"AVAL\",   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_vitals.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. paramcd_levels (character) vector levels paramcd. xaxis (character) name time variable put x-axis. aval Please use aval_var argument instead. aval_var (character) name analysis value variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/template_vitals.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_gee.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"module produces analysis table using Generalized Estimating Equations (GEE).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_gee.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"","code":"tm_a_gee(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   aval_var,   id_var,   arm_var,   visit_var,   cov_var,   arm_ref_comp = NULL,   paramcd,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_gee.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_gee.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_gee.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADQS <- tmc_ex_adqs %>%     filter(ABLFL != \"Y\" & ABLFL2 != \"Y\") %>%     mutate(       AVISIT = as.factor(AVISIT),       AVISITN = rank(AVISITN) %>%         as.factor() %>%         as.numeric() %>%         as.factor(),       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.     ) %>%     droplevels() }) datanames <- c(\"ADSL\", \"ADQS\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_a_gee(       label = \"GEE\",       dataname = \"ADQS\",       aval_var = choices_selected(\"AVALBIN\", fixed = TRUE),       id_var = choices_selected(c(\"USUBJID\", \"SUBJID\"), \"USUBJID\"),       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       visit_var = choices_selected(c(\"AVISIT\", \"AVISITN\"), \"AVISIT\"),       paramcd = choices_selected(         choices = value_choices(data[[\"ADQS\"]], \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       cov_var = choices_selected(c(\"BASE\", \"AGE\", \"SEX\", \"BASE:AVISIT\"), NULL)     )   ) ) #> Initializing tm_a_gee (prototype) #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"module produces analysis tables plots Mixed Model Repeated Measurements.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"","code":"tm_a_mmrm(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   aval_var,   id_var,   arm_var,   visit_var,   cov_var,   arm_ref_comp = NULL,   paramcd,   method = teal.transform::choices_selected(c(\"Satterthwaite\", \"Kenward-Roger\",     \"Kenward-Roger-Linear\"), \"Satterthwaite\", keep_order = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args(),   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. method (teal.transform::choices_selected()) object available choices pre-selected option adjustment method. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings plots named list ggplot2_args objects plot-specific settings. List names match following: c(\"default\", \"lsmeans\", \"diagnostic\"). argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see help vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"ordering input data sets can lead slightly different numerical results different convergence behavior. known observation used package lme4. However, convergence achieved, results reliable numerical precision.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_a_mmrm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"","code":"library(dplyr) arm_ref_comp <- list(   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADQS <- tmc_ex_adqs %>%     filter(ABLFL != \"Y\" & ABLFL2 != \"Y\") %>%     filter(AVISIT %in% c(\"WEEK 1 DAY 8\", \"WEEK 2 DAY 15\", \"WEEK 3 DAY 22\")) %>%     mutate(       AVISIT = as.factor(AVISIT),       AVISITN = rank(AVISITN) %>%         as.factor() %>%         as.numeric() %>%         as.factor() #' making consecutive numeric factor     ) })  datanames <- c(\"ADSL\", \"ADQS\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init(   data = data,   modules = modules(     tm_a_mmrm(       label = \"MMRM\",       dataname = \"ADQS\",       aval_var = choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"),       id_var = choices_selected(c(\"USUBJID\", \"SUBJID\"), \"USUBJID\"),       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       visit_var = choices_selected(c(\"AVISIT\", \"AVISITN\"), \"AVISIT\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         choices = value_choices(data[[\"ADQS\"]], \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       cov_var = choices_selected(c(\"BASE\", \"AGE\", \"SEX\", \"BASE:AVISIT\"), NULL)     )   ) ) #> Initializing tm_a_mmrm #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"module produces ggplot2::ggplot() type bar chart summary table counts per category.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"","code":"tm_g_barchart_simple(   x = NULL,   fill = NULL,   x_facet = NULL,   y_facet = NULL,   label = \"Count Barchart\",   plot_options = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"x (data_extract_spec) variable x-axis. fill (data_extract_spec) grouping variable determine bar colors. x_facet (data_extract_spec) row-wise faceting groups. y_facet (data_extract_spec) column-wise faceting groups. label (character) menu item label module teal app. plot_options (list) list plot options. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"Categories can defined four levels deep defined x, fill, x_facet, y_facet parameters. parameters set NULL (default) ignored.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_barchart_simple.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl %>%   mutate(ITTFL = factor(\"Y\") %>%     with_label(\"Intent-To-Treat Population Flag\")) ADAE <- tmc_ex_adae %>%   filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"ADSL <- tmc_ex_adsl %>%               mutate(ITTFL = factor(\\\"Y\\\") %>%               with_label(\\\"Intent-To-Treat Population Flag\\\"))             ADAE <- tmc_ex_adae %>%               filter(!((AETOXGR == 1) & (AESEV == \\\"MILD\\\") & (ARM == \\\"A: Drug X\\\")))\"   ),   modules = modules(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           choices = variable_choices(             ADSL,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       ),       fill = list(         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = \"SEX\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = NULL,             multiple = FALSE           )         )       ),       x_facet = list(         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = \"AETOXGR\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = NULL,             multiple = FALSE           )         )       ),       y_facet = list(         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = \"AESEV\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = NULL,             multiple = FALSE           )         )       )     )   ) ) #> Initializing tm_g_barchart_simple #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Confidence Interval Plot — tm_g_ci","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"module produces ggplot2::ggplot() type confidence interval plot consistent TLG Catalog template CIG01 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"","code":"tm_g_ci(   label,   x_var,   y_var,   color,   stat = c(\"mean\", \"median\"),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"label (character) menu item label module teal app. x_var (character) name treatment variable put x-axis. y_var (character) name response variable put y-axis. color (data_extract_spec) group variable used determine plot colors, shapes, line types. stat (character) statistic plot. Options \"mean\" \"median\". conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_g_ci(       label = \"Confidence Interval Plot\",       x_var = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           choices = c(\"ARMCD\", \"BMRKR2\"),           selected = c(\"ARMCD\"),           multiple = FALSE,           fixed = FALSE         )       ),       y_var = data_extract_spec(         dataname = \"ADLB\",         filter = list(           filter_spec(             vars = \"PARAMCD\",             choices = levels(ADLB$PARAMCD),             selected = levels(ADLB$PARAMCD)[1],             multiple = FALSE,             label = \"Select lab:\"           ),           filter_spec(             vars = \"AVISIT\",             choices = levels(ADLB$AVISIT),             selected = levels(ADLB$AVISIT)[1],             multiple = FALSE,             label = \"Select visit:\"           )         ),         select = select_spec(           label = \"Analyzed Value\",           choices = c(\"AVAL\", \"CHG\"),           selected = \"AVAL\",           multiple = FALSE,           fixed = FALSE         )       ),       color = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           label = \"Color by variable\",           choices = c(\"SEX\", \"STRATA1\", \"STRATA2\"),           selected = c(\"STRATA1\"),           multiple = FALSE,           fixed = FALSE         )       )     )   ),   header = \"Example of Confidence Interval Plot\",   footer = tags$p(     class = \"text-muted\", \"Source: `teal.modules.clinical::tm_g_ci`\"   ) ) #> Initializing tm_g_ci #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Forest Response Plot — tm_g_forest_rsp","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"module produces grid-style forest plot response data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"","code":"tm_g_forest_rsp(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALC\"), \"AVALC\", fixed = TRUE),   subgroup_var,   strata_var,   stats = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\"),   riskdiff = NULL,   fixed_symbol_size = TRUE,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   default_responses = c(\"CR\", \"PR\", \"Y\", \"Complete Response (CR)\",     \"Partial Response (PR)\"),   plot_height = c(500L, 200L, 2000L),   plot_width = c(1500L, 800L, 3000L),   rel_width_forest = c(25L, 0L, 100L),   font_size = c(15L, 1L, 30L),   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. strata_var (teal.transform::choices_selected()) names variables stratified analysis. stats (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, caption. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   mutate(AVALC = d_onco_rsp_label(AVALC) %>%     with_label(\"Character Result/Finding\")) %>%   filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         mutate(AVALC = d_onco_rsp_label(AVALC) %>%         with_label(\\\"Character Result/Finding\\\")) %>%         filter(PARAMCD != \\\"OVRINV\\\" | AVISIT == \\\"FOLLOW UP\\\")     \"   ),   modules = modules(     tm_g_forest_rsp(       label = \"Forest Response\",       dataname = \"ADRS\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         \"INVET\"       ),       subgroup_var = choices_selected(         variable_choices(ADSL, names(ADSL)),         c(\"BMRKR2\", \"SEX\")       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"STRATA1\", \"STRATA2\")),         \"STRATA2\"       ),       plot_height = c(600L, 200L, 2000L),       default_responses = list(         BESRSPI = list(           rsp = c(\"Stable Disease (SD)\", \"Not Evaluable (NE)\"),           levels = c(             \"Complete Response (CR)\", \"Partial Response (PR)\", \"Stable Disease (SD)\",             \"Progressive Disease (PD)\", \"Not Evaluable (NE)\"           )         ),         INVET = list(           rsp = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),           levels = c(             \"Complete Response (CR)\", \"Not Evaluable (NE)\", \"Partial Response (PR)\",             \"Progressive Disease (PD)\", \"Stable Disease (SD)\"           )         ),         OVRINV = list(           rsp = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\"),           levels = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\", \"Not Evaluable (NE)\")         )       )     )   ) ) #> Initializing tm_g_forest_rsp #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Forest Survival Plot — tm_g_forest_tte","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"module produces grid-style forest plot time--event data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   subgroup_var,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   stats = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   riskdiff = NULL,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   fixed_symbol_size = TRUE,   plot_height = c(500L, 200L, 2000L),   plot_width = c(1500L, 800L, 3000L),   rel_width_forest = c(25L, 0L, 100L),   font_size = c(15L, 1L, 30L),   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. stats (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\"Race\")  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte       ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\\\"Race\\\")     \"   ),   modules = modules(     tm_g_forest_tte(       label = \"Forest Survival\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       subgroup_var = choices_selected(         variable_choices(ADSL, names(ADSL)),         c(\"BMRKR2\", \"SEX\")       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"STRATA1\", \"STRATA2\")),         \"STRATA2\"       )     )   ) ) #> Initializing tm_g_forest_tte #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Individual Patient Plots — tm_g_ipp","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"module produces ggplot2::ggplot() type individual patient plots display trends parameter values time patient, using data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"","code":"tm_g_ipp(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"USUBJID\"), \"USUBJID\", fixed = TRUE),   visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVISIT\"), \"AVISIT\", fixed = TRUE),   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   base_var = lifecycle::deprecated(),   baseline_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"BASE\"),     \"BASE\", fixed = TRUE),   add_baseline_hline = FALSE,   separate_by_obs = FALSE,   suppress_legend = FALSE,   add_avalu = TRUE,   plot_height = c(1200L, 400L, 5000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable values can used arm variable. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. id_var (teal.transform::choices_selected()) object specifying variable name subject id. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. add_baseline_hline (logical) whether horizontal line added plot baseline y-value. separate_by_obs (logical) whether create multi-panel plots. suppress_legend (logical) whether suppress plot legend. add_avalu (logical) whether avalu_first text appended plot title y-axis label. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, x, y. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl %>%   slice(1:20) %>%   df_explicit_na() ADLB <- tmc_ex_adlb %>%   filter(USUBJID %in% ADSL$USUBJID) %>%   df_explicit_na() %>%   filter(AVISIT != \"SCREENING\")  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl %>% slice(1:20) %>% df_explicit_na()       ADLB <- tmc_ex_adlb %>% filter(USUBJID %in% ADSL$USUBJID) %>%         df_explicit_na() %>% filter(AVISIT != \\\"SCREENING\\\")     \"   ),   modules = modules(     tm_g_ipp(       label = \"Individual Patient Plot\",       dataname = \"ADLB\",       arm_var = choices_selected(         value_choices(ADLB, \"ARMCD\"),         \"ARM A\"       ),       paramcd = choices_selected(         value_choices(ADLB, \"PARAMCD\"),         \"ALT\"       ),       aval_var = choices_selected(         variable_choices(ADLB, c(\"AVAL\", \"CHG\")),         \"AVAL\"       ),       avalu_var = choices_selected(         variable_choices(ADLB, c(\"AVALU\")),         \"AVALU\",         fixed = TRUE       ),       id_var = choices_selected(         variable_choices(ADLB, c(\"USUBJID\")),         \"USUBJID\",         fixed = TRUE       ),       visit_var = choices_selected(         variable_choices(ADLB, c(\"AVISIT\")),         \"AVISIT\"       ),       baseline_var = choices_selected(         variable_choices(ADLB, c(\"BASE\")),         \"BASE\",         fixed = TRUE       ),       add_baseline_hline = FALSE,       separate_by_obs = FALSE     )   ) ) #> Initializing tm_g_ipp #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Kaplan-Meier Plot — tm_g_km","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"module produces ggplot-style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   facet_var,   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   font_size = c(11L, 1L, 30),   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),   legend_pos = c(0.9, 0.5),   rel_height_plot = c(80L, 0L, 100L),   plot_height = c(800L, 400L, 5000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. facet_var (teal.transform::choices_selected()) object available choices preselected option names variable can used plot faceting. time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). font_size (numeric) numeric vector length 3 current, minimum maximum font size values. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte     \"   ),   modules = modules(     tm_g_km(       label = \"Kaplan-Meier Plot\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       arm_ref_comp = arm_ref_comp,       strata_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         \"SEX\"       ),       facet_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         NULL       )     )   ) ) #> Initializing tm_g_km #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Line Plot — tm_g_lineplot","title":"teal Module: Line Plot — tm_g_lineplot","text":"module produces ggplot2::ggplot() type line plot, optional summary table, standard ADaM data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Line Plot — tm_g_lineplot","text":"","code":"tm_g_lineplot(   label,   dataname,   parentname = ifelse(inherits(strata, \"data_extract_spec\"),     teal.transform::datanames_input(strata), \"ADSL\"),   strata = teal.transform::choices_selected(teal.transform::variable_choices(parentname,     c(\"ARM\", \"ARMCD\", \"ACTARMCD\")), \"ARM\"),   x = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVISIT\"), \"AVISIT\", fixed = TRUE),   y = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\")), \"AVAL\"),   y_unit = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   paramcd = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"PARAMCD\"), \"PARAMCD\", fixed = TRUE),   param = teal.transform::choices_selected(teal.transform::value_choices(dataname,     \"PARAMCD\", \"PARAM\"), \"ALT\"),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   interval = \"mean_ci\",   mid = \"mean\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = c(\"n\", \"mean_sd\", \"median\", \"range\"),   mid_type = \"pl\",   mid_point_size = c(2, 1, 5),   table_font_size = c(4, 2, 6),   plot_height = c(1000L, 200L, 4000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Line Plot — tm_g_lineplot","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. strata (string NA) group variable name. x (string) x-variable name. y (string) y-variable name. y_unit (string NA) y-axis unit variable name. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. param (character) parameter filter data . conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. table_font_size (numeric(1)) font size text table. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, caption, y, lty. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Line Plot — tm_g_lineplot","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Line Plot — tm_g_lineplot","text":"","code":"library(nestcolor) library(dplyr) library(forcats)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))     \"   ),   modules = modules(     tm_g_lineplot(       label = \"Line Plot\",       dataname = \"ADLB\",       strata = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       y = choices_selected(         variable_choices(ADLB, c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\")),         \"AVAL\"       ),       param = choices_selected(         value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         \"ALT\"       )     )   ) ) #> Initializing tm_g_lineplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_adverse_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"module produces adverse events table ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_adverse_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"","code":"tm_g_pp_adverse_events(   label,   dataname = \"ADAE\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   aeterm = NULL,   tox_grade = NULL,   causality = NULL,   outcome = NULL,   action = NULL,   time = NULL,   decod = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_adverse_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. aeterm (teal.transform::choices_selected()) object available choices preselected option AETERM variable dataname. tox_grade (teal.transform::choices_selected()) object available choices preselected option AETOXGR variable dataname. causality (teal.transform::choices_selected()) object available choices preselected option AEREL variable dataname. outcome (teal.transform::choices_selected()) object available choices preselected option AEOUT variable dataname. action (teal.transform::choices_selected()) object available choices preselected option AEACN variable dataname. time (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname. decod (teal.transform::choices_selected()) object available choices preselected option AEDECOD variable dataname. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_adverse_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_adverse_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"","code":"library(nestcolor) library(dplyr)  ADAE <- tmc_ex_adae ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADAE <- tmc_ex_adae       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)     \"   ),   modules = modules(     tm_g_pp_adverse_events(       label = \"Adverse Events\",       dataname = \"ADAE\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       aeterm = choices_selected(         choices = variable_choices(ADAE, \"AETERM\"),         selected = \"AETERM\"       ),       tox_grade = choices_selected(         choices = variable_choices(ADAE, \"AETOXGR\"),         selected = \"AETOXGR\"       ),       causality = choices_selected(         choices = variable_choices(ADAE, \"AEREL\"),         selected = \"AEREL\"       ),       outcome = choices_selected(         choices = variable_choices(ADAE, \"AEOUT\"),         selected = \"AEOUT\"       ),       action = choices_selected(         choices = variable_choices(ADAE, \"AEACN\"),         selected = \"AEACN\"       ),       time = choices_selected(         choices = variable_choices(ADAE, \"ASTDY\"),         selected = \"ASTDY\"       ),       decod = NULL     )   ) ) #> Initializing tm_g_pp_adverse_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_patient_timeline.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"module produces patient profile timeline ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_patient_timeline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"","code":"tm_g_pp_patient_timeline(   label,   dataname_adcm = \"ADCM\",   dataname_adae = \"ADAE\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   aeterm = NULL,   cmdecod = NULL,   aetime_start = NULL,   aetime_end = NULL,   dstime_start = NULL,   dstime_end = NULL,   aerelday_start = NULL,   aerelday_end = NULL,   dsrelday_start = NULL,   dsrelday_end = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_patient_timeline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"label (character) menu item label module teal app. dataname_adcm (character) name ADCM dataset equivalent. dataname_adae (character) name ADAE dataset equivalent. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. aeterm (teal.transform::choices_selected()) object available choices preselected option AETERM variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname_adcm. aetime_start (teal.transform::choices_selected()) object available choices preselected option ASTDTM variable dataname_adae. aetime_end (teal.transform::choices_selected()) object available choices preselected option AENDTM variable dataname_adae. dstime_start (teal.transform::choices_selected()) object available choices preselected option CMASTDTM variable dataname_adcm. dstime_end (teal.transform::choices_selected()) object available choices preselected option CMAENDTM variable dataname_adcm. aerelday_start (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname_adae. aerelday_end (teal.transform::choices_selected()) object available choices preselected option AENDY variable dataname_adae. dsrelday_start (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname_adcm. dsrelday_end (teal.transform::choices_selected()) object available choices preselected option AENDY variable dataname_adcm. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_patient_timeline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_patient_timeline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"","code":"library(nestcolor) library(dplyr)  data <- teal_data() data <- within(data, {   ADAE <- tmc_ex_adae   ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)   ADCM <- tmc_ex_adcm %>% mutate(     CMSTDY = case_when(       CMCAT == \"medcl B\" ~ 20,       CMCAT == \"medcl C\" ~ 150,       TRUE ~ 1     ) %>% with_label(\"Study Day of Start of Medication\"),     CMENDY = case_when(       CMCAT == \"medcl B\" ~ 700,       CMCAT == \"medcl C\" ~ 1000,       TRUE ~ 500     ) %>% with_label(\"Study Day of End of Medication\"),     CMASTDTM = ASTDTM,     CMAENDTM = AENDTM   ) })  adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\") datanames(data) <- c(\"ADSL\", \"ADAE\", \"ADCM\") join_keys(data) <- default_cdisc_join_keys[c(\"ADSL\", \"ADAE\", \"ADCM\")] join_keys(data)[\"ADCM\", \"ADCM\"] <- adcm_keys join_keys(data)[\"ADAE\", \"ADCM\"] <- c(\"STUDYID\", \"USUBJID\")  app <- init(   data = data,   modules = modules(     tm_g_pp_patient_timeline(       label = \"Patient Timeline\",       dataname_adae = \"ADAE\",       dataname_adcm = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       cmdecod = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMDECOD\"),         selected = \"CMDECOD\",       ),       aeterm = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AETERM\"),         selected = c(\"AETERM\")       ),       aetime_start = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"ASTDTM\"),         selected = c(\"ASTDTM\")       ),       aetime_end = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AENDTM\"),         selected = c(\"AENDTM\")       ),       dstime_start = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMASTDTM\"),         selected = c(\"CMASTDTM\")       ),       dstime_end = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMAENDTM\"),         selected = c(\"CMAENDTM\")       ),       aerelday_start = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"ASTDY\"),         selected = c(\"ASTDY\")       ),       aerelday_end = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AENDY\"),         selected = c(\"AENDY\")       ),       dsrelday_start = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"ASTDY\"),         selected = c(\"ASTDY\")       ),       dsrelday_end = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"AENDY\"),         selected = c(\"AENDY\")       )     )   ) ) #> Initializing tm_g_pp_patient_timeline #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_therapy.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"module produces patient profile therapy table ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_therapy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"","code":"tm_g_pp_therapy(   label,   dataname = \"ADCM\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   atirel = NULL,   cmdecod = NULL,   cmindc = NULL,   cmdose = NULL,   cmtrt = NULL,   cmdosu = NULL,   cmroute = NULL,   cmdosfrq = NULL,   cmstdy = NULL,   cmendy = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_therapy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmdose (teal.transform::choices_selected()) object available choices preselected option CMDOSE variable dataname. cmtrt (teal.transform::choices_selected()) object available choices preselected option CMTRT variable dataname. cmdosu (teal.transform::choices_selected()) object available choices preselected option CMDOSU variable dataname. cmroute (teal.transform::choices_selected()) object available choices preselected option CMROUTE variable dataname. cmdosfrq (teal.transform::choices_selected()) object available choices preselected option CMDOSFRQ variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. cmendy (teal.transform::choices_selected()) object available choices preselected option CMENDY variable dataname. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_therapy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_therapy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"","code":"library(nestcolor) library(dplyr)  ADCM <- tmc_ex_adcm ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID) ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADCM <- tmc_ex_adcm       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)       ADCM$CMASTDTM <- ADCM$ASTDTM       ADCM$CMAENDTM <- ADCM$AENDTM     \",     join_keys = join_keys   ),   modules = modules(     tm_g_pp_therapy(       label = \"Therapy\",       dataname = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       atirel = choices_selected(         choices = variable_choices(ADCM, \"ATIREL\"),         selected = c(\"ATIREL\")       ),       cmdecod = choices_selected(         choices = variable_choices(ADCM, \"CMDECOD\"),         selected = \"CMDECOD\"       ),       cmindc = choices_selected(         choices = variable_choices(ADCM, \"CMINDC\"),         selected = \"CMINDC\"       ),       cmdose = choices_selected(         choices = variable_choices(ADCM, \"CMDOSE\"),         selected = \"CMDOSE\"       ),       cmtrt = choices_selected(         choices = variable_choices(ADCM, \"CMTRT\"),         selected = \"CMTRT\"       ),       cmdosu = choices_selected(         choices = variable_choices(ADCM, \"CMDOSU\"),         selected = c(\"CMDOSU\")       ),       cmroute = choices_selected(         choices = variable_choices(ADCM, \"CMROUTE\"),         selected = \"CMROUTE\"       ),       cmdosfrq = choices_selected(         choices = variable_choices(ADCM, \"CMDOSFRQ\"),         selected = \"CMDOSFRQ\"       ),       cmstdy = choices_selected(         choices = variable_choices(ADCM, \"ASTDY\"),         selected = \"ASTDY\"       ),       cmendy = choices_selected(         choices = variable_choices(ADCM, \"AENDY\"),         selected = \"AENDY\"       )     )   ) ) #> Initializing tm_g_pp_therapy #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"module produces patient profile vitals ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"","code":"tm_g_pp_vitals(   label,   dataname = \"ADVS\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   paramcd = NULL,   aval = lifecycle::deprecated(),   aval_var = NULL,   xaxis = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval Please use aval_var argument instead. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. xaxis (teal.transform::choices_selected()) object available choices preselected option time variable dataname put plot x-axis. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"plot supports horizontal lines following 6 PARAMCD levels present dataname: \"SYSBP\", \"DIABP\", \"TEMP\", \"RESP\", \"OXYSAT\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_g_pp_vitals.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADVS <- tmc_ex_advs  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADVS = ADVS,     code = \"       ADSL <- tmc_ex_adsl       ADVS <- tmc_ex_advs     \"   ),   modules = modules(     tm_g_pp_vitals(       label = \"Vitals\",       dataname = \"ADVS\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       paramcd = choices_selected(         choices = variable_choices(ADVS, \"PARAMCD\"),         selected = \"PARAMCD\"       ),       xaxis = choices_selected(         choices = variable_choices(ADVS, \"ADY\"),         selected = \"ADY\"       ),       aval_var = choices_selected(         choices = variable_choices(ADVS, \"AVAL\"),         selected = \"AVAL\"       )     )   ) ) #> Initializing tm_g_pp_vitals #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Abnormality Summary Table — tm_t_abnormality","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"module produces table summarize abnormality.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"","code":"tm_t_abnormality(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   by_vars,   grade,   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   baseline_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"BNRIND\"), selected = \"BNRIND\", fixed = TRUE),   treatment_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ONTRTFL\"), selected = \"ONTRTFL\", fixed = TRUE),   treatment_flag = teal.transform::choices_selected(\"Y\"),   add_total = TRUE,   total_label = default_total_label(),   exclude_base_abn = FALSE,   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. grade (teal.transform::choices_selected()) object available choices preselected option variable names can used specify abnormality grade. Variable must factor. abnormal (named list) defined user indicate abnormalities displayed. id_var (teal.transform::choices_selected()) object specifying variable name subject id. baseline_var (teal.transform::choices_selected()) variable baseline abnormality grade. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). exclude_base_abn (logical) whether exclude patients abnormal values baseline. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. na_level (character) NA level input dataset, default \"<Missing>\". basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"Patients abnormality baseline treatment visit can excluded accordance GDSR specifications using exclude_base_abn.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"","code":"data <- teal_data() data <- within(data, {   library(dplyr)    ADSL <- tmc_ex_adsl   ADLB <- tmc_ex_adlb %>%     mutate(       ONTRTFL = case_when(         AVISIT %in% c(\"SCREENING\", \"BASELINE\") ~ \"\",         TRUE ~ \"Y\"       ) %>% with_label(\"On Treatment Record Flag\")     ) }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_abnormality(       label = \"Abnormality Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(data[[\"ADSL\"]], subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       add_total = FALSE,       by_vars = choices_selected(         choices = variable_choices(data[[\"ADLB\"]], subset = c(\"LBCAT\", \"PARAM\", \"AVISIT\")),         selected = c(\"LBCAT\", \"PARAM\"),         keep_order = TRUE       ),       baseline_var = choices_selected(         variable_choices(data[[\"ADLB\"]], subset = \"BNRIND\"),         selected = \"BNRIND\", fixed = TRUE       ),       grade = choices_selected(         choices = variable_choices(data[[\"ADLB\"]], subset = \"ANRIND\"),         selected = \"ANRIND\",         fixed = TRUE       ),       abnormal = list(low = \"LOW\", high = \"HIGH\"),       exclude_base_abn = FALSE     )   ) ) #> Initializing tm_t_abnormality #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"module produces table summarize laboratory test results highest grade post-baseline","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"","code":"tm_t_abnormality_by_worst_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   paramcd,   atoxgr_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ATOXGR\"), selected = \"ATOXGR\", fixed = TRUE),   worst_high_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"WGRHIFL\"), selected = \"WGRHIFL\", fixed = TRUE),   worst_low_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"WGRLOFL\"), selected = \"WGRLOFL\", fixed = TRUE),   worst_flag_indicator = teal.transform::choices_selected(\"Y\"),   add_total = TRUE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. id_var (teal.transform::choices_selected()) object specifying variable name subject id. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. atoxgr_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Analysis Toxicity Grade. worst_high_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Worst High Grade flag. worst_low_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Worst Low Grade flag. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_abnormality_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb %>%   filter(!AVISIT %in% c(\"SCREENING\", \"BASELINE\"))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb %>%         filter(!AVISIT %in% c(\\\"SCREENING\\\", \\\"BASELINE\\\"))     \"   ),   modules = modules(     tm_t_abnormality_by_worst_grade(       label = \"Laboratory Test Results with Highest Grade Post-Baseline\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = c(\"ALT\", \"CRP\", \"IGA\")       ),       add_total = FALSE     )   ),   filter = teal_slices(     teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\"),     teal_slice(\"ADLB\", \"ONTRTFL\", selected = \"Y\")   ) ) #> Initializing tm_t_abnormality_by_worst_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: ANCOVA Summary — tm_t_ancova","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"module produces table summarize analysis variance, consistent TLG Catalog template AOVT01 available multiple endpoints selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"","code":"tm_t_ancova(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   aval_var,   cov_var,   include_interact = FALSE,   interact_var = NULL,   interact_y = FALSE,   avisit,   paramcd,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. include_interact (logical) whether interaction term included model. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results interact_var discrete. interaction needed, default option FALSE. avisit (teal.transform::choices_selected()) value analysis visit AVISIT interest. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"single endpoint selected, unadjusted adjusted comparison provided. modules expects analysis data following variables: AVISIT: variable used filter analysis visits. PARAMCD: variable used filter endpoints, filtering paramcd avisit, one observation per patient expected analysis meaningful.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"","code":"ADSL <- tmc_ex_adsl ADQS <- tmc_ex_adqs  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADQS = ADQS,     code = \"       ADSL <- tmc_ex_adsl       ADQS <- tmc_ex_adqs     \"   ),   modules = modules(     tm_t_ancova(       label = \"ANCOVA Table\",       dataname = \"ADQS\",       avisit = choices_selected(         choices = value_choices(ADQS, \"AVISIT\"),         selected = \"WEEK 1 DAY 8\"       ),       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ACTARMCD\", \"ARMCD\")),         selected = \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       aval_var = choices_selected(         choices = variable_choices(ADQS, c(\"CHG\", \"AVAL\")),         selected = \"CHG\"       ),       cov_var = choices_selected(         choices = variable_choices(ADQS, c(\"BASE\", \"STRATA1\", \"SEX\")),         selected = \"STRATA1\"       ),       paramcd = choices_selected(         choices = value_choices(ADQS, \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       interact_var = choices_selected(         choices = variable_choices(ADQS, c(\"BASE\", \"STRATA1\", \"SEX\")),         selected = \"STRATA1\"       )     )   ) ) #> Initializing tm_t_ancova #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Binary Outcome Table — tm_t_binary_outcome","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"module produces binary outcome response summary table, option match template response table RSPT01 available TLG Catalog .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"","code":"tm_t_binary_outcome(   label,   dataname,   parentname = ifelse(test = inherits(arm_var, \"data_extract_spec\"), yes =     teal.transform::datanames_input(arm_var), no = \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(choices =     teal.transform::variable_choices(dataname, c(\"AVALC\", \"SEX\")), selected = \"AVALC\",     fixed = FALSE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   default_responses = c(\"CR\", \"PR\", \"Y\", \"Complete Response (CR)\",     \"Partial Response (PR)\", \"M\"),   rsp_table = FALSE,   control = list(global = list(method = ifelse(rsp_table, \"clopper-pearson\", \"waldcc\"),     conf_level = 0.95), unstrat = list(method_ci = ifelse(rsp_table, \"wald\", \"waldcc\"),     method_test = \"schouten\", odds = TRUE), strat = list(method_ci = \"cmh\", method_test =     \"cmh\")),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. rsp_table (logical) whether initial set-module match RSPT01. Defaults FALSE. control (named list) named list containing 3 named lists follows: global: list settings overall analysis 2 named elements method conf_level. unstrat: list settings unstratified analysis 3 named elements method_ci method_test, odds. See tern::estimate_proportion_diff(), tern::test_proportion_diff(), tern::estimate_odds_ratio(), respectively, options details settings implemented analysis. strat: list settings stratified analysis elements method_ci method_test. See tern::estimate_proportion_diff() tern::test_proportion_diff(), respectively, options details settings implemented analysis. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"display order response categories inherits factor level order source data. Use base::factor() levels argument manipulate source data order include/exclude re-categorize response categories arrange display order. response categories \"Missing\", \"Evaluable (NE)\", \"Missing unevaluable\", 95% confidence interval calculated. Reference arms automatically combined multiple arms selected reference group.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_binary_outcome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   mutate(     AVALC = d_onco_rsp_label(AVALC) %>%       with_label(\"Character Result/Finding\")   ) %>%   filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")  arm_ref_comp <- list(   ARMCD = list(ref = \"ARM B\", comp = c(\"ARM A\", \"ARM C\")),   ARM = list(ref = \"B: Placebo\", comp = c(\"A: Drug X\", \"C: Combination\")) ) app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         mutate(           AVALC = d_onco_rsp_label(AVALC) %>%             with_label(\\\"Character Result/Finding\\\")         ) %>%         filter(PARAMCD != \\\"OVRINV\\\" | AVISIT == \\\"FOLLOW UP\\\")     \"   ),   modules = modules(     tm_t_binary_outcome(       label = \"Responders\",       dataname = \"ADRS\",       paramcd = choices_selected(         choices = value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         selected = \"BESRSPI\"       ),       arm_var = choices_selected(         choices = variable_choices(ADRS, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         selected = \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       strata_var = choices_selected(         choices = variable_choices(ADRS, c(\"SEX\", \"BMRKR2\", \"RACE\")),         selected = \"RACE\"       ),       default_responses = list(         BESRSPI = list(           rsp = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),           levels = c(             \"Complete Response (CR)\", \"Partial Response (PR)\",             \"Stable Disease (SD)\", \"Progressive Disease (PD)\"           )         ),         INVET = list(           rsp = c(\"Stable Disease (SD)\", \"Not Evaluable (NE)\"),           levels = c(             \"Complete Response (CR)\", \"Not Evaluable (NE)\", \"Partial Response (PR)\",             \"Progressive Disease (PD)\", \"Stable Disease (SD)\"           )         ),         OVRINV = list(           rsp = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\"),           levels = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\", \"Not Evaluable (NE)\")         )       )     )   ) ) #> Initializing tm_t_binary_outcome #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Cox Regression Model — tm_t_coxreg","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"module fits Cox univariable multi-variable models, consistent TLG Catalog templates Cox regression tables COXT01 COXT02, respectively. See TLG Catalog entries COXT01 COXT02 .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"","code":"tm_t_coxreg(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   cov_var,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   multivariate = TRUE,   na_level = default_na_str(),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. multivariate (logical) FALSE, univariable approach used instead multi-variable model. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"Cox Proportional Hazards (PH) model commonly used method estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis. modules expects analysis data following variables: AVAL: time event CNSR: 1 record AVAL censored, 0 otherwise PARAMCD: variable used filter endpoint (e.g. OS). filtering PARAMCD one observation per patient expected arm variables stratification/covariate variables taken ADSL data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"likelihood ratio test supported models include strata - Wald test substituted cases. Multi-variable default choice backward compatibility.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"","code":"## First example ## ============= ## The example below is based on the usual approach involving creation of ## a random CDISC dataset and then running the application.  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADTTE <- tmc_ex_adtte }) datanames <- c(\"ADSL\", \"ADTTE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_coxreg(       label = \"Cox Reg.\",       dataname = \"ADTTE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\", \"ACTARMCD\"), \"ARM\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(data[[\"ADTTE\"]], \"PARAMCD\", \"PARAM\"), \"OS\"       ),       strata_var = choices_selected(         c(\"COUNTRY\", \"STRATA1\", \"STRATA2\"), \"STRATA1\"       ),       cov_var = choices_selected(         c(\"AGE\", \"BMRKR1\", \"BMRKR2\", \"REGION1\"), \"AGE\"       ),       multivariate = TRUE     )   ) ) #> Initializing tm_t_coxreg #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  ## Second example ## ============== ## This time, a synthetic pair of ADTTE/ADSL data is fabricated for Cox regression ## where ties and pval_method matter.  ## Dataset fabrication ## -------------------  data <- teal_data() data <- within(data, {   library(dplyr)   ADTTE <- data.frame(     STUDYID = \"LUNG\",     AVAL = c(4, 3, 1, 1, 2, 2, 3, 1, 2),     CNSR = c(1, 1, 1, 0, 1, 1, 0, 0, 0),     ARMCD = factor(       c(0, 1, 1, 1, 1, 0, 0, 0, 0),       labels = c(\"ARM A\", \"ARM B\")     ),     SEX = factor(       c(0, 0, 0, 0, 1, 1, 1, 1, 1),       labels = c(\"F\", \"M\")     ),     INST = factor(c(\"A\", \"A\", \"B\", \"B\", \"A\", \"B\", \"A\", \"B\", \"A\")),     stringsAsFactors = FALSE   )   ADTTE <- rbind(ADTTE, ADTTE, ADTTE, ADTTE)   ADTTE <- as_tibble(ADTTE)   set.seed(1)   ADTTE$INST <- sample(ADTTE$INST)   ADTTE$AGE <- sample(seq(5, 75, 5), size = nrow(ADTTE), replace = TRUE)   ADTTE$USUBJID <- paste(\"sub\", 1:nrow(ADTTE), ADTTE$INST, sep = \"-\")   ADTTE$PARAM <- ADTTE$PARAMCD <- \"OS\"   ADSL <- subset(     ADTTE,     select = c(\"USUBJID\", \"STUDYID\", \"ARMCD\", \"SEX\", \"INST\", \"AGE\")   ) })  datanames <- c(\"ADSL\", \"ADTTE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  ## `teal` application ## ---------------- ## Note that the R code exported by `Show R Code` does not include the data ## pre-processing. You will need to create the dataset as above before ## running the exported R code.  arm_ref_comp <- list(ARMCD = list(ref = \"ARM A\", comp = c(\"ARM B\"))) app <- init(   data = data,   modules = modules(     tm_t_coxreg(       label = \"Cox Reg.\",       dataname = \"ADTTE\",       arm_var = choices_selected(c(\"ARMCD\"), \"ARMCD\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(data[[\"ADTTE\"]], \"PARAMCD\", \"PARAM\"), \"OS\"       ),       strata_var = choices_selected(c(\"INST\"), NULL),       cov_var = choices_selected(c(\"SEX\", \"AGE\"), \"SEX\"),       multivariate = TRUE     )   ) ) #> Initializing tm_t_coxreg #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Events by Term — tm_t_events","title":"teal Module: Events by Term — tm_t_events","text":"module produces table events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Events by Term — tm_t_events","text":"","code":"tm_t_events(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   sort_criteria = c(\"freq_desc\", \"alpha\"),   sort_freq_col = total_label,   prune_freq = 0,   prune_diff = 0,   drop_arm_levels = TRUE,   incl_overall_sum = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Events by Term — tm_t_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. sort_freq_col (character) column sort frequency sort_criteria set freq_desc. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. incl_overall_sum (flag)  whether two rows summarize overall number adverse events included top table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Events by Term — tm_t_events","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Events by Term — tm_t_events","text":"","code":"ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = modules(     tm_t_events(       label = \"Adverse Event Table\",       dataname = \"ADAE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       llt = choices_selected(         choices = variable_choices(ADAE, c(\"AETERM\", \"AEDECOD\")),         selected = c(\"AEDECOD\")       ),       hlt = choices_selected(         choices = variable_choices(ADAE, c(\"AEBODSYS\", \"AESOC\")),         selected = \"AEBODSYS\"       ),       add_total = TRUE,       event_type = \"adverse event\"     )   ) ) #> Initializing tm_t_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Events by Grade — tm_t_events_by_grade","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"module produces table summarize events grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"","code":"tm_t_events_by_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   hlt,   llt,   grade,   grading_groups = list(`Any Grade (%)` = c(\"1\", \"2\", \"3\", \"4\", \"5\"), `Grade 1-2 (%)` =     c(\"1\", \"2\"), `Grade 3-4 (%)` = c(\"3\", \"4\"), `Grade 5 (%)` = \"5\"),   col_by_grade = FALSE,   prune_freq = 0,   prune_diff = 0,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. grade (character) name severity level variable. grading_groups (list) named list grading groups used col_by_grade = TRUE. col_by_grade (logical) whether display grading groups nested columns. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"","code":"data <- teal_data() data <- within(data, {   library(dplyr)    ADSL <- tmc_ex_adsl   lbls_adae <- col_labels(tmc_ex_adae)   ADAE <- tmc_ex_adae %>%     mutate_if(is.character, as.factor) #' be certain of having factors   col_labels(ADAE) <- lbls_adae })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_events_by_grade(       label = \"Adverse Events by Grade Table\",       dataname = \"ADAE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       llt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AETERM\", \"AEDECOD\")),         selected = c(\"AEDECOD\")       ),       hlt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AEBODSYS\", \"AESOC\")),         selected = \"AEBODSYS\"       ),       grade = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AETOXGR\", \"AESEV\")),         selected = \"AETOXGR\"       )     )   ) ) #> Initializing tm_t_events_by_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_patyear.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"module produces table event rates adjusted patient-years.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_patyear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"","code":"tm_t_events_patyear(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   events_var,   paramcd,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_patyear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. events_var (teal.transform::choices_selected()) object available choices preselected option variable event counts. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_patyear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_patyear.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADAETTE <- tmc_ex_adaette %>%   filter(PARAMCD %in% c(\"AETTE1\", \"AETTE2\", \"AETTE3\")) %>%   mutate(is_event = CNSR == 0) %>%   mutate(n_events = as.integer(is_event))  # 1. Basic Example  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAETTE = ADAETTE,     code = \"       ADSL <- tmc_ex_adsl       ADAETTE <- tmc_ex_adaette %>%         filter(PARAMCD %in% c(\\\"AETTE1\\\", \\\"AETTE2\\\", \\\"AETTE3\\\")) %>%         mutate(is_event = CNSR == 0) %>%         mutate(n_events = as.integer(is_event))     \"   ),   modules = modules(     tm_t_events_patyear(       label = \"AE Rate Adjusted for Patient-Years At Risk Table\",       dataname = \"ADAETTE\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         selected = \"ARMCD\"       ),       add_total = TRUE,       events_var = choices_selected(         choices = variable_choices(ADAETTE, \"n_events\"),         selected = \"n_events\",         fixed = TRUE       ),       paramcd = choices_selected(         choices = value_choices(ADAETTE, \"PARAMCD\", \"PARAM\"),         selected = \"AETTE1\"       )     )   ) ) #> Initializing tm_t_events_patyear #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # 2. Example with table split on 2 arm_var variables  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAETTE = ADAETTE,     code = \"       ADSL <- tmc_ex_adsl       ADAETTE <- tmc_ex_adaette %>%         filter(PARAMCD %in% c(\\\"AETTE1\\\", \\\"AETTE2\\\", \\\"AETTE3\\\")) %>%         mutate(is_event = CNSR == 0) %>%         mutate(n_events = as.integer(is_event))     \"   ),   modules = modules(     tm_t_events_patyear(       label = \"AE Rate Adjusted for Patient-Years At Risk Table\",       dataname = \"ADAETTE\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"SEX\")),         selected = c(\"ARM\", \"SEX\")       ),       add_total = TRUE,       events_var = choices_selected(         choices = variable_choices(ADAETTE, \"n_events\"),         selected = \"n_events\",         fixed = TRUE       ),       paramcd = choices_selected(         choices = value_choices(ADAETTE, \"PARAMCD\", \"PARAM\"),         selected = \"AETTE1\"       )     )   ) ) #> Initializing tm_t_events_patyear #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Adverse Events Summary — tm_t_events_summary","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"module produces adverse events summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"","code":"tm_t_events_summary(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   flag_var_anl = NULL,   flag_var_aesi = NULL,   dthfl_var =     teal.transform::choices_selected(teal.transform::variable_choices(parentname,     \"DTHFL\"), \"DTHFL\", fixed = TRUE),   dcsreas_var =     teal.transform::choices_selected(teal.transform::variable_choices(parentname,     \"DCSREAS\"), \"DCSREAS\", fixed = TRUE),   llt = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AEDECOD\"), \"AEDECOD\", fixed = TRUE),   aeseq_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AESEQ\"), \"AESEQ\", fixed = TRUE),   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   count_dth = TRUE,   count_wd = TRUE,   count_subj = TRUE,   count_pt = TRUE,   count_events = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. flag_var_anl (teal.transform::choices_selected() NULL) vector names flag variables dataset used count adverse event sub-groups (e.g. Serious events, Related events, etc.). Variable labels used table row names exist. flag_var_aesi (teal.transform::choices_selected() NULL) vector names flag variables dataset used count adverse event special interest groups. flag variables must type logical. Variable labels used table row names exist. dthfl_var (teal.transform::choices_selected()) object available choices preselected option variable names can used death flag variable. Records `\"Y\"“ summarized table row \"Total number deaths\". dcsreas_var (teal.transform::choices_selected()) object available choices preselected option variable names can used study discontinuation reason variable. Records \"ADVERSE EVENTS\" summarized table row \"Total number patients withdrawn study due AE\". llt (teal.transform::choices_selected()) name variable low level term events. aeseq_var (teal.transform::choices_selected()) variable adverse events sequence number dataset. Used counting total number events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). count_dth (logical) whether show count total deaths (based dthfl_var). Defaults TRUE. count_wd (logical) whether show count patients withdrawn study due adverse event (based dcsreas_var). Defaults TRUE. count_subj (logical) whether show count unique subjects (based USUBJID). applies event flag variables provided. count_pt (logical) whether show count unique preferred terms (based llt). applies event flag variables provided. count_events (logical) whether show count events (based aeseq_var). applies event flag variables provided. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_events_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl %>%     mutate(       DTHFL = case_when(         !is.na(DTHDT) ~ \"Y\",         TRUE ~ \"\"       ) %>% with_label(\"Subject Death Flag\")     )   ADAE <- tmc_ex_adae    add_event_flags <- function(dat) {     dat <- dat %>%       mutate(         TMPFL_SER = AESER == \"Y\",         TMPFL_REL = AEREL == \"Y\",         TMPFL_GR5 = AETOXGR == \"5\",         TMP_SMQ01 = !is.na(SMQ01NAM),         TMP_SMQ02 = !is.na(SMQ02NAM),         TMP_CQ01 = !is.na(CQ01NAM)       )     column_labels <- list(       TMPFL_SER = \"Serious AE\",       TMPFL_REL = \"Related AE\",       TMPFL_GR5 = \"Grade 5 AE\",       TMP_SMQ01 = aesi_label(dat[[\"SMQ01NAM\"]], dat[[\"SMQ01SC\"]]),       TMP_SMQ02 = aesi_label(\"Y.9.9.9.9/Z.9.9.9.9 AESI\"),       TMP_CQ01 = aesi_label(dat[[\"CQ01NAM\"]])     )     col_labels(dat)[names(column_labels)] <- as.character(column_labels)     dat   }    #' Generating user-defined event flags.   ADAE <- ADAE %>% add_event_flags()    ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), \"TMPFL_\")]   aesi_vars <- names(ADAE)[startsWith(names(ADAE), \"TMP_\")] })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_events_summary(       label = \"Adverse Events Summary\",       dataname = \"ADAE\",       arm_var = choices_selected(         choices = variable_choices(\"ADSL\", c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       flag_var_anl = choices_selected(         choices = variable_choices(\"ADAE\", data[[\"ae_anl_vars\"]]),         selected = data[[\"ae_anl_vars\"]][1],         keep_order = TRUE,         fixed = FALSE       ),       flag_var_aesi = choices_selected(         choices = variable_choices(\"ADAE\", data[[\"aesi_vars\"]]),         selected = data[[\"aesi_vars\"]][1],         keep_order = TRUE,         fixed = FALSE       ),       add_total = TRUE     )   ) ) #> Initializing tm_t_events_summary #> Warning: 'package:forcats' may not be available when loading #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"module produces exposure table risk management plan.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"","code":"tm_t_exposure(   label,   dataname,   parentname = ifelse(inherits(col_by_var, \"data_extract_spec\"),     teal.transform::datanames_input(col_by_var), \"ADSL\"),   row_by_var,   col_by_var,   paramcd = teal.transform::choices_selected(choices =     teal.transform::value_choices(dataname, \"PARAMCD\", \"PARAM\"), selected = \"TDURD\"),   paramcd_label = \"PARAM\",   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   parcat,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVAL\"), selected = \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVALU\"), selected = \"AVALU\", fixed = TRUE),   add_total,   total_label = default_total_label(),   add_total_row = TRUE,   total_row_label = \"Total number of patients and patient time*\",   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. row_by_var (teal.transform::choices_selected()) object available choices preselected option variable names can used split rows. col_by_var (teal.transform::choices_selected()) object available choices preselected option variable names can used split columns. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. paramcd_label (character) column dataset value used label argument paramcd. id_var (teal.transform::choices_selected()) object specifying variable name subject id. parcat (teal.transform::choices_selected()) object available choices preselected option parameter category values. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). add_total_row (flag) whether \"total\" level added others includes levels constitute split. custom label can set level via total_row_label argument. total_row_label (character) string display total row label row enabled (see add_total_row). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_exposure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADEX <- tmc_ex_adex    set.seed(1, kind = \"Mersenne-Twister\")   labels <- col_labels(ADEX, fill = FALSE)   ADEX <- ADEX %>%     distinct(USUBJID, .keep_all = TRUE) %>%     mutate(       PARAMCD = \"TDURD\",       PARAM = \"Overall duration (days)\",       AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),       AVALU = \"Days\"     ) %>%     bind_rows(ADEX)   col_labels(ADEX) <- labels })  datanames <- c(\"ADSL\", \"ADEX\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_exposure(       label = \"Duration of Exposure Table\",       dataname = \"ADEX\",       paramcd = choices_selected(         choices = value_choices(data[[\"ADEX\"]], \"PARAMCD\", \"PARAM\"),         selected = \"TDURD\"       ),       col_by_var = choices_selected(         choices = variable_choices(data[[\"ADEX\"]], subset = c(\"SEX\", \"ARM\")),         selected = \"SEX\"       ),       row_by_var = choices_selected(         choices = variable_choices(data[[\"ADEX\"]], subset = c(\"RACE\", \"REGION1\", \"STRATA1\", \"SEX\")),         selected = \"RACE\"       ),       parcat = choices_selected(         choices = value_choices(data[[\"ADEX\"]], \"PARCAT2\"),         selected = \"Drug A\"       ),       add_total = FALSE     )   ),   filter = teal_slices(teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\")) ) #> Initializing tm_t_exposure #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Logistic Regression — tm_t_logistic","title":"teal Module: Logistic Regression — tm_t_logistic","text":"module produces multi-variable logistic regression table consistent TLG Catalog template LGRT02 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Logistic Regression — tm_t_logistic","text":"","code":"tm_t_logistic(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var = NULL,   arm_ref_comp = NULL,   paramcd,   cov_var = NULL,   avalc_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALC\"), \"AVALC\", fixed = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Logistic Regression — tm_t_logistic","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected() NULL) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. NULL, arm/treatment variable included logistic model. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. avalc_var (teal.transform::choices_selected()) object available choices preselected option analysis variable (categorical). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Logistic Regression — tm_t_logistic","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Logistic Regression — tm_t_logistic","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   filter(PARAMCD %in% c(\"BESRSPI\", \"INVET\"))  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         filter(PARAMCD %in% c(\\\"BESRSPI\\\", \\\"INVET\\\"))     \"   ),   modules = modules(     tm_t_logistic(       label = \"Logistic Regression\",       dataname = \"ADRS\",       arm_var = choices_selected(         choices = variable_choices(ADRS, c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         choices = value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         selected = \"BESRSPI\"       ),       cov_var = choices_selected(         choices = c(\"SEX\", \"AGE\", \"BMRKR1\", \"BMRKR2\"),         selected = \"SEX\"       )     )   ) ) #> Initializing tm_t_logistic #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_mult_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Multiple Events by Term — tm_t_mult_events","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"module produces table multiple events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_mult_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"","code":"tm_t_mult_events(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   seq_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_mult_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. seq_var (teal.transform::choices_selected()) object available choices preselected option variable names can used analysis sequence number variable. Used counting unique number events. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_mult_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_mult_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"","code":"ADSL <- tmc_ex_adsl ADCM <- tmc_ex_adcm adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADSL <- tmc_ex_adsl       ADCM <- tmc_ex_adcm     \",     join_keys = join_keys   ),   modules = modules(     tm_t_mult_events(       label = \"Concomitant Medications by Medication Class and Preferred Name\",       dataname = \"ADCM\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       seq_var = choices_selected(\"CMSEQ\", selected = \"CMSEQ\", fixed = TRUE),       hlt = choices_selected(         choices = variable_choices(ADCM, c(\"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")),         selected = c(\"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")       ),       llt = choices_selected(         choices = variable_choices(ADCM, c(\"CMDECOD\")),         selected = c(\"CMDECOD\")       ),       add_total = TRUE,       event_type = \"treatment\"     )   ) ) #> Initializing tm_t_mult_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_basic_info.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"module produces patient profile basic info report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_basic_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"","code":"tm_t_pp_basic_info(   label,   dataname = \"ADSL\",   patient_col = \"USUBJID\",   vars = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_basic_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. patient_col (character) name patient ID variable. vars (teal.transform::choices_selected())  object available choices preselected option variables dataname show table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_basic_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_basic_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"","code":"ADSL <- tmc_ex_adsl  app <- init(   data = cdisc_data(     ADSL = ADSL,     code = \"ADSL <- tmc_ex_adsl\"   ),   modules = modules(     tm_t_pp_basic_info(       label = \"Basic Info\",       dataname = \"ADSL\",       patient_col = \"USUBJID\",       vars = choices_selected(         choices = variable_choices(ADSL),         selected = c(\"ARM\", \"AGE\", \"SEX\", \"COUNTRY\", \"RACE\", \"EOSSTT\")       )     )   ) ) #> Initializing tm_t_pp_basic_info #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_laboratory.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"module produces patient profile laboratory table using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_laboratory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"","code":"tm_t_pp_laboratory(   label,   dataname = \"ADLB\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   timepoints = NULL,   aval = lifecycle::deprecated(),   aval_var = NULL,   avalu = lifecycle::deprecated(),   avalu_var = NULL,   param = NULL,   paramcd = NULL,   anrind = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_laboratory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. timepoints (teal.transform::choices_selected()) object available choices preselected option time variable dataname. aval Please use aval_var argument instead. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu Please use avalu_var argument instead. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. param (teal.transform::choices_selected()) object available choices preselected option PARAM variable dataname. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. anrind (teal.transform::choices_selected()) object available choices preselected option ANRIND variable dataname. Variable following 3 levels: \"HIGH\", \"LOW\", \"NORMAL\". pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_laboratory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_laboratory.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_pp_laboratory(       label = \"Vitals\",       dataname = \"ADLB\",       patient_col = \"USUBJID\",       paramcd = choices_selected(         choices = variable_choices(ADLB, \"PARAMCD\"),         selected = \"PARAMCD\"       ),       param = choices_selected(         choices = variable_choices(ADLB, \"PARAM\"),         selected = \"PARAM\"       ),       timepoints = choices_selected(         choices = variable_choices(ADLB, \"ADY\"),         selected = \"ADY\"       ),       anrind = choices_selected(         choices = variable_choices(ADLB, \"ANRIND\"),         selected = \"ANRIND\"       ),       aval_var = choices_selected(         choices = variable_choices(ADLB, \"AVAL\"),         selected = \"AVAL\"       ),       avalu_var = choices_selected(         choices = variable_choices(ADLB, \"AVALU\"),         selected = \"AVALU\"       )     )   ) ) #> Initializing tm_t_pp_laboratory #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_medical_history.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"module produces patient profile medical history report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_medical_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"","code":"tm_t_pp_medical_history(   label,   dataname = \"ADMH\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   mhterm = NULL,   mhbodsys = NULL,   mhdistat = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_medical_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. mhterm (teal.transform::choices_selected()) object available choices preselected option MHTERM variable dataname. mhbodsys (teal.transform::choices_selected()) object available choices preselected option MHBODSYS variable dataname. mhdistat (teal.transform::choices_selected()) object available choices preselected option MHDISTAT variable dataname. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_medical_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_medical_history.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"","code":"ADSL <- tmc_ex_adsl ADMH <- tmc_ex_admh  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADMH = ADMH,     code = \"       ADSL <- tmc_ex_adsl       ADMH <- tmc_ex_admh     \"   ),   modules = modules(     tm_t_pp_medical_history(       label = \"Medical History\",       dataname = \"ADMH\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       mhterm = choices_selected(         choices = variable_choices(ADMH, c(\"MHTERM\")),         selected = \"MHTERM\"       ),       mhbodsys = choices_selected(         choices = variable_choices(ADMH, \"MHBODSYS\"),         selected = \"MHBODSYS\"       ),       mhdistat = choices_selected(         choices = variable_choices(ADMH, \"MHDISTAT\"),         selected = \"MHDISTAT\"       )     )   ) ) #> Initializing tm_t_pp_medical_history #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_prior_medication.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"module produces patient profile prior medication report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_prior_medication.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"","code":"tm_t_pp_prior_medication(   label,   dataname = \"ADCM\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   atirel = NULL,   cmdecod = NULL,   cmindc = NULL,   cmstdy = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_prior_medication.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_prior_medication.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_pp_prior_medication.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"","code":"library(dplyr)  ADCM <- tmc_ex_adcm ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID) ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADCM <- tmc_ex_adcm       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)       ADCM$CMASTDTM <- ADCM$ASTDTM       ADCM$CMAENDTM <- ADCM$AENDTM     \",     join_keys = join_keys   ),   modules = modules(     tm_t_pp_prior_medication(       label = \"Prior Medication\",       dataname = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       atirel = choices_selected(         choices = variable_choices(ADCM, \"ATIREL\"),         selected = \"ATIREL\"       ),       cmdecod = choices_selected(         choices = variable_choices(ADCM, \"CMDECOD\"),         selected = \"CMDECOD\"       ),       cmindc = choices_selected(         choices = variable_choices(ADCM, \"CMINDC\"),         selected = \"CMINDC\"       ),       cmstdy = choices_selected(         choices = variable_choices(ADCM, \"ASTDY\"),         selected = \"ASTDY\"       )     )   ) ) #> Initializing tm_t_pp_prior_medication #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Shift by Arm — tm_t_shift_by_arm","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"module produces summary table analysis indicator levels arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"","code":"tm_t_shift_by_arm(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   visit_var,   aval_var,   base_var = lifecycle::deprecated(),   baseline_var,   treatment_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ONTRTFL\"), selected = \"ONTRTFL\"),   treatment_flag = teal.transform::choices_selected(\"Y\"),   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"","code":"ADSL <- tmc_ex_adsl ADEG <- tmc_ex_adeg  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADEG = ADEG,     code = \"       ADSL <- tmc_ex_adsl       ADEG <- tmc_ex_adeg     \"   ),   modules = modules(     tm_t_shift_by_arm(       label = \"Shift by Arm Table\",       dataname = \"ADEG\",       arm_var = choices_selected(         variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADEG, \"PARAMCD\"),         selected = \"HR\"       ),       visit_var = choices_selected(         value_choices(ADEG, \"AVISIT\"),         selected = \"POST-BASELINE MINIMUM\"       ),       aval_var = choices_selected(         variable_choices(ADEG, subset = \"ANRIND\"),         selected = \"ANRIND\", fixed = TRUE       ),       baseline_var = choices_selected(         variable_choices(ADEG, subset = \"BNRIND\"),         selected = \"BNRIND\", fixed = TRUE       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_shift_by_arm #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm_by_worst.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"module produces summary table worst analysis indicator variable level per subject arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm_by_worst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"","code":"tm_t_shift_by_arm_by_worst(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   aval_var,   base_var = lifecycle::deprecated(),   baseline_var,   worst_flag_var,   worst_flag,   treatment_flag_var = teal.transform::choices_selected(choices =     teal.transform::variable_choices(dataname, subset = \"ONTRTFL\"), selected = \"ONTRTFL\"),   treatment_flag = teal.transform::choices_selected(\"Y\"),   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm_by_worst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable. worst_flag (character) value indicating worst analysis indicator level. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm_by_worst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_arm_by_worst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"","code":"ADSL <- tmc_ex_adsl ADEG <- tmc_ex_adeg  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADEG = ADEG,     code = \"       ADSL <- tmc_ex_adsl       ADEG <- tmc_ex_adeg     \"   ),   modules = modules(     tm_t_shift_by_arm_by_worst(       label = \"Shift by Arm Table\",       dataname = \"ADEG\",       arm_var = choices_selected(         variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADEG, \"PARAMCD\"),         selected = \"ECGINTP\"       ),       worst_flag_var = choices_selected(         variable_choices(ADEG, c(\"WORS02FL\", \"WORS01FL\")),         selected = \"WORS02FL\"       ),       worst_flag = choices_selected(         value_choices(ADEG, \"WORS02FL\"),         selected = \"Y\", fixed = TRUE       ),       aval_var = choices_selected(         variable_choices(ADEG, c(\"AVALC\", \"ANRIND\")),         selected = \"AVALC\"       ),       baseline_var = choices_selected(         variable_choices(ADEG, c(\"BASEC\", \"BNRIND\")),         selected = \"BASEC\"       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_shift_by_arm_by_worst #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Grade Summary Table — tm_t_shift_by_grade","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"module produces summary table worst grades per subject visit parameter.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"","code":"tm_t_shift_by_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVISIT\"), selected = \"AVISIT\", fixed = TRUE),   paramcd,   worst_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\")), selected = \"WGRLOVFL\"),   worst_flag_indicator =     teal.transform::choices_selected(teal.transform::value_choices(dataname, \"WGRLOVFL\"),     selected = \"Y\", fixed = TRUE),   anl_toxgrade_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"ATOXGR\")), selected = c(\"ATOXGR\"), fixed = TRUE),   base_toxgrade_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"BTOXGR\")), selected = c(\"BTOXGR\"), fixed = TRUE),   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   add_total = FALSE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   na_level = default_na_str(),   code_missing_baseline = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. anl_toxgrade_var (teal.transform::choices_selected()) variable analysis toxicity grade. base_toxgrade_var (teal.transform::choices_selected()) variable baseline toxicity grade. id_var (teal.transform::choices_selected()) object specifying variable name subject id. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). code_missing_baseline (logical) whether missing baseline grades counted grade 0. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_shift_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_shift_by_grade(       label = \"Grade Laboratory Abnormality Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = \"ALT\"       ),       worst_flag_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\")),         selected = c(\"WGRLOVFL\")       ),       worst_flag_indicator = choices_selected(         value_choices(ADLB, \"WGRLOVFL\"),         selected = \"Y\", fixed = TRUE       ),       anl_toxgrade_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"ATOXGR\")),         selected = c(\"ATOXGR\"),         fixed = TRUE       ),       base_toxgrade_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"BTOXGR\")),         selected = c(\"BTOXGR\"),         fixed = TRUE       ),       add_total = FALSE     )   ),   filter = teal_slices(teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\")) ) #> Initializing tm_t_shift_by_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_smq.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"module produces adverse events table Standardized MedDRA Query.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_smq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"","code":"tm_t_smq(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   llt,   add_total = TRUE,   total_label = default_total_label(),   sort_criteria = c(\"freq_desc\", \"alpha\"),   drop_arm_levels = TRUE,   na_level = default_na_str(),   smq_varlabel = \"Standardized MedDRA Query\",   baskets,   scopes,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_smq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). smq_varlabel (character) label use new column SMQ created tern::h_stack_by_baskets(). baskets (teal.transform::choices_selected()) object available choices preselected options standardized/customized queries. scopes (teal.transform::choices_selected()) object available choices scopes standardized queries. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_smq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_smq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"","code":"data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADAE <- tmc_ex_adae    names_baskets <- grep(\"^(SMQ|CQ).*NAM$\", names(ADAE), value = TRUE)   names_scopes <- grep(\"^SMQ.*SC$\", names(ADAE), value = TRUE)    cs_baskets <- choices_selected(     choices = variable_choices(ADAE, subset = names_baskets),     selected = names_baskets   )    cs_scopes <- choices_selected(     choices = variable_choices(ADAE, subset = names_scopes),     selected = names_scopes,     fixed = TRUE   ) })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_smq(       label = \"Adverse Events by SMQ Table\",       dataname = \"ADAE\",       arm_var = choices_selected(         choices = variable_choices(data[[\"ADSL\"]], subset = c(\"ARM\", \"SEX\")),         selected = \"ARM\"       ),       add_total = FALSE,       baskets = data[[\"cs_baskets\"]],       scopes = data[[\"cs_scopes\"]],       llt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], subset = c(\"AEDECOD\")),         selected = \"AEDECOD\"       )     )   ) ) #> Initializing tm_t_smq #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Summary of Variables — tm_t_summary","title":"teal Module: Summary of Variables — tm_t_summary","text":"module produces table summarize variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Summary of Variables — tm_t_summary","text":"","code":"tm_t_summary(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   summarize_vars,   add_total = TRUE,   total_label = default_total_label(),   show_arm_var_labels = TRUE,   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\", \"geom_mean\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Summary of Variables — tm_t_summary","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. summarize_vars (teal.transform::choices_selected()) names variables summarized. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). show_arm_var_labels (flag) whether arm variable label(s) displayed. Defaults TRUE. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Summary of Variables — tm_t_summary","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Summary of Variables — tm_t_summary","text":"","code":"# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data. ADSL <- tmc_ex_adsl ADSL$EOSDY[1] <- NA_integer_  app <- init(   data = cdisc_data(     ADSL = ADSL,     code = \"       ADSL <- tmc_ex_adsl       ADSL$EOSDY[1] <- NA_integer_     \"   ),   modules = modules(     tm_t_summary(       label = \"Demographic Table\",       dataname = \"ADSL\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       add_total = TRUE,       summarize_vars = choices_selected(         c(\"SEX\", \"RACE\", \"BMRKR2\", \"EOSDY\", \"DCSREAS\", \"AGE\"),         c(\"SEX\", \"RACE\")       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_summary #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary_by.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"module produces table summarize variables row groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"","code":"tm_t_summary_by(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   by_vars,   summarize_vars,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   paramcd = NULL,   add_total = TRUE,   total_label = default_total_label(),   parallel_vars = FALSE,   row_groups = FALSE,   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   denominator = teal.transform::choices_selected(c(\"n\", \"N\", \"omit\"), \"omit\", fixed =     TRUE),   drop_arm_levels = TRUE,   drop_zero_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. summarize_vars (teal.transform::choices_selected()) names variables summarized. id_var (teal.transform::choices_selected()) object specifying variable name subject id. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). parallel_vars (logical) whether summarized variables arranged columns. Can set TRUE chosen analysis variables numeric. row_groups (logical) whether summarized variables arranged row groups. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. drop_zero_levels (logical) whether rows zero counts columns removed table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_summary_by.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_summary_by(       label = \"Summary by Row Groups Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       add_total = TRUE,       by_vars = choices_selected(         choices = variable_choices(ADLB, c(\"PARAM\", \"AVISIT\")),         selected = c(\"AVISIT\")       ),       summarize_vars = choices_selected(         choices = variable_choices(ADLB, c(\"AVAL\", \"CHG\")),         selected = c(\"AVAL\")       ),       useNA = \"ifany\",       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = \"ALT\"       )     )   ) ) #> Initializing tm_t_summary_by #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Time-To-Event Table — tm_t_tte","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"module produces time--event analysis summary table, consistent TLG Catalog template TTET01 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"","code":"tm_t_tte(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   conf_level_coxph = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order     = TRUE),   conf_level_survfit = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95,     keep_order = TRUE),   time_points,   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   event_desc_var = teal.transform::choices_selected(\"EVNTDESC\", \"EVNTDESC\", fixed = TRUE),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level_coxph (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). conf_level_survfit (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). time_points (teal.transform::choices_selected()) object available choices preselected option time points can used tern::surv_timepoint(). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. event_desc_var (character data_extract_spec()) variable name event description information, optional. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"core functionality module based coxph_pairwise(), surv_timepoint(), surv_time() tern package. arm stratification variables taken parentname data. following variables used module: AVAL: time event CNSR: 1 record AVAL censored, 0 otherwise PARAMCD: variable used filter endpoint (e.g. OS). filtering PARAMCD one observation per patient expected","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/tm_t_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"","code":"ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte     \"   ),   modules = modules(     tm_t_tte(       label = \"Time To Event Table\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         \"SEX\"       ),       time_points = choices_selected(c(182, 243), 182),       event_desc_var = choices_selected(         variable_choices(ADTTE, \"EVNTDESC\"),         \"EVNTDESC\",         fixed = TRUE       )     )   ) ) #> Initializing tm_t_tte #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"Check vector valid used treatment arm variable","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"","code":"validate_arm(arm_vec)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"arm_vec vector validated","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_arm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"validate error returned vector factor detailed error message entries empty strings","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_standard_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate standard input values for a teal module — validate_standard_inputs","text":"","code":"validate_standard_inputs(   adsl,   adslvars = character(0),   anl,   anlvars = character(0),   need_arm = TRUE,   arm_var,   ref_arm,   comp_arm,   min_n_levels_armvar = 1L,   max_n_levels_armvar = 100L,   min_nrow = 1 )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/reference/validate_standard_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate standard input values for a teal module — validate_standard_inputs","text":"adsl data.frame subject-level data adslvars required variables ADSL anl data.frame analysis data anlvars required variables ANL need_arm flag indicating whether grouping variable arm_var required can optionally NULL. arm_var character name grouping variable, typically arm ref_arm character name reference level arm_var comp_arm character name comparison level arm_var min_n_levels_armvar minimum number levels grouping variable arm_var. Defaults 1, NULL minimum. max_n_levels_armvar maximum number levels grouping variable arm_var. Use NULL maximum. min_nrow minimum number observations ADSL ANL","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-9-1-9023","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.1.9023","text":"Added teal.logger functionality logging changes shiny inputs modules. Introduced ylim parameter tm_g_km module controls width y-axis. Added functionality tm_t_events_patyear split columns multiple (nested) variables via arm_var argument. Added arguments arm_var_labels template_summary show_arm_var_labels tm_t_summary allow user display arm variable (arm_var) labels table header. Added argument stats modules tm_g_forest_rsp tm_g_forest_tte allow users specify statistics include table. Added argument riskdiff modules tm_g_forest_rsp tm_g_forest_tte allow users add risk difference table column. Added count_dth count_wd parameters tm_t_events_summary select/deselect “Total number deaths” “Total number patients withdrawn study due AE” rows, respectively. options correspond “Count deaths” “Count withdrawals due AE” checkboxes available module run.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-9-1-9023","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.1.9023","text":"Removed Show Warnings modals modules. Clarified documentation specifying whether multiple values can selected arm_var argument module. Replaced use rtables::add_colcounts() function show_colcounts argument basic_table(). Began deprecation cycle show_labels argument template_summary effect tm_t_summary module. Replaced instances deprecated strata argument tern::control_lineplot_vars() group_var.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-091","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.9.1","title":"teal.modules.clinical 0.9.1","text":"CRAN release: 2024-04-27","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.1","text":"Updated tm_g_forest_rsp tm_g_forest_tte use refactored version g_forest. Plots now displayed ggplot objects instead grob objects. Added parameters font_size rel_width_forest control font size width plot relative table, respectively. Updated tm_t_summary_by allow NULL input paramcd argument. Updated tm_g_km use refactored version g_km. Plots now displayed ggplot objects instead grob objects. Added parameters rel_height_plot, font_size, control_annot_surv_med, control_annot_coxph control height plot relative table, font size, median survival time table size, Cox-PH table size, respectively. Added control argument tm_t_binary_outcome control settings analysis (methods, confidence intervals, odds ratios) within module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.1","text":"Replaced instances deprecated na_level argument tern functions na_str. Replaced argument/list element name strata instead strat tern function calls following deprecation argument/name within tern. Removed formatters dependencies replaced use functions relating variable labels functions teal.data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-090","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.9.0","title":"teal.modules.clinical 0.9.0","text":"CRAN release: 2024-02-23","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"breaking-changes-0-9-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.modules.clinical 0.9.0","text":"Adapted modules use teal_data objects. Module arguments previously accepted inputs teal.transform::choices_selected() teal.transform::data_extract_spec() now accept input teal.transform::choices_selected(). affected modules : tm_a_gee, tm_a_mmrm, tm_g_ci, tm_g_forest_rsp, tm_g_forest_tte, tm_g_ipp, tm_g_km, tm_g_lineplot, tm_g_pp_adverse_events, tm_g_pp_patient_timeline, tm_g_pp_therapy, tm_g_pp_vitals, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_ancova, tm_t_binary_outcome, tm_t_coxreg, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_logistic, tm_t_mult_events, tm_t_pp_basic_info, tm_t_pp_laboratory, tm_t_pp_medical_history, tm_t_pp_prior_medication, tm_t_shift_by_arm, tm_t_shift_by_arm_by_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, tm_t_tte","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.0","text":"Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Simplify examples vignettes code removing package prefixes possible. Added parameter sort_freq_col tm_t_events allow user select column use sorting decreasing frequency. Added parameter incl_overall_sum tm_t_events allow user choose whether overall summary rows included top table. Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Added default_total_label set_default_total_label functions get set default total column label (total_label) modules. Implemented tern::default_na_str tern::set_default_na_str functions get set default missing value replacement string (na_level) modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.9.0","text":"Fixed bug tm_g_lineplot forcing module initialize table. Fixes partial matching.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.0","text":"Deprecated aval argument tm_t_pp_laboratory tm_g_pp_vitals replaced aval_var argument. Deprecated avalu argument tm_t_pp_laboratory replaced avalu_var argument. Deprecated base_var argument tm_g_ipp, tm_t_shift_by_arm, template_shift_by_arm_by_worst replaced baseline_var argument. Specified minimal version package dependencies. Replaced usage deprecated summarize_vars function analyze_vars. Reduced package dependencies (removed tidyr, rlang, magrittr styler). Introduced tests partial matching.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-16","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.16","text":"Added informative error message grade mapping error occurs tm_t_abnormality_by_worst_grade. Fixed label indentation tm_t_abnormality_by_worst_grade. Added total_label argument enable customization “Patients” column/row label following modules: tm_a_mmrm, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_binary_outcome, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_mult_events, tm_t_shift_by_arm, tm_t_shift_by_arm_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, tm_t_tte. Increased default width tm_g_forest_tte plot prevent overlapping text. Improved default annotation table sizing tm_g_km. Refactored tm_t_exposure display “total” row last row table instead summary row. Added parameters add_total_row set whether total row displayed total_row_label set total row label. Updated tm_t_events maintain indentation pruning. Updated default reference/comparison arm level selection work arm variable levels filtered . Updated tm_t_coxreg drop factor covariate variable levels present avoid errors filtering. Updated tm_t_pp_basic_info, tm_t_pp_medical_history, tm_g_pp_therapy, tm_g_pp_adverse_events, tm_t_pp_laboratory print patient ID table. Updated tm_t_pp_basic_info, tm_g_pp_therapy, tm_g_pp_adverse_events, tm_t_pp_laboratory use rlistings print data neatly reports. Updated tm_g_lineplot allow user remove interval plot. Updated documentation vignettes demonstrate method pass teal_data object teal::init().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-16","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.16","text":"Fixed bug tm_t_coxreg preventing table displayed covariates selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-16","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.16","text":"Updated control_incidence_rate parameter names tm_t_events_patyear time_unit_input time_unit_output input_time_unit num_pt_year, respectively, parameter names changed tern. Hid datasets used patient profile modules filter panel. Replaced datanames = \"\" parameter datasets used internally module.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"breaking-changes-0-8-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.clinical 0.8.15","text":"Replaced chunks simpler qenv class. Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.15","text":"Replaced synthetic_cdisc_data refactored synthetic_cdisc_dataset function speed dataset loading tests/examples. Added new GEE module tm_a_gee. Added interface selecting interaction term tm_t_ancova. Updated encoding input checks use shinyvalidate::InputValidator better UI experience. Previously used shiny::validate. Added option tm_a_mmrm allow Kenward-Roger adjustments standard errors p-values. Added option choose facet scale options tm_g_barchart_simple. Added label parameter cs_to_select_spec/cs_to_des_select cs_to_filter_spec/cs_to_des_filter allow user customize label printed selection field. Updated tm_t_coxreg module refactoring summarize_coxreg tern fix indentation. Updated tm_t_exposure module use new function analyze_patients_exposure_in_cols fix table structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-15","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.15","text":"Fixed bug causing overlapping bars tm_g_barchart_simple. Fixed bug figures svg format. Fixed bug tm_t_summary tm_t_summary_by preventing users specifying numeric_stats argument.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.15","text":"Updated package Suggests use scda.2022 rather scda.2021. Removed unused argument param tm_g_pp_vitals. Removed optimizer choice tm_a_mmrm since can always use automatically determined optimizer. Created datasets use examples/tests adsl, adae, adaette, adcm, adeg, adex, adlb, admh, adqs, adrs, adtte, advs. datasets stored data folder accessible via tmc_ex_* prefix. Updated examples tests use datasets teal.modules.clinical package instead scda datasets. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Implemented lubridate package date variables internal data. Changed default value plot_width tm_g_forest_rsp prevent clutter.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.14","text":"Updated synthetic data tests version rcd_2022_02_28. Updated test files tests/testthat/ synthetic_cdisc_data(\"2022_02_28\") Reverted missing data checkbox tm_t_summary (encoding filtering separate). Implemented new widget allows dragging dropping select comparison groups. Added teal.reporter functionality modules. Enhanced tm_t_pp_medical_history module use table_with_settings module return rtables object. Implemented nestcolor examples, refactored tm_g_barchart_simple allow use nestcolor. Added descriptive title/labels visit name subtitle tm_g_ci. Updated tm_a_mmrm column name deselecting treatment “obs” “Patients”, added subtitles footnotes. Added title parameter category subtitle tm_t_exposure, cleaned labels. Added titles worse flag variable subtitles tm_t_shift_by_grade tm_t_shift_by_arm_by_worst. Added footnote tm_t_events_patyear CI method. Added subtitle footnotes tm_g_km. Added Stratified Analysis CI method option panel tm_t_binary_outcome. Added validation covariate/visit conflicts tm_a_mmrm. Remove unnecessary brackets header tm_t_exposure. Hid footnotes tm_g_km tm_t_tte “Compare Treatments” .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-14","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.14","text":"Fixed bug tm_g_barchart_simple prevented display graph. Fixed broken example tm_t_abnormality_by_worst_grade. Fixed bug tm_a_mmrm prevented table headers displaying. Fixed bug tm_g_forest_rsp deselecting endpoint. Fixed bug tm_t_binary_outcome crashed app deselecting paramcd. Fixed teal.reporter card names tm_t_smq. Fixed bug tm_t_shift_by_arm_by_worst adding validations choosing different endpoint values. Fixed bug tm_t_coxreg preventing footnotes displaying univariate models.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.14","text":"Added nestcolor dependency replaced deprecated function tern::color_palette nestcolor::color_palette.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tm_g_pp_adverse_events-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_g_pp_adverse_events","title":"teal.modules.clinical 0.8.13","text":"Updated position labels. Updated plot render color legend.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tm_t_summary_by-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_t_summary_by","title":"teal.modules.clinical 0.8.13","text":"Enhanced module support geometric mean encoding panel.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tm_t_summary-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_t_summary","title":"teal.modules.clinical 0.8.13","text":"Updated added footnote. Enhanced module support geometric mean encoding panel. Updated module display checkboxes numeric variables statistics numeric variables part selected. Updated validations warn users using dataset non unique identifiers selecting variables non supported types (.e. Date, POSIXt). Added checkbox remove column generated missing values.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"other-modules-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"Other modules","title":"teal.modules.clinical 0.8.13","text":"Updated tm_t_binary_outcome enable option apply continuity correction Newcombe method. Simplified show R code tm_g_pp_patient_timeline module. Improved names code chunks shown Debug Info. Improved validation treatment variable factor.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-13","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.13","text":"Fixed summarize_logistic implementation broken empty string error. upstream. _NA_ new standard flag allow pivot empty entries data frames. Took @title tm_t_binary_outcome.R producing warning. Updated validation account error selecting single variable tm_g_pp_patient_timeline module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.13","text":"Added pkgdown template documentation. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.12","text":"Changed input Covariates tm_t_coxreg.R track user input reflect order table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-features-0-8-12","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.12","text":"Added new module tm_t_shift_by_arm_by_worst analysis laboratory abnormalities severe grade flag. Enhanced tm_t_events_patyear include selected parameter title table. Enhanced tm_t_mult_events include selected parameter title table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-12","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.12","text":"Rewrote modules use moduleServer updated calls teal.devel modules also written use moduleServer. Changed way obtaining selection ordered changes teal.devel. Use ordered = TRUE cs_to_des_select cs_to_select_spec return ordered selection. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. tm_t_events_summary now allows nested arm_var columns matching outputs tm_t_events. Added validation tm_t_abnormality_by_worst_grade arm_var selected. Enhanced tm_t_binary_outcome include responders response table default. Added subtitle tm_g_forest_tte, tm_t_coxreg, tm_t_binary_outcome listing stratification factors.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-12","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.12","text":"Fixed bug prevent processing empty sets data tm_g_forest_rsp.R causing shiny errors runtime. Fixed bug closed Compare Treatments conditional panel marked Combine comparison groups? option conflicted adding column patients tables tm_t_binary_outcome.R tm_t_tte.R.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-12-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.12","text":"Replaced deprecated rtables::var_labels calls documentation examples. Add import tern.mmrm package change references split tern. Adjusted package imports take account changes teal framework. Ensure consistent vertical order tm_g_pp_patient_timeline output switching absolute relative days.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"breaking-changes-0-8-11","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.clinical 0.8.11","text":"Updated tm_t_abnormality due changes count_abnormal abnormal argument taking list input now. Changed tm_g_pp_patient_timeline parameter, cmtrt, cmdecod.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-features-0-8-11","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.11","text":"Added new module tm_t_abnormality_by_worst_grade analysis laboratory test results highest grade post-baseline. Enhanced tm_t_ancova include selected parameter(s), visit(s) analysis variable title table. Added new module tm_g_lineplot creating line plots. Enhanced tm_t_logistic include selected parameter title table. Enhanced tm_g_forest_rsp include selected parameter title table. Enhanced tm_g_forest_tte include selected parameter title table. Enhanced tm_g_pp_patient_timeline bold axes labels integer values axis. Enhanced tm_g_ipp allow users display AVALU title y axis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-11","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.11","text":"Added support logging logger package added info level logs upon initialization module. Added default_responses argument tm_t_binary_outcome tm_g_forest_rsp allow user specify default selected responses possible response levels. Updated tm_t_binary_outcome show selected responses output table selecting “Show Selected Response Categories”. Added rsp_table argument tm_t_binary_outcome allow user initialize module matching RSPT01 STREAM template. Added support custom arguments ggplot2::labs ggplot2::theme plot based modules. Added support custom arguments rtables::basic_table table based modules. Updated tm_t_binary_outcome enable option apply continuity correction Wilson method.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-11","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.11","text":"Updated required R version >= 3.6. Refactored calls defunct teal.devel::data_extract_input calls replacement teal.devel::data_extract_ui. Updated modules use new data_merge_module interface provided teal.devel removed usage now deprecated function teal.devel::get_input_order. Updated tm_t_binary_outcome module add template removed now deprecated module tm_t_rsp. Removed utils.nest dependency replaced calls checkmate equivalents.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-11","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.clinical 0.8.11","text":"Fixed bug tm_g_pp_therapy cmstdy cmendy argument type integer causes plot crash.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-features-0-8-10","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.10","text":"Added new module tm_t_smq analysis adverse events Standardized MedDRA Query. Added new module tm_t_shift_by_grade analysis grade laboratory abnormalities. Added new module tm_t_exposure analysis duration exposure risk management plan. Added new module tm_t_shift_by_arm can display shift table ECG interval data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-10","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.10","text":"Corrected tm_a_mmrm able consider treatment variable interactions. Fixed tm_t_binary_outcome tm_t_rsp choose correct CI estimation method Proportions Difference Stratified Analysis (.e. Wald-type confidence interval CMH weights).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.10","text":"Added validation checks tm_t_rsp tm_t_binary_outcome stratification errors applied filters. Added tm_g_km validation check plot tables font size. Enhanced tm_g_km add selected paramcd plot title. tm_t_events now can display layouts two nested column treatment variables. options pruning sorting available. Exported package helper functions. Updated tm_t_events_by_grade display grading groups nested columns col_by_grade option support pruning sorting options like tm_t_events. Used format_count_fraction fix formatting inconsistency tm_t_events_summary. Updated count_occurrences vars argument tm_t_shift_by_grade. Updated tm_t_pp_laboratory display 4 decimals default. Updated tm_t_events_by_grade use trim_levels_in_group split function instead trim_rows function. Added table title tm_t_tte. Added table titles tm_t_rsp tm_t_binary_outcome.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.10","text":"Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr. Removed insert_rrow updated usage count_patients_by_flags tm_t_events_summary. Changed package calls functions dplyr package. functions now fully specified (e.g. dplyr::filter).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-features-0-8-9","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.9","text":"Added capability remember order user input encoding UI elements. Inputs marked double arrow icon tracking enabled. affected modules : tm_t_summary, tm_t_summary_by, tm_g_forest_rsp, tm_g_forest_tte, tm_t_events_summary, tm_t_abnormality, tm_t_mult_events. Added new argument numeric_stats tm_t_summary tm_t_summary_by control displayed summary statistics numeric variables. Added new argument drop_zero_levels tm_t_summary_by can drop rows zeros result table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-9","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.9","text":"Split tm_g_patient_profile tabs 8 separate new modules. Added option select patient ID filter panel modules patient profile. Added validation tm_g_patient_timeline plot empty. Enhanced tm_a_mmrm work without treatment variable. Added option choose number decimal places rounding tm_t_pp_laboratory. Added check box tm_g_pp_patient_timeline hiding/showing relative study days x-axis. Added title patient’s id plots patient profile modules. Made gray error message tm_g_forest_tte informative deselecting Endpoint column left-hand encoding panel. Added twenty-fifth seventy-fifth quantile summary statistics tm_t_summary. Added interaction p-value column tm_t_coxreg. Added validation tm_t_ancova selected covariate variables contain one level. Added validation tm_t_events_patyear events variable empty. Changed font size input description tm_g_km precisely describe controls. Enhanced tm_t_logistic interaction choices depend selected covariates. Enhanced tm_t_rsp strata input visible comparing treatments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-9","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.9","text":"Fixed Get R Code output tm_t_pp_laboratory return identical HTML formatted table displayed app. Added validation tm_t_coxreg ensure treatment, strata covariate variables overlap. Limited label repel feature tm_g_pp_patient_timeline X-axis consistent look. Updated tm_t_summary_by paramcd required analyzing ADSL variables. Updated tm_t_coxreg can work covariate selected. Updated tm_a_mmrm can work treatment variable selected. Updated tm_g_forest_tte total number events also shown table. Updated tm_t_events_summary work pooled studies. Updated validation level tm_t_coxreg. Updated validation level tm_t_logistic. Added validation tm_t_binary_outcome tm_t_rsp ensure strata variable contains one level selecting one strata variable. Updated warning message deselecting statistics tm_t_summary tm_t_summary_by explain need select least one statistic.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.8","text":"Added option download expand tables. tm_g_km added support downloading images updated x-axis label show title case. Added slider font size plots. Added persistence selected table lengths. timeline plot now supports edge cases. vitals tab, removed unused label text legend, updated plot display stable colors per levels, cleared x-axis limit fixed legend update filtering. Also added note clarify supported horizontal lines cases. Updated adverse events tab show warning message instead empty plot data empty. Fixed PARAMCD selected levels current patient. Updated pre-processing code inside template_tte dataset without events still produces table. Updated code use correct denominator duration response endpoints. Modified parameter arm_var accept one column. selecting two columns arm_var, second variable nest first one. Added argument show_labels template_summary show label single summary variable table. Added new parameter conf_arg tm_t_rsp consistent efficacy modules. Added validation statement tm_g_ipp module print message deselecting Timepoint Variable drop-. Removed header definition tm_g_forest_rsp tm_g_forest_tte now default header g_forest. Fixed validation statement tm_t_coxreg models without strata using likelihood tests return result. Clarified functionality drop_arm_levels tm_t_summary tm_t_summary_by. encodings panel, checkbox show parent dataset analysis dataset different.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.8","text":"Replaced remaining two observe function calls observeEvent optimize performance. Fixed grammar “Select patient’s id” error message tm_g_patient_profile. Fixed font_size default templates 12L instead vector 3 integers cleaned associated unnecessary code. Fixed deprecated function warning tm_g_barchart_simple. Fixed subgroup_var definition truncation tm_g_forest_rsp tm_g_forest_tte. Clarified labeling related regression type encoding panel tm_t_coxreg.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-8","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.8","text":"Added validation case filtering rows therapy tab tm_g_patient_profile. Updated internals modules read data correct field filter_spec objects. Fixed reactivity filter panel PARAMCD variable levels input tm_g_patient_profile vitals tab plot get reset filtering. Updated vitals plot tab tm_g_patient_profile drop NA entries plot. Updated tm_t_coxreg take values account. Added check tm_t_coxreg interactions univariate models multivariate models. Updated tm_t_events_summary work pooled studies.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-module-0-8-7","dir":"Changelog","previous_headings":"","what":"New Module","title":"teal.modules.clinical 0.8.7","text":"Added new module tm_g_patient_profile profile patients based predefined categories. Added new module tm_g_ipp individual patient plots.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.7","text":"Added argument drop_arm_levels safety modules. allows removal columns based factor levels found filtered data. Updated tm_g_km allow plot failure probability y-axis, tick interval selection x-axis option create plot without confidence interval ribbon (new default). Added argument time_unit_var template_g_km add time unit x-axis label.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.7","text":"Removed redundant Analysis Data: label Encodings Panel. Removed limit requiring 15 fewer columns tabulation modules. New upper threshold 100 columns. Decreased lower limit number observations required modules. Safety tables require least one record. Requirements efficacy outputs per treatment group: tm_a_mmrm requires five records, tm_t_logistic tm_t_coxreg require two records, remaining modules require least one record per treatment group. graphs, lower threshold two records. Removed argument cnsr_val tm_t_events_patyear added new argument events_var. arm_ref_comp_observer include parentname argument. Show R code include datasets retrieved data_extract_spec objects. Refactored stringr dependency patient profile module. Added missing table calls chunks tm_t_events tm_t_events_by_grade.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"new-features-0-8-6","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.clinical 0.8.6","text":"Added new module tm_g_ci confidence interval plots. Added new module tm_t_ancova analysis variance summary tables. Added new module tm_t_mult_events multi-event tables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"enhancements-0-8-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.6","text":"Refactored modules using redesigned rtables tern packages. Enhanced modules. now take advantage data_extract_spec data_merge_module functionality teal. Reduced clutter repeated datasets encodings panels. Updated modules use OptionalSelectInput conf_level.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"miscellaneous-0-8-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.6","text":"Added vignette substitute can helpful developing analysis template functions teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"bug-fixes-0-8-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.6","text":"Updated tm_t_events module use user’s non-default choices prune_freq prune_diff.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-085","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.5","title":"teal.modules.clinical 0.8.5","text":"graph modules now accept plot_width argument specifies plot width renders slider adjust width interactively module. FilteredData object now passed arm_ref_comp_observer modules now support nested lists containing delayed_data objects. Replace plot_with_height module new plot_with_settings module. Update examples use code argument inside cdisc_dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-084","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.4","title":"teal.modules.clinical 0.8.4","text":"Extend tm_t_coxreg optionally produce univariate Cox regressions. Updated tm_t_binary_outcome display Odds Ratio estimates, include new methods CIs p-values display summary individual response categories. Updated tm_t_tte optionally compare arms, removed conf_level argument. Updated tm_g_km optionally compare arms. Extend tm_g_km optionally scale X axis range case one plot. New tm_a_mmrm MMRM analysis. Deprecated tm_t_mmrm (superseded tm_a_mmrm).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-083","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.3","title":"teal.modules.clinical 0.8.3","text":"New tm_t_coxreg module multi-variable Cox regressions. New tm_t_binary_outcome module. New tm_t_events_patyear module: events rate adjusted patient-year risk table. Remove grade_levels argument tm_t_events_by_grade. Updated response table single arm. New tm_t_abnormality module. Removed get_relabel_call get_relabel_call2 favor teal.devel::get_relabel_call teal.devel::get_anl_relabel_call.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-082","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.2","title":"teal.modules.clinical 0.8.2","text":"Add confidence level survfit, coxph, ztest; add confidence type, ties, percentiles tm_t_tte. Optionally use single term tm_t_events tm_t_events_by_grade modules. New tm_t_logistic module. New tm_t_mmrm module. New modules tm_t_summary_by tm_t_events_summary. Add stratified analysis tm_g_forest_tte tm_g_forest_rsp. Add confidence level plotting symbol size options tm_g_forest_rsp tm_g_forest_tte.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-081","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.1","title":"teal.modules.clinical 0.8.1","text":"New tm_t_events tm_t_events_by_grade modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-080","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.0","title":"teal.modules.clinical 0.8.0","text":"Optionally show KM CoxPH table tm_g_km.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-070","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.7.0","title":"teal.modules.clinical 0.7.0","text":"Use teal.devel.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/news/index.html","id":"tealmodulesclinical-060","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.6.0","title":"teal.modules.clinical 0.6.0","text":"Package renamed teal.modules.clinical. Rename tm_t_summarize_variables tm_t_summary. Usage teal::choices_selected() function instead *_var *_var_choices arguments.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"generating-minimal-data-to-test-teal-modules-clinical","dir":"Articles","previous_headings":"","what":"Generating minimal data to test teal.modules.clinical","title":"Example Data Generation","text":"following script used create save cached synthetic CDISC data data/ directory use examples tests teal.modules.clinical package. script/vignette initialized Emily de la Rua tern. Disclaimer: vignette concerns mainly development minimal stable test data kept internal feature tracking.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"setup-helper-functions","dir":"Articles","previous_headings":"","what":"Setup & Helper Functions","title":"Example Data Generation","text":"","code":"library(dplyr) library(teal.data)  study_duration_secs <- lubridate::seconds(lubridate::years(2))  sample_fct <- function(x, N, ...) {    checkmate::assert_number(N)   factor(sample(x, N, replace = TRUE, ...), levels = if (is.factor(x)) levels(x) else x) }  retain <- function(df, value_var, event, outside = NA) {   indices <- c(1, which(event == TRUE), nrow(df) + 1)   values <- c(outside, value_var[event == TRUE])   rep(values, diff(indices)) }  relvar_init <- function(relvar1, relvar2) {   if (length(relvar1) != length(relvar2)) {     message(simpleError(       \"The argument value length of relvar1 and relvar2 differ. They must contain the same number of elements.\"     ))     return(NA)   }   return(list(\"relvar1\" = relvar1, \"relvar2\" = relvar2)) }  rel_var <- function(df = NULL, var_name = NULL, var_values = NULL, related_var = NULL) {   if (is.null(df)) {     message(\"Missing data frame argument value.\")     return(NA)   } else {     n_relvar1 <- length(unique(df[, related_var, drop = TRUE]))     n_relvar2 <- length(var_values)     if (n_relvar1 != n_relvar2) {       message(paste(\"Unequal vector lengths for\", related_var, \"and\", var_name))       return(NA)     } else {       relvar1 <- unique(df[, related_var, drop = TRUE])       relvar2_values <- rep(NA, nrow(df))       for (r in seq_len(length(relvar1))) {         matched <- which(df[, related_var, drop = TRUE] == relvar1[r])         relvar2_values[matched] <- var_values[r]       }       return(relvar2_values)     }   } }  visit_schedule <- function(visit_format = \"WEEK\",                            n_assessments = 10L,                            n_days = 5L) {   if (!(toupper(visit_format) %in% c(\"WEEK\", \"CYCLE\"))) {     message(\"Visit format value must either be: WEEK or CYCLE\")     return(NA)   }   if (toupper(visit_format) == \"WEEK\") {     assessments <- 1:n_assessments     assessments_ord <- -1:n_assessments     visit_values <- c(\"SCREENING\", \"BASELINE\", paste(toupper(visit_format), assessments, \"DAY\", (assessments * 7) + 1))   } else if (toupper(visit_format) == \"CYCLE\") {     cycles <- sort(rep(1:n_assessments, times = 1, each = n_days))     days <- rep(seq(1:n_days), times = n_assessments, each = 1)     assessments_ord <- 0:(n_assessments * n_days)     visit_values <- c(\"SCREENING\", paste(toupper(visit_format), cycles, \"DAY\", days))   }   visit_values <- stats::reorder(factor(visit_values), assessments_ord) }  rtpois <- function(n, lambda) stats::qpois(stats::runif(n, stats::dpois(0, lambda), 1), lambda)  rtexp <- function(n, rate, l = NULL, r = NULL) {   if (!is.null(l)) {     l - log(1 - stats::runif(n)) / rate   } else if (!is.null(r)) {     -log(1 - stats::runif(n) * (1 - exp(-r * rate))) / rate   } else {     stats::rexp(n, rate)   } }  str_extract <- function(string, pattern) regmatches(string, gregexpr(pattern, string))  with_label <- function(x, label) {   attr(x, \"label\") <- as.vector(label)   x }  common_var_labels <- c(   USUBJID = \"Unique Subject Identifier\",   STUDYID = \"Study Identifier\",   PARAM = \"Parameter\",   PARAMCD = \"Parameter Code\",   AVISIT = \"Analysis Visit\",   AVISITN = \"Analysis Visit (N)\",   AVAL = \"Analysis Value\",   AVALU = \"Analysis Value Unit\",   AVALC = \"Character Result/Finding\",   BASE = \"Baseline Value\",   BASE2 = \"Screening Value\",   ABLFL = \"Baseline Record Flag\",   ABLFL2 = \"Screening Record Flag\",   CHG = \"Absolute Change from Baseline\",   PCHG = \"Percentage Change from Baseline\",   ANRIND = \"Analysis Reference Range Indicator\",   BNRIND = \"Baseline Reference Range Indicator\",   ANRLO = \"Analysis Normal Range Lower Limit\",   ANRHI = \"Analysis Normal Range Upper Limit\",   CNSR = \"Censor\",   ADTM = \"Analysis Datetime\",   ADY = \"Analysis Relative Day\",   ASTDY = \"Analysis Start Relative Day\",   AENDY = \"Analysis End Relative Day\",   ASTDTM = \"Analysis Start Datetime\",   AENDTM = \"Analysis End Datetime\",   VISITDY = \"Planned Study Day of Visit\",   EVNTDESC = \"Event or Censoring Description\",   CNSDTDSC = \"Censor Date Description\",   BASETYPE = \"Baseline Type\",   DTYPE = \"Derivation Type\",   ONTRTFL = \"On Treatment Record Flag\",   WORS01FL = \"Worst Observation in Window Flag 01\",   WORS02FL = \"Worst Post-Baseline Observation\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adsl","dir":"Articles","previous_headings":"","what":"ADSL","title":"Example Data Generation","text":"","code":"generate_adsl <- function(N = 200) {    set.seed(1)   sys_dtm <- lubridate::fast_strptime(\"20/2/2019 11:16:16.683\", \"%d/%m/%Y %H:%M:%OS\", tz = \"UTC\")   country_site_prob <- c(.5, .121, .077, .077, .075, .052, .046, .025, .014, .003)    adsl <- tibble::tibble(     STUDYID = rep(\"AB12345\", N) %>% with_label(\"Study Identifier\"),     COUNTRY = sample_fct(       c(\"CHN\", \"USA\", \"BRA\", \"PAK\", \"NGA\", \"RUS\", \"JPN\", \"GBR\", \"CAN\", \"CHE\"),       N,       prob = country_site_prob     ) %>% with_label(\"Country\"),     SITEID = sample_fct(1:20, N, prob = rep(country_site_prob, times = 2)),     SUBJID = paste(\"id\", seq_len(N), sep = \"-\") %>% with_label(\"Subject Identifier for the Study\"),     AGE = (sapply(stats::rchisq(N, df = 5, ncp = 10), max, 0) + 20) %>% with_label(\"Age\"),     SEX = c(\"F\", \"M\") %>% sample_fct(N, prob = c(.52, .48)) %>% with_label(\"Sex\"),     ARMCD = c(\"ARM A\", \"ARM B\", \"ARM C\") %>% sample_fct(N) %>% with_label(\"Planned Arm Code\"),     ARM = dplyr::recode(       .data$ARMCD,       \"ARM A\" = \"A: Drug X\", \"ARM B\" = \"B: Placebo\", \"ARM C\" = \"C: Combination\"     ) %>% with_label(\"Description of Planned Arm\"),     ACTARMCD = .data$ARMCD %>% with_label(\"Actual Arm Code\"),     ACTARM = .data$ARM %>% with_label(\"Description of Actual Arm\"),     RACE = c(       \"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\", \"AMERICAN INDIAN OR ALASKA NATIVE\",       \"MULTIPLE\", \"NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER\", \"OTHER\", \"UNKNOWN\"     ) %>%       sample_fct(N, prob = c(.55, .23, .16, .05, .004, .003, .002, .002)) %>%       with_label(\"Race\"),     TRTSDTM = sys_dtm + sample(seq(0, study_duration_secs), size = N, replace = TRUE) %>%       with_label(\"Datetime of First Exposure to Treatment\"),     TRTEDTM = c(TRTSDTM + study_duration_secs) %>%       with_label(\"Datetime of Last Exposure to Treatment\"),     EOSDY = ceiling(as.numeric(difftime(TRTEDTM, TRTSDTM, units = \"days\"))) %>%       with_label(\"End of Study Relative Day\"),     EOSDT = lubridate::date(TRTEDTM) %>% with_label(\"End of Study Date\"),     STRATA1 = c(\"A\", \"B\", \"C\") %>% sample_fct(N) %>% with_label(\"Stratification Factor 1\"),     STRATA2 = c(\"S1\", \"S2\") %>% sample_fct(N) %>% with_label(\"Stratification Factor 2\"),     BMRKR1 = stats::rchisq(N, 6) %>% with_label(\"Continuous Level Biomarker 1\"),     BMRKR2 = sample_fct(c(\"LOW\", \"MEDIUM\", \"HIGH\"), N) %>% with_label(\"Continuous Level Biomarker 2\")   )    # associate sites with countries and regions   adsl <- adsl %>%     dplyr::mutate(       SITEID = paste0(.data$COUNTRY, \"-\", .data$SITEID) %>% with_label(\"Study Site Identifier\"),       REGION1 = factor(dplyr::case_when(         COUNTRY %in% c(\"NGA\") ~ \"Africa\",         COUNTRY %in% c(\"CHN\", \"JPN\", \"PAK\") ~ \"Asia\",         COUNTRY %in% c(\"RUS\") ~ \"Eurasia\",         COUNTRY %in% c(\"GBR\") ~ \"Europe\",         COUNTRY %in% c(\"CAN\", \"USA\") ~ \"North America\",         COUNTRY %in% c(\"BRA\") ~ \"South America\",         TRUE ~ as.character(NA)       )) %>% with_label(\"Geographic Region 1\"),       SAFFL = factor(\"Y\") %>% with_label(\"Safety Population Flag\")     ) %>%     dplyr::mutate(       USUBJID = paste(.data$STUDYID, .data$SITEID, .data$SUBJID, sep = \"-\") %>%         with_label(\"Unique Subject Identifier\")     )    # disposition related variables   # using probability of 1 for the \"DEATH\" level to ensure at least one death record exists   l_dcsreas <- list(     choices = c(       \"ADVERSE EVENT\", \"DEATH\", \"LACK OF EFFICACY\", \"PHYSICIAN DECISION\",       \"PROTOCOL VIOLATION\", \"WITHDRAWAL BY PARENT/GUARDIAN\", \"WITHDRAWAL BY SUBJECT\"     ),     prob = c(.2, 1, .1, .1, .2, .1, .1)   )   l_dthcat_other <- list(     choices = c(       \"Post-study reporting of death\", \"LOST TO FOLLOW UP\", \"MISSING\", \"SUICIDE\", \"UNKNOWN\"     ),     prob = c(.1, .3, .3, .2, .1)   )    adsl <- adsl %>%     dplyr::mutate(       EOSSTT = dplyr::case_when(         EOSDY == max(EOSDY, na.rm = TRUE) ~ \"COMPLETED\",         EOSDY < max(EOSDY, na.rm = TRUE) ~ \"DISCONTINUED\",         is.na(TRTEDTM) ~ \"ONGOING\"       ) %>% with_label(\"End of Study Status\")     ) %>%     dplyr::mutate(       EOTSTT = .data$EOSSTT %>% with_label(\"End of Treatment Status\")     ) %>%     dplyr::mutate(       DCSREAS = ifelse(         .data$EOSSTT == \"DISCONTINUED\",         sample(x = l_dcsreas$choices, size = N, replace = TRUE, prob = l_dcsreas$prob),         as.character(NA)       ) %>% with_label(\"Reason for Discontinuation from Study\")     )    tmc_ex_adsl <- adsl %>%     dplyr::mutate(DTHDT = dplyr::case_when(       DCSREAS == \"DEATH\" ~ lubridate::date(TRTEDTM + lubridate::days(sample(0:50, size = N, replace = TRUE)))     ) %>% with_label(\"Date of Death\"))    save(tmc_ex_adsl, file = \"data/tmc_ex_adsl.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adae","dir":"Articles","previous_headings":"","what":"ADAE","title":"Example Data Generation","text":"","code":"generate_adae <- function(adsl = tmc_ex_adsl,                           max_n_aes = 5) {   set.seed(1)   lookup_ae <- tibble::tribble(     ~AEBODSYS, ~AELLT, ~AEDECOD, ~AEHLT, ~AEHLGT, ~AETOXGR, ~AESOC, ~AESER, ~AEREL,     \"cl A.1\", \"llt A.1.1.1.1\", \"dcd A.1.1.1.1\", \"hlt A.1.1.1\", \"hlgt A.1.1\", \"1\", \"cl A\", \"N\", \"N\",     \"cl A.1\", \"llt A.1.1.1.2\", \"dcd A.1.1.1.2\", \"hlt A.1.1.1\", \"hlgt A.1.1\", \"2\", \"cl A\", \"Y\", \"N\",     \"cl B.1\", \"llt B.1.1.1.1\", \"dcd B.1.1.1.1\", \"hlt B.1.1.1\", \"hlgt B.1.1\", \"5\", \"cl B\", \"Y\", \"Y\",     \"cl B.2\", \"llt B.2.1.2.1\", \"dcd B.2.1.2.1\", \"hlt B.2.1.2\", \"hlgt B.2.1\", \"3\", \"cl B\", \"N\", \"N\",     \"cl B.2\", \"llt B.2.2.3.1\", \"dcd B.2.2.3.1\", \"hlt B.2.2.3\", \"hlgt B.2.2\", \"1\", \"cl B\", \"Y\", \"N\",     \"cl C.1\", \"llt C.1.1.1.3\", \"dcd C.1.1.1.3\", \"hlt C.1.1.1\", \"hlgt C.1.1\", \"4\", \"cl C\", \"N\", \"Y\",     \"cl C.2\", \"llt C.2.1.2.1\", \"dcd C.2.1.2.1\", \"hlt C.2.1.2\", \"hlgt C.2.1\", \"2\", \"cl C\", \"N\", \"Y\",     \"cl D.1\", \"llt D.1.1.1.1\", \"dcd D.1.1.1.1\", \"hlt D.1.1.1\", \"hlgt D.1.1\", \"5\", \"cl D\", \"Y\", \"Y\",     \"cl D.1\", \"llt D.1.1.4.2\", \"dcd D.1.1.4.2\", \"hlt D.1.1.4\", \"hlgt D.1.1\", \"3\", \"cl D\", \"N\", \"N\",     \"cl D.2\", \"llt D.2.1.5.3\", \"dcd D.2.1.5.3\", \"hlt D.2.1.5\", \"hlgt D.2.1\", \"1\", \"cl D\", \"N\", \"Y\"   )    aag <- utils::read.table(     sep = \",\", header = TRUE,     text = paste(       \"NAMVAR,SRCVAR,GRPTYPE,REFNAME,REFTERM,SCOPE\",       \"CQ01NAM,AEDECOD,CUSTOM,D.2.1.5.3/A.1.1.1.1 aesi,dcd D.2.1.5.3,\",       \"CQ01NAM,AEDECOD,CUSTOM,D.2.1.5.3/A.1.1.1.1 aesi,dcd A.1.1.1.1,\",       \"SMQ01NAM,AEDECOD,SMQ,C.1.1.1.3/B.2.2.3.1 aesi,dcd C.1.1.1.3,BROAD\",       \"SMQ01NAM,AEDECOD,SMQ,C.1.1.1.3/B.2.2.3.1 aesi,dcd B.2.2.3.1,BROAD\",       \"SMQ02NAM,AEDECOD,SMQ,Y.9.9.9.9/Z.9.9.9.9 aesi,dcd Y.9.9.9.9,NARROW\",       \"SMQ02NAM,AEDECOD,SMQ,Y.9.9.9.9/Z.9.9.9.9 aesi,dcd Z.9.9.9.9,NARROW\",       sep = \"\\n\"     ), stringsAsFactors = FALSE   )    adae <- Map(     function(id, sid) {       n_aes <- sample(c(0, seq_len(max_n_aes)), 1)       i <- sample(seq_len(nrow(lookup_ae)), n_aes, TRUE)       dplyr::mutate(         lookup_ae[i, ],         USUBJID = id,         STUDYID = sid       )     },     adsl$USUBJID,     adsl$STUDYID   ) %>%     Reduce(rbind, .) %>%     `[`(c(10, 11, 1, 2, 3, 4, 5, 6, 7, 8, 9)) %>%     dplyr::mutate(       AETERM = gsub(\"dcd\", \"trm\", .data$AEDECOD) %>% with_label(\"Reported Term for the Adverse Event\"),       AESEV = dplyr::case_when(         AETOXGR == 1 ~ \"MILD\",         AETOXGR %in% c(2, 3) ~ \"MODERATE\",         AETOXGR %in% c(4, 5) ~ \"SEVERE\"       ) %>% with_label(\"Severity/Intensity\")     )    # merge adsl to be able to add AE date and study day variables   adae <- dplyr::inner_join(adae, adsl, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ASTDY = ceiling(difftime(ASTDTM, TRTSDTM, units = \"days\"))) %>%     # add 1 to end of range incase both values passed to sample() are the same     dplyr::mutate(AENDTM = sample(       seq(lubridate::as_datetime(ASTDTM), lubridate::as_datetime(TRTENDT + 1), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(AENDY = ceiling(difftime(AENDTM, TRTSDTM, units = \"days\"))) %>%     dplyr::mutate(LDOSEDTM = dplyr::case_when(       TRTSDTM < ASTDTM ~ lubridate::as_datetime(stats::runif(1, TRTSDTM, ASTDTM)),       TRUE ~ ASTDTM     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$AETERM)    adae <- adae %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(AESEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$ASTDTM,       .data$AETERM,       .data$AESEQ     )    outcomes <- c(     \"UNKNOWN\",     \"NOT RECOVERED/NOT RESOLVED\",     \"RECOVERED/RESOLVED WITH SEQUELAE\",     \"RECOVERING/RESOLVING\",     \"RECOVERED/RESOLVED\"   )    adae <- adae %>%     dplyr::mutate(       AEOUT = factor(ifelse(         .data$AETOXGR == \"5\",         \"FATAL\",         as.character(sample_fct(outcomes, nrow(adae), prob = c(0.1, 0.2, 0.1, 0.3, 0.3)))       )) %>% with_label(\"Outcome of Adverse Event\"),       TRTEMFL = ifelse(.data$ASTDTM >= .data$TRTSDTM, \"Y\", \"\") %>%         with_label(\"Treatment Emergent Analysis Flag\")     )    l_aag <- split(aag, interaction(aag$NAMVAR, aag$SRCVAR, aag$GRPTYPE, drop = TRUE))    # Create aesi flags   l_aesi <- lapply(l_aag, function(d_adag, d_adae) {     names(d_adag)[names(d_adag) == \"REFTERM\"] <- d_adag$SRCVAR[1]     names(d_adag)[names(d_adag) == \"REFNAME\"] <- d_adag$NAMVAR[1]      if (d_adag$GRPTYPE[1] == \"CUSTOM\") {       d_adag <- d_adag[-which(names(d_adag) == \"SCOPE\")]     } else if (d_adag$GRPTYPE[1] == \"SMQ\") {       names(d_adag)[names(d_adag) == \"SCOPE\"] <- paste0(substr(d_adag$NAMVAR[1], 1, 5), \"SC\")     }      d_adag <- d_adag[-which(names(d_adag) %in% c(\"NAMVAR\", \"SRCVAR\", \"GRPTYPE\"))]     d_new <- dplyr::left_join(x = d_adae, y = d_adag, by = intersect(names(d_adae), names(d_adag)))     d_new[, dplyr::setdiff(names(d_new), names(d_adae)), drop = FALSE]   }, adae)   adae <- dplyr::bind_cols(adae, l_aesi)    actions <- c(     \"DOSE RATE REDUCED\",     \"UNKNOWN\",     \"NOT APPLICABLE\",     \"DRUG INTERRUPTED\",     \"DRUG WITHDRAWN\",     \"DOSE INCREASED\",     \"DOSE NOT CHANGED\",     \"DOSE REDUCED\",     \"NOT EVALUABLE\"   )    tmc_ex_adae <- adae %>%     dplyr::mutate(       AEACN = factor(ifelse(         .data$AETOXGR == \"5\",         \"NOT EVALUABLE\",         as.character(sample_fct(actions, nrow(adae), prob = c(0.05, 0.05, 0.05, 0.01, 0.05, 0.1, 0.45, 0.1, 0.05)))       )) %>% with_label(\"Action Taken With Study Treatment\")     ) %>%     col_relabel(       AEBODSYS = \"Body System or Organ Class\",       AELLT = \"Lowest Level Term\",       AEDECOD = \"Dictionary-Derived Term\",       AEHLT = \"High Level Term\",       AEHLGT = \"High Level Group Term\",       AETOXGR = \"Analysis Toxicity Grade\",       AESOC = \"Primary System Organ Class\",       AESER = \"Serious Event\",       AEREL = \"Analysis Causality\",       AESEQ = \"Sponsor-Defined Identifier\",       LDOSEDTM = \"End Time/Time of Last Dose\",       CQ01NAM = \"CQ 01 Reference Name\",       SMQ01NAM = \"SMQ 01 Reference Name\",       SMQ01SC = \"SMQ 01 Scope\",       SMQ02NAM = \"SMQ 02 Reference Name\",       SMQ02SC = \"SMQ 02 Scope\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adae)[is.na(col_labels(tmc_ex_adae))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adae[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adae, file = \"data/tmc_ex_adae.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adaette","dir":"Articles","previous_headings":"","what":"ADAETTE","title":"Example Data Generation","text":"","code":"generate_adaette <- function(adsl = tmc_ex_adsl) {   set.seed(1)   lookup_adaette <- tibble::tribble(     ~ARM, ~CATCD, ~CAT, ~LAMBDA, ~CNSR_P,     \"ARM A\", \"1\", \"any adverse event\", 1 / 80, 0.4,     \"ARM B\", \"1\", \"any adverse event\", 1 / 100, 0.2,     \"ARM C\", \"1\", \"any adverse event\", 1 / 60, 0.42,     \"ARM A\", \"2\", \"any serious adverse event\", 1 / 100, 0.3,     \"ARM B\", \"2\", \"any serious adverse event\", 1 / 150, 0.1,     \"ARM C\", \"2\", \"any serious adverse event\", 1 / 80, 0.32,     \"ARM A\", \"3\", \"a grade 3-5 adverse event\", 1 / 80, 0.2,     \"ARM B\", \"3\", \"a grade 3-5 adverse event\", 1 / 100, 0.08,     \"ARM C\", \"3\", \"a grade 3-5 adverse event\", 1 / 60, 0.23   )   evntdescr_sel <- \"Preferred Term\"   cnsdtdscr_sel <- c(     \"Clinical Cut Off\",     \"Completion or Discontinuation\",     \"End of AE Reporting Period\"   )    random_patient_data <- function(patient_info) {     startdt <- lubridate::date(patient_info$TRTSDTM)     trtedtm <- lubridate::floor_date(dplyr::case_when(       is.na(patient_info$TRTEDTM) ~ lubridate::date(patient_info$TRTSDTM) + study_duration_secs,       TRUE ~ lubridate::date(patient_info$TRTEDTM)     ), unit = \"day\")     enddts <- c(patient_info$EOSDT, lubridate::date(trtedtm))     enddts_min_index <- which.min(enddts)     adt <- enddts[enddts_min_index]     adtm <- lubridate::as_datetime(adt)     ady <- as.numeric(adt - startdt + 1)     data.frame(       ARM = patient_info$ARM,       STUDYID = patient_info$STUDYID,       SITEID = patient_info$SITEID,       USUBJID = patient_info$USUBJID,       PARAMCD = \"AEREPTTE\",       PARAM = \"Time to end of AE reporting period\",       CNSR = 0,       AVAL = lubridate::days(ady) / lubridate::years(1),       AVALU = \"YEARS\",       EVNTDESC = ifelse(enddts_min_index == 1, \"Completion or Discontinuation\", \"End of AE Reporting Period\"),       CNSDTDSC = NA,       ADTM = adtm,       ADY = ady,       stringsAsFactors = FALSE     )   }    paramcd_hy <- c(\"HYSTTEUL\", \"HYSTTEBL\")   param_hy <- c(\"Time to Hy's Law Elevation in relation to ULN\", \"Time to Hy's Law Elevation in relation to Baseline\")   param_init_list <- relvar_init(param_hy, paramcd_hy)   adsl_hy <- dplyr::select(adsl, \"STUDYID\", \"USUBJID\", \"TRTSDTM\", \"SITEID\", \"ARM\")   adaette_hy <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     stringsAsFactors = FALSE   )    adaette_hy <- dplyr::left_join(adaette_hy, adsl_hy, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::mutate(       PARAMCD = factor(rel_var(         df = as.data.frame(adaette_hy),         var_values = param_init_list$relvar2,         related_var = \"PARAM\"       ))     ) %>%     dplyr::mutate(       CNSR = sample(c(0, 1), prob = c(0.1, 0.9), size = dplyr::n(), replace = TRUE),       EVNTDESC = dplyr::if_else(         .data$CNSR == 0,         \"First Post-Baseline Raised ALT or AST Elevation Result\",         NA_character_       ),       CNSDTDSC = dplyr::if_else(.data$CNSR == 0, NA_character_,         sample(c(\"Last Post-Baseline ALT or AST Result\", \"Treatment Start\"),           prob = c(0.9, 0.1),           size = dplyr::n(), replace = TRUE         )       )     ) %>%     dplyr::rowwise() %>%     dplyr::mutate(ADTM = dplyr::case_when(       CNSDTDSC == \"Treatment Start\" ~ TRTSDTM,       TRUE ~ TRTSDTM + sample(seq(0, study_duration_secs), size = dplyr::n(), replace = TRUE)     )) %>%     dplyr::mutate(       ADY_int = lubridate::date(ADTM) - lubridate::date(TRTSDTM) + 1,       ADY = as.numeric(ADY_int),       AVAL = lubridate::days(ADY_int) / lubridate::weeks(1),       AVALU = \"WEEKS\"     ) %>%     dplyr::select(-TRTSDTM, -ADY_int)    random_ae_data <- function(lookup_info, patient_info, patient_data) {     cnsr <- sample(c(0, 1), 1, prob = c(1 - lookup_info$CNSR_P, lookup_info$CNSR_P))     ae_rep_tte <- patient_data$AVAL[patient_data$PARAMCD == \"AEREPTTE\"]     data.frame(       ARM = rep(patient_data$ARM, 2),       STUDYID = rep(patient_data$STUDYID, 2),       SITEID = rep(patient_data$SITEID, 2),       USUBJID = rep(patient_data$USUBJID, 2),       PARAMCD = c(         paste0(\"AETTE\", lookup_info$CATCD),         paste0(\"AETOT\", lookup_info$CATCD)       ),       PARAM = c(         paste(\"Time to first occurrence of\", lookup_info$CAT),         paste(\"Number of occurrences of\", lookup_info$CAT)       ),       CNSR = c(cnsr, NA),       AVAL = c(         ifelse(cnsr == 1, ae_rep_tte, rtexp(1, lookup_info$LAMBDA * 365.25, r = ae_rep_tte)),         ifelse(cnsr == 1, 0, rtpois(1, lookup_info$LAMBDA * 365.25))       ),       AVALU = c(\"YEARS\", NA),       EVNTDESC = c(ifelse(cnsr == 0, sample(evntdescr_sel, 1), \"\"), NA),       CNSDTDSC = c(ifelse(cnsr == 1, sample(cnsdtdscr_sel, 1), \"\"), NA),       stringsAsFactors = FALSE     ) %>% dplyr::mutate(       ADY = dplyr::if_else(is.na(AVALU), NA_real_, ceiling(as.numeric(lubridate::dyears(AVAL), \"days\"))),       ADTM = dplyr::if_else(         is.na(AVALU),         lubridate::as_datetime(NA),         patient_info$TRTSDTM + lubridate::days(ADY)       )     )   }    adaette <- split(adsl, adsl$USUBJID) %>%     lapply(function(patient_info) {       patient_data <- random_patient_data(patient_info)       lookup_arm <- lookup_adaette %>%         dplyr::filter(.data$ARM == as.character(patient_info$ARMCD))       ae_data <- split(lookup_arm, lookup_arm$CATCD) %>%         lapply(random_ae_data, patient_data = patient_data, patient_info = patient_info) %>%         Reduce(rbind, .)       dplyr::bind_rows(patient_data, ae_data)     }) %>%     Reduce(rbind, .)   adaette <- rbind(adaette, adaette_hy)    tmc_ex_adaette <- adsl %>%     dplyr::inner_join(       dplyr::select(adaette, -\"SITEID\", -\"ARM\"),       by = c(\"STUDYID\", \"USUBJID\"),       multiple = \"all\"     ) %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::arrange(.data$ADTM) %>%     dplyr::mutate(PARAM = as.factor(.data$PARAM)) %>%     dplyr::mutate(PARAMCD = as.factor(.data$PARAMCD)) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adaette)[is.na(col_labels(tmc_ex_adaette))]),     function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adaette[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adaette, file = \"data/tmc_ex_adaette.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adcm","dir":"Articles","previous_headings":"","what":"ADCM","title":"Example Data Generation","text":"","code":"generate_adcm <- function(adsl = tmc_ex_adsl,                           max_n_cms = 5L) {   set.seed(1)   lookup_cm <- tibble::tribble(     ~CMCLAS, ~CMDECOD, ~ATIREL,     \"medcl A\", \"medname A_1/3\", \"PRIOR\",     \"medcl A\", \"medname A_2/3\", \"CONCOMITANT\",     \"medcl A\", \"medname A_3/3\", \"CONCOMITANT\",     \"medcl B\", \"medname B_1/4\", \"CONCOMITANT\",     \"medcl B\", \"medname B_2/4\", \"PRIOR\",     \"medcl B\", \"medname B_3/4\", \"PRIOR\",     \"medcl B\", \"medname B_4/4\", \"CONCOMITANT\",     \"medcl C\", \"medname C_1/2\", \"CONCOMITANT\",     \"medcl C\", \"medname C_2/2\", \"CONCOMITANT\"   )    adcm <- Map(function(id, sid) {     n_cms <- sample(c(0, seq_len(max_n_cms)), 1)     i <- sample(seq_len(nrow(lookup_cm)), n_cms, TRUE)     dplyr::mutate(       lookup_cm[i, ],       USUBJID = id,       STUDYID = sid     )   }, adsl$USUBJID, adsl$STUDYID) %>%     Reduce(rbind, .) %>%     `[`(c(4, 5, 1, 2, 3)) %>%     dplyr::mutate(CMCAT = .data$CMCLAS %>% with_label(\"Category for Medication\"))    # merge adsl to be able to add CM date and study day variables   adcm <- dplyr::inner_join(     adcm,     adsl,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ASTDY = ceiling(difftime(ASTDTM, TRTSDTM, units = \"days\"))) %>%     # add 1 to end of range incase both values passed to sample() are the same     dplyr::mutate(AENDTM = sample(       seq(lubridate::as_datetime(ASTDTM), lubridate::as_datetime(TRTENDT + 1), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(AENDY = ceiling(difftime(AENDTM, TRTSDTM, units = \"days\"))) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(STUDYID, USUBJID, ASTDTM)    tmc_ex_adcm <- adcm %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(CMSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$CMSEQ) %>%     dplyr::mutate(       ATC1 = paste(\"ATCCLAS1\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 1 Text\"),       ATC2 = paste(\"ATCCLAS2\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 2 Text\"),       ATC3 = paste(\"ATCCLAS3\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 3 Text\"),       ATC4 = paste(\"ATCCLAS4\", substr(.data$CMDECOD, 9, 9)) %>% with_label(\"ATC Level 4 Text\")     ) %>%     dplyr::mutate(       CMINDC = sample(c(         \"Nausea\", \"Hypertension\", \"Urticaria\", \"Fever\",         \"Asthma\", \"Infection\", \"Diabete\", \"Diarrhea\", \"Pneumonia\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Indication\"),       CMDOSE = sample(1:99, dplyr::n(), replace = TRUE) %>% with_label(\"Dose per Administration\"),       CMTRT = substr(.data$CMDECOD, 9, 13) %>% with_label(\"Reported Name of Drug, Med, or Therapy\"),       CMDOSU = sample(c(         \"ug/mL\", \"ug/kg/day\", \"%\", \"uL\", \"DROP\",         \"umol/L\", \"mg\", \"mg/breath\", \"ug\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Dose Units\")     ) %>%     dplyr::mutate(       CMROUTE = sample(c(         \"INTRAVENOUS\", \"ORAL\", \"NASAL\",         \"INTRAMUSCULAR\", \"SUBCUTANEOUS\", \"INHALED\", \"RECTAL\", \"UNKNOWN\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Route of Administration\"),       CMDOSFRQ = sample(c(         \"Q4W\", \"QN\", \"Q4H\", \"UNKNOWN\", \"TWICE\",         \"Q4H\", \"QD\", \"TID\", \"4 TIMES PER MONTH\"       ), dplyr::n(), replace = TRUE) %>% with_label(\"Dosing Frequency per Interval\")     ) %>%     col_relabel(       CMCLAS = \"Medication Class\",       CMDECOD = \"Standardized Medication Name\",       ATIREL = \"Time Relation of Medication\",       CMSEQ = \"Sponsor-Defined Identifier\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adcm)[is.na(col_labels(tmc_ex_adcm))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adcm[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adcm, file = \"data/tmc_ex_adcm.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adeg","dir":"Articles","previous_headings":"","what":"ADEG","title":"Example Data Generation","text":"","code":"generate_adeg <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_eg = 3L) {   set.seed(1)   param <- c(\"QT Duration\", \"RR Duration\", \"Heart Rate\", \"ECG Interpretation\")   paramcd <- c(\"QT\", \"RR\", \"HR\", \"ECGINTP\")   paramu <- c(\"msec\", \"msec\", \"beats/min\", \"\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adeg <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    adeg$PARAMCD <- as.factor(rel_var(     df = adeg,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adeg <- adeg %>% dplyr::mutate(AVAL = dplyr::case_when(     .data$PARAMCD == \"QT\" ~ stats::rnorm(nrow(adeg), mean = 350, sd = 100),     .data$PARAMCD == \"RR\" ~ stats::rnorm(nrow(adeg), mean = 1050, sd = 300),     .data$PARAMCD == \"HR\" ~ stats::rnorm(nrow(adeg), mean = 70, sd = 20),     .data$PARAMCD == \"ECGINTP\" ~ NA_real_   ))    adeg <- adeg %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ NA_real_   ))    adeg$AVALU <- as.factor(rel_var(     df = adeg,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adeg <- adeg[order(adeg$STUDYID, adeg$USUBJID, adeg$PARAMCD, adeg$AVISITN), ]   adeg <- Reduce(rbind, lapply(split(adeg, adeg$USUBJID), function(x) {     x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]     x$ABLFL <- ifelse(toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",       \"Y\",       ifelse(toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\", \"Y\", \"\")     )     x   }))    adeg$BASE <- ifelse(adeg$AVISITN >= 0, retain(adeg, adeg$AVAL, adeg$ABLFL == \"Y\"), adeg$AVAL)   adeg <- adeg %>%     dplyr::mutate(ANRLO = dplyr::case_when(       .data$PARAMCD == \"QT\" ~ 200,       .data$PARAMCD == \"RR\" ~ 600,       .data$PARAMCD == \"HR\" ~ 40,       .data$PARAMCD == \"ECGINTP\" ~ NA_real_     )) %>%     dplyr::mutate(ANRHI = dplyr::case_when(       .data$PARAMCD == \"QT\" ~ 500,       .data$PARAMCD == \"RR\" ~ 1500,       .data$PARAMCD == \"HR\" ~ 100,       .data$PARAMCD == \"ECGINTP\" ~ NA_real_     )) %>%     dplyr::mutate(ANRIND = factor(dplyr::case_when(       .data$AVAL < .data$ANRLO ~ \"LOW\",       .data$AVAL >= .data$ANRLO & .data$AVAL <= .data$ANRHI ~ \"NORMAL\",       .data$AVAL > .data$ANRHI ~ \"HIGH\"     )))    adeg <- adeg %>%     dplyr::mutate(CHG = ifelse(.data$AVISITN > 0, .data$AVAL - .data$BASE, NA)) %>%     dplyr::mutate(PCHG = ifelse(.data$AVISITN > 0, 100 * (.data$CHG / .data$BASE), NA)) %>%     dplyr::mutate(BASETYPE = \"LAST\") %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BNRIND = .data$ANRIND[.data$ABLFL == \"Y\"]) %>%     dplyr::ungroup() %>%     dplyr::mutate(DTYPE = NA)    adeg$ANRIND <- factor(adeg$ANRIND, levels = c(\"LOW\", \"NORMAL\", \"HIGH\"))   adeg$BNRIND <- factor(adeg$BNRIND, levels = c(\"LOW\", \"NORMAL\", \"HIGH\"))    adeg <- dplyr::inner_join(     adsl,     adeg,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::ungroup() %>%     dplyr::group_by(USUBJID) %>%     dplyr::arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adeg <- adeg %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$BASETYPE,       .data$AVISITN,       .data$DTYPE,       .data$ADTM     )    adeg <- adeg %>%     dplyr::mutate(ONTRTFL = factor(dplyr::case_when(       is.na(.data$TRTSDTM) ~ \"\",       is.na(.data$ADTM) ~ \"Y\",       (.data$ADTM < .data$TRTSDTM) ~ \"\",       (.data$ADTM > .data$TRTEDTM) ~ \"\",       TRUE ~ \"Y\"     ))) %>%     dplyr::mutate(AVALC = ifelse(       .data$PARAMCD == \"ECGINTP\",       as.character(sample_fct(c(\"ABNORMAL\", \"NORMAL\"), nrow(adeg), prob = c(0.25, 0.75))),       as.character(.data$AVAL)     ))    adeg <- adeg %>% dplyr::mutate(row_check = seq_len(nrow(adeg)))   get_groups <- function(data, minimum) {     data <- data %>%       dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%       dplyr::arrange(.data$ADTM) %>%       dplyr::filter(         (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &           (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)       ) %>%       {         if (minimum == TRUE) {           dplyr::filter(., .data$AVAL == min(.data$AVAL)) %>%             dplyr::mutate(., DTYPE = \"MINIMUM\", AVISIT = \"POST-BASELINE MINIMUM\")         } else {           dplyr::filter(., .data$AVAL == max(.data$AVAL)) %>%             dplyr::mutate(., DTYPE = \"MAXIMUM\", AVISIT = \"POST-BASELINE MAXIMUM\")         }       } %>%       dplyr::slice(1) %>%       dplyr::ungroup()     return(data)   }    lbls <- col_labels(adeg)   adeg <- rbind(adeg, get_groups(adeg, TRUE), get_groups(adeg, FALSE)) %>%     dplyr::arrange(.data$row_check) %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::arrange(.data$AVISIT, .by_group = TRUE) %>%     dplyr::ungroup()   col_labels(adeg) <- lbls    adeg <- adeg[, -which(names(adeg) %in% c(\"row_check\"))]   flag_variables <- function(data, worst_obs) {     data_compare <- data %>%       dplyr::mutate(row_check = seq_len(nrow(data)))     data <- data_compare %>%       {         if (worst_obs == FALSE) {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE, .data$AVISIT) %>%             dplyr::arrange(., .data$ADTM)         } else {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE)         }       } %>%       dplyr::filter(         .data$AVISITN > 0 & (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM) &           is.na(.data$DTYPE)       ) %>%       {         if (worst_obs == TRUE) {           dplyr::arrange(., .data$AVALC) %>% dplyr::filter(., ifelse(             .data$PARAMCD == \"ECGINTP\",             ifelse(.data$AVALC == \"ABNORMAL\", .data$AVALC == \"ABNORMAL\", .data$AVALC == \"NORMAL\"),             .data$AVAL == min(.data$AVAL)           ))         } else {           dplyr::filter(., ifelse(             .data$PARAMCD == \"ECGINTP\",             .data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\",             .data$AVAL == min(.data$AVAL)           ))         }       } %>%       dplyr::slice(1) %>%       {         if (worst_obs == TRUE) {           dplyr::mutate(., new_var = dplyr::case_when(             (.data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\") ~ \"Y\",             (!is.na(.data$AVAL) & is.na(.data$DTYPE)) ~ \"Y\",             TRUE ~ \"\"           ))         } else {           dplyr::mutate(., new_var = dplyr::case_when(             (.data$AVALC == \"ABNORMAL\" | .data$AVALC == \"NORMAL\") ~ \"Y\",             (!is.na(.data$AVAL) & is.na(.data$DTYPE)) ~ \"Y\",             TRUE ~ \"\"           ))         }       } %>%       dplyr::ungroup()      data_compare$new_var <- ifelse(data_compare$row_check %in% data$row_check, \"Y\", \"\")     data_compare <- data_compare[, -which(names(data_compare) %in% c(\"row_check\"))]      return(data_compare)   }   adeg <- flag_variables(adeg, FALSE) %>% dplyr::rename(WORS01FL = \"new_var\")   adeg <- flag_variables(adeg, TRUE) %>% dplyr::rename(WORS02FL = \"new_var\")    tmc_ex_adeg <- adeg %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BASEC = ifelse(       .data$PARAMCD == \"ECGINTP\",       .data$AVALC[.data$AVISIT == \"BASELINE\"],       as.character(.data$BASE)     )) %>%     dplyr::ungroup() %>%     col_relabel(BASEC = \"Baseline Character Value\")    i_lbls <- sapply(     names(col_labels(tmc_ex_adeg)[is.na(col_labels(tmc_ex_adeg))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adeg[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adeg, file = \"data/tmc_ex_adeg.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adex","dir":"Articles","previous_headings":"","what":"ADEX","title":"Example Data Generation","text":"","code":"generate_adex <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_exs = 3L) {   set.seed(1)   param <- c(     \"Dose administered during constant dosing interval\",     \"Number of doses administered during constant dosing interval\",     \"Total dose administered\",     \"Total number of doses administered\"   )   paramcd <- c(\"DOSE\", \"NDOSE\", \"TDOSE\", \"TNDOSE\")   paramu <- c(\"mg\", \" \", \"mg\", \" \")   parcat1 <- c(\"INDIVIDUAL\", \"OVERALL\")   parcat2 <- c(\"Drug A\", \"Drug B\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adex <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = c(       rep(         param_init_list$relvar1[1],         length(levels(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days)))       ),       rep(         param_init_list$relvar1[2],         length(levels(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days)))       ),       param_init_list$relvar1[3:4]     ),     stringsAsFactors = FALSE   )    adex$PARAMCD <- as.factor(rel_var(     df = adex,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adex$AVALU <- as.factor(rel_var(     df = adex,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adex <- adex %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(PARCAT_ind = sample(c(1, 2), size = 1)) %>%     dplyr::mutate(PARCAT2 = ifelse(.data$PARCAT_ind == 1, parcat2[1], parcat2[2])) %>%     dplyr::select(-\"PARCAT_ind\")    adex <- adex %>% dplyr::mutate(PARCAT1 = dplyr::case_when(     (.data$PARAMCD == \"TNDOSE\" | .data$PARAMCD == \"TDOSE\") ~ \"OVERALL\",     .data$PARAMCD == \"DOSE\" | .data$PARAMCD == \"NDOSE\" ~ \"INDIVIDUAL\"   ))    adex_visit <- adex %>%     dplyr::filter(.data$PARAMCD == \"DOSE\" | .data$PARAMCD == \"NDOSE\") %>%     dplyr::mutate(       AVISIT = rep(visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days), 2)     )    adex <- dplyr::left_join(     adex %>%       dplyr::group_by(         .data$USUBJID,         .data$STUDYID,         .data$PARAM,         .data$PARAMCD,         .data$AVALU,         .data$PARCAT1,         .data$PARCAT2       ) %>%       dplyr::mutate(id = dplyr::row_number()),     adex_visit %>%       dplyr::group_by(         .data$USUBJID,         .data$STUDYID,         .data$PARAM,         .data$PARAMCD,         .data$AVALU,         .data$PARCAT1,         .data$PARCAT2       ) %>%       dplyr::mutate(id = dplyr::row_number()),     by = c(\"USUBJID\", \"STUDYID\", \"PARCAT1\", \"PARCAT2\", \"id\", \"PARAMCD\", \"PARAM\", \"AVALU\")   ) %>%     dplyr::select(-\"id\")    adex <- adex %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ 999000   ))    adex2 <- split(adex, adex$USUBJID) %>%     lapply(function(pinfo) {       pinfo %>%         dplyr::filter(.data$PARAMCD == \"DOSE\") %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2, .data$AVISIT) %>%         dplyr::mutate(changeind = dplyr::case_when(           .data$AVISIT == \"SCREENING\" ~ 0,           .data$AVISIT != \"SCREENING\" ~ sample(c(-1, 0, 1),             size = 1,             prob = c(0.25, 0.5, 0.25),             replace = TRUE           )         )) %>%         dplyr::ungroup() %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2) %>%         dplyr::mutate(           csum = cumsum(.data$changeind),           changeind = dplyr::case_when(             .data$csum <= -3 ~ sample(c(0, 1), size = 1, prob = c(0.5, 0.5)),             .data$csum >= 3 ~ sample(c(0, -1), size = 1, prob = c(0.5, 0.5)),             TRUE ~ .data$changeind           )         ) %>%         dplyr::mutate(csum = cumsum(.data$changeind)) %>%         dplyr::ungroup() %>%         dplyr::group_by(.data$USUBJID, .data$PARCAT2, .data$AVISIT) %>%         dplyr::mutate(AVAL = dplyr::case_when(           .data$csum == -2 ~ 480,           .data$csum == -1 ~ 720,           .data$csum == 0 ~ 960,           .data$csum == 1 ~ 1200,           .data$csum == 2 ~ 1440         )) %>%         dplyr::select(-c(\"csum\", \"changeind\")) %>%         dplyr::ungroup()     }) %>%     Reduce(rbind, .)    adextmp <- dplyr::full_join(adex2, adex, by = names(adex))   adex <- adextmp %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(AVAL = ifelse(.data$PARAMCD == \"NDOSE\", 1, .data$AVAL)) %>%     dplyr::mutate(AVAL = ifelse(       .data$PARAMCD == \"TNDOSE\",       sum(.data$AVAL[.data$PARAMCD == \"NDOSE\"]),       .data$AVAL     )) %>%     dplyr::ungroup() %>%     dplyr::group_by(.data$USUBJID, .data$STUDYID, .data$PARCAT2) %>%     dplyr::mutate(AVAL = ifelse(       .data$PARAMCD == \"TDOSE\",       sum(.data$AVAL[.data$PARAMCD == \"DOSE\"]),       .data$AVAL     ))    adex <- dplyr::inner_join(adsl, adex, by = c(\"STUDYID\", \"USUBJID\"), multiple = \"all\") %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM)    adex <- adex %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(EXSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ASTDTM,       .data$AVISITN     ) %>%     col_relabel(       PARCAT1 = \"Parameter Category (Individual/Overall)\",       PARCAT2 = \"Parameter Category (Drug A/Drug B)\",       EXSEQ = \"Analysis Sequence Number\"     )    visit_levels <- str_extract(levels(adex$AVISIT), pattern = \"[0-9]+\")   vl_extracted <- vapply(visit_levels, function(x) as.numeric(x[2]), numeric(1))   vl_extracted <- c(-1, 1, vl_extracted[!is.na(vl_extracted)])    tmc_ex_adex <- adex %>%     dplyr::mutate(VISITDY = as.numeric(as.character(factor(AVISIT, labels = vl_extracted)))) %>%     dplyr::mutate(ASTDTM = lubridate::as_datetime(TRTSDTM) + lubridate::days(VISITDY)) %>%     dplyr::distinct(USUBJID, .keep_all = TRUE)    i_lbls <- sapply(     names(col_labels(tmc_ex_adex)[is.na(col_labels(tmc_ex_adex))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adex[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adex, file = \"data/tmc_ex_adex.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adlb","dir":"Articles","previous_headings":"","what":"ADLB","title":"Example Data Generation","text":"","code":"generate_adlb <- function(adsl = tmc_ex_adsl,                           n_assessments = 3L,                           n_days = 3L,                           max_n_lbs = 3L) {   set.seed(1)   lbcat <- c(\"CHEMISTRY\", \"CHEMISTRY\", \"IMMUNOLOGY\")   param <- c(     \"Alanine Aminotransferase Measurement\",     \"C-Reactive Protein Measurement\",     \"Immunoglobulin A Measurement\"   )   paramcd <- c(\"ALT\", \"CRP\", \"IGA\")   paramu <- c(\"U/L\", \"mg/L\", \"g/L\")   aval_mean <- c(20, 1, 2)   visit_format <- \"WEEK\"    # validate and initialize related variables   lbcat_init_list <- relvar_init(param, lbcat)   param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    adlb <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    # assign AVAL based on different test   adlb <- adlb %>%     dplyr::mutate(AVAL = stats::rnorm(nrow(adlb), mean = 1, sd = 0.2)) %>%     dplyr::left_join(data.frame(PARAM = param, ADJUST = aval_mean), by = \"PARAM\") %>%     dplyr::mutate(AVAL = .data$AVAL * .data$ADJUST) %>%     dplyr::select(-\"ADJUST\")    # assign related variable values: PARAMxLBCAT are related   adlb$LBCAT <- as.factor(rel_var(     df = adlb,     var_name = \"LBCAT\",     var_values = lbcat_init_list$relvar2,     related_var = \"PARAM\"   ))    # assign related variable values: PARAMxPARAMCD are related   adlb$PARAMCD <- as.factor(rel_var(     df = adlb,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))    adlb$AVALU <- as.factor(rel_var(     df = adlb,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    adlb <- adlb %>% dplyr::mutate(AVISITN = dplyr::case_when(     AVISIT == \"SCREENING\" ~ -1,     AVISIT == \"BASELINE\" ~ 0,     (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,     TRUE ~ NA_real_   ))    adlb <- adlb %>%     dplyr::mutate(AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     ))    # order to prepare for change from screening and baseline values   adlb <- adlb[order(adlb$STUDYID, adlb$USUBJID, adlb$PARAMCD, adlb$AVISITN), ]    adlb <- Reduce(rbind, lapply(split(adlb, adlb$USUBJID), function(x) {     x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]     x$ABLFL2 <- ifelse(x$AVISIT == \"SCREENING\", \"Y\", \"\")     x$ABLFL <- ifelse(toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",       \"Y\",       ifelse(toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\", \"Y\", \"\")     )     x   }))    adlb$BASE <- ifelse(adlb$ABLFL2 != \"Y\", retain(adlb, adlb$AVAL, adlb$ABLFL == \"Y\"), NA)   anrind_choices <- c(\"HIGH\", \"LOW\", \"NORMAL\")   adlb <- adlb %>%     dplyr::mutate(BASETYPE = \"LAST\") %>%     dplyr::mutate(ANRIND = sample_fct(anrind_choices, nrow(adlb), prob = c(0.1, 0.1, 0.8))) %>%     dplyr::mutate(ANRLO = dplyr::case_when(       .data$PARAMCD == \"ALT\" ~ 7,       .data$PARAMCD == \"CRP\" ~ 8,       .data$PARAMCD == \"IGA\" ~ 0.8     )) %>%     dplyr::mutate(ANRHI = dplyr::case_when(       .data$PARAMCD == \"ALT\" ~ 55,       .data$PARAMCD == \"CRP\" ~ 10,       .data$PARAMCD == \"IGA\" ~ 3     )) %>%     dplyr::mutate(DTYPE = NA) %>%     dplyr::mutate(       ATOXGR = factor(dplyr::case_when(         .data$ANRIND == \"LOW\" ~ sample(           c(\"-1\", \"-2\", \"-3\", \"-4\", \"-5\"),           nrow(adlb),           replace = TRUE,           prob = c(0.30, 0.25, 0.20, 0.15, 0)         ),         .data$ANRIND == \"HIGH\" ~ sample(           c(\"1\", \"2\", \"3\", \"4\", \"5\"),           nrow(adlb),           replace = TRUE,           prob = c(0.30, 0.25, 0.20, 0.15, 0)         ),         .data$ANRIND == \"NORMAL\" ~ \"0\"       )) %>% with_label(\"Analysis Toxicity Grade\")     ) %>%     dplyr::group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     dplyr::mutate(BTOXGR = .data$ATOXGR[.data$ABLFL == \"Y\"]) %>%     dplyr::ungroup() %>%     col_relabel(BTOXGR = \"Baseline Toxicity Grade\")    # High and low descriptions of the different PARAMCD values   # This is currently hard coded as the GDSR does not have these descriptions yet   grade_lookup <- tibble::tribble(     ~PARAMCD, ~ATOXDSCL, ~ATOXDSCH,     \"ALB\", \"Hypoalbuminemia\", NA_character_,     \"ALKPH\", NA_character_, \"Alkaline phosphatase increased\",     \"ALT\", NA_character_, \"Alanine aminotransferase increased\",     \"AST\", NA_character_, \"Aspartate aminotransferase increased\",     \"BILI\", NA_character_, \"Blood bilirubin increased\",     \"CA\", \"Hypocalcemia\", \"Hypercalcemia\",     \"CHOLES\", NA_character_, \"Cholesterol high\",     \"CK\", NA_character_, \"CPK increased\",     \"CREAT\", NA_character_, \"Creatinine increased\",     \"CRP\", NA_character_, \"C reactive protein increased\",     \"GGT\", NA_character_, \"GGT increased\",     \"GLUC\", \"Hypoglycemia\", \"Hyperglycemia\",     \"HGB\", \"Anemia\", \"Hemoglobin increased\",     \"IGA\", NA_character_, \"Immunoglobulin A increased\",     \"POTAS\", \"Hypokalemia\", \"Hyperkalemia\",     \"LYMPH\", \"CD4 lymphocytes decreased\", NA_character_,     \"PHOS\", \"Hypophosphatemia\", NA_character_,     \"PLAT\", \"Platelet count decreased\", NA_character_,     \"SODIUM\", \"Hyponatremia\", \"Hypernatremia\",     \"WBC\", \"White blood cell decreased\", \"Leukocytosis\",   )    # merge grade_lookup onto adlb   adlb <- dplyr::left_join(adlb, grade_lookup, by = \"PARAMCD\")    # merge adsl to be able to add LB date and study day variables   adlb <- dplyr::inner_join(     adsl,     adlb,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::ungroup() %>%     dplyr::group_by(USUBJID) %>%     dplyr::arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adlb <- adlb %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(LBSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$BASETYPE,       .data$AVISITN,       .data$DTYPE,       .data$ADTM,       .data$LBSEQ     ) %>%     col_relabel(LBSEQ = \"Lab Test or Examination Sequence Number\")    adlb <- adlb %>% dplyr::mutate(ONTRTFL = factor(dplyr::case_when(     is.na(.data$TRTSDTM) ~ \"\",     is.na(.data$ADTM) ~ \"Y\",     (.data$ADTM < .data$TRTSDTM) ~ \"\",     (.data$ADTM > .data$TRTEDTM) ~ \"\",     TRUE ~ \"Y\"   )))    flag_variables <- function(data,                              apply_grouping,                              apply_filter,                              apply_mutate) {     data_compare <- data %>% dplyr::mutate(row_check = seq_len(nrow(data)))     data <- data_compare %>%       {         if (apply_grouping == TRUE) {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE, .data$AVISIT)         } else {           dplyr::group_by(., .data$USUBJID, .data$PARAMCD, .data$BASETYPE)         }       } %>%       dplyr::arrange(.data$ADTM, .data$LBSEQ) %>%       {         if (apply_filter == TRUE) {           dplyr::filter(             .,             (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           ) %>%             dplyr::filter(.data$ATOXGR == max(as.numeric(as.character(.data$ATOXGR))))         } else if (apply_filter == FALSE) {           dplyr::filter(             .,             (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           ) %>%             dplyr::filter(.data$ATOXGR == min(as.numeric(as.character(.data$ATOXGR))))         } else {           dplyr::filter(             .,             .data$AVAL == min(.data$AVAL) &               (.data$AVISIT != \"BASELINE\" & .data$AVISIT != \"SCREENING\") &               (.data$ONTRTFL == \"Y\" | .data$ADTM <= .data$TRTSDTM)           )         }       } %>%       dplyr::slice(1) %>%       {         if (apply_mutate == TRUE) {           dplyr::mutate(., new_var = ifelse(is.na(.data$DTYPE), \"Y\", \"\"))         } else {           dplyr::mutate(., new_var = ifelse(is.na(.data$AVAL) == FALSE & is.na(.data$DTYPE), \"Y\", \"\"))         }       } %>%       dplyr::ungroup()      data_compare$new_var <- ifelse(data_compare$row_check %in% data$row_check, \"Y\", \"\")     data_compare <- data_compare[, -which(names(data_compare) %in% c(\"row_check\"))]     return(data_compare)   }   adlb <- flag_variables(adlb, TRUE, \"ELSE\", FALSE) %>% dplyr::rename(WORS01FL = \"new_var\")   adlb <- flag_variables(adlb, FALSE, TRUE, TRUE) %>% dplyr::rename(WGRHIFL = \"new_var\")   adlb <- flag_variables(adlb, FALSE, FALSE, TRUE) %>% dplyr::rename(WGRLOFL = \"new_var\")   adlb <- flag_variables(adlb, TRUE, TRUE, TRUE) %>% dplyr::rename(WGRHIVFL = \"new_var\")   adlb <- flag_variables(adlb, TRUE, FALSE, TRUE) %>% dplyr::rename(WGRLOVFL = \"new_var\")    tmc_ex_adlb <- adlb %>% dplyr::mutate(     ANL01FL = ifelse(       (.data$ABLFL == \"Y\" | (.data$WORS01FL == \"Y\" & is.na(.data$DTYPE))) &         (.data$AVISIT != \"SCREENING\"),       \"Y\",       \"\"     ) %>% with_label(\"Analysis Flag 01 Baseline Post-Baseline\"),     PARAM = as.factor(.data$PARAM)   )    tmc_ex_adlb <- tmc_ex_adlb %>%     group_by(.data$USUBJID, .data$PARAMCD, .data$BASETYPE) %>%     mutate(BNRIND = .data$ANRIND[.data$ABLFL == \"Y\"]) %>%     ungroup() %>%     dplyr::mutate(ADY = ceiling(as.numeric(difftime(.data$ADTM, .data$TRTSDTM, units = \"days\"))))    tmc_ex_adlb$PARAMCD <- as.factor(tmc_ex_adlb$PARAMCD)   tmc_ex_adlb <- tmc_ex_adlb %>%     dplyr::mutate(CHG = .data$AVAL - .data$BASE) %>%     dplyr::mutate(PCHG = 100 * (.data$CHG / .data$BASE)) %>%     col_relabel(       LBCAT = \"Category for Lab Test\",       ATOXDSCL = \"Analysis Toxicity Description Low\",       ATOXDSCH = \"Analysis Toxicity Description High\",       WGRHIFL = \"Worst High Grade per Patient\",       WGRLOFL = \"Worst Low Grade per Patient\",       WGRHIVFL = \"Worst High Grade per Patient per Visit\",       WGRLOVFL = \"Worst Low Grade per Patient per Visit\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adlb)[is.na(col_labels(tmc_ex_adlb))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adlb[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adlb, file = \"data/tmc_ex_adlb.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"admh","dir":"Articles","previous_headings":"","what":"ADMH","title":"Example Data Generation","text":"","code":"generate_admh <- function(adsl = tmc_ex_adsl,                           max_n_mhs = 10L) {   set.seed(1)   lookup_mh <- tibble::tribble(     ~MHBODSYS, ~MHDECOD, ~MHSOC,     \"cl A\", \"trm A_1/2\", \"cl A\",     \"cl A\", \"trm A_2/2\", \"cl A\",     \"cl B\", \"trm B_1/3\", \"cl B\",     \"cl B\", \"trm B_2/3\", \"cl B\",     \"cl B\", \"trm B_3/3\", \"cl B\",     \"cl C\", \"trm C_1/2\", \"cl C\",     \"cl C\", \"trm C_2/2\", \"cl C\",     \"cl D\", \"trm D_1/3\", \"cl D\",     \"cl D\", \"trm D_2/3\", \"cl D\",     \"cl D\", \"trm D_3/3\", \"cl D\"   )    admh <- Map(     function(id, sid) {       n_mhs <- sample(0:max_n_mhs, 1)       i <- sample(seq_len(nrow(lookup_mh)), n_mhs, TRUE)       dplyr::mutate(         lookup_mh[i, ],         USUBJID = id,         STUDYID = sid       )     },     adsl$USUBJID,     adsl$STUDYID   ) %>%     Reduce(rbind, .) %>%     `[`(c(4, 5, 1, 2, 3)) %>%     dplyr::mutate(MHTERM = .data$MHDECOD %>% with_label(\"Reported Term for the Medical History\"))    admh <- dplyr::inner_join(     adsl,     admh,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ASTDTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM, .data$MHTERM) %>%     dplyr::mutate(MHDISTAT = sample(       x = c(\"Resolved\", \"Ongoing with treatment\", \"Ongoing without treatment\"),       prob = c(0.6, 0.2, 0.2),       size = dplyr::n(),       replace = TRUE     ) %>% with_label(\"Status of Disease\"))    tmc_ex_admh <- admh %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(MHSEQ = seq_len(dplyr::n())) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ASTDTM) %>%     col_relabel(       MHBODSYS = \"Body System or Organ Class\",       MHDECOD = \"Dictionary-Derived Term\",       MHSOC = \"Primary System Organ Class\",       MHSEQ = \"Sponsor-Defined Identifier\"     )    i_lbls <- sapply(     names(col_labels(tmc_ex_admh)[is.na(col_labels(tmc_ex_admh))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_admh[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_admh, file = \"data/tmc_ex_admh.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adqs","dir":"Articles","previous_headings":"","what":"ADQS","title":"Example Data Generation","text":"","code":"generate_adqs <- function(adsl = tmc_ex_adsl,                           n_assessments = 5L,                           n_days = 5L) {   set.seed(1)   param <- c(     \"BFI All Questions\",     \"Fatigue Interference\",     \"Function/Well-Being (GF1,GF3,GF7)\",     \"Treatment Side Effects (GP2,C5,GP5)\",     \"FKSI-19 All Questions\"   )   paramcd <- c(\"BFIALL\", \"FATIGI\", \"FKSI-FWB\", \"FKSI-TSE\", \"FKSIALL\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)    adqs <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = param_init_list$relvar1,     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments, n_days = n_days),     stringsAsFactors = FALSE   )    adqs <- dplyr::mutate(     adqs,     AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     )   )    adqs$PARAMCD <- rel_var(df = adqs, var_name = \"PARAMCD\", var_values = param_init_list$relvar2, related_var = \"PARAM\")   adqs$AVAL <- stats::rnorm(nrow(adqs), mean = 50, sd = 8) + adqs$AVISITN * stats::rnorm(nrow(adqs), mean = 5, sd = 2)   adqs <- adqs[order(adqs$STUDYID, adqs$USUBJID, adqs$PARAMCD, adqs$AVISITN), ]    adqs <- Reduce(     rbind,     lapply(       split(adqs, adqs$USUBJID),       function(x) {         x$STUDYID <- adsl$STUDYID[which(adsl$USUBJID == x$USUBJID[1])]         x$ABLFL2 <- ifelse(x$AVISIT == \"SCREENING\", \"Y\", \"\")         x$ABLFL <- ifelse(           toupper(visit_format) == \"WEEK\" & x$AVISIT == \"BASELINE\",           \"Y\",           ifelse(             toupper(visit_format) == \"CYCLE\" & x$AVISIT == \"CYCLE 1 DAY 1\",             \"Y\",             \"\"           )         )         x       }     )   )    adqs$BASE <- ifelse(adqs$ABLFL2 != \"Y\", retain(adqs, adqs$AVAL, adqs$ABLFL == \"Y\"), NA)   adqs <- adqs %>% dplyr::mutate(CHG = .data$AVAL - .data$BASE)    adqs <- dplyr::inner_join(     adsl,     adqs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     ungroup() %>%     group_by(USUBJID) %>%     arrange(USUBJID, AVISITN) %>%     dplyr::mutate(ADTM = rep(       sort(sample(         seq(lubridate::as_datetime(TRTSDTM[1]), lubridate::as_datetime(TRTENDT[1]), by = \"day\"),         size = nlevels(AVISIT)       )),       each = n() / nlevels(AVISIT)     )) %>%     dplyr::ungroup() %>%     dplyr::select(-TRTENDT) %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    tmc_ex_adqs <- adqs %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adqs)[is.na(col_labels(tmc_ex_adqs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adqs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adqs, file = \"data/tmc_ex_adqs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adrs","dir":"Articles","previous_headings":"","what":"ADRS","title":"Example Data Generation","text":"","code":"generate_adrs <- function(adsl = tmc_ex_adsl) {   set.seed(1)   param_codes <- stats::setNames(1:5, c(\"CR\", \"PR\", \"SD\", \"PD\", \"NE\"))    lookup_ars <- expand.grid(     ARM = c(\"A: Drug X\", \"B: Placebo\", \"C: Combination\"),     AVALC = names(param_codes)   ) %>% dplyr::mutate(     AVAL = param_codes[.data$AVALC],     p_scr = c(rep(0, 3), rep(0, 3), c(1, 1, 1), c(0, 0, 0), c(0, 0, 0)),     p_bsl = c(rep(0, 3), rep(0, 3), c(1, 1, 1), c(0, 0, 0), c(0, 0, 0)),     p_cycle = c(c(.35, .25, .4), c(.30, .20, .20), c(.2, .25, .3), c(.14, 0.20, 0.18), c(.01, 0.1, 0.02)),     p_eoi = c(c(.35, .25, .4), c(.30, .20, .20), c(.2, .25, .3), c(.14, 0.20, 0.18), c(.01, 0.1, 0.02)),     p_fu = c(c(.25, .15, .3), c(.15, .05, .25), c(.3, .25, .3), c(.3, .55, .25), rep(0, 3))   )    adrs <- split(adsl, adsl$USUBJID) %>%     lapply(function(pinfo) {       probs <- dplyr::filter(lookup_ars, .data$ARM == as.character(pinfo$ACTARM))       # screening       rsp_screen <- sample(probs$AVALC, 1, prob = probs$p_scr) %>% as.character()       # baseline       rsp_bsl <- sample(probs$AVALC, 1, prob = probs$p_bsl) %>% as.character()       # cycle       rsp_c2d1 <- sample(probs$AVALC, 1, prob = probs$p_cycle) %>% as.character()       rsp_c4d1 <- sample(probs$AVALC, 1, prob = probs$p_cycle) %>% as.character()       # end of induction       rsp_eoi <- sample(probs$AVALC, 1, prob = probs$p_eoi) %>% as.character()       # follow up       rsp_fu <- sample(probs$AVALC, 1, prob = probs$p_fu) %>% as.character()        best_rsp <- min(param_codes[c(rsp_screen, rsp_bsl, rsp_eoi, rsp_fu, rsp_c2d1, rsp_c4d1)])       best_rsp_i <- which.min(param_codes[c(rsp_screen, rsp_bsl, rsp_eoi, rsp_fu, rsp_c2d1, rsp_c4d1)])        avisit <- c(\"SCREENING\", \"BASELINE\", \"CYCLE 2 DAY 1\", \"CYCLE 4 DAY 1\", \"END OF INDUCTION\", \"FOLLOW UP\")        # meaningful date information       TRTSTDT <- lubridate::date(pinfo$TRTSDTM)        TRTENDT <- lubridate::date(dplyr::if_else(          !is.na(pinfo$TRTEDTM), pinfo$TRTEDTM,         lubridate::floor_date(TRTSTDT + study_duration_secs, unit = \"day\")       ))       scr_date <- TRTSTDT - lubridate::days(100)       bs_date <- TRTSTDT       flu_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       eoi_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       c2d1_date <- sample(seq(lubridate::as_datetime(TRTSTDT), lubridate::as_datetime(TRTENDT), by = \"day\"), size = 1)       c4d1_date <- min(lubridate::date(c2d1_date + lubridate::days(60)), TRTENDT)        tibble::tibble(         STUDYID = pinfo$STUDYID,         USUBJID = pinfo$USUBJID,         PARAMCD = as.factor(c(rep(\"OVRINV\", 6), \"BESRSPI\", \"INVET\")),         PARAM = as.factor(dplyr::recode(           .data$PARAMCD,           OVRINV = \"Overall Response by Investigator - by visit\",           OVRSPI = \"Best Overall Response by Investigator (no confirmation required)\",           BESRSPI = \"Best Confirmed Overall Response by Investigator\",           INVET = \"Investigator End Of Induction Response\"         )),         AVALC = c(           rsp_screen, rsp_bsl, rsp_c2d1, rsp_c4d1, rsp_eoi, rsp_fu,           names(param_codes)[best_rsp],           rsp_eoi         ),         AVAL = param_codes[.data$AVALC],         AVISIT = factor(c(avisit, avisit[best_rsp_i], avisit[5]), levels = avisit)       ) %>%         merge(           tibble::tibble(             AVISIT = avisit,             ADTM = c(scr_date, bs_date, c2d1_date, c4d1_date, eoi_date, flu_date),             AVISITN = c(-1, 0, 2, 4, 999, 999),             TRTSDTM = pinfo$TRTSDTM           ) %>%             dplyr::select(-\"TRTSDTM\"),           by = \"AVISIT\"         )     }) %>%     Reduce(rbind, .) %>%     dplyr::mutate(       AVALC = factor(.data$AVALC, levels = names(param_codes)),       DTHFL = factor(sample(c(\"Y\", \"N\"), nrow(.), replace = TRUE, prob = c(1, 0.8))) %>%         with_label(\"Death Flag\")     )    # merge ADSL to be able to add RS date and study day variables   adrs <- dplyr::inner_join(     adsl,     adrs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   )    tmc_ex_adrs <- adrs %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_adrs)[is.na(col_labels(tmc_ex_adrs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adrs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adrs, file = \"data/tmc_ex_adrs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"adtte","dir":"Articles","previous_headings":"","what":"ADTTE","title":"Example Data Generation","text":"","code":"generate_adtte <- function(adsl = tmc_ex_adsl) {   set.seed(1)   lookup_tte <- tibble::tribble(     ~ARM, ~PARAMCD, ~PARAM, ~LAMBDA, ~CNSR_P,     \"ARM A\", \"OS\", \"Overall Survival\", log(2) / 610, 0.4,     \"ARM B\", \"OS\", \"Overall Survival\", log(2) / 490, 0.3,     \"ARM C\", \"OS\", \"Overall Survival\", log(2) / 365, 0.2,     \"ARM A\", \"PFS\", \"Progression Free Survival\", log(2) / 365, 0.4,     \"ARM B\", \"PFS\", \"Progression Free Survival\", log(2) / 305, 0.3,     \"ARM C\", \"PFS\", \"Progression Free Survival\", log(2) / 243, 0.2,     \"ARM A\", \"EFS\", \"Event Free Survival\", log(2) / 365, 0.4,     \"ARM B\", \"EFS\", \"Event Free Survival\", log(2) / 305, 0.3,     \"ARM C\", \"EFS\", \"Event Free Survival\", log(2) / 243, 0.2,     \"ARM A\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 305, 0.4,     \"ARM B\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 243, 0.3,     \"ARM C\", \"CRSD\", \"Duration of Confirmed Response\", log(2) / 182, 0.2   )    evntdescr_sel <- c(     \"Death\",     \"Disease Progression\",     \"Last Tumor Assessment\",     \"Adverse Event\",     \"Last Date Known To Be Alive\"   )    cnsdtdscr_sel <- c(     \"Preferred Term\",     \"Clinical Cut Off\",     \"Completion or Discontinuation\",     \"End of AE Reporting Period\"   )    adtte <- split(adsl, adsl$USUBJID) %>%     lapply(FUN = function(pinfo) {       lookup_tte %>%         dplyr::filter(.data$ARM == as.character(pinfo$ACTARMCD)) %>%         dplyr::rowwise() %>%         dplyr::mutate(           STUDYID = pinfo$STUDYID,           USUBJID = pinfo$USUBJID,           CNSR = sample(c(0, 1), 1, prob = c(1 - .data$CNSR_P, .data$CNSR_P)),           AVAL = stats::rexp(1, .data$LAMBDA),           AVALU = \"DAYS\",           EVNTDESC = if (.data$CNSR == 1) {             sample(evntdescr_sel[-c(1:2)], 1)           } else {             ifelse(.data$PARAMCD == \"OS\",               sample(evntdescr_sel[1], 1),               sample(evntdescr_sel[c(1:2)], 1)             )           }         ) %>%         dplyr::select(-\"LAMBDA\", -\"CNSR_P\")     }) %>%     Reduce(rbind, .)    # merge ADSL to be able to add TTE date and study day variables   adtte <- dplyr::inner_join(     adsl,     dplyr::select(adtte, -\"ARM\"),     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ADTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    adtte <- adtte %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::mutate(PARAM = as.factor(.data$PARAM)) %>%     dplyr::mutate(PARAMCD = as.factor(.data$PARAMCD)) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )   lbls <- col_labels(adtte)    # adding adverse event counts and log follow-up time   tmc_ex_adtte <- dplyr::bind_rows(     adtte,     data.frame(adtte %>%       dplyr::group_by(.data$USUBJID) %>%       dplyr::slice_head(n = 1) %>%       dplyr::mutate(         PARAMCD = \"TNE\",         PARAM = \"Total Number of Exacerbations\",         AVAL = stats::rpois(1, 3),         AVALU = \"COUNT\",         lgTMATRSK = log(stats::rexp(1, rate = 3)),         dplyr::across(c(\"ADTM\", \"EVNTDESC\"), ~NA)       ))   ) %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$ADTM     )   col_labels(tmc_ex_adtte) <- c(lbls, lgTMATRSK = \"Log Time At Risk\")    i_lbls <- sapply(     names(col_labels(tmc_ex_adtte)[is.na(col_labels(tmc_ex_adtte))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_adtte[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_adtte, file = \"data/tmc_ex_adtte.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"advs","dir":"Articles","previous_headings":"","what":"ADVS","title":"Example Data Generation","text":"","code":"generate_advs <- function(adsl = tmc_ex_adsl,                           n_assessments = 5L,                           n_days = 5L) {   set.seed(1)   param <- c(     \"Diastolic Blood Pressure\",     \"Pulse Rate\",     \"Respiratory Rate\",     \"Systolic Blood Pressure\",     \"Temperature\", \"Weight\"   )   paramcd <- c(\"DIABP\", \"PULSE\", \"RESP\", \"SYSBP\", \"TEMP\", \"WEIGHT\")   paramu <- c(\"Pa\", \"beats/min\", \"breaths/min\", \"Pa\", \"C\", \"Kg\")   visit_format <- \"WEEK\"    param_init_list <- relvar_init(param, paramcd)   unit_init_list <- relvar_init(param, paramu)    advs <- expand.grid(     STUDYID = unique(adsl$STUDYID),     USUBJID = adsl$USUBJID,     PARAM = as.factor(param_init_list$relvar1),     AVISIT = visit_schedule(visit_format = visit_format, n_assessments = n_assessments),     stringsAsFactors = FALSE   )    advs <- dplyr::mutate(     advs,     AVISITN = dplyr::case_when(       AVISIT == \"SCREENING\" ~ -1,       AVISIT == \"BASELINE\" ~ 0,       (grepl(\"^WEEK\", AVISIT) | grepl(\"^CYCLE\", AVISIT)) ~ as.numeric(AVISIT) - 2,       TRUE ~ NA_real_     )   )    advs$PARAMCD <- as.factor(rel_var(     df = advs,     var_name = \"PARAMCD\",     var_values = param_init_list$relvar2,     related_var = \"PARAM\"   ))   advs$AVALU <- as.factor(rel_var(     df = advs,     var_name = \"AVALU\",     var_values = unit_init_list$relvar2,     related_var = \"PARAM\"   ))    advs$AVAL <- stats::rnorm(nrow(advs), mean = 50, sd = 8)   advs <- advs[order(advs$STUDYID, advs$USUBJID, advs$PARAMCD, advs$AVISITN), ]    advs <- dplyr::inner_join(     adsl,     advs,     by = c(\"STUDYID\", \"USUBJID\"),     multiple = \"all\"   ) %>%     dplyr::rowwise() %>%     dplyr::mutate(TRTENDT = lubridate::date(dplyr::case_when(       is.na(TRTEDTM) ~ lubridate::floor_date(lubridate::date(TRTSDTM) + study_duration_secs, unit = \"day\"),       TRUE ~ TRTEDTM     ))) %>%     dplyr::mutate(ADTM = sample(       seq(lubridate::as_datetime(TRTSDTM), lubridate::as_datetime(TRTENDT), by = \"day\"),       size = 1     )) %>%     dplyr::mutate(ADY = ceiling(difftime(ADTM, TRTSDTM, units = \"days\"))) %>%     dplyr::select(-TRTENDT) %>%     dplyr::ungroup() %>%     dplyr::arrange(.data$STUDYID, .data$USUBJID, .data$ADTM)    tmc_ex_advs <- advs %>%     dplyr::group_by(.data$USUBJID) %>%     dplyr::ungroup() %>%     dplyr::arrange(       .data$STUDYID,       .data$USUBJID,       .data$PARAMCD,       .data$AVISITN,       .data$ADTM     )    i_lbls <- sapply(     names(col_labels(tmc_ex_advs)[is.na(col_labels(tmc_ex_advs))]), function(x) which(names(common_var_labels) == x)   )   col_labels(tmc_ex_advs[names(i_lbls)]) <- common_var_labels[i_lbls]    save(tmc_ex_advs, file = \"data/tmc_ex_advs.rda\", compress = \"xz\") }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/generate_tmc_test_data.html","id":"generate-data","dir":"Articles","previous_headings":"","what":"Generate Data","title":"Example Data Generation","text":"","code":"# Generate & load adsl tmp_fol <- getwd() setwd(dirname(tmp_fol)) generate_adsl() load(\"data/tmc_ex_adsl.rda\")  # Generate other datasets generate_adae() generate_adaette() generate_adcm() generate_adeg() generate_adex() generate_adlb() generate_admh() generate_adqs() generate_adrs() generate_adtte() generate_advs()  setwd(tmp_fol)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"section","dir":"Articles","previous_headings":"","what":"Quick start: `substitute` for NSE","title":"Quick start: `substitute` for NSE","text":"Considering expression, R usually evaluates returns value. Instead focusing value, also possible work code generated value. non standard evaluation, NSE, starts. function substitute important element non-standard evaluation. instance, consider defined <- 5, expression returns 5, substitute() returns code obtain value: . principle teal relies : generate expressions. return result expression result panel app. return corresponding code (expression) Show R Code. expression returning displayed value must reactive. information encoding one hand, filtering panel hand modify expression displayed value. , teal needs work expressions values relies heavily NSE. NSE advanced notion mixing Shiny app development source difficulties : hindered coding efficiency Shiny app must run order check correct execution code. limited possibilities testing. alternative, possible focus first NSE aspects plain R, ready, integrate Shiny App. following practical examples demonstrating NSE works. choice made focus substitute.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"nse-principle","dir":"Articles","previous_headings":"The Basics","what":"NSE Principle","title":"Quick start: `substitute` for NSE","text":"happened? substitute returns code value, attempt run code, therefore possible return expression make sense (yet), instance involving two non defined objects. values b exist, expression can run without error: Now, function name substitute reason. returning expression, also operates substitutions terms within given expression. happened? objects b exist function environment substitute called. terms expression within substitute replaced values b. Indeed, returning expression, substitute verifies b don’t value existing evaluation environment. , values b used expression. also possible use second argument substitute, env, environment (list) containing objects. expression submitted substitute corresponding objects env, terms within expression substituted provided values: happened? environment values b taken directly declared within substitute expression (argument expr) values substituted (argument env). substitute returned non-evaluated expression, use eval() evaluate . slightly elaborate expression:  Note : x argument name plot preserved, x object replaced.","code":"non_evaluated_expression <- substitute(expr = a + b) non_evaluated_expression ## a + b eval(non_evaluated_expression) ## Error in eval(non_evaluated_expression): object 'b' not found non_evaluated_expression <- substitute(expr = a + b) a <- 1 b <- 5 eval(non_evaluated_expression) ## [1] 6 fun <- function(a, b) {   substitute(expr = a + b) } non_evaluated_expression <- fun(5, -2) non_evaluated_expression ## 5 + -2 eval(non_evaluated_expression) ## [1] 3 non_evaluated_expression <- substitute(   expr = a + b,   env = list(a = 5, b = 5) ) non_evaluated_expression ## 5 + 5 eval(non_evaluated_expression) ## [1] 10 non_evaluated_expression <- substitute(   expr = plot(x = x, y = exp(x), main = text),   env = list(x = 0:10, text = \"A graph\") ) non_evaluated_expression ## plot(x = 0:10, y = exp(0:10), main = \"A graph\") eval(non_evaluated_expression)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"replace-an-object-name","dir":"Articles","previous_headings":"The Basics","what":"Replace an object name","title":"Quick start: `substitute` for NSE","text":"formulas, character strings accepted, execute substitution? object names specific class (name); .names coerces character string object name (alternatively, .symbol provides identical result):","code":"# Error expected: plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = Sepal.Length,     y = Sepal.Width,     text = \"Iris, again ...\"   ) ) ## Error in eval(expr, envir, enclos): object 'Sepal.Length' not found # Error expected: plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = \"Sepal.Length\",     y = \"Sepal.Width\",     text = \"Iris, again ...\"   ) ) plot_expr ## plot(\"Sepal.Width\" ~ \"Sepal.Length\", data = iris, main = \"Iris, again ...\") eval(plot_expr) ## Error in terms.formula(formula, data = data): invalid term in model formula plot_expr <- substitute(   expr = plot(y ~ x, data = iris, main = text),   env = list(     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) plot_expr ## plot(Sepal.Width ~ Sepal.Length, data = iris, main = \"Iris, again ...\") eval(plot_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"what-about-dataframe-names","dir":"Articles","previous_headings":"The Basics","what":"What about dataframe names?","title":"Quick start: `substitute` for NSE","text":"Lets imagine pipe-flavored expression, df term corresponding dataframe substituted: df %>% plot(y ~ x, data = ., main = text). principle exposed can work directly without addition. However, df expression replaced directly value object provided expression generating dataframe: pipeline working humanly readable.  can replace value expression generating value? pretty much topic vignette: substitute.","code":"library(dplyr) ##  ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ##  ##     filter, lag ## The following objects are masked from 'package:base': ##  ##     intersect, setdiff, setequal, union  short_iris <- head(iris) plot_expr <- substitute(   expr = df %>% plot(y ~ x, data = ., main = text),   env = list(     df = short_iris,     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) eval(plot_expr) plot_expr ## list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4), Sepal.Width = c(3.5,  ## 3, 3.2, 3.1, 3.6, 3.9), Petal.Length = c(1.4, 1.4, 1.3, 1.5,  ## 1.4, 1.7), Petal.Width = c(0.2, 0.2, 0.2, 0.2, 0.2, 0.4), Species = c(1L,  ## 1L, 1L, 1L, 1L, 1L)) %>% plot(Sepal.Width ~ Sepal.Length, data = .,  ##     main = \"Iris, again ...\") plot_expr <- substitute(   expr = df %>% plot(y ~ x, data = ., main = text),   env = list(     df = substitute(iris),     x = as.name(\"Sepal.Length\"),     y = as.symbol(\"Sepal.Width\"),     text = \"Iris, again ...\"   ) ) plot_expr ## iris %>% plot(Sepal.Width ~ Sepal.Length, data = ., main = \"Iris, again ...\") eval(plot_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"in-a-nutshell","dir":"Articles","previous_headings":"The Basics","what":"In a nutshell","title":"Quick start: `substitute` for NSE","text":"expr expression (eventually) substituted. env environment potential replacement value might needed. object name (like formulas e.g. y ~ x) , use .name .symbol. data frame name (like iris) , use substitute.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"direct-use-of-substitute","dir":"Articles","previous_headings":"rtables","what":"Direct use of substitute","title":"Quick start: `substitute` for NSE","text":"substitute approach can used rtables pipelines. Lets prepare example reporting data LB domain. example based template LBT01; target report columns lab test result per study arm, values (AVAL) changes baseline (CHG), per analysis visit rows. data can prepared follows: rtables expression obtained : expression valid … : … easily readable …: … can arranged:","code":"library(teal.modules.clinical) library(dplyr)  adlb <- tmc_ex_adlb adlb_f <- adlb %>%   filter(     PARAM == \"Alanine Aminotransferase Measurement\" &       ARMCD %in% c(\"ARM A\", \"ARM B\") & AVISIT == \"WEEK 1 DAY 8\"   ) rtables_expr <- substitute(   expr = basic_table() %>%     split_cols_by(arm, split_fun = drop_split_levels) %>%     split_rows_by(visit, split_fun = drop_split_levels) %>%     split_cols_by_multivar(       vars = c(\"AVAL\", \"CHG\"),       varlabels = c(\"Value\", \"Change\")     ) %>%     summarize_colvars() %>%     build_table(df = df),   env = list(     df = substitute(adlb_f),     arm = \"ARM\",     visit = \"AVISIT\"   ) ) eval(rtables_expr) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 rtables_expr ## basic_table() %>% split_cols_by(\"ARM\", split_fun = drop_split_levels) %>%  ##     split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>%  ##     split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c(\"Value\",  ##         \"Change\")) %>% summarize_colvars() %>% build_table(df = adlb_f) library(teal) library(styler)  #' Stylish code #' #' Deparse an expression and display the code following NEST conventions. #' #' @param expr (`call`)\\cr or possibly understood as so. #' styled_expr <- function(expr) {   print(     styler::style_text(text = deparse(expr)),     colored = FALSE   ) } #' #' @examples styled_expr(rtables_expr) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"substitute-in-a-function","dir":"Articles","previous_headings":"rtables","what":"substitute in a function","title":"Quick start: `substitute` for NSE","text":"Moving , substitute can actually wrapped function, way rtables pipelines programmatically obtained: results obtained … , fine tuning easier. instance, variable designating study arm visit can changed, expected feature teal module encoding panel.","code":"rtables_expr <- function(df,                          arm,                          visit) {   substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ) %>%       summarize_colvars() %>%       build_table(df = df),     env = list(       df = substitute(df),       arm = arm,       visit = visit     )   ) } result <- rtables_expr(df = adlb_f, arm = \"ARM\", visit = \"AVISIT\") styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f) eval(result) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 result <- rtables_expr(df = adlb_f, arm = \"ARMCD\", visit = \"AVISITN\") eval(result) ## Split var [AVISITN] was not character or factor. Converting to factor ##                         ARM A                        ARM B            ##                  Value         Change         Value         Change    ## ————————————————————————————————————————————————————————————————————— ## 1                                                                     ##   n               69             69            73             73      ##   Mean (SD)   20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median         20.4           2.4           20.0           -0.2     ##   Min - Max   12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARMCD\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISITN\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"chain-expressions-in-a-pipeline","dir":"Articles","previous_headings":"rtables","what":"Chain expressions in a pipeline","title":"Quick start: `substitute` for NSE","text":"also possible manipulate expressions, instance, expressions might chained pipeline. Expressions can arranged list, way, possible conditional editing expressions. context rtables, layers enclosing analyze call handle .stats option. lean expression include .stats option, default value changed. expected feature teal module rendering code Show R Code: First application standard statistics: statistics specifications:","code":"#' Expressions as a pipeline #' #' Accepts expressions to be chained using the `magrittr` pipeline-flavor. #' @param ... (`call`)\\cr or object which can be interpreted as so. #'    (e.g. `name`) #' pipe_expr <- function(...) {   exprs <- unlist(list(...))   exprs <- lapply(     exprs,     function(x) {       x <- deparse(x)       paste(x, collapse = \" \")     }   )   exprs <- unlist(exprs)   exprs <- paste(exprs, collapse = \" %>% \")   str2lang(exprs) }  #' @examples result <- pipe_expr(   expr1 = substitute(df),   expr2 = substitute(head) ) result ## df %>% head rtables_expr <- function(df,                          arm,                          visit,                          .stats = NULL) {   # The rtables layout is decomposed into a list of expressions.   lyt <- list()   # 1. First the columns and rows:   lyt$structure <- substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ),     env = list(       arm = arm,       visit = visit     )   )   # 2. The analyze layer which depends on the use of .stats.   lyt$analyze <- if (is.null(.stats)) {     substitute(       summarize_colvars()     )   } else {     substitute(       summarize_colvars(.stats = .stats),       list(.stats = .stats)     )   }   # 3. And finishing with rtables::build_table.   lyt$build <- substitute(     build_table(df = df),     list(df = substitute(df))   )   # As previously demonstrated, expressions can be manipulated and   # chained in a pipeline.   pipe_expr(lyt) } result <- rtables_expr(df = adlb_f, arm = \"ARM\", visit = \"AVISIT\") styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars() %>% ##   build_table(df = adlb_f) eval(result) ##                        A: Drug X                    B: Placebo         ##                   Value         Change         Value         Change    ## —————————————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                           ##   n                69             69            73             73      ##   Mean (SD)    20.8 (4.1)     1.6 (6.1)     20.2 (4.1)     -0.2 (5.6)  ##   Median          20.4           2.4           20.0           -0.2     ##   Min - Max    12.8 - 34.6   -11.3 - 14.2   12.6 - 29.0   -12.8 - 10.8 result <- rtables_expr(   df = adlb_f, arm = \"ARM\", visit = \"AVISIT\",   .stats = c(\"n\", \"mean_sd\") ) styled_expr(result) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars(.stats = c(\"n\", \"mean_sd\")) %>% ##   build_table(df = adlb_f) eval(result) ##                      A: Drug X                B: Placebo        ##                  Value       Change       Value        Change   ## ——————————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                    ##   n                69          69           73           73     ##   Mean (SD)    20.8 (4.1)   1.6 (6.1)   20.2 (4.1)   -0.2 (5.6)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"including-pre-processing","dir":"Articles","previous_headings":"rtables","what":"Including pre-processing","title":"Quick start: `substitute` for NSE","text":"Finally, also possible wrap several expressions single function. instance, teal module generally includes pre-processing section: now possible modify studied parameter (PARAMCD) addition study arm visit variables names. two expressions consistent: two expressions can executed return rtables:","code":"rtables_expr <- function(df,                          paramcd,                          arm,                          visit,                          .stats = NULL) {   # y is a list which will collect two expressions:   # 1. y$data with the preprocessing steps.   # 2. y$rtables the table layout and build.   y <- list()   # 1. Preprocessing ---   y$data <- substitute(     df <- df %>%       filter(         PARAMCD == paramcd &           ARMCD %in% c(\"ARM A\", \"ARM B\") & AVISIT == \"WEEK 1 DAY 8\"       ),     list(       df = substitute(df),       paramcd = paramcd     )   )   # 2. rtables layout ---   lyt <- list()   lyt$structure <- substitute(     expr = basic_table() %>%       split_cols_by(arm, split_fun = drop_split_levels) %>%       split_rows_by(visit, split_fun = drop_split_levels) %>%       split_cols_by_multivar(         vars = c(\"AVAL\", \"CHG\"),         varlabels = c(\"Value\", \"Change\")       ),     env = list(       arm = arm,       visit = visit     )   )   lyt$analyze <- if (is.null(.stats)) {     substitute(       summarize_colvars()     )   } else {     substitute(       summarize_colvars(.stats = .stats),       list(.stats = .stats)     )   }   lyt$build <- substitute(     build_table(df = df),     list(df = substitute(df))   )   y$rtables <- pipe_expr(lyt)   # Finally returns y as a list with two expressions.   y } adlb <- tmc_ex_adlb result <- rtables_expr(   df = adlb, paramcd = \"CRP\", arm = \"ARM\", visit = \"AVISIT\",   .stats = c(\"n\", \"mean_sd\") ) styled_expr(result$data) ## adlb <- adlb %>% filter(PARAMCD == \"CRP\" & ARMCD %in% c( ##   \"ARM A\", ##   \"ARM B\" ## ) & AVISIT == \"WEEK 1 DAY 8\") styled_expr(result$rtables) ## basic_table() %>% ##   split_cols_by(\"ARM\", split_fun = drop_split_levels) %>% ##   split_rows_by(\"AVISIT\", split_fun = drop_split_levels) %>% ##   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\"), varlabels = c( ##     \"Value\", ##     \"Change\" ##   )) %>% ##   summarize_colvars(.stats = c(\"n\", \"mean_sd\")) %>% ##   build_table(df = adlb) result_exec <- mapply(eval, result) result_exec$rtables ##                      A: Drug X              B: Placebo       ##                  Value      Change       Value      Change   ## ———————————————————————————————————————————————————————————— ## WEEK 1 DAY 8                                                 ##   n               69          69          73          73     ##   Mean (SD)    1.0 (0.2)   0.0 (0.3)   1.0 (0.2)   0.0 (0.3)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/quickstart_substitute.html","id":"in-a-nutshell-1","dir":"Articles","previous_headings":"rtables","what":"In a nutshell","title":"Quick start: `substitute` for NSE","text":"point, possible : generate rtables pipelines. chain expressions pipeline (e.g. pipe_expr) decompose rtables pipeline add conditional layers (e.g. .stats). group expressions single list control pre-processing rtables pipeline.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/teal-modules-clinical.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started with {teal.modules.clinical}","text":"teal.modules.clinical package implementing number teal modules helpful exploring clinical trials data, specifically targeted towards data following ADaM standards. teal.modules.clinical modules can used data ADaM standard clinical data, features package tailored towards data type. concepts presented require knowledge core features teal, specifically launch teal application pass data . Therefore, highly recommended refer home page introductory vignette teal package.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/teal-modules-clinical.html","id":"main-features","dir":"Articles","previous_headings":"","what":"Main Features","title":"Getting Started with {teal.modules.clinical}","text":"package provides ready--use teal modules can embed teal application. modules generate highly customizable tables, plots, outputs often used exploratory data analysis, including: ANCOVA - tm_t_ancova() Cox regression - tm_t_coxreg() Kaplan-Meier plot - tm_g_km() Logistic regression - tm_t_logistic() Bar chart - tm_g_barchart_simple() Confidence interval plot - tm_g_ci() Binary outcome response table - tm_t_binary_outcome() Summary adverse events table - tm_t_events_summary() SMQ table - tm_t_smq() Time--event table - tm_t_tte() library also offers group patient profile modules targeted clinical statisticians physicians want review data per patient basis. modules present data patient’s adverse events, severity, current therapy, laboratory results . See full index package functions & modules .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/articles/teal-modules-clinical.html","id":"a-simple-application","dir":"Articles","previous_headings":"","what":"A Simple Application","title":"Getting Started with {teal.modules.clinical}","text":"teal.modules.clinical module needs embedded inside shiny/teal application interact . simple application including bar chart module look like : Consider consulting documentation examples module (e.g. ?tm_g_barchart_simple). many, can also find useful links TLG Catalog additional example apps can found. teal.modules.clinical exports modules needs support libraries run teal app flesh functionality. example , tm_g_barchart_simple() function teal.modules.clinical whereas init() teal function, data_extract_spec(), select_spec(), variable_choices() teal.transform functions, cdisc_data() teal.data function. Let’s break app pieces: lines load libraries used example. use example data provided teal.modules.clinical package: nestcolor optional package can loaded apply standardized NEST color palette module plots. need load teal teal.modules.clinical already depends . next step, use teal create shiny UI server functions can launch using shiny. data argument tells teal input data - ADaM datasets ADSL ADAE - modules argument indicates modules included application. , include one module: tm_g_barchart_simple(). Finally, use shiny launch application: teal.modules.clinical modules allow specification arguments using teal.transform::choices_selected(), tm_t_summary() module following example. Please refer API reference specific modules examples information customization options available.","code":"library(teal.modules.clinical) library(nestcolor)  ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = list(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADAE\",         select = select_spec(           choices = variable_choices(             ADAE,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       )     )   ) )  if (interactive()) shinyApp(app$ui, app$server) library(teal.modules.clinical) library(nestcolor) ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = list(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADAE\",         select = select_spec(           choices = variable_choices(             ADAE,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       )     )   ) ) if (interactive()) shinyApp(app$ui, app$server) ADSL <- tmc_ex_adsl  app <- init(   data = cdisc_data(ADSL = ADSL, code = \"ADSL <- tmc_ex_adsl\"),   modules = list(     tm_t_summary(       label = \"Demographic Table\",       dataname = \"ADSL\",       arm_var = choices_selected(choices = c(\"ARM\", \"ARMCD\"), selected = \"ARM\"),       summarize_vars = choices_selected(         choices = c(\"SEX\", \"RACE\", \"BMRKR2\", \"EOSDY\", \"DCSREAS\", \"AGE\"),         selected = c(\"SEX\", \"RACE\")       )     )   ) )  if (interactive()) shinyApp(app$ui, app$server)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Mahmoud Hallal. Author. Dawid Kaledkowski. Author. Rosemary Li. Author. Heng Wang. Author. Pawel Rucki. Author. Nikolas Burkoff. Author. Konrad Pagacz. Author. Vaakesan Sundrelingam. Contributor. Francois Collin. Contributor. Imanol Zubizarreta. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Hallal M, Kaledkowski D, Li R, Wang H, Rucki P, Burkoff N, Pagacz K (2024). teal.modules.clinical: 'teal' Modules Standard Clinical Outputs. R package version 0.9.1.9023, https://github.com/insightsengineering/teal.modules.clinical/, https://insightsengineering.github.io/teal.modules.clinical/main/.","code":"@Manual{,   title = {teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs},   author = {Joe Zhu and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Mahmoud Hallal and Dawid Kaledkowski and Rosemary Li and Heng Wang and Pawel Rucki and Nikolas Burkoff and Konrad Pagacz},   year = {2024},   note = {R package version 0.9.1.9023,     https://github.com/insightsengineering/teal.modules.clinical/},   url = {https://insightsengineering.github.io/teal.modules.clinical/main/}, }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/index.html","id":"tealmodulesclinical","dir":"","previous_headings":"","what":"teal Modules for Standard Clinical Outputs","title":"teal Modules for Standard Clinical Outputs","text":"package contains set standard teal modules used CDISC data order generate many standard outputs used clinical trials. modules include, limited : Forest plots (tm_g_forest_rsp()/tm_g_forest_tte()) Line plots (tm_g_lineplot()) Kaplan-Meier plots (tm_g_km()) … MMRM (tm_a_mmrm()) Logistic regression (tm_t_logistic()) Cox regression (tm_t_coxreg()) … Unique patients (tm_t_summary()) Exposure across patients (tm_t_exposure()) Change baseline parameters (tm_t_summary_by()) … Table basic information chosen patient (tm_t_pp_basic_info()) Plot patient vitals time (tm_g_pp_vitals()) General timeline individual patients (tm_g_pp_patient_timeline()) … modules package implemented using functions R package tern order produce output. Please see Teal Gallery TLG Catalog examples shiny apps created using modules package.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"teal Modules for Standard Clinical Outputs","text":"Alternatively, might want use development version.","code":"install.packages('teal.modules.clinical') # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.modules.clinical\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"teal Modules for Standard Clinical Outputs","text":"understand use package, please refer Getting Started article, provides multiple examples code implementation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"teal Modules for Standard Clinical Outputs","text":"encounter bug feature request, please file issue. questions, discussions, staying date, please use teal channel pharmaverse slack workspace.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"teal Modules for Standard Clinical Outputs","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression List — add_expr","title":"Expression List — add_expr","text":"Add new expression list (expressions).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression List — add_expr","text":"","code":"add_expr(expr_ls, new_expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression List — add_expr","text":"expr_ls (list call) list new expression added. new_expr (call) new expression add.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression List — add_expr","text":"list call.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Expression List — add_expr","text":"Offers stricter control add new expressions existing list. list expressions can later used generate pipeline, instance pipe_expr.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/add_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression List — add_expr","text":"","code":"library(rtables)  lyt <- list() lyt <- add_expr(lyt, substitute(basic_table())) lyt <- add_expr(   lyt, substitute(split_cols_by(var = arm), env = list(armcd = \"ARMCD\")) ) lyt <- add_expr(   lyt,   substitute(     test_proportion_diff(       vars = \"rsp\", method = \"cmh\", variables = list(strata = \"strata\")     )   ) ) lyt <- add_expr(lyt, quote(build_table(df = dta))) pipe_expr(lyt) #> basic_table() %>% split_cols_by(var = arm) %>% test_proportion_diff(vars = \"rsp\",  #>     method = \"cmh\", variables = list(strata = \"strata\")) %>%  #>     build_table(df = dta)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/arm_ref_comp_observer.html","id":null,"dir":"Reference","previous_headings":"","what":"Observer for Treatment reference variable — arm_ref_comp_observer","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"Updates reference comparison Treatments selected Treatment variable changes","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/arm_ref_comp_observer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"","code":"arm_ref_comp_observer(   session,   input,   output,   id_ref = \"Ref\",   id_comp = \"Comp\",   id_arm_var,   data,   arm_ref_comp,   module,   on_off = reactive(TRUE),   input_id = \"buckets\",   output_id = \"arms_buckets\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/arm_ref_comp_observer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"session (environment) shiny session input (character) shiny input output (character) shiny input id_ref (character) id reference Treatment input UI element id_comp (character) id comparison group input UI element id_arm_var (character) id Treatment variable input UI element data (reactive data.frame) dataset used validate Treatment reference inputs set id_ref input. arm_ref_comp (unknown) Treatment reference compare variables provided nested list Treatment variable corresponds list specifying default levels reference comparison treatments. module (character) name module called (used produce informative error messages) on_off (logical) reactive can used stop whole observer FALSE. input_id (character) unique id buckets referenced . output_id (character) name UI id output written .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/arm_ref_comp_observer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Observer for Treatment reference variable — arm_ref_comp_observer","text":"Returns shinyvalidate::InputValidator checks least one reference comparison arm","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse text input to numeric vector — as_num","title":"Parse text input to numeric vector — as_num","text":"Generic parse text numeric vectors. initially designed robust interpretation text input teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse text input to numeric vector — as_num","text":"","code":"as_num(str)  # Default S3 method as_num(str)  # S3 method for class 'character' as_num(str)  # S3 method for class 'numeric' as_num(str)  # S3 method for class 'factor' as_num(str)  # S3 method for class 'logical' as_num(str)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse text input to numeric vector — as_num","text":"str (vector) extract numeric .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse text input to numeric vector — as_num","text":"vector numeric directly parsed numeric boolean. list numeric parsed character string, character string associated list item.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse text input to numeric vector — as_num","text":"function intended extract numeric character string, factor levels, boolean return vector numeric.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/as_num.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse text input to numeric vector — as_num","text":"","code":"dta <- list(   character = c(\"text10,20.5letter30.!\", \"!-.40$$-50e5[\", NA),   factor    = factor(c(\"]+60e-6, 7.7%%8L\", \"%90sep.100\\\"1L\", NA_character_)),   numeric   = c(1, -5e+2, NA),   logical   = c(TRUE, FALSE, NA) ) lapply(dta, as_num) #> $character #> $character[[1]] #> [1] 10.0 20.5 30.0 #>  #> $character[[2]] #> [1] -4e-01 -5e+06 #>  #> $character[[3]] #> [1] NA #>  #>  #> $factor #> $factor[[1]] #> [1] 0.00006 7.70000 8.00000 #>  #> $factor[[2]] #> [1] 90.0  0.1  1.0 #>  #> $factor[[3]] #> [1] NA #>  #>  #> $numeric #> [1]    1 -500   NA #>  #> $logical #> [1]  1  0 NA #>"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/bracket_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expressions in Brackets — bracket_expr","title":"Expressions in Brackets — bracket_expr","text":"Groups several expressions single bracketed expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/bracket_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expressions in Brackets — bracket_expr","text":"","code":"bracket_expr(exprs)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/bracket_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expressions in Brackets — bracket_expr","text":"exprs (list call) expressions concatenate single bracketed expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/bracket_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expressions in Brackets — bracket_expr","text":"{ object. See base::Paren() details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/bracket_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expressions in Brackets — bracket_expr","text":"","code":"adsl <- tmc_ex_adsl adrs <- tmc_ex_adrs  expr1 <- substitute(   expr = anl <- subset(df, PARAMCD == param),   env = list(df = as.name(\"adrs\"), param = \"INVET\") ) expr2 <- substitute(expr = anl$rsp_lab <- d_onco_rsp_label(anl$AVALC)) expr3 <- substitute(   expr = {     anl$is_rsp <- anl$rsp_lab %in%       c(\"Complete Response (CR)\", \"Partial Response (PR)\")   } )  res <- bracket_expr(list(expr1, expr2, expr3)) eval(res) table(anl$rsp_lab, anl$is_rsp) #>                            #>                            FALSE TRUE #>   Complete Response (CR)       0   60 #>   Partial Response (PR)        0   45 #>   Stable Disease (SD)         50    0 #>   Progressive Disease (PD)    39    0 #>   Not Evaluable (NE)           6    0"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/call_concatenate.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate expressions via a binary operator — call_concatenate","title":"Concatenate expressions via a binary operator — call_concatenate","text":"e.g. combine + ggplot without introducing parentheses due associativity","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/call_concatenate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate expressions via a binary operator — call_concatenate","text":"","code":"call_concatenate(args, bin_op = \"+\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/call_concatenate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate expressions via a binary operator — call_concatenate","text":"args arguments concatenate operator bin_op binary operator concatenate ","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/call_concatenate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate expressions via a binary operator — call_concatenate","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/call_concatenate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Concatenate expressions via a binary operator — call_concatenate","text":"","code":"library(ggplot2)  # What we want to achieve call(\"+\", quote(f), quote(g)) #> f + g call(\"+\", quote(f), call(\"+\", quote(g), quote(h))) # parentheses not wanted #> f + (g + h) call(\"+\", call(\"+\", quote(f), quote(g)), quote(h)) # as expected without unnecessary parentheses #> f + g + h Reduce(function(existing, new) call(\"+\", existing, new), list(quote(f), quote(g), quote(h))) #> f + g + h  # how we do it call_concatenate(list(quote(f), quote(g), quote(h))) #> f + g + h call_concatenate(list(quote(f))) #> f call_concatenate(list()) #> NULL call_concatenate(   list(quote(ggplot(mtcars)), quote(geom_point(aes(wt, mpg)))) ) #> ggplot(mtcars) + geom_point(aes(wt, mpg))  eval(   call_concatenate(     list(quote(ggplot(mtcars)), quote(geom_point(aes(wt, mpg))))   ) )"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/check_arm_ref_comp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"","code":"check_arm_ref_comp(x, df_to_check, module)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/check_arm_ref_comp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"x (character) Name variable df_to_check (data.frame) table check module (character) teal module ref comp called ","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/check_arm_ref_comp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the Treatment variable is reference or compare — check_arm_ref_comp","text":"TRUE FALSE whether variable ref comp","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/clean_description.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up categorical variable description — clean_description","title":"Clean up categorical variable description — clean_description","text":"Cleaning categorical variable descriptions presenting.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/clean_description.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up categorical variable description — clean_description","text":"","code":"clean_description(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/clean_description.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up categorical variable description — clean_description","text":"x (character) vector categories descriptions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/clean_description.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean up categorical variable description — clean_description","text":"string","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/clean_description.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean up categorical variable description — clean_description","text":"","code":"clean_description(\"Level A (other text)\") #> [1] \"Level A\" clean_description(\"A long string that should be shortened\") #> [1] \"A long string tha...\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/color_lab_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Mapping function for Laboratory Table — color_lab_values","title":"Mapping function for Laboratory Table — color_lab_values","text":"Map value level characters values proper html tags, colors icons.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/color_lab_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mapping function for Laboratory Table — color_lab_values","text":"","code":"color_lab_values(   x,   classes = c(\"HIGH\", \"NORMAL\", \"LOW\"),   colors = list(HIGH = \"red\", NORMAL = \"grey\", LOW = \"blue\"),   default_color = \"black\",   icons = list(HIGH = \"glyphicon glyphicon-arrow-up\", LOW =     \"glyphicon glyphicon-arrow-down\") )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/color_lab_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mapping function for Laboratory Table — color_lab_values","text":"x (character) vector elements format (value level). classes (character) classes vector. colors (list) color per class. default_color (character) default color. icons (list) certain icons per level.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/color_lab_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mapping function for Laboratory Table — color_lab_values","text":"character vector element formatted HTML tag corresponding value x.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/color_lab_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mapping function for Laboratory Table — color_lab_values","text":"","code":"color_lab_values(c(\"LOW\", \"LOW\", \"HIGH\", \"NORMAL\", \"HIGH\")) #>                                                                                           LOW  #> \"<span style='color:blue!important'>LOW<i class='glyphicon glyphicon-arrow-down'><\/i><\/span>\"  #>                                                                                           LOW  #> \"<span style='color:blue!important'>LOW<i class='glyphicon glyphicon-arrow-down'><\/i><\/span>\"  #>                                                                                          HIGH  #>   \"<span style='color:red!important'>HIGH<i class='glyphicon glyphicon-arrow-up'><\/i><\/span>\"  #>                                                                                        NORMAL  #>                        \"<span style='color:grey!important'>NORMAL<i class='NULL'><\/i><\/span>\"  #>                                                                                          HIGH  #>   \"<span style='color:red!important'>HIGH<i class='glyphicon glyphicon-arrow-up'><\/i><\/span>\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/column_annotation_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Get full label, useful for annotating plots — column_annotation_label","title":"Get full label, useful for annotating plots — column_annotation_label","text":"Get full label, useful annotating plots","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/column_annotation_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get full label, useful for annotating plots — column_annotation_label","text":"","code":"column_annotation_label(dataset, column, omit_raw_name = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/column_annotation_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get full label, useful for annotating plots — column_annotation_label","text":"dataset (data.frame) dataset column (character) column get label omit_raw_name (logical) omits raw name square brackets label found","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/column_annotation_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get full label, useful for annotating plots — column_annotation_label","text":"\"Label [Column name]\" label exists, otherwise \"Column name\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/column_annotation_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get full label, useful for annotating plots — column_annotation_label","text":"","code":"data <- mtcars column_annotation_label(data, \"cyl\") #> [1] \"cyl\" attr(data[[\"cyl\"]], \"label\") <- \"Cylinder\" column_annotation_label(data, \"cyl\") #> [1] \"Cylinder [cyl]\" column_annotation_label(data, \"cyl\", omit_raw_name = TRUE) #> [1] \"Cylinder\" column_annotation_label(tmc_ex_adsl, \"ACTARM\") #> [1] \"Description of Actual Arm [ACTARM]\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/control_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Control Function for Time-To-Event teal Module — control_tte","title":"Control Function for Time-To-Event teal Module — control_tte","text":"Controls arguments Cox regression survival analysis results.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/control_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control Function for Time-To-Event teal Module — control_tte","text":"","code":"control_tte(   surv_time = list(conf_level = 0.95, conf_type = \"plain\", quantiles = c(0.25, 0.75)),   coxph = list(pval_method = \"log-rank\", ties = \"efron\", conf_level = 0.95),   surv_timepoint = control_surv_timepoint(conf_level = 0.95, conf_type = c(\"plain\",     \"none\", \"log\", \"log-log\")) )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/control_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control Function for Time-To-Event teal Module — control_tte","text":"surv_time (list) control parameters survfit model. See tern::control_surv_time() details. coxph (list) control parameters Cox-PH model. See tern::control_coxph() details. surv_timepoint (list) control parameters survfit model time point. See tern::control_surv_timepoint() details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"Convert choices_selected data_extract_spec filter_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"","code":"cs_to_des_filter(   cs,   dataname,   multiple = FALSE,   include_vars = FALSE,   label = \"Filter by\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. dataname (character) name data multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). include_vars (flag) whether include filter variables fixed selection result. can useful preserving reuse rtables code e.g. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to data_extract_spec with only filter_spec — cs_to_des_filter","text":"(teal.transform::data_extract_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_select.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"Convert choices_selected data_extract_spec select_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_select.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"","code":"cs_to_des_select(   cs,   dataname,   multiple = FALSE,   ordered = FALSE,   label = \"Select\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_select.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. dataname (character) name data multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). ordered (logical(1)) Flags whether selection order tracked. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_des_select.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to data_extract_spec with only select_spec — cs_to_des_select","text":"(teal.transform::data_extract_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_filter_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to filter_spec — cs_to_filter_spec","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"Convert choices_selected filter_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_filter_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"","code":"cs_to_filter_spec(cs, multiple = FALSE, label = \"Filter by\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_filter_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_filter_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to filter_spec — cs_to_filter_spec","text":"(teal.transform::filter_spec())","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_select_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert choices_selected to select_spec — cs_to_select_spec","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"Convert choices_selected select_spec","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_select_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"","code":"cs_to_select_spec(cs, multiple = FALSE, ordered = FALSE, label = \"Select\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_select_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"cs (choices_selected) object transformed. See teal.transform::choices_selected() details. multiple (logical) Whether multiple values shall allowed shiny shiny::selectInput(). ordered (logical(1)) Flags whether selection order tracked. label (character) Label print selection field. label, set NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/cs_to_select_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert choices_selected to select_spec — cs_to_select_spec","text":"(select_spec)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string for total column label — default_total_label","title":"Default string for total column label — default_total_label","text":"default string used label \"total\" column. value used default value total_label argument throughout teal.modules.clinical package. specified module user via total_label argument, R environment options via set_default_total_label(), \"Patients\" used.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string for total column label — default_total_label","text":"","code":"default_total_label()  set_default_total_label(total_label)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string for total column label — default_total_label","text":"total_label (string) Single string value set R environment options default label use \"total\" column. Use getOption(\"tmc_default_total_label\") check current value set R environment (defaults \"Patients\" set).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string for total column label — default_total_label","text":"default_total_label returns current value R environment option set \"tmc_default_total_label\", \"Patients\" otherwise. set_default_total_label return value.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string for total column label — default_total_label","text":"default_total_label(): Getter default total column label. set_default_total_label(): Setter default total column label. Sets option \"tmc_default_total_label\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/default_total_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string for total column label — default_total_label","text":"","code":"# Default settings default_total_label() #> [1] \"All Patients\" getOption(\"tmc_default_total_label\") #> NULL  # Set custom value set_default_total_label(\"All Patients\")  # Settings after value has been set default_total_label() #> [1] \"All Patients\" getOption(\"tmc_default_total_label\") #> [1] \"All Patients\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC Data for Examples — ex_data","title":"Simulated CDISC Data for Examples — ex_data","text":"Simulated CDISC Data Examples","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC Data for Examples — ex_data","text":"","code":"tmc_ex_adsl  tmc_ex_adae  tmc_ex_adaette  tmc_ex_adcm  tmc_ex_adeg  tmc_ex_adex  tmc_ex_adlb  tmc_ex_admh  tmc_ex_adqs  tmc_ex_adrs  tmc_ex_adtte  tmc_ex_advs"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC Data for Examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 26 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 51 columns. object class tbl_df (inherits tbl, data.frame) 1800 rows 35 columns. object class tbl_df (inherits tbl, data.frame) 512 rows 45 columns. object class tbl_df (inherits tbl, data.frame) 5200 rows 48 columns. object class tbl_df (inherits tbl, data.frame) 200 rows 37 columns. object class tbl_df (inherits tbl, data.frame) 3000 rows 58 columns. object class tbl_df (inherits tbl, data.frame) 1077 rows 33 columns. object class tbl_df (inherits tbl, data.frame) 7000 rows 36 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 34 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 34 columns. object class tbl_df (inherits tbl, data.frame) 8400 rows 34 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC Data for Examples — ex_data","text":"tmc_ex_adsl: ADSL data tmc_ex_adae: ADAE data tmc_ex_adaette: ADAETTE data tmc_ex_adcm: ADCM data tmc_ex_adeg: ADEG data tmc_ex_adex: ADEX data tmc_ex_adlb: ADLB data tmc_ex_admh: ADMH data tmc_ex_adqs: ADQS data tmc_ex_adrs: ADRS data tmc_ex_adtte: ADTTE data tmc_ex_advs: ADVS data","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/extract_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracts html id for data_extract_ui — extract_input","title":"Extracts html id for data_extract_ui — extract_input","text":"data_extract_ui located extended html id. use ns(\"original id\") reference, extended specific suffixes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/extract_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts html id for data_extract_ui — extract_input","text":"","code":"extract_input(varname, dataname, filter = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/extract_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts html id for data_extract_ui — extract_input","text":"varname (character) original html id.  retrieved ns(\"original id\") UI function session$ns(\"original id\")/\"original id\" server function. dataname (character)dataname data_extract input. might retrieved like data_extract_spec(...)[[1]]$dataname. filter (logical) optional, connected extract_data_spec objects passed filter argument","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/extract_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts html id for data_extract_ui — extract_input","text":"string","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/extract_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracts html id for data_extract_ui — extract_input","text":"","code":"extract_input(\"ARM\", \"ADSL\") #> [1] \"ARM-dataset_ADSL_singleextract-select\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/facet_grid_formula.html","id":null,"dir":"Reference","previous_headings":"","what":"Facetting formula x_facet ~ y_facet — facet_grid_formula","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"Replaces x_facet y_facet . empty character","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/facet_grid_formula.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"","code":"facet_grid_formula(x_facet, y_facet)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/facet_grid_formula.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"x_facet (character(1)) name x facet, empty, facet along x. y_facet (character(1)) name y facet, empty, facet along y.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/facet_grid_formula.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Facetting formula x_facet ~ y_facet — facet_grid_formula","text":"facet grid formula formula(x_facet ~ y_facet)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_g_forest_obj_var_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"Utility function extracting paramcd forest plots","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_g_forest_obj_var_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"","code":"get_g_forest_obj_var_name(paramcd, input, filter_idx = 1)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_g_forest_obj_var_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function for extracting paramcd for forest plots — get_g_forest_obj_var_name","text":"paramcd teal.transform::data_extract_spec() variable value designating studied parameter. input shiny app input filter_idx filter section index (default 1)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_paramcd_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the associated parameter value for paramcd — get_paramcd_label","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"Utility function extracting parameter value associated paramcd value label. parameter value paramcd label, paramcd value returned. used generating title.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_paramcd_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"","code":"get_paramcd_label(anl, paramcd)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_paramcd_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the associated parameter value for paramcd — get_paramcd_label","text":"anl Analysis dataset paramcd teal.transform::data_extract_spec() variable value designating studied parameter.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_var_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get variable labels — get_var_labels","text":"","code":"get_var_labels(datasets, dataname, vars)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_var_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get variable labels — get_var_labels","text":"datasets (teal::FilteredData) Data built teal dataname (character) name dataset vars (character) Column names data","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/get_var_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get variable labels — get_var_labels","text":"character variable labels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/h_concat_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression Deparsing — h_concat_expr","title":"Expression Deparsing — h_concat_expr","text":"Deparse expression string.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/h_concat_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression Deparsing — h_concat_expr","text":"","code":"h_concat_expr(expr)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/h_concat_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression Deparsing — h_concat_expr","text":"expr (call) object can used .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/h_concat_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression Deparsing — h_concat_expr","text":"string.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/h_concat_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression Deparsing — h_concat_expr","text":"","code":"expr <- quote({   library(rtables)   basic_table() %>%     split_cols_by(var = \"ARMCD\") %>%     test_proportion_diff(       vars = \"rsp\", method = \"cmh\", variables = list(strata = \"strata\")     ) %>%     build_table(df = dta) })  h_concat_expr(expr) #> [1] \"{\\n    library(rtables)\\n    basic_table() %>% split_cols_by(var = \\\"ARMCD\\\") %>% test_proportion_diff(vars = \\\"rsp\\\", \\n        method = \\\"cmh\\\", variables = list(strata = \\\"strata\\\")) %>% \\n        build_table(df = dta)\\n}\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/is.cs_or_des.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"Whether object class teal.transform::choices_selected()","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/is.cs_or_des.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"","code":"is.cs_or_des(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/is.cs_or_des.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"x object checked","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/is.cs_or_des.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Whether object is of class teal.transform::choices_selected() — is.cs_or_des","text":"(logical)","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/make_barchart_simple_call.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"ggplot2 call generate simple bar chart","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/make_barchart_simple_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"","code":"make_barchart_simple_call(   y_name,   x_name = NULL,   fill_name = NULL,   x_facet_name = NULL,   y_facet_name = NULL,   label_bars = TRUE,   barlayout = c(\"side_by_side\", \"stacked\"),   flip_axis = FALSE,   rotate_bar_labels = FALSE,   rotate_x_label = FALSE,   rotate_y_label = FALSE,   expand_y_range = 0,   facet_scales = \"free_x\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/make_barchart_simple_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"y_name (character NULL) name y-axis variable. x_name (character NULL) name x-axis variable. Defaults NULL dependent extract input can empty. fill_name (character NULL) name variable determine bar fill color. x_facet_name (character NULL) name variable use horizontal plot faceting. y_facet_name (character NULL) name variable use vertical plot faceting. label_bars (logical NULL) whether bars labeled. TRUE, label bar numbers also drawn text. barlayout (character NULL) type bar layout. Options \"stacked\" (default) \"side_by_side\". flip_axis (character NULL) whether flip plot axis. rotate_bar_labels (logical NULL) whether bar labels rotated 45 degrees. rotate_x_label (logical NULL) whether x-axis labels rotated 45 degrees. rotate_y_label (logical NULL) whether y-axis labels rotated 45 degrees. expand_y_range (numeric NULL) fraction y-axis range expand . facet_scales (character) value passed scales argument ggplot2::facet_grid(). Options fixed, free_x, free_y, free. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/make_barchart_simple_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot2 call to generate simple bar chart — make_barchart_simple_call","text":"call produce ggplot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists arguments teal modules used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. avisit (teal.transform::choices_selected()) value analysis visit AVISIT interest. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. dataname (character) analysis data used teal module. default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. hlt (teal.transform::choices_selected()) name variable high level term events. id_var (teal.transform::choices_selected()) object specifying variable name subject id. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results interact_var discrete. interaction needed, default option FALSE. label (character) menu item label module teal app. llt (teal.transform::choices_selected()) name variable low level term events. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. pre_output (shiny.tag) optional, text placed output put output context. example title. strata_var (teal.transform::choices_selected()) names variables stratified analysis. summarize_vars (teal.transform::choices_selected()) names variables summarized. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. time_points (teal.transform::choices_selected()) object available choices preselected option time points can used tern::surv_timepoint(). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. useNA (character) whether missing data (NA) displayed level. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/module_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Module Arguments — module_arguments","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/module_arguments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Module Arguments — module_arguments","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams module_arguments Parameters identical descriptions & input types Standard Template Arguments section excluded reduce duplication module function inherits parameters corresponding template function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/pipe_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Expressions as a Pipeline — pipe_expr","title":"Expressions as a Pipeline — pipe_expr","text":"Concatenate expressions single pipeline-flavor expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/pipe_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expressions as a Pipeline — pipe_expr","text":"","code":"pipe_expr(exprs, pipe_str = \"%>%\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/pipe_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expressions as a Pipeline — pipe_expr","text":"exprs (list call) expressions concatenate pipeline (%>%). pipe_str (character) character separates expressions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/pipe_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expressions as a Pipeline — pipe_expr","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/pipe_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expressions as a Pipeline — pipe_expr","text":"","code":"pipe_expr(   list(     expr1 = substitute(df),     expr2 = substitute(head)   ) ) #> df %>% head"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression: Arm Preparation — prepare_arm","title":"Expression: Arm Preparation — prepare_arm","text":"function generate standard expression pre-processing dataset teal module applications. especially interest preprocessing steps needs applied similarly several datasets (e.g. ADSL ADRS).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression: Arm Preparation — prepare_arm","text":"","code":"prepare_arm(   dataname,   arm_var,   ref_arm,   comp_arm,   compare_arm = !is.null(ref_arm),   ref_arm_val = paste(ref_arm, collapse = \"/\"),   drop = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression: Arm Preparation — prepare_arm","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. ref_arm_val (character) replacement name reference level. drop (logical) drop unused variable levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression: Arm Preparation — prepare_arm","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Expression: Arm Preparation — prepare_arm","text":"teal.modules.clinical, user interface includes manipulation study arms. Classically: arm variable (e.g. ARM, ACTARM), reference arm (0 ), comparison arm (1 ) possibility combine comparison arms. Note arms compared , produced expression reduced optionally dropping non-represented levels arm. comparing arms, pre-processing includes three steps: Filtering dataset retain arms interest (reference comparison). Optional, one arm designated reference combined single level. reference explicitly reassigned non-represented levels arm dropped.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression: Arm Preparation — prepare_arm","text":"","code":"prepare_arm(   dataname = \"adrs\",   arm_var = \"ARMCD\",   ref_arm = \"ARM A\",   comp_arm = c(\"ARM B\", \"ARM C\") ) #> adrs %>% dplyr::filter(ARMCD %in% c(\"ARM A\", \"ARM B\", \"ARM C\")) %>%  #>     dplyr::mutate(ARMCD = stats::relevel(ARMCD, ref = \"ARM A\")) %>%  #>     dplyr::mutate(ARMCD = droplevels(ARMCD))  prepare_arm(   dataname = \"adsl\",   arm_var = \"ARMCD\",   ref_arm = c(\"ARM B\", \"ARM C\"),   comp_arm = \"ARM A\" ) #> adsl %>% dplyr::filter(ARMCD %in% c(\"ARM B\", \"ARM C\", \"ARM A\")) %>%  #>     dplyr::mutate(ARMCD = combine_levels(ARMCD, levels = c(\"ARM B\",  #>         \"ARM C\"), new_level = \"ARM B/ARM C\")) %>% dplyr::mutate(ARMCD = stats::relevel(ARMCD,  #>     ref = \"ARM B/ARM C\")) %>% dplyr::mutate(ARMCD = droplevels(ARMCD))"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Expression: Prepare Arm Levels — prepare_arm_levels","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"function generates standard expression pre-processing dataset arm levels used apply steps safety teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"","code":"prepare_arm_levels(dataname, parentname, arm_var, drop_arm_levels = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"{ object. See base::Paren() details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/prepare_arm_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expression: Prepare Arm Levels — prepare_arm_levels","text":"","code":"prepare_arm_levels(   dataname = \"adae\",   parentname = \"adsl\",   arm_var = \"ARMCD\",   drop_arm_levels = TRUE ) #> { #>     adae <- adae %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #>     arm_levels <- levels(adae[[\"ARMCD\"]]) #>     adsl <- adsl %>% dplyr::filter(ARMCD %in% arm_levels) #>     adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #> }  prepare_arm_levels(   dataname = \"adae\",   parentname = \"adsl\",   arm_var = \"ARMCD\",   drop_arm_levels = FALSE ) #> { #>     adsl <- adsl %>% dplyr::mutate(ARMCD = droplevels(ARMCD)) #>     arm_levels <- levels(adsl[[\"ARMCD\"]]) #>     adae <- adae %>% dplyr::mutate(ARMCD = factor(ARMCD, levels = arm_levels)) #> }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":null,"dir":"Reference","previous_headings":"","what":"Split choices_selected objects with interactions into their component variables — split_choices","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"Split choices_selected objects interactions component variables","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"","code":"split_choices(x)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"x (choices_selected) object interaction terms","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"choices_selected() object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"uses regex \\\\*|: perform split.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_choices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split choices_selected objects with interactions into their component variables — split_choices","text":"","code":"split_choices(choices_selected(choices = c(\"x:y\", \"a*b\"), selected = all_choices())) #> $choices #> [1] \"x\" \"y\" \"a\" \"b\" #>  #> $selected #> [1] \"x\" \"y\" \"a\" \"b\" #>  #> $fixed #> [1] FALSE #>  #> attr(,\"class\") #> [1] \"choices_selected\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_col_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Split-Column Expression — split_col_expr","title":"Split-Column Expression — split_col_expr","text":"Renders expression column split rtables depending : expected arm comparison expected arm combination","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_col_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split-Column Expression — split_col_expr","text":"","code":"split_col_expr(compare, combine, ref, arm_var)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_col_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split-Column Expression — split_col_expr","text":"compare (logical) TRUE reference level included. combine (logical) TRUE group combination included. ref (character) reference level (used combine = TRUE). arm_var (character) arm grouping variable name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_col_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split-Column Expression — split_col_expr","text":"call","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_col_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split-Column Expression — split_col_expr","text":"","code":"split_col_expr(   compare = TRUE,   combine = FALSE,   ref = \"ARM A\",   arm_var = \"ARMCD\" ) #> rtables::split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_interactions.html","id":null,"dir":"Reference","previous_headings":"","what":"Split interaction terms into their component variables — split_interactions","title":"Split interaction terms into their component variables — split_interactions","text":"Split interaction terms component variables","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_interactions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split interaction terms into their component variables — split_interactions","text":"","code":"split_interactions(x, by = \"\\\\*|:\")"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_interactions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split interaction terms into their component variables — split_interactions","text":"x (character) string representing interaction usually form x:y x*y. (character) regex split interaction term .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_interactions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split interaction terms into their component variables — split_interactions","text":"vector strings element component variable extracted interaction term x.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/split_interactions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split interaction terms into their component variables — split_interactions","text":"","code":"split_interactions(\"x:y\") #> [1] \"x\" \"y\" split_interactions(\"x*y\") #> [1] \"x\" \"y\""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitute Names in a Quoted Expression — substitute_names","title":"Substitute Names in a Quoted Expression — substitute_names","text":"function substitutes names left- right-hand sides quoted expression. addition can also standard substitutions right-hand side.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitute Names in a Quoted Expression — substitute_names","text":"","code":"substitute_names(expr, names, others = list())  h_subst_lhs_names(qexpr, names)  substitute_lhs_names(qexpr, names)  substitute_rhs(qexpr, env)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitute Names in a Quoted Expression — substitute_names","text":"expr (language) expression. names (named list name) requested name substitutions. others (named list) requested substitutions happen right-hand side. qexpr (language) quoted expression. env (environment list) requested variable substitutions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitute Names in a Quoted Expression — substitute_names","text":"modified expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_names.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Substitute Names in a Quoted Expression — substitute_names","text":"h_subst_lhs_names(): Helper function just substitute top-level names left-hand side quoted expression. substitute_lhs_names(): recursively substitutes names left-hand sides quoted expression. substitute_rhs(): substitutes right-hand side quoted expression. Note just synonym substitute_q().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_q.html","id":null,"dir":"Reference","previous_headings":"","what":"Substitute in Quoted Expressions — substitute_q","title":"Substitute in Quoted Expressions — substitute_q","text":"version substitute needed substitute() evaluate first argument, often useful able modify quoted expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_q.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Substitute in Quoted Expressions — substitute_q","text":"","code":"substitute_q(qexpr, env)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_q.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Substitute in Quoted Expressions — substitute_q","text":"qexpr (language) quoted expression. env (environment list) requested variable substitutions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_q.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Substitute in Quoted Expressions — substitute_q","text":"modified expression.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/substitute_q.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Substitute in Quoted Expressions — substitute_q","text":"simplified package pryr avoid another dependency.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/teal.modules.clinical-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","title":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","text":"Provides teal modules standard clinical trials outputs. teal modules add encoding panel interactively change encodings within teal.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/teal.modules.clinical-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal Modules for Standard Clinical Outputs — teal.modules.clinical-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Mahmoud Hallal mahmoud.hallal@roche.com Dawid Kaledkowski dawid.kaledkowski@roche.com Rosemary Li li.yaqiong@gene.com Heng Wang wang.heng@gene.com Pawel Rucki pawel.rucki@roche.com Nikolas Burkoff Konrad Pagacz contributors: Vaakesan Sundrelingam [contributor] Francois Collin [contributor] Imanol Zubizarreta [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_a_gee.html","id":null,"dir":"Reference","previous_headings":"","what":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"Creates valid expression generate analysis table using Generalized Estimating Equations (GEE).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_a_gee.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"","code":"template_a_gee(   output_table,   data_model_fit = \"ANL\",   dataname_lsmeans = \"ANL_ADSL\",   input_arm_var = \"ARM\",   ref_group = \"A: Drug X\",   aval_var,   id_var,   arm_var,   visit_var,   split_covariates,   cor_struct,   conf_level = 0.95,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_a_gee.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"output_table (character) type output table (\"t_gee_cov\", \"t_gee_coef\", \"t_gee_lsmeans\"). data_model_fit (character) dataset used fit model tern.gee::fit_gee(). dataname_lsmeans (character) dataset used alt_counts_df argument rtables::build_table(). aval_var (character) name analysis value variable. id_var (character) variable name subject id. arm_var (character) variable names can used arm_var. visit_var (character) variable names can used visit variable. Must factor dataname. split_covariates (character) vector names variables use covariates tern.gee::vars_gee(). cor_struct (character) assumed correlation structure tern.gee::fit_gee. conf_level (numeric) value confidence level within range (0, 1). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_a_gee.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template for Generalized Estimating Equations (GEE) analysis module — template_a_gee","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Abnormality Summary Table — template_abnormality","title":"Template: Abnormality Summary Table — template_abnormality","text":"Creates valid expression generate table summarize abnormality.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Abnormality Summary Table — template_abnormality","text":"","code":"template_abnormality(   parentname,   dataname,   arm_var,   id_var = \"USUBJID\",   by_vars,   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   grade = \"ANRIND\",   baseline_var = \"BNRIND\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   add_total = FALSE,   total_label = default_total_label(),   exclude_base_abn = FALSE,   drop_arm_levels = TRUE,   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args(),   tbl_title )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Abnormality Summary Table — template_abnormality","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. by_vars (character) variable names used split summary rows. abnormal (named list) indicating abnormality direction grades. grade (character) name variable used specify abnormality grade. Variable must factor. baseline_var (character) name variable specifying baseline abnormality grade. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). exclude_base_abn (logical) whether exclude patients abnormal values baseline. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (character) NA level input dataset, defaults \"<Missing>\". basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). tbl_title (character) Title label variables bars","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Abnormality Summary Table — template_abnormality","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"Creates valid expression generate table summarize abnormality grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"","code":"template_abnormality_by_worst_grade(   parentname,   dataname,   arm_var,   id_var = \"USUBJID\",   paramcd = \"PARAMCD\",   atoxgr_var = \"ATOXGR\",   worst_high_flag_var = \"WGRHIFL\",   worst_low_flag_var = \"WGRLOFL\",   worst_flag_indicator = \"Y\",   add_total = FALSE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. paramcd (character) name parameter code variable. atoxgr_var (character) name variable indicating Analysis Toxicity Grade. worst_high_flag_var (character) name variable indicating Worst High Grade flag worst_low_flag_var (character) name variable indicating Worst Low Grade flag worst_flag_indicator (character) flag value indicating worst grade. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_abnormality_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Laboratory test results with highest grade post-baseline — template_abnormality_by_worst_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_adverse_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"Creates valid expression generate adverse events table ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_adverse_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"","code":"template_adverse_events(   dataname = \"ANL\",   aeterm = \"AETERM\",   tox_grade = \"AETOXGR\",   causality = \"AEREL\",   outcome = \"AEOUT\",   action = \"AEACN\",   time = \"ASTDY\",   decod = NULL,   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_adverse_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"dataname (character) analysis data used teal module. aeterm (character) name reported term adverse event variable. tox_grade (character) name standard toxicity grade variable. causality (character) name causality variable. outcome (character) name outcome adverse event variable. action (character) name action taken study treatment variable. time (character) name study day start adverse event variable. decod (character) name dictionary derived term variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_adverse_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Adverse Events Table and Plot — template_adverse_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: ANCOVA Summary — template_ancova","title":"Template: ANCOVA Summary — template_ancova","text":"Creates valid expression generate analysis variance summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: ANCOVA Summary — template_ancova","text":"","code":"template_ancova(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   combine_comp_arms = FALSE,   aval_var,   label_aval = NULL,   cov_var,   include_interact = FALSE,   interact_var = NULL,   interact_y = FALSE,   paramcd_levels = \"\",   paramcd_var = \"PARAMCD\",   label_paramcd = NULL,   visit_levels = \"\",   visit_var = \"AVISIT\",   conf_level = 0.95,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: ANCOVA Summary — template_ancova","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. label_aval (character) label value variable used title rendering. cov_var (character) names covariates variables. include_interact (logical) whether interaction term included model. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results. interaction needed, default option FALSE. paramcd_levels (character) variable levels studied parameter. paramcd_var (character) variable name studied parameter. label_paramcd (character) variable label used title rendering. visit_levels (character) variable levels studied visits. visit_var (character) variable names can used visit variable. Must factor dataname. conf_level (numeric) value confidence level within range (0, 1). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: ANCOVA Summary — template_ancova","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Template Arguments — template_arguments","title":"Standard Template Arguments — template_arguments","text":"documentation function lists arguments teal module templates used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Template Arguments — template_arguments","text":"add_total (logical) whether include column total number patients. anl_name (character) analysis data used teal module. arm_var (character) variable names can used arm_var. atirel (character) name time relation medication variable. aval Please use aval_var argument instead. avalu Please use avalu_var argument instead. avalu_var (character) name analysis value unit variable. aval_var (character) name analysis value variable. baseline_var (character) name variable baseline values analysis variable. base_var Please use baseline_var argument instead. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). by_vars (character) variable names used split summary rows. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmstdy (character) name study relative day start medication variable. cnsr_var (character) name censoring variable. combine_comp_arms (logical) triggers combination comparison arms. compare_arm (logical) triggers comparison study arms. comp_arm (character) level comparison arm case arm comparison. conf_level (numeric) value confidence level within range (0, 1). control (list) list settings analysis. cov_var (character) names covariates variables. dataname (character) analysis data used teal module. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\"). hlt (character) name variable high level term events. id_var (character) variable name subject id. include_interact (logical) whether interaction term included model. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. llt (character) name variable low level term events. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). na.rm (logical) whether NA values removed prior analysis. numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. paramcd (character) name parameter code variable. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_id (character) patient ID. prune_diff (number) threshold use trimming table using criteria difference rates two columns. prune_freq (number) threshold use trimming table using event incidence rate column. ref_arm (character) level reference arm case arm comparison. sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. strata_var (character) names variables stratified analysis. subgroup_var (character) variable names can used subgroups. sum_vars (character) names variables summarized. time_points (character) time points can used tern::surv_timepoint(). time_unit_var (character) name variable representing time units. title (character) title output. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). treatment_flag (character) name value indicating treatment records treatment_flag_var. treatment_flag_var (character) name treatment flag variable. useNA (character) whether missing data (NA) displayed level. var_labels (named character) optional variable labels relabeling analysis variables. visit_var (character) variable names can used visit variable. Must factor dataname. worst_flag_indicator (character) value indicating worst grade. worst_flag_var (character) name worst flag variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standard Template Arguments — template_arguments","text":"list expressions generate table plot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_arguments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard Template Arguments — template_arguments","text":"Although function just returns NULL two uses, teal module users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams template_arguments","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_basic_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Basic Info — template_basic_info","title":"Template: Patient Profile Basic Info — template_basic_info","text":"Creates valid expression generate patient profile basic info report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_basic_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Basic Info — template_basic_info","text":"","code":"template_basic_info(dataname = \"ANL\", vars, patient_id = NULL)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_basic_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Basic Info — template_basic_info","text":"dataname (character) analysis data used teal module. vars (character) names variables shown table. patient_id (character) patient ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_basic_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Basic Info — template_basic_info","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_binary_outcome.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Binary Outcome — template_binary_outcome","title":"Template: Binary Outcome — template_binary_outcome","text":"Creates valid expression generate binary outcome analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_binary_outcome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Binary Outcome — template_binary_outcome","text":"","code":"template_binary_outcome(   dataname,   parentname,   arm_var,   paramcd,   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVALC\",   show_rsp_cat = TRUE,   responder_val = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),   responder_val_levels = responder_val,   control = list(global = list(method = \"waldcc\", conf_level = 0.95), unstrat =     list(method_ci = \"waldcc\", method_test = \"schouten\", odds = TRUE), strat =     list(method_ci = \"cmh\", method_test = \"cmh\", strat = NULL)),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_binary_outcome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Binary Outcome — template_binary_outcome","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) response parameter value use table title. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. show_rsp_cat (logical) display multinomial response estimations. responder_val (character) short label observations translate AVALC responder/non-responder. responder_val_levels (character) levels responses shown multinomial response estimations. control (list) list settings analysis. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_binary_outcome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Binary Outcome — template_binary_outcome","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_m.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Multi-Variable Cox Regression — template_coxreg_m","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"Creates valid expression generate multi-variable Cox regression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_m.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"","code":"template_coxreg_m(   dataname,   cov_var,   arm_var,   cnsr_var,   aval_var,   ref_arm,   comp_arm,   paramcd,   at = list(),   strata_var = NULL,   combine_comp_arms = FALSE,   control = control_coxreg(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_m.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"dataname (character) analysis data used teal module. cov_var (character) names covariates variables. arm_var (character) variable names can used arm_var. cnsr_var (character) name censoring variable. aval_var (character) name analysis value variable. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. paramcd (character) name parameter code variable. (list numeric) candidate covariate numeric type variable, use specify value covariate effect estimated. strata_var (character) names variables stratified analysis. combine_comp_arms (logical) triggers combination comparison arms. control (list) list settings analysis (see control_coxreg()). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_m.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Multi-Variable Cox Regression — template_coxreg_m","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_u.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Univariable Cox Regression — template_coxreg_u","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"Creates valid expression generate univariable Cox regression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_u.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"","code":"template_coxreg_u(   dataname,   cov_var,   arm_var,   cnsr_var,   aval_var,   ref_arm,   comp_arm,   paramcd,   at = list(),   strata_var = NULL,   combine_comp_arms = FALSE,   control = control_coxreg(),   na_level = default_na_str(),   append = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_u.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"dataname (character) analysis data used teal module. cov_var (character) names covariates variables. arm_var (character) variable names can used arm_var. cnsr_var (character) name censoring variable. aval_var (character) name analysis value variable. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. paramcd (character) name parameter code variable. (list numeric) candidate covariate numeric type variable, use specify value covariate effect estimated. strata_var (character) names variables stratified analysis. combine_comp_arms (logical) triggers combination comparison arms. control (list) list settings analysis (see control_coxreg()). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). append (logical) whether result appended previous one. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_coxreg_u.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Univariable Cox Regression — template_coxreg_u","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Events by Term — template_events","title":"Template: Events by Term — template_events","text":"Creates valid expression generate table events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Events by Term — template_events","text":"","code":"template_events(   dataname,   parentname,   arm_var,   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   sort_criteria = c(\"freq_desc\", \"alpha\"),   sort_freq_col = total_label,   prune_freq = 0,   prune_diff = 0,   drop_arm_levels = TRUE,   incl_overall_sum = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Events by Term — template_events","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. sort_freq_col (character) column sort frequency sort_criteria set freq_desc. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. incl_overall_sum (flag)  whether two rows summarize overall number adverse events included top table. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Events by Term — template_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Events by Grade — template_events_by_grade","title":"Template: Events by Grade — template_events_by_grade","text":"Creates valid expression generate table summarize events grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Events by Grade — template_events_by_grade","text":"","code":"template_events_by_grade(   dataname,   parentname,   arm_var,   id = \"\",   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   grade,   label_grade = NULL,   prune_freq = 0,   prune_diff = 0,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Events by Grade — template_events_by_grade","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. id (character) unique identifier patients datasets, default \"USUBJID\". hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. grade (character) name severity level variable. label_grade (string) label grade variable dataname. label extracted module. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Events by Grade — template_events_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_col_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"Creates valid expression generate table summarize adverse events grouped grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_col_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"","code":"template_events_col_by_grade(   dataname,   parentname,   arm_var,   grading_groups = list(`Any Grade (%)` = c(\"1\", \"2\", \"3\", \"4\", \"5\"), `Grade 1-2 (%)` =     c(\"1\", \"2\"), `Grade 3-4 (%)` = c(\"3\", \"4\"), `Grade 5 (%)` = \"5\"),   add_total = TRUE,   total_label = default_total_label(),   id = \"USUBJID\",   hlt,   llt,   label_hlt = NULL,   label_llt = NULL,   grade = \"AETOXGR\",   label_grade = NULL,   prune_freq = 0.1,   prune_diff = 0,   na_level = default_na_str(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_col_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. grading_groups (list) named list grading groups. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). id (character) name variable uniquely identify patients datasets. hlt (character) name variable high level term events. llt (character) name variable low level term events. label_hlt (string) label hlt variable dataname. label extracted module. label_llt (string) label llt variable dataname. label extracted module. grade (character) name grade variable base grading_groups . label_grade (character) label grade variable dataname. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_col_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Grouped by Grade with Threshold — template_events_col_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_patyear.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"Creates valid expression generate table event rates adjusted patient-years.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_patyear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"","code":"template_events_patyear(   dataname,   parentname,   arm_var,   events_var,   label_paramcd,   aval_var = \"AVAL\",   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   control = control_incidence_rate(),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_patyear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. events_var (character) name variable number observed events. label_paramcd (character)paramcd variable text use table title. aval_var (character) name analysis value variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). control (list) list settings analysis. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_patyear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Event Rates Adjusted for Patient-Years — template_events_patyear","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Summary — template_events_summary","title":"Template: Adverse Events Summary — template_events_summary","text":"Creates valid expression generate adverse events summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Summary — template_events_summary","text":"","code":"template_events_summary(   anl_name,   parentname,   arm_var,   dthfl_var = \"DTHFL\",   dcsreas_var = \"DCSREAS\",   flag_var_anl = NULL,   flag_var_aesi = NULL,   aeseq_var = \"AESEQ\",   llt = \"AEDECOD\",   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   count_dth = TRUE,   count_wd = TRUE,   count_subj = TRUE,   count_pt = TRUE,   count_events = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Summary — template_events_summary","text":"anl_name (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. dthfl_var (character) name variable subject death flag parentname. Records \"Y\" summarized table row \"Total number deaths\". dcsreas_var (character) name variable study discontinuation reason parentname. Records \"ADVERSE EVENTS\" summarized table row \"Total number patients withdrawn study due AE\". flag_var_anl (character) name flag variable dataset used count adverse event sub-groups (e.g. Serious events, Related events, etc.). Variable labels used table row names exist. flag_var_aesi (character) name flag variable dataset used count adverse event special interest groups. flag variables must type logical. Variable labels used table row names exist. aeseq_var (character) name variable adverse events sequence number dataset. Used counting total number events. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). count_dth (logical) whether show count total deaths (based dthfl_var). Defaults TRUE. count_wd (logical) whether show count patients withdrawn study due adverse event (based dcsreas_var). Defaults TRUE. count_subj (logical) whether show count unique subjects (based USUBJID). applies event flag variables provided. count_pt (logical) whether show count unique preferred terms (based llt). applies event flag variables provided. count_events (logical) whether show count events (based aeseq_var). applies event flag variables provided.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_events_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Summary — template_events_summary","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Exposure Table for Risk management plan — template_exposure","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"Creates valid expression generate exposure table risk management plan.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"","code":"template_exposure(   parentname,   dataname,   id_var,   paramcd,   paramcd_label = NULL,   row_by_var,   col_by_var = NULL,   add_total = FALSE,   total_label = \"Total\",   add_total_row = TRUE,   total_row_label = \"Total number of patients and patient time*\",   drop_levels = TRUE,   na_level = default_na_str(),   aval_var,   avalu_var,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. id_var (character) variable name subject id. paramcd (character) name parameter code variable. paramcd_label (character) column dataname dataset value used label argument paramcd. row_by_var (character) variable name used split values rows. col_by_var (character) variable name used split values columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). add_total_row (flag) whether \"total\" level added others includes levels constitute split. custom label can set level via total_row_label argument. total_row_label (character) string display total row label row enabled (see add_total_row). drop_levels (flag) whether empty rows removed table. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). aval_var (character) name analysis value variable. avalu_var (character) name analysis value unit variable. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Exposure Table for Risk management plan — template_exposure","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_fit_mmrm.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"Creates valid expression generate analysis tables plots Mixed Model Repeated Measurements.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_fit_mmrm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"","code":"template_fit_mmrm(   parentname,   dataname,   aval_var,   arm_var,   ref_arm,   comp_arm = NULL,   combine_comp_arms = FALSE,   id_var,   visit_var,   cov_var,   conf_level = 0.95,   method = \"Satterthwaite\",   cor_struct = \"unstructured\",   weights_emmeans = \"proportional\",   parallel = FALSE )  template_mmrm_tables(   parentname,   dataname,   fit_name,   arm_var,   ref_arm,   visit_var,   paramcd,   show_relative = c(\"increase\", \"reduction\", \"none\"),   table_type = \"t_mmrm_cov\",   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )  template_mmrm_plots(   fit_name,   lsmeans_plot = list(select = c(\"estimates\", \"contrasts\"), width = 0.6, show_pval =     FALSE),   diagnostic_plot = list(type = \"fit-residual\", z_threshold = NULL),   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_fit_mmrm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. aval_var (character) name analysis value variable. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. combine_comp_arms (logical) triggers combination comparison arms. id_var (character) variable name subject id. visit_var (character) variable names can used visit variable. Must factor dataname. cov_var (character) names covariates variables. conf_level (numeric) value confidence level within range (0, 1). method (string) string specifying adjustment method. cor_struct (string) string specifying correlation structure, defaults \"unstructured\". See tern.mmrm::build_formula() options. weights_emmeans argument emmeans::emmeans(), \"proportional\" default. parallel (flag) flag controls whether optimizer search can use available free cores machine (default). fit_name (string) name fitted MMRM object. paramcd (character) name parameter code variable. show_relative (string) \"reduction\" (control - treatment, default) \"increase\" (treatment - control) shown relative change baseline. table_type (string) type table output. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). lsmeans_plot (named list) list controls LS means plot. See tern.mmrm::g_mmrm_lsmeans(). diagnostic_plot (named list) list controls diagnostic_plot. See tern.mmrm::g_mmrm_diagnostic(). ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_fit_mmrm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"list expressions generate table plot object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_fit_mmrm.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Template: Mixed Model Repeated Measurements (MMRM) Analysis — template_fit_mmrm","text":"template_mmrm_tables(): Creates valid expressions generate MMRM LS means, covariance matrix, fixed effects, diagnostic tables. template_mmrm_plots(): Creates valid expressions generate MMRM LS means diagnostic plots.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Response Forest Plot — template_forest_rsp","title":"Template: Response Forest Plot — template_forest_rsp","text":"Creates valid expression generate response forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Response Forest Plot — template_forest_rsp","text":"","code":"template_forest_rsp(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   obj_var_name = \"\",   aval_var = \"AVALC\",   responders = c(\"CR\", \"PR\"),   subgroup_var,   strata_var = NULL,   stats = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\"),   riskdiff = NULL,   conf_level = 0.95,   col_symbol_size = NULL,   rel_width_forest = 0.25,   font_size = 15,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Response Forest Plot — template_forest_rsp","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. obj_var_name (character) additional text append table title. aval_var (character) name analysis value variable. responders (character) values aval_var considered responders. subgroup_var (character) variable names can used subgroups. strata_var (character) names variables stratified analysis. stats (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (numeric) value confidence level within range (0, 1). col_symbol_size (integer NULL) column index used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, caption. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Response Forest Plot — template_forest_rsp","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Survival Forest Plot — template_forest_tte","title":"Template: Survival Forest Plot — template_forest_tte","text":"Creates valid expression generate survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Survival Forest Plot — template_forest_tte","text":"","code":"template_forest_tte(   dataname = \"ANL\",   parentname = \"ANL_ADSL\",   arm_var,   ref_arm = NULL,   comp_arm = NULL,   obj_var_name = \"\",   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   subgroup_var,   strata_var = NULL,   stats = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   riskdiff = NULL,   conf_level = 0.95,   col_symbol_size = NULL,   time_unit_var = \"AVALU\",   rel_width_forest = 0.25,   font_size = 15,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Survival Forest Plot — template_forest_tte","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. obj_var_name (character) additional text append table title. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. subgroup_var (character) variable names can used subgroups. strata_var (character) names variables stratified analysis. stats (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (numeric) value confidence level within range (0, 1). col_symbol_size (integer NULL) column index used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. time_unit_var (character) name variable representing time units. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Survival Forest Plot — template_forest_tte","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Confidence Interval Plot — template_g_ci","title":"Template: Confidence Interval Plot — template_g_ci","text":"Creates valid expression generate ggplot2::ggplot() confidence interval plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Confidence Interval Plot — template_g_ci","text":"","code":"template_g_ci(   dataname,   x_var,   y_var,   grp_var = NULL,   stat = c(\"mean\", \"median\"),   conf_level = 0.95,   unit_var = \"AVALU\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Confidence Interval Plot — template_g_ci","text":"dataname (character) analysis data used teal module. x_var (character) name treatment variable put x-axis. y_var (character) name response variable put y-axis. grp_var (character) name group variable used determine plot colors, point shapes, line types. stat (character) statistic plot. Options \"mean\" \"median\". conf_level (numeric) value confidence level within range (0, 1). unit_var (character) name unit variable. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Confidence Interval Plot — template_g_ci","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Individual Patient Plots — template_g_ipp","title":"Template: Individual Patient Plots — template_g_ipp","text":"Creates valid expression generate ggplot2::ggplot() plots individual patients.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Individual Patient Plots — template_g_ipp","text":"","code":"template_g_ipp(   dataname = \"ANL\",   paramcd,   arm_var,   arm_levels,   avalu_first,   paramcd_first,   aval_var = \"AVAL\",   avalu_var = \"AVALU\",   id_var = \"USUBJID\",   visit_var = \"AVISIT\",   base_var = lifecycle::deprecated(),   baseline_var = \"BASE\",   add_baseline_hline = FALSE,   separate_by_obs = FALSE,   ggplot2_args = teal.widgets::ggplot2_args(),   suppress_legend = FALSE,   add_avalu = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Individual Patient Plots — template_g_ipp","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. arm_var (character) variable names can used arm_var. arm_levels (character) vector levels arm_var. avalu_first (character)avalu_var text append plot title y-axis label add_avalu TRUE. paramcd_first (character)paramcd text append plot title y-axis label. aval_var (character) name analysis value variable. avalu_var (character) name analysis value unit variable. id_var (character) variable name subject id. visit_var (character) name variable visit timepoints. base_var Please use baseline_var argument instead. baseline_var (character) name variable baseline values analysis variable. add_baseline_hline (logical) whether horizontal line added plot baseline y-value. separate_by_obs (logical) whether create multi-panel plots. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, x, y. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\"). suppress_legend (logical) whether suppress plot legend. add_avalu (logical) whether avalu_first text appended plot title y-axis label.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Individual Patient Plots — template_g_ipp","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Kaplan-Meier Plot — template_g_km","title":"Template: Kaplan-Meier Plot — template_g_km","text":"Creates valid expression generate Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Kaplan-Meier Plot — template_g_km","text":"","code":"template_g_km(   dataname = \"ANL\",   arm_var = \"ARM\",   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   xticks = NULL,   strata_var = NULL,   time_points = NULL,   facet_var = \"SEX\",   font_size = 11,   conf_level = 0.95,   ties = \"efron\",   xlab = \"Survival time\",   time_unit_var = \"AVALU\",   yval = \"Survival\",   ylim = NULL,   pval_method = \"log-rank\",   annot_surv_med = TRUE,   annot_coxph = TRUE,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),   legend_pos = NULL,   position_coxph = lifecycle::deprecated(),   width_annots = lifecycle::deprecated(),   rel_height_plot = 0.8,   ci_ribbon = FALSE,   title = \"KM Plot\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Kaplan-Meier Plot — template_g_km","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. strata_var (character) names variables stratified analysis. time_points (character) time points can used tern::surv_timepoint(). facet_var (character) name variable use facet plot. font_size (numeric) font size value. conf_level (numeric) value confidence level within range (0, 1). ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. xlab (string) x-axis label. time_unit_var (character) name variable representing time units. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. pval_method (string) method used estimation p.values; wald (default) likelihood. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. position_coxph Please use x y elements control_annot_coxph instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\" rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. title (character) title output.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Kaplan-Meier Plot — template_g_km","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Line Plot — template_g_lineplot","title":"Template: Line Plot — template_g_lineplot","text":"Creates valid expression generate ggplot2::ggplot() line plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Line Plot — template_g_lineplot","text":"","code":"template_g_lineplot(   dataname = \"ANL\",   strata = \"ARM\",   x = \"AVISIT\",   y = \"AVAL\",   y_unit = \"AVALU\",   paramcd = \"PARAMCD\",   param = \"ALT\",   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = c(\"n\", \"mean_sd\", \"median\", \"range\"),   mid_type = \"pl\",   conf_level = 0.95,   incl_screen = TRUE,   mid_point_size = 2,   table_font_size = 4,   title = \"Line Plot\",   y_lab = \"\",   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Line Plot — template_g_lineplot","text":"dataname (character) analysis data used teal module. strata (string NA) group variable name. x (string) x-variable name. y (string) y-variable name. y_unit (string NA) y-axis unit variable name. paramcd (string NA) parameter code variable name. param (character) parameter filter data . mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). conf_level (numeric) value confidence level within range (0, 1). incl_screen (logical) whether screening visit included. mid_point_size (numeric(1)) font size mid plot points. table_font_size (numeric(1)) font size text table. title (string) plot title. y_lab (string NULL) y-axis label. NULL label added. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, caption, y, lty. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Line Plot — template_g_lineplot","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_laboratory.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Laboratory Table — template_laboratory","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"Creates valid expression generate patient profile laboratory table using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_laboratory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"","code":"template_laboratory(   dataname = \"ANL\",   paramcd = \"PARAMCD\",   param = \"PARAM\",   anrind = \"ANRIND\",   timepoints = \"ADY\",   aval = lifecycle::deprecated(),   aval_var = \"AVAL\",   avalu = lifecycle::deprecated(),   avalu_var = \"AVALU\",   patient_id = NULL,   round_value = 0L )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_laboratory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. param (character) name parameter variable. anrind (character) name analysis reference range indicator variable. timepoints (character) name time variable. aval Please use aval_var argument instead. aval_var (character) name analysis value variable. avalu Please use avalu_var argument instead. avalu_var (character) name analysis value unit variable. patient_id (character) patient ID. round_value (numeric) number decimal places round .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_laboratory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Laboratory Table — template_laboratory","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Logistic Regression — template_logistic","title":"Template: Logistic Regression — template_logistic","text":"Creates valid expression generate logistic regression table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Logistic Regression — template_logistic","text":"","code":"template_logistic(   dataname,   arm_var,   aval_var,   paramcd = lifecycle::deprecated(),   label_paramcd,   cov_var,   interaction_var,   ref_arm,   comp_arm,   topleft = \"Logistic Regression\",   conf_level = 0.95,   combine_comp_arms = FALSE,   responder_val = c(\"CR\", \"PR\"),   at = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Logistic Regression — template_logistic","text":"dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. fit logistic model arm/treatment variable, set NULL. aval_var (character) name analysis value variable. paramcd paramcd argument used function. label_paramcd (character) label response parameter value print table title. cov_var (character) names covariates variables. interaction_var (character) names variables can used interaction variable selection. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. topleft (character) text use top-left annotation table. conf_level (numeric) value confidence level within range (0, 1). combine_comp_arms (logical) triggers combination comparison arms. responder_val (character) values responder variable corresponding successful response. (numeric NULL) optional values interaction variable. Otherwise median used. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Logistic Regression — template_logistic","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_medical_history.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Medical History — template_medical_history","title":"Template: Patient Profile Medical History — template_medical_history","text":"Creates valid expression generate patient profile medical history report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_medical_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Medical History — template_medical_history","text":"","code":"template_medical_history(   dataname = \"ANL\",   mhterm = \"MHTERM\",   mhbodsys = \"MHBODSYS\",   mhdistat = \"MHDISTAT\",   patient_id = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_medical_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Medical History — template_medical_history","text":"dataname (character) analysis data used teal module. mhterm (character) name reported term medical history variable. mhbodsys (character) name body system organ class variable. mhdistat (character) name status disease variable. patient_id (character) patient ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_medical_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Medical History — template_medical_history","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_mult_events.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Multiple Events by Term — template_mult_events","title":"Template: Multiple Events by Term — template_mult_events","text":"Creates valid expression generate table multiple events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_mult_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Multiple Events by Term — template_mult_events","text":"","code":"template_mult_events(   dataname,   parentname,   arm_var,   seq_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_mult_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Multiple Events by Term — template_mult_events","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. seq_var (character) name analysis sequence number variable. Used counting unique number events. hlt (character) name variable high level term events. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_mult_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Multiple Events by Term — template_mult_events","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_patient_timeline.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Timeline Plot — template_patient_timeline","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"Creates valid expression generate patient profile timeline ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_patient_timeline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"","code":"template_patient_timeline(   dataname = \"ANL\",   aeterm = \"AETERM\",   aetime_start = \"ASTDTM\",   aetime_end = \"AENDTM\",   dstime_start = \"CMASTDTM\",   dstime_end = \"CMAENDTM\",   cmdecod = \"CMDECOD\",   aerelday_start = NULL,   aerelday_end = NULL,   dsrelday_start = NULL,   dsrelday_end = NULL,   relative_day = FALSE,   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_patient_timeline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"dataname (character) analysis data used teal module. aeterm (character) name reported term adverse event variable. aetime_start (character) name start date/time adverse event variable. aetime_end (character) name end date/time adverse event variable. dstime_start (character) name date/time first exposure treatment variable. dstime_end (character) name date/time last exposure treatment variable. cmdecod (character) name standardized medication name variable. aerelday_start (character) name adverse event study start day variable. aerelday_end (character) name adverse event study end day variable. dsrelday_start (character) name concomitant medications study start day variable. dsrelday_end (character) name concomitant medications study day start variable. relative_day (logical) whether use relative days (TRUE) absolute dates (FALSE). patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_patient_timeline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Timeline Plot — template_patient_timeline","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_prior_medication.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Prior Medication — template_prior_medication","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"Creates valid expression generate patient profile prior medication report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_prior_medication.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"","code":"template_prior_medication(   dataname = \"ANL\",   atirel = \"ATIREL\",   cmdecod = \"CMDECOD\",   cmindc = \"CMINDC\",   cmstdy = \"CMSTDY\" )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_prior_medication.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"dataname (character) analysis data used teal module. atirel (character) name time relation medication variable. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmstdy (character) name study relative day start medication variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_prior_medication.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Prior Medication — template_prior_medication","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Shift by Arm — template_shift_by_arm","title":"Template: Shift by Arm — template_shift_by_arm","text":"Creates valid expression generate summary table analysis indicator levels arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Shift by Arm — template_shift_by_arm","text":"","code":"template_shift_by_arm(   dataname,   parentname,   arm_var = \"ARM\",   paramcd = \"PARAMCD\",   visit_var = \"AVISIT\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   aval_var = \"ANRIND\",   base_var = lifecycle::deprecated(),   baseline_var = \"BNRIND\",   na.rm = FALSE,   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Shift by Arm — template_shift_by_arm","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) name parameter code variable. visit_var (character) variable names can used visit variable. Must factor dataname. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. aval_var (character) name analysis reference range indicator variable. base_var Please use baseline_var argument instead. baseline_var (character) name baseline reference range indicator variable. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Shift by Arm — template_shift_by_arm","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm_by_worst.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"Creates valid expression generate summary table worst analysis indicator variable level per subject arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm_by_worst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"","code":"template_shift_by_arm_by_worst(   dataname,   parentname,   arm_var = \"ARM\",   paramcd = \"PARAMCD\",   worst_flag_var = \"WORS02FL\",   worst_flag = \"Y\",   treatment_flag_var = \"ONTRTFL\",   treatment_flag = \"Y\",   aval_var = \"ANRIND\",   base_var = lifecycle::deprecated(),   baseline_var = \"BNRIND\",   na.rm = FALSE,   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm_by_worst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) name parameter code variable. worst_flag_var (character) name worst flag variable. worst_flag (character) value indicating worst analysis indicator level. treatment_flag_var (character) name treatment flag variable. treatment_flag (character) name value indicating treatment records treatment_flag_var. aval_var (character) name analysis reference range indicator variable. base_var Please use baseline_var argument instead. baseline_var (character) name baseline reference range indicator variable. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_arm_by_worst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Shift by Arm by Worst Analysis Indicator Level — template_shift_by_arm_by_worst","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Grade Summary Table — template_shift_by_grade","title":"Template: Grade Summary Table — template_shift_by_grade","text":"Creates valid expression generate grade summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Grade Summary Table — template_shift_by_grade","text":"","code":"template_shift_by_grade(   parentname,   dataname,   arm_var = \"ARM\",   id_var = \"USUBJID\",   visit_var = \"AVISIT\",   worst_flag_var = c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\"),   worst_flag_indicator = \"Y\",   anl_toxgrade_var = \"ATOXGR\",   base_toxgrade_var = \"BTOXGR\",   paramcd = \"PARAMCD\",   drop_arm_levels = TRUE,   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   code_missing_baseline = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Grade Summary Table — template_shift_by_grade","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. visit_var (character) variable names can used visit variable. Must factor dataname. worst_flag_var (character) name worst flag variable. worst_flag_indicator (character) value indicating worst grade. anl_toxgrade_var (character) name variable indicating analysis toxicity grade. base_toxgrade_var (character) name variable indicating baseline toxicity grade. paramcd (character) name parameter code variable. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). code_missing_baseline (logical) whether missing baseline grades counted grade 0. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_shift_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Grade Summary Table — template_shift_by_grade","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_smq.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"Creates valid expression generate adverse events table Standardized MedDRA Query.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_smq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"","code":"template_smq(   dataname,   parentname,   arm_var,   llt = \"AEDECOD\",   add_total = TRUE,   total_label = default_total_label(),   sort_criteria = c(\"freq_desc\", \"alpha\"),   drop_arm_levels = TRUE,   na_level = default_na_str(),   smq_varlabel = \"Standardized MedDRA Query\",   baskets = c(\"SMQ01NAM\", \"SMQ02NAM\", \"CQ01NAM\"),   id_var = \"USUBJID\",   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_smq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. llt (character) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). smq_varlabel (character) label use new column SMQ created tern::h_stack_by_baskets(). baskets (character) names selected standardized/customized queries variables. id_var (character) variable name subject id. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_smq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Adverse Events Table by Standardized MedDRA Query — template_smq","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Summary of Variables — template_summary","title":"Template: Summary of Variables — template_summary","text":"Creates valid expression generate table summarize variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Summary of Variables — template_summary","text":"","code":"template_summary(   dataname,   parentname,   arm_var,   sum_vars,   show_labels = lifecycle::deprecated(),   add_total = TRUE,   total_label = default_total_label(),   var_labels = character(),   arm_var_labels = NULL,   na.rm = FALSE,   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\", \"geom_mean\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Summary of Variables — template_summary","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. sum_vars (character) names variables summarized. show_labels  add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). var_labels (named character) optional variable labels relabeling analysis variables. arm_var_labels (character NULL) vector column variable labels display, length arm_var. NULL, labels displayed. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Summary of Variables — template_summary","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary_by.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Summarize Variables by Row Groups Module — template_summary_by","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"Creates valid expression generate table summarize variables row groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"","code":"template_summary_by(   parentname,   dataname,   arm_var,   id_var,   sum_vars,   by_vars,   var_labels = character(),   add_total = TRUE,   total_label = default_total_label(),   parallel_vars = FALSE,   row_groups = FALSE,   na.rm = FALSE,   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   drop_zero_levels = TRUE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"parentname (character) parent analysis data used teal module, usually refers ADSL. dataname (character) analysis data used teal module. arm_var (character) variable names can used arm_var. id_var (character) variable name subject id. sum_vars (character) names variables summarized. by_vars (character) variable names used split summary rows. var_labels (named character) optional variable labels relabeling analysis variables. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). parallel_vars (logical) whether summarized variables arranged columns. Can set TRUE chosen analysis variables numeric. row_groups (logical) whether summarized variables arranged row groups. na.rm (logical) whether NA values removed prior analysis. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. drop_zero_levels (logical) whether rows zero counts columns removed table. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_summary_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Summarize Variables by Row Groups Module — template_summary_by","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_therapy.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Therapy Table and Plot — template_therapy","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"Creates valid expression generate patient profile therapy table ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_therapy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"","code":"template_therapy(   dataname = \"ANL\",   atirel = \"ATIREL\",   cmdecod = \"CMDECOD\",   cmindc = \"CMINDC\",   cmdose = \"CMDOSE\",   cmtrt = \"CMTRT\",   cmdosu = \"CMDOSU\",   cmroute = \"CMROUTE\",   cmdosfrq = \"CMDOSFRQ\",   cmstdy = \"CMSTDY\",   cmendy = \"CMENDY\",   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_therapy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"dataname (character) analysis data used teal module. atirel (character) name time relation medication variable. cmdecod (character) name standardized medication name variable. cmindc (character) name indication variable. cmdose (character) name dose per administration variable. cmtrt (character) name reported name drug, med, therapy variable. cmdosu (character) name dose units variable. cmroute (character) name route administration variable. cmdosfrq (character) name dosing frequency per interval variable. cmstdy (character) name study relative day start medication variable. cmendy (character) name study day end medication variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_therapy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Therapy Table and Plot — template_therapy","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Time-To-Event — template_tte","title":"Template: Time-To-Event — template_tte","text":"Creates valid expression generate time--event analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Time-To-Event — template_tte","text":"","code":"template_tte(   dataname = \"ANL\",   parentname = \"ADSL\",   arm_var = \"ARM\",   paramcd,   ref_arm = NULL,   comp_arm = NULL,   compare_arm = FALSE,   combine_comp_arms = FALSE,   aval_var = \"AVAL\",   cnsr_var = \"CNSR\",   strata_var = NULL,   time_points = NULL,   time_unit_var = \"AVALU\",   event_desc_var = \"EVNTDESC\",   control = control_tte(),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Time-To-Event — template_tte","text":"dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (character) variable names can used arm_var. paramcd (character) endpoint parameter value use table title. ref_arm (character) level reference arm case arm comparison. comp_arm (character) level comparison arm case arm comparison. compare_arm (logical) triggers comparison study arms. combine_comp_arms (logical) triggers combination comparison arms. aval_var (character) name analysis value variable. cnsr_var (character) name censoring variable. strata_var (character) names variables stratified analysis. time_points (character) time points can used tern::surv_timepoint(). time_unit_var (character) name variable representing time units. event_desc_var (character) name variable events description. control (list) list settings analysis. See control_tte() details. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Time-To-Event — template_tte","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_vitals.html","id":null,"dir":"Reference","previous_headings":"","what":"Template: Patient Profile Vitals Plot — template_vitals","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"Creates valid expression generate patient profile vitals ggplot2::ggplot() plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_vitals.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"","code":"template_vitals(   dataname = \"ANL\",   paramcd = \"PARAMCD\",   paramcd_levels = c(\"SYSBP\", \"DIABP\", \"PUL\", \"RESP\", \"OXYSAT\", \"WGHT\", \"TEMP\"),   xaxis = \"ADY\",   aval = lifecycle::deprecated(),   aval_var = \"AVAL\",   patient_id,   font_size = 12L,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_vitals.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"dataname (character) analysis data used teal module. paramcd (character) name parameter code variable. paramcd_levels (character) vector levels paramcd. xaxis (character) name time variable put x-axis. aval Please use aval_var argument instead. aval_var (character) name analysis value variable. patient_id (character) patient ID. font_size (numeric) font size value. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/template_vitals.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Template: Patient Profile Vitals Plot — template_vitals","text":"list expressions generate table plot object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_gee.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"module produces analysis table using Generalized Estimating Equations (GEE).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_gee.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"","code":"tm_a_gee(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   aval_var,   id_var,   arm_var,   visit_var,   cov_var,   arm_ref_comp = NULL,   paramcd,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_gee.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_gee.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_gee.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Generalized Estimating Equations (GEE) analysis — tm_a_gee","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADQS <- tmc_ex_adqs %>%     filter(ABLFL != \"Y\" & ABLFL2 != \"Y\") %>%     mutate(       AVISIT = as.factor(AVISIT),       AVISITN = rank(AVISITN) %>%         as.factor() %>%         as.numeric() %>%         as.factor(),       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.     ) %>%     droplevels() }) datanames <- c(\"ADSL\", \"ADQS\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_a_gee(       label = \"GEE\",       dataname = \"ADQS\",       aval_var = choices_selected(\"AVALBIN\", fixed = TRUE),       id_var = choices_selected(c(\"USUBJID\", \"SUBJID\"), \"USUBJID\"),       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       visit_var = choices_selected(c(\"AVISIT\", \"AVISITN\"), \"AVISIT\"),       paramcd = choices_selected(         choices = value_choices(data[[\"ADQS\"]], \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       cov_var = choices_selected(c(\"BASE\", \"AGE\", \"SEX\", \"BASE:AVISIT\"), NULL)     )   ) ) #> Initializing tm_a_gee (prototype) #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"module produces analysis tables plots Mixed Model Repeated Measurements.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"","code":"tm_a_mmrm(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   aval_var,   id_var,   arm_var,   visit_var,   cov_var,   arm_ref_comp = NULL,   paramcd,   method = teal.transform::choices_selected(c(\"Satterthwaite\", \"Kenward-Roger\",     \"Kenward-Roger-Linear\"), \"Satterthwaite\", keep_order = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args(),   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. method (teal.transform::choices_selected()) object available choices pre-selected option adjustment method. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\"). ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings plots named list ggplot2_args objects plot-specific settings. List names match following: c(\"default\", \"lsmeans\", \"diagnostic\"). argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see help vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"ordering input data sets can lead slightly different numerical results different convergence behavior. known observation used package lme4. However, convergence achieved, results reliable numerical precision.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_a_mmrm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Mixed Model Repeated Measurements (MMRM) Analysis — tm_a_mmrm","text":"","code":"library(dplyr) arm_ref_comp <- list(   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADQS <- tmc_ex_adqs %>%     filter(ABLFL != \"Y\" & ABLFL2 != \"Y\") %>%     filter(AVISIT %in% c(\"WEEK 1 DAY 8\", \"WEEK 2 DAY 15\", \"WEEK 3 DAY 22\")) %>%     mutate(       AVISIT = as.factor(AVISIT),       AVISITN = rank(AVISITN) %>%         as.factor() %>%         as.numeric() %>%         as.factor() #' making consecutive numeric factor     ) })  datanames <- c(\"ADSL\", \"ADQS\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] app <- init(   data = data,   modules = modules(     tm_a_mmrm(       label = \"MMRM\",       dataname = \"ADQS\",       aval_var = choices_selected(c(\"AVAL\", \"CHG\"), \"AVAL\"),       id_var = choices_selected(c(\"USUBJID\", \"SUBJID\"), \"USUBJID\"),       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       visit_var = choices_selected(c(\"AVISIT\", \"AVISITN\"), \"AVISIT\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         choices = value_choices(data[[\"ADQS\"]], \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       cov_var = choices_selected(c(\"BASE\", \"AGE\", \"SEX\", \"BASE:AVISIT\"), NULL)     )   ) ) #> Initializing tm_a_mmrm #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"module produces ggplot2::ggplot() type bar chart summary table counts per category.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"","code":"tm_g_barchart_simple(   x = NULL,   fill = NULL,   x_facet = NULL,   y_facet = NULL,   label = \"Count Barchart\",   plot_options = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"x (data_extract_spec) variable x-axis. fill (data_extract_spec) grouping variable determine bar colors. x_facet (data_extract_spec) row-wise faceting groups. y_facet (data_extract_spec) column-wise faceting groups. label (character) menu item label module teal app. plot_options (list) list plot options. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"Categories can defined four levels deep defined x, fill, x_facet, y_facet parameters. parameters set NULL (default) ignored.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_barchart_simple.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Simple Bar Chart and Table of Counts per Category — tm_g_barchart_simple","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl %>%   mutate(ITTFL = factor(\"Y\") %>%     with_label(\"Intent-To-Treat Population Flag\")) ADAE <- tmc_ex_adae %>%   filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"ADSL <- tmc_ex_adsl %>%               mutate(ITTFL = factor(\\\"Y\\\") %>%               with_label(\\\"Intent-To-Treat Population Flag\\\"))             ADAE <- tmc_ex_adae %>%               filter(!((AETOXGR == 1) & (AESEV == \\\"MILD\\\") & (ARM == \\\"A: Drug X\\\")))\"   ),   modules = modules(     tm_g_barchart_simple(       label = \"ADAE Analysis\",       x = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           choices = variable_choices(             ADSL,             c(               \"ARM\", \"ACTARM\", \"SEX\",               \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"             )           ),           selected = \"ACTARM\",           multiple = FALSE         )       ),       fill = list(         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = \"SEX\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = NULL,             multiple = FALSE           )         )       ),       x_facet = list(         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = \"AETOXGR\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = NULL,             multiple = FALSE           )         )       ),       y_facet = list(         data_extract_spec(           dataname = \"ADAE\",           select = select_spec(             choices = variable_choices(ADAE, c(\"AETOXGR\", \"AESEV\", \"AESER\")),             selected = \"AESEV\",             multiple = FALSE           )         ),         data_extract_spec(           dataname = \"ADSL\",           select = select_spec(             choices = variable_choices(               ADSL,               c(                 \"ARM\", \"ACTARM\", \"SEX\",                 \"RACE\", \"ITTFL\", \"SAFFL\", \"STRATA2\"               )             ),             selected = NULL,             multiple = FALSE           )         )       )     )   ) ) #> Initializing tm_g_barchart_simple #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Confidence Interval Plot — tm_g_ci","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"module produces ggplot2::ggplot() type confidence interval plot consistent TLG Catalog template CIG01 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"","code":"tm_g_ci(   label,   x_var,   y_var,   color,   stat = c(\"mean\", \"median\"),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"label (character) menu item label module teal app. x_var (character) name treatment variable put x-axis. y_var (character) name response variable put y-axis. color (data_extract_spec) group variable used determine plot colors, shapes, line types. stat (character) statistic plot. Options \"mean\" \"median\". conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Confidence Interval Plot — tm_g_ci","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_g_ci(       label = \"Confidence Interval Plot\",       x_var = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           choices = c(\"ARMCD\", \"BMRKR2\"),           selected = c(\"ARMCD\"),           multiple = FALSE,           fixed = FALSE         )       ),       y_var = data_extract_spec(         dataname = \"ADLB\",         filter = list(           filter_spec(             vars = \"PARAMCD\",             choices = levels(ADLB$PARAMCD),             selected = levels(ADLB$PARAMCD)[1],             multiple = FALSE,             label = \"Select lab:\"           ),           filter_spec(             vars = \"AVISIT\",             choices = levels(ADLB$AVISIT),             selected = levels(ADLB$AVISIT)[1],             multiple = FALSE,             label = \"Select visit:\"           )         ),         select = select_spec(           label = \"Analyzed Value\",           choices = c(\"AVAL\", \"CHG\"),           selected = \"AVAL\",           multiple = FALSE,           fixed = FALSE         )       ),       color = data_extract_spec(         dataname = \"ADSL\",         select = select_spec(           label = \"Color by variable\",           choices = c(\"SEX\", \"STRATA1\", \"STRATA2\"),           selected = c(\"STRATA1\"),           multiple = FALSE,           fixed = FALSE         )       )     )   ),   header = \"Example of Confidence Interval Plot\",   footer = tags$p(     class = \"text-muted\", \"Source: `teal.modules.clinical::tm_g_ci`\"   ) ) #> Initializing tm_g_ci #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Forest Response Plot — tm_g_forest_rsp","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"module produces grid-style forest plot response data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"","code":"tm_g_forest_rsp(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALC\"), \"AVALC\", fixed = TRUE),   subgroup_var,   strata_var,   stats = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\"),   riskdiff = NULL,   fixed_symbol_size = TRUE,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   default_responses = c(\"CR\", \"PR\", \"Y\", \"Complete Response (CR)\",     \"Partial Response (PR)\"),   plot_height = c(500L, 200L, 2000L),   plot_width = c(1500L, 800L, 3000L),   rel_width_forest = c(25L, 0L, 100L),   font_size = c(15L, 1L, 30L),   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. strata_var (teal.transform::choices_selected()) names variables stratified analysis. stats (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, caption. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Forest Response Plot — tm_g_forest_rsp","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   mutate(AVALC = d_onco_rsp_label(AVALC) %>%     with_label(\"Character Result/Finding\")) %>%   filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         mutate(AVALC = d_onco_rsp_label(AVALC) %>%         with_label(\\\"Character Result/Finding\\\")) %>%         filter(PARAMCD != \\\"OVRINV\\\" | AVISIT == \\\"FOLLOW UP\\\")     \"   ),   modules = modules(     tm_g_forest_rsp(       label = \"Forest Response\",       dataname = \"ADRS\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         \"INVET\"       ),       subgroup_var = choices_selected(         variable_choices(ADSL, names(ADSL)),         c(\"BMRKR2\", \"SEX\")       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"STRATA1\", \"STRATA2\")),         \"STRATA2\"       ),       plot_height = c(600L, 200L, 2000L),       default_responses = list(         BESRSPI = list(           rsp = c(\"Stable Disease (SD)\", \"Not Evaluable (NE)\"),           levels = c(             \"Complete Response (CR)\", \"Partial Response (PR)\", \"Stable Disease (SD)\",             \"Progressive Disease (PD)\", \"Not Evaluable (NE)\"           )         ),         INVET = list(           rsp = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),           levels = c(             \"Complete Response (CR)\", \"Not Evaluable (NE)\", \"Partial Response (PR)\",             \"Progressive Disease (PD)\", \"Stable Disease (SD)\"           )         ),         OVRINV = list(           rsp = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\"),           levels = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\", \"Not Evaluable (NE)\")         )       )     )   ) ) #> Initializing tm_g_forest_rsp #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Forest Survival Plot — tm_g_forest_tte","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"module produces grid-style forest plot time--event data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   subgroup_var,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   stats = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   riskdiff = NULL,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   fixed_symbol_size = TRUE,   plot_height = c(500L, 200L, 2000L),   plot_width = c(1500L, 800L, 3000L),   rel_width_forest = c(25L, 0L, 100L),   font_size = c(15L, 1L, 30L),   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. subgroup_var (teal.transform::choices_selected()) object available choices preselected option variable names can used default subgroups. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. stats (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. fixed_symbol_size (logical) (TRUE), symbol size used plotting estimate. Otherwise, symbol size proportional sample size subgroup. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Forest Survival Plot — tm_g_forest_tte","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\"Race\")  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte       ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\\\"Race\\\")     \"   ),   modules = modules(     tm_g_forest_tte(       label = \"Forest Survival\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       subgroup_var = choices_selected(         variable_choices(ADSL, names(ADSL)),         c(\"BMRKR2\", \"SEX\")       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"STRATA1\", \"STRATA2\")),         \"STRATA2\"       )     )   ) ) #> Initializing tm_g_forest_tte #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Individual Patient Plots — tm_g_ipp","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"module produces ggplot2::ggplot() type individual patient plots display trends parameter values time patient, using data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"","code":"tm_g_ipp(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"USUBJID\"), \"USUBJID\", fixed = TRUE),   visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVISIT\"), \"AVISIT\", fixed = TRUE),   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   base_var = lifecycle::deprecated(),   baseline_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"BASE\"),     \"BASE\", fixed = TRUE),   add_baseline_hline = FALSE,   separate_by_obs = FALSE,   suppress_legend = FALSE,   add_avalu = TRUE,   plot_height = c(1200L, 400L, 5000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable values can used arm variable. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. id_var (teal.transform::choices_selected()) object specifying variable name subject id. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. add_baseline_hline (logical) whether horizontal line added plot baseline y-value. separate_by_obs (logical) whether create multi-panel plots. suppress_legend (logical) whether suppress plot legend. add_avalu (logical) whether avalu_first text appended plot title y-axis label. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, x, y. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Individual Patient Plots — tm_g_ipp","text":"","code":"library(nestcolor) library(dplyr)  ADSL <- tmc_ex_adsl %>%   slice(1:20) %>%   df_explicit_na() ADLB <- tmc_ex_adlb %>%   filter(USUBJID %in% ADSL$USUBJID) %>%   df_explicit_na() %>%   filter(AVISIT != \"SCREENING\")  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl %>% slice(1:20) %>% df_explicit_na()       ADLB <- tmc_ex_adlb %>% filter(USUBJID %in% ADSL$USUBJID) %>%         df_explicit_na() %>% filter(AVISIT != \\\"SCREENING\\\")     \"   ),   modules = modules(     tm_g_ipp(       label = \"Individual Patient Plot\",       dataname = \"ADLB\",       arm_var = choices_selected(         value_choices(ADLB, \"ARMCD\"),         \"ARM A\"       ),       paramcd = choices_selected(         value_choices(ADLB, \"PARAMCD\"),         \"ALT\"       ),       aval_var = choices_selected(         variable_choices(ADLB, c(\"AVAL\", \"CHG\")),         \"AVAL\"       ),       avalu_var = choices_selected(         variable_choices(ADLB, c(\"AVALU\")),         \"AVALU\",         fixed = TRUE       ),       id_var = choices_selected(         variable_choices(ADLB, c(\"USUBJID\")),         \"USUBJID\",         fixed = TRUE       ),       visit_var = choices_selected(         variable_choices(ADLB, c(\"AVISIT\")),         \"AVISIT\"       ),       baseline_var = choices_selected(         variable_choices(ADLB, c(\"BASE\")),         \"BASE\",         fixed = TRUE       ),       add_baseline_hline = FALSE,       separate_by_obs = FALSE     )   ) ) #> Initializing tm_g_ipp #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Kaplan-Meier Plot — tm_g_km","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"module produces ggplot-style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   facet_var,   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   font_size = c(11L, 1L, 30),   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),   legend_pos = c(0.9, 0.5),   rel_height_plot = c(80L, 0L, 100L),   plot_height = c(800L, 400L, 5000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. facet_var (teal.transform::choices_selected()) object available choices preselected option names variable can used plot faceting. time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). font_size (numeric) numeric vector length 3 current, minimum maximum font size values. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Kaplan-Meier Plot — tm_g_km","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte     \"   ),   modules = modules(     tm_g_km(       label = \"Kaplan-Meier Plot\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       arm_ref_comp = arm_ref_comp,       strata_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         \"SEX\"       ),       facet_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         NULL       )     )   ) ) #> Initializing tm_g_km #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Line Plot — tm_g_lineplot","title":"teal Module: Line Plot — tm_g_lineplot","text":"module produces ggplot2::ggplot() type line plot, optional summary table, standard ADaM data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Line Plot — tm_g_lineplot","text":"","code":"tm_g_lineplot(   label,   dataname,   parentname = ifelse(inherits(strata, \"data_extract_spec\"),     teal.transform::datanames_input(strata), \"ADSL\"),   strata = teal.transform::choices_selected(teal.transform::variable_choices(parentname,     c(\"ARM\", \"ARMCD\", \"ACTARMCD\")), \"ARM\"),   x = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVISIT\"), \"AVISIT\", fixed = TRUE),   y = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\")), \"AVAL\"),   y_unit = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   paramcd = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"PARAMCD\"), \"PARAMCD\", fixed = TRUE),   param = teal.transform::choices_selected(teal.transform::value_choices(dataname,     \"PARAMCD\", \"PARAM\"), \"ALT\"),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   interval = \"mean_ci\",   mid = \"mean\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = c(\"n\", \"mean_sd\", \"median\", \"range\"),   mid_type = \"pl\",   mid_point_size = c(2, 1, 5),   table_font_size = c(4, 2, 6),   plot_height = c(1000L, 200L, 4000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Line Plot — tm_g_lineplot","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. strata (string NA) group variable name. x (string) x-variable name. y (string) y-variable name. y_unit (string NA) y-axis unit variable name. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. param (character) parameter filter data . conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. table_font_size (numeric(1)) font size text table. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. module, argument accept ggplot2_args object labs list following child elements: title, subtitle, caption, y, lty. elements taken account. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Line Plot — tm_g_lineplot","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Line Plot — tm_g_lineplot","text":"","code":"library(nestcolor) library(dplyr) library(forcats)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))     \"   ),   modules = modules(     tm_g_lineplot(       label = \"Line Plot\",       dataname = \"ADLB\",       strata = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       y = choices_selected(         variable_choices(ADLB, c(\"AVAL\", \"BASE\", \"CHG\", \"PCHG\")),         \"AVAL\"       ),       param = choices_selected(         value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         \"ALT\"       )     )   ) ) #> Initializing tm_g_lineplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_adverse_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"module produces adverse events table ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_adverse_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"","code":"tm_g_pp_adverse_events(   label,   dataname = \"ADAE\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   aeterm = NULL,   tox_grade = NULL,   causality = NULL,   outcome = NULL,   action = NULL,   time = NULL,   decod = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_adverse_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. aeterm (teal.transform::choices_selected()) object available choices preselected option AETERM variable dataname. tox_grade (teal.transform::choices_selected()) object available choices preselected option AETOXGR variable dataname. causality (teal.transform::choices_selected()) object available choices preselected option AEREL variable dataname. outcome (teal.transform::choices_selected()) object available choices preselected option AEOUT variable dataname. action (teal.transform::choices_selected()) object available choices preselected option AEACN variable dataname. time (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname. decod (teal.transform::choices_selected()) object available choices preselected option AEDECOD variable dataname. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_adverse_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_adverse_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse_events","text":"","code":"library(nestcolor) library(dplyr)  ADAE <- tmc_ex_adae ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADAE <- tmc_ex_adae       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)     \"   ),   modules = modules(     tm_g_pp_adverse_events(       label = \"Adverse Events\",       dataname = \"ADAE\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       aeterm = choices_selected(         choices = variable_choices(ADAE, \"AETERM\"),         selected = \"AETERM\"       ),       tox_grade = choices_selected(         choices = variable_choices(ADAE, \"AETOXGR\"),         selected = \"AETOXGR\"       ),       causality = choices_selected(         choices = variable_choices(ADAE, \"AEREL\"),         selected = \"AEREL\"       ),       outcome = choices_selected(         choices = variable_choices(ADAE, \"AEOUT\"),         selected = \"AEOUT\"       ),       action = choices_selected(         choices = variable_choices(ADAE, \"AEACN\"),         selected = \"AEACN\"       ),       time = choices_selected(         choices = variable_choices(ADAE, \"ASTDY\"),         selected = \"ASTDY\"       ),       decod = NULL     )   ) ) #> Initializing tm_g_pp_adverse_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_patient_timeline.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"module produces patient profile timeline ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_patient_timeline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"","code":"tm_g_pp_patient_timeline(   label,   dataname_adcm = \"ADCM\",   dataname_adae = \"ADAE\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   aeterm = NULL,   cmdecod = NULL,   aetime_start = NULL,   aetime_end = NULL,   dstime_start = NULL,   dstime_end = NULL,   aerelday_start = NULL,   aerelday_end = NULL,   dsrelday_start = NULL,   dsrelday_end = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_patient_timeline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"label (character) menu item label module teal app. dataname_adcm (character) name ADCM dataset equivalent. dataname_adae (character) name ADAE dataset equivalent. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. aeterm (teal.transform::choices_selected()) object available choices preselected option AETERM variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname_adcm. aetime_start (teal.transform::choices_selected()) object available choices preselected option ASTDTM variable dataname_adae. aetime_end (teal.transform::choices_selected()) object available choices preselected option AENDTM variable dataname_adae. dstime_start (teal.transform::choices_selected()) object available choices preselected option CMASTDTM variable dataname_adcm. dstime_end (teal.transform::choices_selected()) object available choices preselected option CMAENDTM variable dataname_adcm. aerelday_start (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname_adae. aerelday_end (teal.transform::choices_selected()) object available choices preselected option AENDY variable dataname_adae. dsrelday_start (teal.transform::choices_selected()) object available choices preselected option ASTDY variable dataname_adcm. dsrelday_end (teal.transform::choices_selected()) object available choices preselected option AENDY variable dataname_adcm. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_patient_timeline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_patient_timeline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Timeline Plot — tm_g_pp_patient_timeline","text":"","code":"library(nestcolor) library(dplyr)  data <- teal_data() data <- within(data, {   ADAE <- tmc_ex_adae   ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)   ADCM <- tmc_ex_adcm %>% mutate(     CMSTDY = case_when(       CMCAT == \"medcl B\" ~ 20,       CMCAT == \"medcl C\" ~ 150,       TRUE ~ 1     ) %>% with_label(\"Study Day of Start of Medication\"),     CMENDY = case_when(       CMCAT == \"medcl B\" ~ 700,       CMCAT == \"medcl C\" ~ 1000,       TRUE ~ 500     ) %>% with_label(\"Study Day of End of Medication\"),     CMASTDTM = ASTDTM,     CMAENDTM = AENDTM   ) })  adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\") datanames(data) <- c(\"ADSL\", \"ADAE\", \"ADCM\") join_keys(data) <- default_cdisc_join_keys[c(\"ADSL\", \"ADAE\", \"ADCM\")] join_keys(data)[\"ADCM\", \"ADCM\"] <- adcm_keys join_keys(data)[\"ADAE\", \"ADCM\"] <- c(\"STUDYID\", \"USUBJID\")  app <- init(   data = data,   modules = modules(     tm_g_pp_patient_timeline(       label = \"Patient Timeline\",       dataname_adae = \"ADAE\",       dataname_adcm = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       cmdecod = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMDECOD\"),         selected = \"CMDECOD\",       ),       aeterm = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AETERM\"),         selected = c(\"AETERM\")       ),       aetime_start = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"ASTDTM\"),         selected = c(\"ASTDTM\")       ),       aetime_end = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AENDTM\"),         selected = c(\"AENDTM\")       ),       dstime_start = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMASTDTM\"),         selected = c(\"CMASTDTM\")       ),       dstime_end = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"CMAENDTM\"),         selected = c(\"CMAENDTM\")       ),       aerelday_start = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"ASTDY\"),         selected = c(\"ASTDY\")       ),       aerelday_end = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], \"AENDY\"),         selected = c(\"AENDY\")       ),       dsrelday_start = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"ASTDY\"),         selected = c(\"ASTDY\")       ),       dsrelday_end = choices_selected(         choices = variable_choices(data[[\"ADCM\"]], \"AENDY\"),         selected = c(\"AENDY\")       )     )   ) ) #> Initializing tm_g_pp_patient_timeline #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_therapy.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"module produces patient profile therapy table ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_therapy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"","code":"tm_g_pp_therapy(   label,   dataname = \"ADCM\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   atirel = NULL,   cmdecod = NULL,   cmindc = NULL,   cmdose = NULL,   cmtrt = NULL,   cmdosu = NULL,   cmroute = NULL,   cmdosfrq = NULL,   cmstdy = NULL,   cmendy = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_therapy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmdose (teal.transform::choices_selected()) object available choices preselected option CMDOSE variable dataname. cmtrt (teal.transform::choices_selected()) object available choices preselected option CMTRT variable dataname. cmdosu (teal.transform::choices_selected()) object available choices preselected option CMDOSU variable dataname. cmroute (teal.transform::choices_selected()) object available choices preselected option CMROUTE variable dataname. cmdosfrq (teal.transform::choices_selected()) object available choices preselected option CMDOSFRQ variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. cmendy (teal.transform::choices_selected()) object available choices preselected option CMENDY variable dataname. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_therapy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_therapy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Therapy Table and Plot — tm_g_pp_therapy","text":"","code":"library(nestcolor) library(dplyr)  ADCM <- tmc_ex_adcm ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID) ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADCM <- tmc_ex_adcm       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)       ADCM$CMASTDTM <- ADCM$ASTDTM       ADCM$CMAENDTM <- ADCM$AENDTM     \",     join_keys = join_keys   ),   modules = modules(     tm_g_pp_therapy(       label = \"Therapy\",       dataname = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       atirel = choices_selected(         choices = variable_choices(ADCM, \"ATIREL\"),         selected = c(\"ATIREL\")       ),       cmdecod = choices_selected(         choices = variable_choices(ADCM, \"CMDECOD\"),         selected = \"CMDECOD\"       ),       cmindc = choices_selected(         choices = variable_choices(ADCM, \"CMINDC\"),         selected = \"CMINDC\"       ),       cmdose = choices_selected(         choices = variable_choices(ADCM, \"CMDOSE\"),         selected = \"CMDOSE\"       ),       cmtrt = choices_selected(         choices = variable_choices(ADCM, \"CMTRT\"),         selected = \"CMTRT\"       ),       cmdosu = choices_selected(         choices = variable_choices(ADCM, \"CMDOSU\"),         selected = c(\"CMDOSU\")       ),       cmroute = choices_selected(         choices = variable_choices(ADCM, \"CMROUTE\"),         selected = \"CMROUTE\"       ),       cmdosfrq = choices_selected(         choices = variable_choices(ADCM, \"CMDOSFRQ\"),         selected = \"CMDOSFRQ\"       ),       cmstdy = choices_selected(         choices = variable_choices(ADCM, \"ASTDY\"),         selected = \"ASTDY\"       ),       cmendy = choices_selected(         choices = variable_choices(ADCM, \"AENDY\"),         selected = \"AENDY\"       )     )   ) ) #> Initializing tm_g_pp_therapy #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"module produces patient profile vitals ggplot2::ggplot() type plot using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"","code":"tm_g_pp_vitals(   label,   dataname = \"ADVS\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   paramcd = NULL,   aval = lifecycle::deprecated(),   aval_var = NULL,   xaxis = NULL,   font_size = c(12L, 12L, 25L),   plot_height = c(700L, 200L, 2000L),   plot_width = NULL,   pre_output = NULL,   post_output = NULL,   ggplot2_args = teal.widgets::ggplot2_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval Please use aval_var argument instead. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. xaxis (teal.transform::choices_selected()) object available choices preselected option time variable dataname put plot x-axis. font_size (numeric) numeric vector length 3 current, minimum maximum font size values. plot_height (numeric) optional vector length three c(value, min, max). Specifies height main plot renders slider plot interactively adjust plot height. plot_width (numeric) optional vector length three c(value, min, max). Specifies width main plot renders slider plot interactively adjust plot width. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. ggplot2_args (ggplot2_args) optional object created teal.widgets::ggplot2_args() settings module plot. argument merged option teal.ggplot2_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-ggplot2-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"plot supports horizontal lines following 6 PARAMCD levels present dataname: \"SYSBP\", \"DIABP\", \"TEMP\", \"RESP\", \"OXYSAT\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_g_pp_vitals.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Vitals Plot — tm_g_pp_vitals","text":"","code":"library(nestcolor)  ADSL <- tmc_ex_adsl ADVS <- tmc_ex_advs  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADVS = ADVS,     code = \"       ADSL <- tmc_ex_adsl       ADVS <- tmc_ex_advs     \"   ),   modules = modules(     tm_g_pp_vitals(       label = \"Vitals\",       dataname = \"ADVS\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       plot_height = c(600L, 200L, 2000L),       paramcd = choices_selected(         choices = variable_choices(ADVS, \"PARAMCD\"),         selected = \"PARAMCD\"       ),       xaxis = choices_selected(         choices = variable_choices(ADVS, \"ADY\"),         selected = \"ADY\"       ),       aval_var = choices_selected(         choices = variable_choices(ADVS, \"AVAL\"),         selected = \"AVAL\"       )     )   ) ) #> Initializing tm_g_pp_vitals #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Abnormality Summary Table — tm_t_abnormality","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"module produces table summarize abnormality.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"","code":"tm_t_abnormality(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   by_vars,   grade,   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   baseline_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"BNRIND\"), selected = \"BNRIND\", fixed = TRUE),   treatment_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ONTRTFL\"), selected = \"ONTRTFL\", fixed = TRUE),   treatment_flag = teal.transform::choices_selected(\"Y\"),   add_total = TRUE,   total_label = default_total_label(),   exclude_base_abn = FALSE,   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   na_level = default_na_str(),   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. grade (teal.transform::choices_selected()) object available choices preselected option variable names can used specify abnormality grade. Variable must factor. abnormal (named list) defined user indicate abnormalities displayed. id_var (teal.transform::choices_selected()) object specifying variable name subject id. baseline_var (teal.transform::choices_selected()) variable baseline abnormality grade. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). exclude_base_abn (logical) whether exclude patients abnormal values baseline. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. na_level (character) NA level input dataset, default \"<Missing>\". basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"Patients abnormality baseline treatment visit can excluded accordance GDSR specifications using exclude_base_abn.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Abnormality Summary Table — tm_t_abnormality","text":"","code":"data <- teal_data() data <- within(data, {   library(dplyr)    ADSL <- tmc_ex_adsl   ADLB <- tmc_ex_adlb %>%     mutate(       ONTRTFL = case_when(         AVISIT %in% c(\"SCREENING\", \"BASELINE\") ~ \"\",         TRUE ~ \"Y\"       ) %>% with_label(\"On Treatment Record Flag\")     ) }) datanames <- c(\"ADSL\", \"ADLB\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_abnormality(       label = \"Abnormality Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(data[[\"ADSL\"]], subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       add_total = FALSE,       by_vars = choices_selected(         choices = variable_choices(data[[\"ADLB\"]], subset = c(\"LBCAT\", \"PARAM\", \"AVISIT\")),         selected = c(\"LBCAT\", \"PARAM\"),         keep_order = TRUE       ),       baseline_var = choices_selected(         variable_choices(data[[\"ADLB\"]], subset = \"BNRIND\"),         selected = \"BNRIND\", fixed = TRUE       ),       grade = choices_selected(         choices = variable_choices(data[[\"ADLB\"]], subset = \"ANRIND\"),         selected = \"ANRIND\",         fixed = TRUE       ),       abnormal = list(low = \"LOW\", high = \"HIGH\"),       exclude_base_abn = FALSE     )   ) ) #> Initializing tm_t_abnormality #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"module produces table summarize laboratory test results highest grade post-baseline","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"","code":"tm_t_abnormality_by_worst_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   paramcd,   atoxgr_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ATOXGR\"), selected = \"ATOXGR\", fixed = TRUE),   worst_high_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"WGRHIFL\"), selected = \"WGRHIFL\", fixed = TRUE),   worst_low_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"WGRLOFL\"), selected = \"WGRLOFL\", fixed = TRUE),   worst_flag_indicator = teal.transform::choices_selected(\"Y\"),   add_total = TRUE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. id_var (teal.transform::choices_selected()) object specifying variable name subject id. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. atoxgr_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Analysis Toxicity Grade. worst_high_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Worst High Grade flag. worst_low_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used Worst Low Grade flag. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_abnormality_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Laboratory test results with highest grade post-baseline — tm_t_abnormality_by_worst_grade","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb %>%   filter(!AVISIT %in% c(\"SCREENING\", \"BASELINE\"))  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb %>%         filter(!AVISIT %in% c(\\\"SCREENING\\\", \\\"BASELINE\\\"))     \"   ),   modules = modules(     tm_t_abnormality_by_worst_grade(       label = \"Laboratory Test Results with Highest Grade Post-Baseline\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = c(\"ALT\", \"CRP\", \"IGA\")       ),       add_total = FALSE     )   ),   filter = teal_slices(     teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\"),     teal_slice(\"ADLB\", \"ONTRTFL\", selected = \"Y\")   ) ) #> Initializing tm_t_abnormality_by_worst_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: ANCOVA Summary — tm_t_ancova","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"module produces table summarize analysis variance, consistent TLG Catalog template AOVT01 available multiple endpoints selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"","code":"tm_t_ancova(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   aval_var,   cov_var,   include_interact = FALSE,   interact_var = NULL,   interact_y = FALSE,   avisit,   paramcd,   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. include_interact (logical) whether interaction term included model. interact_var (character) name variable interactions arm. interaction needed, default option NULL. interact_y (character) selected item interact_var column used select specific ANCOVA results interact_var discrete. interaction needed, default option FALSE. avisit (teal.transform::choices_selected()) value analysis visit AVISIT interest. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"single endpoint selected, unadjusted adjusted comparison provided. modules expects analysis data following variables: AVISIT: variable used filter analysis visits. PARAMCD: variable used filter endpoints, filtering paramcd avisit, one observation per patient expected analysis meaningful.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: ANCOVA Summary — tm_t_ancova","text":"","code":"ADSL <- tmc_ex_adsl ADQS <- tmc_ex_adqs  arm_ref_comp <- list(   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ),   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADQS = ADQS,     code = \"       ADSL <- tmc_ex_adsl       ADQS <- tmc_ex_adqs     \"   ),   modules = modules(     tm_t_ancova(       label = \"ANCOVA Table\",       dataname = \"ADQS\",       avisit = choices_selected(         choices = value_choices(ADQS, \"AVISIT\"),         selected = \"WEEK 1 DAY 8\"       ),       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ACTARMCD\", \"ARMCD\")),         selected = \"ARMCD\"       ),       arm_ref_comp = arm_ref_comp,       aval_var = choices_selected(         choices = variable_choices(ADQS, c(\"CHG\", \"AVAL\")),         selected = \"CHG\"       ),       cov_var = choices_selected(         choices = variable_choices(ADQS, c(\"BASE\", \"STRATA1\", \"SEX\")),         selected = \"STRATA1\"       ),       paramcd = choices_selected(         choices = value_choices(ADQS, \"PARAMCD\", \"PARAM\"),         selected = \"FKSI-FWB\"       ),       interact_var = choices_selected(         choices = variable_choices(ADQS, c(\"BASE\", \"STRATA1\", \"SEX\")),         selected = \"STRATA1\"       )     )   ) ) #> Initializing tm_t_ancova #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Binary Outcome Table — tm_t_binary_outcome","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"module produces binary outcome response summary table, option match template response table RSPT01 available TLG Catalog .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"","code":"tm_t_binary_outcome(   label,   dataname,   parentname = ifelse(test = inherits(arm_var, \"data_extract_spec\"), yes =     teal.transform::datanames_input(arm_var), no = \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(choices =     teal.transform::variable_choices(dataname, c(\"AVALC\", \"SEX\")), selected = \"AVALC\",     fixed = FALSE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   default_responses = c(\"CR\", \"PR\", \"Y\", \"Complete Response (CR)\",     \"Partial Response (PR)\", \"M\"),   rsp_table = FALSE,   control = list(global = list(method = ifelse(rsp_table, \"clopper-pearson\", \"waldcc\"),     conf_level = 0.95), unstrat = list(method_ci = ifelse(rsp_table, \"wald\", \"waldcc\"),     method_test = \"schouten\", odds = TRUE), strat = list(method_ci = \"cmh\", method_test =     \"cmh\")),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). default_responses (list character) defines default codes response variable module per value paramcd. passed vector transmitted paramcd values. passed list must named contain arrays, name corresponding single value paramcd. array may contain default response values named arrays rsp default selected response values levels default level choices. rsp_table (logical) whether initial set-module match RSPT01. Defaults FALSE. control (named list) named list containing 3 named lists follows: global: list settings overall analysis 2 named elements method conf_level. unstrat: list settings unstratified analysis 3 named elements method_ci method_test, odds. See tern::estimate_proportion_diff(), tern::test_proportion_diff(), tern::estimate_odds_ratio(), respectively, options details settings implemented analysis. strat: list settings stratified analysis elements method_ci method_test. See tern::estimate_proportion_diff() tern::test_proportion_diff(), respectively, options details settings implemented analysis. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"display order response categories inherits factor level order source data. Use base::factor() levels argument manipulate source data order include/exclude re-categorize response categories arrange display order. response categories \"Missing\", \"Evaluable (NE)\", \"Missing unevaluable\", 95% confidence interval calculated. Reference arms automatically combined multiple arms selected reference group.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_binary_outcome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Binary Outcome Table — tm_t_binary_outcome","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   mutate(     AVALC = d_onco_rsp_label(AVALC) %>%       with_label(\"Character Result/Finding\")   ) %>%   filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")  arm_ref_comp <- list(   ARMCD = list(ref = \"ARM B\", comp = c(\"ARM A\", \"ARM C\")),   ARM = list(ref = \"B: Placebo\", comp = c(\"A: Drug X\", \"C: Combination\")) ) app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         mutate(           AVALC = d_onco_rsp_label(AVALC) %>%             with_label(\\\"Character Result/Finding\\\")         ) %>%         filter(PARAMCD != \\\"OVRINV\\\" | AVISIT == \\\"FOLLOW UP\\\")     \"   ),   modules = modules(     tm_t_binary_outcome(       label = \"Responders\",       dataname = \"ADRS\",       paramcd = choices_selected(         choices = value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         selected = \"BESRSPI\"       ),       arm_var = choices_selected(         choices = variable_choices(ADRS, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         selected = \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       strata_var = choices_selected(         choices = variable_choices(ADRS, c(\"SEX\", \"BMRKR2\", \"RACE\")),         selected = \"RACE\"       ),       default_responses = list(         BESRSPI = list(           rsp = c(\"Complete Response (CR)\", \"Partial Response (PR)\"),           levels = c(             \"Complete Response (CR)\", \"Partial Response (PR)\",             \"Stable Disease (SD)\", \"Progressive Disease (PD)\"           )         ),         INVET = list(           rsp = c(\"Stable Disease (SD)\", \"Not Evaluable (NE)\"),           levels = c(             \"Complete Response (CR)\", \"Not Evaluable (NE)\", \"Partial Response (PR)\",             \"Progressive Disease (PD)\", \"Stable Disease (SD)\"           )         ),         OVRINV = list(           rsp = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\"),           levels = c(\"Progressive Disease (PD)\", \"Stable Disease (SD)\", \"Not Evaluable (NE)\")         )       )     )   ) ) #> Initializing tm_t_binary_outcome #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Cox Regression Model — tm_t_coxreg","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"module fits Cox univariable multi-variable models, consistent TLG Catalog templates Cox regression tables COXT01 COXT02, respectively. See TLG Catalog entries COXT01 COXT02 .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"","code":"tm_t_coxreg(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   cov_var,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   multivariate = TRUE,   na_level = default_na_str(),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. multivariate (logical) FALSE, univariable approach used instead multi-variable model. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"Cox Proportional Hazards (PH) model commonly used method estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis. modules expects analysis data following variables: AVAL: time event CNSR: 1 record AVAL censored, 0 otherwise PARAMCD: variable used filter endpoint (e.g. OS). filtering PARAMCD one observation per patient expected arm variables stratification/covariate variables taken ADSL data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"likelihood ratio test supported models include strata - Wald test substituted cases. Multi-variable default choice backward compatibility.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Cox Regression Model — tm_t_coxreg","text":"","code":"## First example ## ============= ## The example below is based on the usual approach involving creation of ## a random CDISC dataset and then running the application.  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADTTE <- tmc_ex_adtte }) datanames <- c(\"ADSL\", \"ADTTE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_coxreg(       label = \"Cox Reg.\",       dataname = \"ADTTE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\", \"ACTARMCD\"), \"ARM\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(data[[\"ADTTE\"]], \"PARAMCD\", \"PARAM\"), \"OS\"       ),       strata_var = choices_selected(         c(\"COUNTRY\", \"STRATA1\", \"STRATA2\"), \"STRATA1\"       ),       cov_var = choices_selected(         c(\"AGE\", \"BMRKR1\", \"BMRKR2\", \"REGION1\"), \"AGE\"       ),       multivariate = TRUE     )   ) ) #> Initializing tm_t_coxreg #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  ## Second example ## ============== ## This time, a synthetic pair of ADTTE/ADSL data is fabricated for Cox regression ## where ties and pval_method matter.  ## Dataset fabrication ## -------------------  data <- teal_data() data <- within(data, {   library(dplyr)   ADTTE <- data.frame(     STUDYID = \"LUNG\",     AVAL = c(4, 3, 1, 1, 2, 2, 3, 1, 2),     CNSR = c(1, 1, 1, 0, 1, 1, 0, 0, 0),     ARMCD = factor(       c(0, 1, 1, 1, 1, 0, 0, 0, 0),       labels = c(\"ARM A\", \"ARM B\")     ),     SEX = factor(       c(0, 0, 0, 0, 1, 1, 1, 1, 1),       labels = c(\"F\", \"M\")     ),     INST = factor(c(\"A\", \"A\", \"B\", \"B\", \"A\", \"B\", \"A\", \"B\", \"A\")),     stringsAsFactors = FALSE   )   ADTTE <- rbind(ADTTE, ADTTE, ADTTE, ADTTE)   ADTTE <- as_tibble(ADTTE)   set.seed(1)   ADTTE$INST <- sample(ADTTE$INST)   ADTTE$AGE <- sample(seq(5, 75, 5), size = nrow(ADTTE), replace = TRUE)   ADTTE$USUBJID <- paste(\"sub\", 1:nrow(ADTTE), ADTTE$INST, sep = \"-\")   ADTTE$PARAM <- ADTTE$PARAMCD <- \"OS\"   ADSL <- subset(     ADTTE,     select = c(\"USUBJID\", \"STUDYID\", \"ARMCD\", \"SEX\", \"INST\", \"AGE\")   ) })  datanames <- c(\"ADSL\", \"ADTTE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  ## `teal` application ## ---------------- ## Note that the R code exported by `Show R Code` does not include the data ## pre-processing. You will need to create the dataset as above before ## running the exported R code.  arm_ref_comp <- list(ARMCD = list(ref = \"ARM A\", comp = c(\"ARM B\"))) app <- init(   data = data,   modules = modules(     tm_t_coxreg(       label = \"Cox Reg.\",       dataname = \"ADTTE\",       arm_var = choices_selected(c(\"ARMCD\"), \"ARMCD\"),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(data[[\"ADTTE\"]], \"PARAMCD\", \"PARAM\"), \"OS\"       ),       strata_var = choices_selected(c(\"INST\"), NULL),       cov_var = choices_selected(c(\"SEX\", \"AGE\"), \"SEX\"),       multivariate = TRUE     )   ) ) #> Initializing tm_t_coxreg #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Events by Term — tm_t_events","title":"teal Module: Events by Term — tm_t_events","text":"module produces table events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Events by Term — tm_t_events","text":"","code":"tm_t_events(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   sort_criteria = c(\"freq_desc\", \"alpha\"),   sort_freq_col = total_label,   prune_freq = 0,   prune_diff = 0,   drop_arm_levels = TRUE,   incl_overall_sum = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Events by Term — tm_t_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. sort_freq_col (character) column sort frequency sort_criteria set freq_desc. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. incl_overall_sum (flag)  whether two rows summarize overall number adverse events included top table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Events by Term — tm_t_events","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Events by Term — tm_t_events","text":"","code":"ADSL <- tmc_ex_adsl ADAE <- tmc_ex_adae  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAE = ADAE,     code = \"       ADSL <- tmc_ex_adsl       ADAE <- tmc_ex_adae     \"   ),   modules = modules(     tm_t_events(       label = \"Adverse Event Table\",       dataname = \"ADAE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       llt = choices_selected(         choices = variable_choices(ADAE, c(\"AETERM\", \"AEDECOD\")),         selected = c(\"AEDECOD\")       ),       hlt = choices_selected(         choices = variable_choices(ADAE, c(\"AEBODSYS\", \"AESOC\")),         selected = \"AEBODSYS\"       ),       add_total = TRUE,       event_type = \"adverse event\"     )   ) ) #> Initializing tm_t_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Events by Grade — tm_t_events_by_grade","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"module produces table summarize events grade.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"","code":"tm_t_events_by_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   hlt,   llt,   grade,   grading_groups = list(`Any Grade (%)` = c(\"1\", \"2\", \"3\", \"4\", \"5\"), `Grade 1-2 (%)` =     c(\"1\", \"2\"), `Grade 3-4 (%)` = c(\"3\", \"4\"), `Grade 5 (%)` = \"5\"),   col_by_grade = FALSE,   prune_freq = 0,   prune_diff = 0,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. grade (character) name severity level variable. grading_groups (list) named list grading groups used col_by_grade = TRUE. col_by_grade (logical) whether display grading groups nested columns. prune_freq (number) threshold use trimming table using event incidence rate column. prune_diff (number) threshold use trimming table using criteria difference rates two columns. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Events by Grade — tm_t_events_by_grade","text":"","code":"data <- teal_data() data <- within(data, {   library(dplyr)    ADSL <- tmc_ex_adsl   lbls_adae <- col_labels(tmc_ex_adae)   ADAE <- tmc_ex_adae %>%     mutate_if(is.character, as.factor) #' be certain of having factors   col_labels(ADAE) <- lbls_adae })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_events_by_grade(       label = \"Adverse Events by Grade Table\",       dataname = \"ADAE\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       llt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AETERM\", \"AEDECOD\")),         selected = c(\"AEDECOD\")       ),       hlt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AEBODSYS\", \"AESOC\")),         selected = \"AEBODSYS\"       ),       grade = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], c(\"AETOXGR\", \"AESEV\")),         selected = \"AETOXGR\"       )     )   ) ) #> Initializing tm_t_events_by_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_patyear.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"module produces table event rates adjusted patient-years.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_patyear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"","code":"tm_t_events_patyear(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   events_var,   paramcd,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALU\"), \"AVALU\", fixed = TRUE),   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_patyear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. events_var (teal.transform::choices_selected()) object available choices preselected option variable event counts. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_patyear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_patyear.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Event Rates Adjusted for Patient-Years — tm_t_events_patyear","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADAETTE <- tmc_ex_adaette %>%   filter(PARAMCD %in% c(\"AETTE1\", \"AETTE2\", \"AETTE3\")) %>%   mutate(is_event = CNSR == 0) %>%   mutate(n_events = as.integer(is_event))  # 1. Basic Example  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAETTE = ADAETTE,     code = \"       ADSL <- tmc_ex_adsl       ADAETTE <- tmc_ex_adaette %>%         filter(PARAMCD %in% c(\\\"AETTE1\\\", \\\"AETTE2\\\", \\\"AETTE3\\\")) %>%         mutate(is_event = CNSR == 0) %>%         mutate(n_events = as.integer(is_event))     \"   ),   modules = modules(     tm_t_events_patyear(       label = \"AE Rate Adjusted for Patient-Years At Risk Table\",       dataname = \"ADAETTE\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         selected = \"ARMCD\"       ),       add_total = TRUE,       events_var = choices_selected(         choices = variable_choices(ADAETTE, \"n_events\"),         selected = \"n_events\",         fixed = TRUE       ),       paramcd = choices_selected(         choices = value_choices(ADAETTE, \"PARAMCD\", \"PARAM\"),         selected = \"AETTE1\"       )     )   ) ) #> Initializing tm_t_events_patyear #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # 2. Example with table split on 2 arm_var variables  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADAETTE = ADAETTE,     code = \"       ADSL <- tmc_ex_adsl       ADAETTE <- tmc_ex_adaette %>%         filter(PARAMCD %in% c(\\\"AETTE1\\\", \\\"AETTE2\\\", \\\"AETTE3\\\")) %>%         mutate(is_event = CNSR == 0) %>%         mutate(n_events = as.integer(is_event))     \"   ),   modules = modules(     tm_t_events_patyear(       label = \"AE Rate Adjusted for Patient-Years At Risk Table\",       dataname = \"ADAETTE\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"SEX\")),         selected = c(\"ARM\", \"SEX\")       ),       add_total = TRUE,       events_var = choices_selected(         choices = variable_choices(ADAETTE, \"n_events\"),         selected = \"n_events\",         fixed = TRUE       ),       paramcd = choices_selected(         choices = value_choices(ADAETTE, \"PARAMCD\", \"PARAM\"),         selected = \"AETTE1\"       )     )   ) ) #> Initializing tm_t_events_patyear #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Adverse Events Summary — tm_t_events_summary","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"module produces adverse events summary table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"","code":"tm_t_events_summary(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   flag_var_anl = NULL,   flag_var_aesi = NULL,   dthfl_var =     teal.transform::choices_selected(teal.transform::variable_choices(parentname,     \"DTHFL\"), \"DTHFL\", fixed = TRUE),   dcsreas_var =     teal.transform::choices_selected(teal.transform::variable_choices(parentname,     \"DCSREAS\"), \"DCSREAS\", fixed = TRUE),   llt = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AEDECOD\"), \"AEDECOD\", fixed = TRUE),   aeseq_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AESEQ\"), \"AESEQ\", fixed = TRUE),   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   count_dth = TRUE,   count_wd = TRUE,   count_subj = TRUE,   count_pt = TRUE,   count_events = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. flag_var_anl (teal.transform::choices_selected() NULL) vector names flag variables dataset used count adverse event sub-groups (e.g. Serious events, Related events, etc.). Variable labels used table row names exist. flag_var_aesi (teal.transform::choices_selected() NULL) vector names flag variables dataset used count adverse event special interest groups. flag variables must type logical. Variable labels used table row names exist. dthfl_var (teal.transform::choices_selected()) object available choices preselected option variable names can used death flag variable. Records `\"Y\"“ summarized table row \"Total number deaths\". dcsreas_var (teal.transform::choices_selected()) object available choices preselected option variable names can used study discontinuation reason variable. Records \"ADVERSE EVENTS\" summarized table row \"Total number patients withdrawn study due AE\". llt (teal.transform::choices_selected()) name variable low level term events. aeseq_var (teal.transform::choices_selected()) variable adverse events sequence number dataset. Used counting total number events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). count_dth (logical) whether show count total deaths (based dthfl_var). Defaults TRUE. count_wd (logical) whether show count patients withdrawn study due adverse event (based dcsreas_var). Defaults TRUE. count_subj (logical) whether show count unique subjects (based USUBJID). applies event flag variables provided. count_pt (logical) whether show count unique preferred terms (based llt). applies event flag variables provided. count_events (logical) whether show count events (based aeseq_var). applies event flag variables provided. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_events_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Adverse Events Summary — tm_t_events_summary","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl %>%     mutate(       DTHFL = case_when(         !is.na(DTHDT) ~ \"Y\",         TRUE ~ \"\"       ) %>% with_label(\"Subject Death Flag\")     )   ADAE <- tmc_ex_adae    add_event_flags <- function(dat) {     dat <- dat %>%       mutate(         TMPFL_SER = AESER == \"Y\",         TMPFL_REL = AEREL == \"Y\",         TMPFL_GR5 = AETOXGR == \"5\",         TMP_SMQ01 = !is.na(SMQ01NAM),         TMP_SMQ02 = !is.na(SMQ02NAM),         TMP_CQ01 = !is.na(CQ01NAM)       )     column_labels <- list(       TMPFL_SER = \"Serious AE\",       TMPFL_REL = \"Related AE\",       TMPFL_GR5 = \"Grade 5 AE\",       TMP_SMQ01 = aesi_label(dat[[\"SMQ01NAM\"]], dat[[\"SMQ01SC\"]]),       TMP_SMQ02 = aesi_label(\"Y.9.9.9.9/Z.9.9.9.9 AESI\"),       TMP_CQ01 = aesi_label(dat[[\"CQ01NAM\"]])     )     col_labels(dat)[names(column_labels)] <- as.character(column_labels)     dat   }    #' Generating user-defined event flags.   ADAE <- ADAE %>% add_event_flags()    ae_anl_vars <- names(ADAE)[startsWith(names(ADAE), \"TMPFL_\")]   aesi_vars <- names(ADAE)[startsWith(names(ADAE), \"TMP_\")] })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_events_summary(       label = \"Adverse Events Summary\",       dataname = \"ADAE\",       arm_var = choices_selected(         choices = variable_choices(\"ADSL\", c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       flag_var_anl = choices_selected(         choices = variable_choices(\"ADAE\", data[[\"ae_anl_vars\"]]),         selected = data[[\"ae_anl_vars\"]][1],         keep_order = TRUE,         fixed = FALSE       ),       flag_var_aesi = choices_selected(         choices = variable_choices(\"ADAE\", data[[\"aesi_vars\"]]),         selected = data[[\"aesi_vars\"]][1],         keep_order = TRUE,         fixed = FALSE       ),       add_total = TRUE     )   ) ) #> Initializing tm_t_events_summary #> Warning: 'package:forcats' may not be available when loading #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"module produces exposure table risk management plan.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"","code":"tm_t_exposure(   label,   dataname,   parentname = ifelse(inherits(col_by_var, \"data_extract_spec\"),     teal.transform::datanames_input(col_by_var), \"ADSL\"),   row_by_var,   col_by_var,   paramcd = teal.transform::choices_selected(choices =     teal.transform::value_choices(dataname, \"PARAMCD\", \"PARAM\"), selected = \"TDURD\"),   paramcd_label = \"PARAM\",   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   parcat,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVAL\"), selected = \"AVAL\", fixed = TRUE),   avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVALU\"), selected = \"AVALU\", fixed = TRUE),   add_total,   total_label = default_total_label(),   add_total_row = TRUE,   total_row_label = \"Total number of patients and patient time*\",   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. row_by_var (teal.transform::choices_selected()) object available choices preselected option variable names can used split rows. col_by_var (teal.transform::choices_selected()) object available choices preselected option variable names can used split columns. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. paramcd_label (character) column dataset value used label argument paramcd. id_var (teal.transform::choices_selected()) object specifying variable name subject id. parcat (teal.transform::choices_selected()) object available choices preselected option parameter category values. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). add_total_row (flag) whether \"total\" level added others includes levels constitute split. custom label can set level via total_row_label argument. total_row_label (character) string display total row label row enabled (see add_total_row). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_exposure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Exposure Table for Risk management plan — tm_t_exposure","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADEX <- tmc_ex_adex    set.seed(1, kind = \"Mersenne-Twister\")   labels <- col_labels(ADEX, fill = FALSE)   ADEX <- ADEX %>%     distinct(USUBJID, .keep_all = TRUE) %>%     mutate(       PARAMCD = \"TDURD\",       PARAM = \"Overall duration (days)\",       AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),       AVALU = \"Days\"     ) %>%     bind_rows(ADEX)   col_labels(ADEX) <- labels })  datanames <- c(\"ADSL\", \"ADEX\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_exposure(       label = \"Duration of Exposure Table\",       dataname = \"ADEX\",       paramcd = choices_selected(         choices = value_choices(data[[\"ADEX\"]], \"PARAMCD\", \"PARAM\"),         selected = \"TDURD\"       ),       col_by_var = choices_selected(         choices = variable_choices(data[[\"ADEX\"]], subset = c(\"SEX\", \"ARM\")),         selected = \"SEX\"       ),       row_by_var = choices_selected(         choices = variable_choices(data[[\"ADEX\"]], subset = c(\"RACE\", \"REGION1\", \"STRATA1\", \"SEX\")),         selected = \"RACE\"       ),       parcat = choices_selected(         choices = value_choices(data[[\"ADEX\"]], \"PARCAT2\"),         selected = \"Drug A\"       ),       add_total = FALSE     )   ),   filter = teal_slices(teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\")) ) #> Initializing tm_t_exposure #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Logistic Regression — tm_t_logistic","title":"teal Module: Logistic Regression — tm_t_logistic","text":"module produces multi-variable logistic regression table consistent TLG Catalog template LGRT02 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Logistic Regression — tm_t_logistic","text":"","code":"tm_t_logistic(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var = NULL,   arm_ref_comp = NULL,   paramcd,   cov_var = NULL,   avalc_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVALC\"), \"AVALC\", fixed = TRUE),   conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =     TRUE),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Logistic Regression — tm_t_logistic","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected() NULL) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. NULL, arm/treatment variable included logistic model. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. cov_var (teal.transform::choices_selected()) object available choices preselected option covariates variables. avalc_var (teal.transform::choices_selected()) object available choices preselected option analysis variable (categorical). conf_level (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Logistic Regression — tm_t_logistic","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Logistic Regression — tm_t_logistic","text":"","code":"library(dplyr)  ADSL <- tmc_ex_adsl ADRS <- tmc_ex_adrs %>%   filter(PARAMCD %in% c(\"BESRSPI\", \"INVET\"))  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADRS = ADRS,     code = \"       ADSL <- tmc_ex_adsl       ADRS <- tmc_ex_adrs %>%         filter(PARAMCD %in% c(\\\"BESRSPI\\\", \\\"INVET\\\"))     \"   ),   modules = modules(     tm_t_logistic(       label = \"Logistic Regression\",       dataname = \"ADRS\",       arm_var = choices_selected(         choices = variable_choices(ADRS, c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         choices = value_choices(ADRS, \"PARAMCD\", \"PARAM\"),         selected = \"BESRSPI\"       ),       cov_var = choices_selected(         choices = c(\"SEX\", \"AGE\", \"BMRKR1\", \"BMRKR2\"),         selected = \"SEX\"       )     )   ) ) #> Initializing tm_t_logistic #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_mult_events.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Multiple Events by Term — tm_t_mult_events","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"module produces table multiple events term.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_mult_events.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"","code":"tm_t_mult_events(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   seq_var,   hlt,   llt,   add_total = TRUE,   total_label = default_total_label(),   na_level = default_na_str(),   event_type = \"event\",   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_mult_events.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. seq_var (teal.transform::choices_selected()) object available choices preselected option variable names can used analysis sequence number variable. Used counting unique number events. hlt (teal.transform::choices_selected()) name variable high level term events. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). event_type (character) type event summarized (e.g. adverse event, treatment). Default \"event\". drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_mult_events.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_mult_events.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Multiple Events by Term — tm_t_mult_events","text":"","code":"ADSL <- tmc_ex_adsl ADCM <- tmc_ex_adcm adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADSL <- tmc_ex_adsl       ADCM <- tmc_ex_adcm     \",     join_keys = join_keys   ),   modules = modules(     tm_t_mult_events(       label = \"Concomitant Medications by Medication Class and Preferred Name\",       dataname = \"ADCM\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       seq_var = choices_selected(\"CMSEQ\", selected = \"CMSEQ\", fixed = TRUE),       hlt = choices_selected(         choices = variable_choices(ADCM, c(\"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")),         selected = c(\"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")       ),       llt = choices_selected(         choices = variable_choices(ADCM, c(\"CMDECOD\")),         selected = c(\"CMDECOD\")       ),       add_total = TRUE,       event_type = \"treatment\"     )   ) ) #> Initializing tm_t_mult_events #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_basic_info.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"module produces patient profile basic info report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_basic_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"","code":"tm_t_pp_basic_info(   label,   dataname = \"ADSL\",   patient_col = \"USUBJID\",   vars = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_basic_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. patient_col (character) name patient ID variable. vars (teal.transform::choices_selected())  object available choices preselected option variables dataname show table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_basic_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_basic_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Basic Info — tm_t_pp_basic_info","text":"","code":"ADSL <- tmc_ex_adsl  app <- init(   data = cdisc_data(     ADSL = ADSL,     code = \"ADSL <- tmc_ex_adsl\"   ),   modules = modules(     tm_t_pp_basic_info(       label = \"Basic Info\",       dataname = \"ADSL\",       patient_col = \"USUBJID\",       vars = choices_selected(         choices = variable_choices(ADSL),         selected = c(\"ARM\", \"AGE\", \"SEX\", \"COUNTRY\", \"RACE\", \"EOSSTT\")       )     )   ) ) #> Initializing tm_t_pp_basic_info #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_laboratory.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"module produces patient profile laboratory table using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_laboratory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"","code":"tm_t_pp_laboratory(   label,   dataname = \"ADLB\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   timepoints = NULL,   aval = lifecycle::deprecated(),   aval_var = NULL,   avalu = lifecycle::deprecated(),   avalu_var = NULL,   param = NULL,   paramcd = NULL,   anrind = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_laboratory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. timepoints (teal.transform::choices_selected()) object available choices preselected option time variable dataname. aval Please use aval_var argument instead. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. avalu Please use avalu_var argument instead. avalu_var (teal.transform::choices_selected()) object available choices preselected option analysis unit variable. param (teal.transform::choices_selected()) object available choices preselected option PARAM variable dataname. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. anrind (teal.transform::choices_selected()) object available choices preselected option ANRIND variable dataname. Variable following 3 levels: \"HIGH\", \"LOW\", \"NORMAL\". pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_laboratory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_laboratory.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Laboratory Table — tm_t_pp_laboratory","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_pp_laboratory(       label = \"Vitals\",       dataname = \"ADLB\",       patient_col = \"USUBJID\",       paramcd = choices_selected(         choices = variable_choices(ADLB, \"PARAMCD\"),         selected = \"PARAMCD\"       ),       param = choices_selected(         choices = variable_choices(ADLB, \"PARAM\"),         selected = \"PARAM\"       ),       timepoints = choices_selected(         choices = variable_choices(ADLB, \"ADY\"),         selected = \"ADY\"       ),       anrind = choices_selected(         choices = variable_choices(ADLB, \"ANRIND\"),         selected = \"ANRIND\"       ),       aval_var = choices_selected(         choices = variable_choices(ADLB, \"AVAL\"),         selected = \"AVAL\"       ),       avalu_var = choices_selected(         choices = variable_choices(ADLB, \"AVALU\"),         selected = \"AVALU\"       )     )   ) ) #> Initializing tm_t_pp_laboratory #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_medical_history.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"module produces patient profile medical history report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_medical_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"","code":"tm_t_pp_medical_history(   label,   dataname = \"ADMH\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   mhterm = NULL,   mhbodsys = NULL,   mhdistat = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_medical_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. mhterm (teal.transform::choices_selected()) object available choices preselected option MHTERM variable dataname. mhbodsys (teal.transform::choices_selected()) object available choices preselected option MHBODSYS variable dataname. mhdistat (teal.transform::choices_selected()) object available choices preselected option MHDISTAT variable dataname. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_medical_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_medical_history.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Medical History — tm_t_pp_medical_history","text":"","code":"ADSL <- tmc_ex_adsl ADMH <- tmc_ex_admh  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADMH = ADMH,     code = \"       ADSL <- tmc_ex_adsl       ADMH <- tmc_ex_admh     \"   ),   modules = modules(     tm_t_pp_medical_history(       label = \"Medical History\",       dataname = \"ADMH\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       mhterm = choices_selected(         choices = variable_choices(ADMH, c(\"MHTERM\")),         selected = \"MHTERM\"       ),       mhbodsys = choices_selected(         choices = variable_choices(ADMH, \"MHBODSYS\"),         selected = \"MHBODSYS\"       ),       mhdistat = choices_selected(         choices = variable_choices(ADMH, \"MHDISTAT\"),         selected = \"MHDISTAT\"       )     )   ) ) #> Initializing tm_t_pp_medical_history #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_prior_medication.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"module produces patient profile prior medication report using ADaM datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_prior_medication.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"","code":"tm_t_pp_prior_medication(   label,   dataname = \"ADCM\",   parentname = \"ADSL\",   patient_col = \"USUBJID\",   atirel = NULL,   cmdecod = NULL,   cmindc = NULL,   cmstdy = NULL,   pre_output = NULL,   post_output = NULL )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_prior_medication.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. patient_col (character) name patient ID variable. atirel (teal.transform::choices_selected()) object available choices preselected option ATIREL variable dataname. cmdecod (teal.transform::choices_selected()) object available choices preselected option CMDECOD variable dataname. cmindc (teal.transform::choices_selected()) object available choices preselected option CMINDC variable dataname. cmstdy (teal.transform::choices_selected()) object available choices preselected option CMSTDY variable dataname. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_prior_medication.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_pp_prior_medication.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Patient Profile Prior Medication — tm_t_pp_prior_medication","text":"","code":"library(dplyr)  ADCM <- tmc_ex_adcm ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID) ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM adcm_keys <- c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"CMSEQ\", \"ATC1\", \"ATC2\", \"ATC3\", \"ATC4\")  join_keys <- default_cdisc_join_keys[c(\"ADSL\", \"ADCM\")] join_keys[\"ADCM\", \"ADCM\"] <- adcm_keys  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADCM = ADCM,     code = \"       ADCM <- tmc_ex_adcm       ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)       ADCM$CMASTDTM <- ADCM$ASTDTM       ADCM$CMAENDTM <- ADCM$AENDTM     \",     join_keys = join_keys   ),   modules = modules(     tm_t_pp_prior_medication(       label = \"Prior Medication\",       dataname = \"ADCM\",       parentname = \"ADSL\",       patient_col = \"USUBJID\",       atirel = choices_selected(         choices = variable_choices(ADCM, \"ATIREL\"),         selected = \"ATIREL\"       ),       cmdecod = choices_selected(         choices = variable_choices(ADCM, \"CMDECOD\"),         selected = \"CMDECOD\"       ),       cmindc = choices_selected(         choices = variable_choices(ADCM, \"CMINDC\"),         selected = \"CMINDC\"       ),       cmstdy = choices_selected(         choices = variable_choices(ADCM, \"ASTDY\"),         selected = \"ASTDY\"       )     )   ) ) #> Initializing tm_t_pp_prior_medication #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Shift by Arm — tm_t_shift_by_arm","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"module produces summary table analysis indicator levels arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"","code":"tm_t_shift_by_arm(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   visit_var,   aval_var,   base_var = lifecycle::deprecated(),   baseline_var,   treatment_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     \"ONTRTFL\"), selected = \"ONTRTFL\"),   treatment_flag = teal.transform::choices_selected(\"Y\"),   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Shift by Arm — tm_t_shift_by_arm","text":"","code":"ADSL <- tmc_ex_adsl ADEG <- tmc_ex_adeg  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADEG = ADEG,     code = \"       ADSL <- tmc_ex_adsl       ADEG <- tmc_ex_adeg     \"   ),   modules = modules(     tm_t_shift_by_arm(       label = \"Shift by Arm Table\",       dataname = \"ADEG\",       arm_var = choices_selected(         variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADEG, \"PARAMCD\"),         selected = \"HR\"       ),       visit_var = choices_selected(         value_choices(ADEG, \"AVISIT\"),         selected = \"POST-BASELINE MINIMUM\"       ),       aval_var = choices_selected(         variable_choices(ADEG, subset = \"ANRIND\"),         selected = \"ANRIND\", fixed = TRUE       ),       baseline_var = choices_selected(         variable_choices(ADEG, subset = \"BNRIND\"),         selected = \"BNRIND\", fixed = TRUE       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_shift_by_arm #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm_by_worst.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"module produces summary table worst analysis indicator variable level per subject arm.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm_by_worst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"","code":"tm_t_shift_by_arm_by_worst(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   paramcd,   aval_var,   base_var = lifecycle::deprecated(),   baseline_var,   worst_flag_var,   worst_flag,   treatment_flag_var = teal.transform::choices_selected(choices =     teal.transform::variable_choices(dataname, subset = \"ONTRTFL\"), selected = \"ONTRTFL\"),   treatment_flag = teal.transform::choices_selected(\"Y\"),   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   add_total = FALSE,   total_label = default_total_label(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm_by_worst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. base_var Please use baseline_var argument instead. baseline_var (teal.transform::choices_selected()) object available choices preselected option variable values can used baseline_var. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable. worst_flag (character) value indicating worst analysis indicator level. treatment_flag_var (teal.transform::choices_selected()) treatment flag variable. treatment_flag (teal.transform::choices_selected()) value indicating treatment records treatment_flag_var. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). add_total (logical) whether include row total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm_by_worst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_arm_by_worst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Shift by Arm by Worst Analysis Indicator Level — tm_t_shift_by_arm_by_worst","text":"","code":"ADSL <- tmc_ex_adsl ADEG <- tmc_ex_adeg  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADEG = ADEG,     code = \"       ADSL <- tmc_ex_adsl       ADEG <- tmc_ex_adeg     \"   ),   modules = modules(     tm_t_shift_by_arm_by_worst(       label = \"Shift by Arm Table\",       dataname = \"ADEG\",       arm_var = choices_selected(         variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         value_choices(ADEG, \"PARAMCD\"),         selected = \"ECGINTP\"       ),       worst_flag_var = choices_selected(         variable_choices(ADEG, c(\"WORS02FL\", \"WORS01FL\")),         selected = \"WORS02FL\"       ),       worst_flag = choices_selected(         value_choices(ADEG, \"WORS02FL\"),         selected = \"Y\", fixed = TRUE       ),       aval_var = choices_selected(         variable_choices(ADEG, c(\"AVALC\", \"ANRIND\")),         selected = \"AVALC\"       ),       baseline_var = choices_selected(         variable_choices(ADEG, c(\"BASEC\", \"BNRIND\")),         selected = \"BASEC\"       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_shift_by_arm_by_worst #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Grade Summary Table — tm_t_shift_by_grade","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"module produces summary table worst grades per subject visit parameter.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"","code":"tm_t_shift_by_grade(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"AVISIT\"), selected = \"AVISIT\", fixed = TRUE),   paramcd,   worst_flag_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\")), selected = \"WGRLOVFL\"),   worst_flag_indicator =     teal.transform::choices_selected(teal.transform::value_choices(dataname, \"WGRLOVFL\"),     selected = \"Y\", fixed = TRUE),   anl_toxgrade_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"ATOXGR\")), selected = c(\"ATOXGR\"), fixed = TRUE),   base_toxgrade_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, subset =     c(\"BTOXGR\")), selected = c(\"BTOXGR\"), fixed = TRUE),   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   add_total = FALSE,   total_label = default_total_label(),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   na_level = default_na_str(),   code_missing_baseline = FALSE,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. visit_var (teal.transform::choices_selected()) object available choices preselected option variable names can used visit variable. Must factor dataname. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. worst_flag_var (teal.transform::choices_selected()) object available choices preselected option variable names can used worst flag variable. worst_flag_indicator (teal.transform::choices_selected()) value indicating worst grade. anl_toxgrade_var (teal.transform::choices_selected()) variable analysis toxicity grade. base_toxgrade_var (teal.transform::choices_selected()) variable baseline toxicity grade. id_var (teal.transform::choices_selected()) object specifying variable name subject id. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). code_missing_baseline (logical) whether missing baseline grades counted grade 0. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_shift_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Grade Summary Table — tm_t_shift_by_grade","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_shift_by_grade(       label = \"Grade Laboratory Abnormality Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, subset = c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = \"ALT\"       ),       worst_flag_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"WGRLOVFL\", \"WGRLOFL\", \"WGRHIVFL\", \"WGRHIFL\")),         selected = c(\"WGRLOVFL\")       ),       worst_flag_indicator = choices_selected(         value_choices(ADLB, \"WGRLOVFL\"),         selected = \"Y\", fixed = TRUE       ),       anl_toxgrade_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"ATOXGR\")),         selected = c(\"ATOXGR\"),         fixed = TRUE       ),       base_toxgrade_var = choices_selected(         choices = variable_choices(ADLB, subset = c(\"BTOXGR\")),         selected = c(\"BTOXGR\"),         fixed = TRUE       ),       add_total = FALSE     )   ),   filter = teal_slices(teal_slice(\"ADSL\", \"SAFFL\", selected = \"Y\")) ) #> Initializing tm_t_shift_by_grade #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_smq.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"module produces adverse events table Standardized MedDRA Query.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_smq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"","code":"tm_t_smq(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   llt,   add_total = TRUE,   total_label = default_total_label(),   sort_criteria = c(\"freq_desc\", \"alpha\"),   drop_arm_levels = TRUE,   na_level = default_na_str(),   smq_varlabel = \"Standardized MedDRA Query\",   baskets,   scopes,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_smq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. id_var (teal.transform::choices_selected()) object specifying variable name subject id. llt (teal.transform::choices_selected()) name variable low level term events. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). sort_criteria (character) sort final table. Default option freq_desc sorts column sort_freq_col decreasing number patients event. Alternative option alpha sorts events alphabetically. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). smq_varlabel (character) label use new column SMQ created tern::h_stack_by_baskets(). baskets (teal.transform::choices_selected()) object available choices preselected options standardized/customized queries. scopes (teal.transform::choices_selected()) object available choices scopes standardized queries. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_smq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_smq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Adverse Events Table by Standardized MedDRA Query — tm_t_smq","text":"","code":"data <- teal_data() data <- within(data, {   ADSL <- tmc_ex_adsl   ADAE <- tmc_ex_adae    names_baskets <- grep(\"^(SMQ|CQ).*NAM$\", names(ADAE), value = TRUE)   names_scopes <- grep(\"^SMQ.*SC$\", names(ADAE), value = TRUE)    cs_baskets <- choices_selected(     choices = variable_choices(ADAE, subset = names_baskets),     selected = names_baskets   )    cs_scopes <- choices_selected(     choices = variable_choices(ADAE, subset = names_scopes),     selected = names_scopes,     fixed = TRUE   ) })  datanames <- c(\"ADSL\", \"ADAE\") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames]  app <- init(   data = data,   modules = modules(     tm_t_smq(       label = \"Adverse Events by SMQ Table\",       dataname = \"ADAE\",       arm_var = choices_selected(         choices = variable_choices(data[[\"ADSL\"]], subset = c(\"ARM\", \"SEX\")),         selected = \"ARM\"       ),       add_total = FALSE,       baskets = data[[\"cs_baskets\"]],       scopes = data[[\"cs_scopes\"]],       llt = choices_selected(         choices = variable_choices(data[[\"ADAE\"]], subset = c(\"AEDECOD\")),         selected = \"AEDECOD\"       )     )   ) ) #> Initializing tm_t_smq #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Summary of Variables — tm_t_summary","title":"teal Module: Summary of Variables — tm_t_summary","text":"module produces table summarize variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Summary of Variables — tm_t_summary","text":"","code":"tm_t_summary(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   summarize_vars,   add_total = TRUE,   total_label = default_total_label(),   show_arm_var_labels = TRUE,   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"mean_ci\", \"median\", \"median_ci\", \"quantiles\",     \"range\", \"geom_mean\"),   denominator = c(\"N\", \"n\", \"omit\"),   drop_arm_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Summary of Variables — tm_t_summary","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. summarize_vars (teal.transform::choices_selected()) names variables summarized. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). show_arm_var_labels (flag) whether arm variable label(s) displayed. Defaults TRUE. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Summary of Variables — tm_t_summary","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Summary of Variables — tm_t_summary","text":"","code":"# Preparation of the test case - use `EOSDY` and `DCSREAS` variables to demonstrate missing data. ADSL <- tmc_ex_adsl ADSL$EOSDY[1] <- NA_integer_  app <- init(   data = cdisc_data(     ADSL = ADSL,     code = \"       ADSL <- tmc_ex_adsl       ADSL$EOSDY[1] <- NA_integer_     \"   ),   modules = modules(     tm_t_summary(       label = \"Demographic Table\",       dataname = \"ADSL\",       arm_var = choices_selected(c(\"ARM\", \"ARMCD\"), \"ARM\"),       add_total = TRUE,       summarize_vars = choices_selected(         c(\"SEX\", \"RACE\", \"BMRKR2\", \"EOSDY\", \"DCSREAS\", \"AGE\"),         c(\"SEX\", \"RACE\")       ),       useNA = \"ifany\"     )   ) ) #> Initializing tm_t_summary #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary_by.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"module produces table summarize variables row groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary_by.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"","code":"tm_t_summary_by(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   by_vars,   summarize_vars,   id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     subset = \"USUBJID\"), selected = \"USUBJID\", fixed = TRUE),   paramcd = NULL,   add_total = TRUE,   total_label = default_total_label(),   parallel_vars = FALSE,   row_groups = FALSE,   useNA = c(\"ifany\", \"no\"),   na_level = default_na_str(),   numeric_stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   denominator = teal.transform::choices_selected(c(\"n\", \"N\", \"omit\"), \"omit\", fixed =     TRUE),   drop_arm_levels = TRUE,   drop_zero_levels = TRUE,   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary_by.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable(s) results table. two elements selected arm_var, second variable nested first variable. by_vars (teal.transform::choices_selected()) object available choices preselected option variable names used split summary rows. summarize_vars (teal.transform::choices_selected()) names variables summarized. id_var (teal.transform::choices_selected()) object specifying variable name subject id. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). parallel_vars (logical) whether summarized variables arranged columns. Can set TRUE chosen analysis variables numeric. row_groups (logical) whether summarized variables arranged row groups. useNA (character) whether missing data (NA) displayed level. na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). numeric_stats (character) names statistics display numeric summary variables. Available statistics n, mean_sd, mean_ci, median, median_ci, quantiles, range, geom_mean. denominator (character) chooses percentages calculated. option N, reference population column total used denominator. option n, number non-missing records row column intersection used denominator. omit chosen, percentage omitted. drop_arm_levels (logical) whether drop unused levels arm_var. TRUE, arm_var levels set used dataname dataset. FALSE, arm_var levels set used parentname dataset. dataname parentname , drop_arm_levels set TRUE user input parameter ignored. drop_zero_levels (logical) whether rows zero counts columns removed table. pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary_by.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"teal_module object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_summary_by.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Summarize Variables by Row Groups — tm_t_summary_by","text":"","code":"ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADLB = ADLB,     code = \"       ADSL <- tmc_ex_adsl       ADLB <- tmc_ex_adlb     \"   ),   modules = modules(     tm_t_summary_by(       label = \"Summary by Row Groups Table\",       dataname = \"ADLB\",       arm_var = choices_selected(         choices = variable_choices(ADSL, c(\"ARM\", \"ARMCD\")),         selected = \"ARM\"       ),       add_total = TRUE,       by_vars = choices_selected(         choices = variable_choices(ADLB, c(\"PARAM\", \"AVISIT\")),         selected = c(\"AVISIT\")       ),       summarize_vars = choices_selected(         choices = variable_choices(ADLB, c(\"AVAL\", \"CHG\")),         selected = c(\"AVAL\")       ),       useNA = \"ifany\",       paramcd = choices_selected(         choices = value_choices(ADLB, \"PARAMCD\", \"PARAM\"),         selected = \"ALT\"       )     )   ) ) #> Initializing tm_t_summary_by #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"teal Module: Time-To-Event Table — tm_t_tte","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"module produces time--event analysis summary table, consistent TLG Catalog template TTET01 available .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"","code":"tm_t_tte(   label,   dataname,   parentname = ifelse(inherits(arm_var, \"data_extract_spec\"),     teal.transform::datanames_input(arm_var), \"ADSL\"),   arm_var,   arm_ref_comp = NULL,   paramcd,   strata_var,   aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"AVAL\"), \"AVAL\", fixed = TRUE),   cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,     \"CNSR\"), \"CNSR\", fixed = TRUE),   conf_level_coxph = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order     = TRUE),   conf_level_survfit = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95,     keep_order = TRUE),   time_points,   time_unit_var =     teal.transform::choices_selected(teal.transform::variable_choices(dataname, \"AVALU\"),     \"AVALU\", fixed = TRUE),   event_desc_var = teal.transform::choices_selected(\"EVNTDESC\", \"EVNTDESC\", fixed = TRUE),   add_total = FALSE,   total_label = default_total_label(),   na_level = default_na_str(),   pre_output = NULL,   post_output = NULL,   basic_table_args = teal.widgets::basic_table_args() )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"label (character) menu item label module teal app. dataname (character) analysis data used teal module. parentname (character) parent analysis data used teal module, usually refers ADSL. arm_var (teal.transform::choices_selected()) object available choices preselected option variable names can used arm_var. defines grouping variable results table. arm_ref_comp (list) optional, specified must named list element corresponding arm variable ADSL element must another list (possibly delayed teal.transform::variable_choices() delayed teal.transform::value_choices() elements named ref comp defined default reference comparison arms arm variable changed. paramcd (teal.transform::choices_selected()) object available choices preselected option parameter code variable dataname. strata_var (teal.transform::choices_selected()) names variables stratified analysis. aval_var (teal.transform::choices_selected()) object available choices pre-selected option analysis variable. cnsr_var (teal.transform::choices_selected()) object available choices preselected option censoring variable. conf_level_coxph (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). conf_level_survfit (teal.transform::choices_selected()) object available choices pre-selected option confidence level, within range (0, 1). time_points (teal.transform::choices_selected()) object available choices preselected option time points can used tern::surv_timepoint(). time_unit_var (teal.transform::choices_selected()) object available choices pre-selected option time unit variable. event_desc_var (character data_extract_spec()) variable name event description information, optional. add_total (logical) whether include column total number patients. total_label (string) string display total column/row label column/row enabled (see add_total). Defaults \"Patients\". set new default total_label apply modules, run set_default_total_label(\"new_default\"). na_level (string) used replace NA empty values character factor variables data. Defaults \"<Missing>\". set default na_level apply modules, run set_default_na_str(\"new_default\"). pre_output (shiny.tag) optional, text placed output put output context. example title. post_output (shiny.tag) optional, text placed output put output context. example shiny::helpText() elements useful. basic_table_args (basic_table_args) optional object created teal.widgets::basic_table_args() settings module table. argument merged option teal.basic_table_args default module arguments (hard coded module body). details, see vignette: vignette(\"custom-basic-table-arguments\", package = \"teal.widgets\").","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"teal_module object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"core functionality module based coxph_pairwise(), surv_timepoint(), surv_time() tern package. arm stratification variables taken parentname data. following variables used module: AVAL: time event CNSR: 1 record AVAL censored, 0 otherwise PARAMCD: variable used filter endpoint (e.g. OS). filtering PARAMCD one observation per patient expected","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/tm_t_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"teal Module: Time-To-Event Table — tm_t_tte","text":"","code":"ADSL <- tmc_ex_adsl ADTTE <- tmc_ex_adtte  arm_ref_comp <- list(   ACTARMCD = list(     ref = \"ARM B\",     comp = c(\"ARM A\", \"ARM C\")   ),   ARM = list(     ref = \"B: Placebo\",     comp = c(\"A: Drug X\", \"C: Combination\")   ) )  app <- init(   data = cdisc_data(     ADSL = ADSL,     ADTTE = ADTTE,     code = \"       ADSL <- tmc_ex_adsl       ADTTE <- tmc_ex_adtte     \"   ),   modules = modules(     tm_t_tte(       label = \"Time To Event Table\",       dataname = \"ADTTE\",       arm_var = choices_selected(         variable_choices(ADSL, c(\"ARM\", \"ARMCD\", \"ACTARMCD\")),         \"ARM\"       ),       arm_ref_comp = arm_ref_comp,       paramcd = choices_selected(         value_choices(ADTTE, \"PARAMCD\", \"PARAM\"),         \"OS\"       ),       strata_var = choices_selected(         variable_choices(ADSL, c(\"SEX\", \"BMRKR2\")),         \"SEX\"       ),       time_points = choices_selected(c(182, 243), 182),       event_desc_var = choices_selected(         variable_choices(ADTTE, \"EVNTDESC\"),         \"EVNTDESC\",         fixed = TRUE       )     )   ) ) #> Initializing tm_t_tte #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"Check vector valid used treatment arm variable","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"","code":"validate_arm(arm_vec)"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"arm_vec vector validated","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_arm.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check if vector is valid as to be used as a treatment arm variable — validate_arm","text":"validate error returned vector factor detailed error message entries empty strings","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_standard_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate standard input values for a teal module — validate_standard_inputs","text":"","code":"validate_standard_inputs(   adsl,   adslvars = character(0),   anl,   anlvars = character(0),   need_arm = TRUE,   arm_var,   ref_arm,   comp_arm,   min_n_levels_armvar = 1L,   max_n_levels_armvar = 100L,   min_nrow = 1 )"},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/reference/validate_standard_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate standard input values for a teal module — validate_standard_inputs","text":"adsl data.frame subject-level data adslvars required variables ADSL anl data.frame analysis data anlvars required variables ANL need_arm flag indicating whether grouping variable arm_var required can optionally NULL. arm_var character name grouping variable, typically arm ref_arm character name reference level arm_var comp_arm character name comparison level arm_var min_n_levels_armvar minimum number levels grouping variable arm_var. Defaults 1, NULL minimum. max_n_levels_armvar maximum number levels grouping variable arm_var. Use NULL maximum. min_nrow minimum number observations ADSL ANL","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-9-1-9023","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.1.9023","text":"Added teal.logger functionality logging changes shiny inputs modules. Introduced ylim parameter tm_g_km module controls width y-axis. Added functionality tm_t_events_patyear split columns multiple (nested) variables via arm_var argument. Added arguments arm_var_labels template_summary show_arm_var_labels tm_t_summary allow user display arm variable (arm_var) labels table header. Added argument stats modules tm_g_forest_rsp tm_g_forest_tte allow users specify statistics include table. Added argument riskdiff modules tm_g_forest_rsp tm_g_forest_tte allow users add risk difference table column. Added count_dth count_wd parameters tm_t_events_summary select/deselect “Total number deaths” “Total number patients withdrawn study due AE” rows, respectively. options correspond “Count deaths” “Count withdrawals due AE” checkboxes available module run.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-9-1-9023","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.1.9023","text":"Removed Show Warnings modals modules. Clarified documentation specifying whether multiple values can selected arm_var argument module. Replaced use rtables::add_colcounts() function show_colcounts argument basic_table(). Began deprecation cycle show_labels argument template_summary effect tm_t_summary module. Replaced instances deprecated strata argument tern::control_lineplot_vars() group_var.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-091","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.9.1","title":"teal.modules.clinical 0.9.1","text":"CRAN release: 2024-04-27","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.1","text":"Updated tm_g_forest_rsp tm_g_forest_tte use refactored version g_forest. Plots now displayed ggplot objects instead grob objects. Added parameters font_size rel_width_forest control font size width plot relative table, respectively. Updated tm_t_summary_by allow NULL input paramcd argument. Updated tm_g_km use refactored version g_km. Plots now displayed ggplot objects instead grob objects. Added parameters rel_height_plot, font_size, control_annot_surv_med, control_annot_coxph control height plot relative table, font size, median survival time table size, Cox-PH table size, respectively. Added control argument tm_t_binary_outcome control settings analysis (methods, confidence intervals, odds ratios) within module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.1","text":"Replaced instances deprecated na_level argument tern functions na_str. Replaced argument/list element name strata instead strat tern function calls following deprecation argument/name within tern. Removed formatters dependencies replaced use functions relating variable labels functions teal.data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-090","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.9.0","title":"teal.modules.clinical 0.9.0","text":"CRAN release: 2024-02-23","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"breaking-changes-0-9-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"teal.modules.clinical 0.9.0","text":"Adapted modules use teal_data objects. Module arguments previously accepted inputs teal.transform::choices_selected() teal.transform::data_extract_spec() now accept input teal.transform::choices_selected(). affected modules : tm_a_gee, tm_a_mmrm, tm_g_ci, tm_g_forest_rsp, tm_g_forest_tte, tm_g_ipp, tm_g_km, tm_g_lineplot, tm_g_pp_adverse_events, tm_g_pp_patient_timeline, tm_g_pp_therapy, tm_g_pp_vitals, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_ancova, tm_t_binary_outcome, tm_t_coxreg, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_logistic, tm_t_mult_events, tm_t_pp_basic_info, tm_t_pp_laboratory, tm_t_pp_medical_history, tm_t_pp_prior_medication, tm_t_shift_by_arm, tm_t_shift_by_arm_by_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, tm_t_tte","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.9.0","text":"Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Simplify examples vignettes code removing package prefixes possible. Added parameter sort_freq_col tm_t_events allow user select column use sorting decreasing frequency. Added parameter incl_overall_sum tm_t_events allow user choose whether overall summary rows included top table. Updated documentation vignettes demonstrate method pass teal_data object teal::init(). Added default_total_label set_default_total_label functions get set default total column label (total_label) modules. Implemented tern::default_na_str tern::set_default_na_str functions get set default missing value replacement string (na_level) modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.9.0","text":"Fixed bug tm_g_lineplot forcing module initialize table. Fixes partial matching.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.9.0","text":"Deprecated aval argument tm_t_pp_laboratory tm_g_pp_vitals replaced aval_var argument. Deprecated avalu argument tm_t_pp_laboratory replaced avalu_var argument. Deprecated base_var argument tm_g_ipp, tm_t_shift_by_arm, template_shift_by_arm_by_worst replaced baseline_var argument. Specified minimal version package dependencies. Replaced usage deprecated summarize_vars function analyze_vars. Reduced package dependencies (removed tidyr, rlang, magrittr styler). Introduced tests partial matching.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-16","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.16","text":"Added informative error message grade mapping error occurs tm_t_abnormality_by_worst_grade. Fixed label indentation tm_t_abnormality_by_worst_grade. Added total_label argument enable customization “Patients” column/row label following modules: tm_a_mmrm, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_binary_outcome, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_mult_events, tm_t_shift_by_arm, tm_t_shift_by_arm_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, tm_t_tte. Increased default width tm_g_forest_tte plot prevent overlapping text. Improved default annotation table sizing tm_g_km. Refactored tm_t_exposure display “total” row last row table instead summary row. Added parameters add_total_row set whether total row displayed total_row_label set total row label. Updated tm_t_events maintain indentation pruning. Updated default reference/comparison arm level selection work arm variable levels filtered . Updated tm_t_coxreg drop factor covariate variable levels present avoid errors filtering. Updated tm_t_pp_basic_info, tm_t_pp_medical_history, tm_g_pp_therapy, tm_g_pp_adverse_events, tm_t_pp_laboratory print patient ID table. Updated tm_t_pp_basic_info, tm_g_pp_therapy, tm_g_pp_adverse_events, tm_t_pp_laboratory use rlistings print data neatly reports. Updated tm_g_lineplot allow user remove interval plot. Updated documentation vignettes demonstrate method pass teal_data object teal::init().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-16","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.16","text":"Fixed bug tm_t_coxreg preventing table displayed covariates selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-16","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.16","text":"Updated control_incidence_rate parameter names tm_t_events_patyear time_unit_input time_unit_output input_time_unit num_pt_year, respectively, parameter names changed tern. Hid datasets used patient profile modules filter panel. Replaced datanames = \"\" parameter datasets used internally module.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"breaking-changes-0-8-15","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.clinical 0.8.15","text":"Replaced chunks simpler qenv class. Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-15","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.15","text":"Replaced synthetic_cdisc_data refactored synthetic_cdisc_dataset function speed dataset loading tests/examples. Added new GEE module tm_a_gee. Added interface selecting interaction term tm_t_ancova. Updated encoding input checks use shinyvalidate::InputValidator better UI experience. Previously used shiny::validate. Added option tm_a_mmrm allow Kenward-Roger adjustments standard errors p-values. Added option choose facet scale options tm_g_barchart_simple. Added label parameter cs_to_select_spec/cs_to_des_select cs_to_filter_spec/cs_to_des_filter allow user customize label printed selection field. Updated tm_t_coxreg module refactoring summarize_coxreg tern fix indentation. Updated tm_t_exposure module use new function analyze_patients_exposure_in_cols fix table structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-15","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.15","text":"Fixed bug causing overlapping bars tm_g_barchart_simple. Fixed bug figures svg format. Fixed bug tm_t_summary tm_t_summary_by preventing users specifying numeric_stats argument.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-15","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.15","text":"Updated package Suggests use scda.2022 rather scda.2021. Removed unused argument param tm_g_pp_vitals. Removed optimizer choice tm_a_mmrm since can always use automatically determined optimizer. Created datasets use examples/tests adsl, adae, adaette, adcm, adeg, adex, adlb, admh, adqs, adrs, adtte, advs. datasets stored data folder accessible via tmc_ex_* prefix. Updated examples tests use datasets teal.modules.clinical package instead scda datasets. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Implemented lubridate package date variables internal data. Changed default value plot_width tm_g_forest_rsp prevent clutter.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-14","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.14","text":"Updated synthetic data tests version rcd_2022_02_28. Updated test files tests/testthat/ synthetic_cdisc_data(\"2022_02_28\") Reverted missing data checkbox tm_t_summary (encoding filtering separate). Implemented new widget allows dragging dropping select comparison groups. Added teal.reporter functionality modules. Enhanced tm_t_pp_medical_history module use table_with_settings module return rtables object. Implemented nestcolor examples, refactored tm_g_barchart_simple allow use nestcolor. Added descriptive title/labels visit name subtitle tm_g_ci. Updated tm_a_mmrm column name deselecting treatment “obs” “Patients”, added subtitles footnotes. Added title parameter category subtitle tm_t_exposure, cleaned labels. Added titles worse flag variable subtitles tm_t_shift_by_grade tm_t_shift_by_arm_by_worst. Added footnote tm_t_events_patyear CI method. Added subtitle footnotes tm_g_km. Added Stratified Analysis CI method option panel tm_t_binary_outcome. Added validation covariate/visit conflicts tm_a_mmrm. Remove unnecessary brackets header tm_t_exposure. Hid footnotes tm_g_km tm_t_tte “Compare Treatments” .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-14","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.14","text":"Fixed bug tm_g_barchart_simple prevented display graph. Fixed broken example tm_t_abnormality_by_worst_grade. Fixed bug tm_a_mmrm prevented table headers displaying. Fixed bug tm_g_forest_rsp deselecting endpoint. Fixed bug tm_t_binary_outcome crashed app deselecting paramcd. Fixed teal.reporter card names tm_t_smq. Fixed bug tm_t_shift_by_arm_by_worst adding validations choosing different endpoint values. Fixed bug tm_t_coxreg preventing footnotes displaying univariate models.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-14","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.14","text":"Added nestcolor dependency replaced deprecated function tern::color_palette nestcolor::color_palette.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tm_g_pp_adverse_events-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_g_pp_adverse_events","title":"teal.modules.clinical 0.8.13","text":"Updated position labels. Updated plot render color legend.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tm_t_summary_by-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_t_summary_by","title":"teal.modules.clinical 0.8.13","text":"Enhanced module support geometric mean encoding panel.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tm_t_summary-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"tm_t_summary","title":"teal.modules.clinical 0.8.13","text":"Updated added footnote. Enhanced module support geometric mean encoding panel. Updated module display checkboxes numeric variables statistics numeric variables part selected. Updated validations warn users using dataset non unique identifiers selecting variables non supported types (.e. Date, POSIXt). Added checkbox remove column generated missing values.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"other-modules-0-8-13","dir":"Changelog","previous_headings":"Enhancements","what":"Other modules","title":"teal.modules.clinical 0.8.13","text":"Updated tm_t_binary_outcome enable option apply continuity correction Newcombe method. Simplified show R code tm_g_pp_patient_timeline module. Improved names code chunks shown Debug Info. Improved validation treatment variable factor.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-13","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.13","text":"Fixed summarize_logistic implementation broken empty string error. upstream. _NA_ new standard flag allow pivot empty entries data frames. Took @title tm_t_binary_outcome.R producing warning. Updated validation account error selecting single variable tm_g_pp_patient_timeline module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-13","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.13","text":"Added pkgdown template documentation. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-12","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.12","text":"Changed input Covariates tm_t_coxreg.R track user input reflect order table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-features-0-8-12","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.12","text":"Added new module tm_t_shift_by_arm_by_worst analysis laboratory abnormalities severe grade flag. Enhanced tm_t_events_patyear include selected parameter title table. Enhanced tm_t_mult_events include selected parameter title table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-12","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.12","text":"Rewrote modules use moduleServer updated calls teal.devel modules also written use moduleServer. Changed way obtaining selection ordered changes teal.devel. Use ordered = TRUE cs_to_des_select cs_to_select_spec return ordered selection. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. tm_t_events_summary now allows nested arm_var columns matching outputs tm_t_events. Added validation tm_t_abnormality_by_worst_grade arm_var selected. Enhanced tm_t_binary_outcome include responders response table default. Added subtitle tm_g_forest_tte, tm_t_coxreg, tm_t_binary_outcome listing stratification factors.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-12","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.12","text":"Fixed bug prevent processing empty sets data tm_g_forest_rsp.R causing shiny errors runtime. Fixed bug closed Compare Treatments conditional panel marked Combine comparison groups? option conflicted adding column patients tables tm_t_binary_outcome.R tm_t_tte.R.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-12-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.12","text":"Replaced deprecated rtables::var_labels calls documentation examples. Add import tern.mmrm package change references split tern. Adjusted package imports take account changes teal framework. Ensure consistent vertical order tm_g_pp_patient_timeline output switching absolute relative days.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"breaking-changes-0-8-11","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.clinical 0.8.11","text":"Updated tm_t_abnormality due changes count_abnormal abnormal argument taking list input now. Changed tm_g_pp_patient_timeline parameter, cmtrt, cmdecod.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-features-0-8-11","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.11","text":"Added new module tm_t_abnormality_by_worst_grade analysis laboratory test results highest grade post-baseline. Enhanced tm_t_ancova include selected parameter(s), visit(s) analysis variable title table. Added new module tm_g_lineplot creating line plots. Enhanced tm_t_logistic include selected parameter title table. Enhanced tm_g_forest_rsp include selected parameter title table. Enhanced tm_g_forest_tte include selected parameter title table. Enhanced tm_g_pp_patient_timeline bold axes labels integer values axis. Enhanced tm_g_ipp allow users display AVALU title y axis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-11","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.11","text":"Added support logging logger package added info level logs upon initialization module. Added default_responses argument tm_t_binary_outcome tm_g_forest_rsp allow user specify default selected responses possible response levels. Updated tm_t_binary_outcome show selected responses output table selecting “Show Selected Response Categories”. Added rsp_table argument tm_t_binary_outcome allow user initialize module matching RSPT01 STREAM template. Added support custom arguments ggplot2::labs ggplot2::theme plot based modules. Added support custom arguments rtables::basic_table table based modules. Updated tm_t_binary_outcome enable option apply continuity correction Wilson method.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-11","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.11","text":"Updated required R version >= 3.6. Refactored calls defunct teal.devel::data_extract_input calls replacement teal.devel::data_extract_ui. Updated modules use new data_merge_module interface provided teal.devel removed usage now deprecated function teal.devel::get_input_order. Updated tm_t_binary_outcome module add template removed now deprecated module tm_t_rsp. Removed utils.nest dependency replaced calls checkmate equivalents.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-11","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.clinical 0.8.11","text":"Fixed bug tm_g_pp_therapy cmstdy cmendy argument type integer causes plot crash.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-features-0-8-10","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.10","text":"Added new module tm_t_smq analysis adverse events Standardized MedDRA Query. Added new module tm_t_shift_by_grade analysis grade laboratory abnormalities. Added new module tm_t_exposure analysis duration exposure risk management plan. Added new module tm_t_shift_by_arm can display shift table ECG interval data.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-10","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.10","text":"Corrected tm_a_mmrm able consider treatment variable interactions. Fixed tm_t_binary_outcome tm_t_rsp choose correct CI estimation method Proportions Difference Stratified Analysis (.e. Wald-type confidence interval CMH weights).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.10","text":"Added validation checks tm_t_rsp tm_t_binary_outcome stratification errors applied filters. Added tm_g_km validation check plot tables font size. Enhanced tm_g_km add selected paramcd plot title. tm_t_events now can display layouts two nested column treatment variables. options pruning sorting available. Exported package helper functions. Updated tm_t_events_by_grade display grading groups nested columns col_by_grade option support pruning sorting options like tm_t_events. Used format_count_fraction fix formatting inconsistency tm_t_events_summary. Updated count_occurrences vars argument tm_t_shift_by_grade. Updated tm_t_pp_laboratory display 4 decimals default. Updated tm_t_events_by_grade use trim_levels_in_group split function instead trim_rows function. Added table title tm_t_tte. Added table titles tm_t_rsp tm_t_binary_outcome.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.10","text":"Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr. Removed insert_rrow updated usage count_patients_by_flags tm_t_events_summary. Changed package calls functions dplyr package. functions now fully specified (e.g. dplyr::filter).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-features-0-8-9","dir":"Changelog","previous_headings":"","what":"New features","title":"teal.modules.clinical 0.8.9","text":"Added capability remember order user input encoding UI elements. Inputs marked double arrow icon tracking enabled. affected modules : tm_t_summary, tm_t_summary_by, tm_g_forest_rsp, tm_g_forest_tte, tm_t_events_summary, tm_t_abnormality, tm_t_mult_events. Added new argument numeric_stats tm_t_summary tm_t_summary_by control displayed summary statistics numeric variables. Added new argument drop_zero_levels tm_t_summary_by can drop rows zeros result table.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-9","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.9","text":"Split tm_g_patient_profile tabs 8 separate new modules. Added option select patient ID filter panel modules patient profile. Added validation tm_g_patient_timeline plot empty. Enhanced tm_a_mmrm work without treatment variable. Added option choose number decimal places rounding tm_t_pp_laboratory. Added check box tm_g_pp_patient_timeline hiding/showing relative study days x-axis. Added title patient’s id plots patient profile modules. Made gray error message tm_g_forest_tte informative deselecting Endpoint column left-hand encoding panel. Added twenty-fifth seventy-fifth quantile summary statistics tm_t_summary. Added interaction p-value column tm_t_coxreg. Added validation tm_t_ancova selected covariate variables contain one level. Added validation tm_t_events_patyear events variable empty. Changed font size input description tm_g_km precisely describe controls. Enhanced tm_t_logistic interaction choices depend selected covariates. Enhanced tm_t_rsp strata input visible comparing treatments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-9","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.9","text":"Fixed Get R Code output tm_t_pp_laboratory return identical HTML formatted table displayed app. Added validation tm_t_coxreg ensure treatment, strata covariate variables overlap. Limited label repel feature tm_g_pp_patient_timeline X-axis consistent look. Updated tm_t_summary_by paramcd required analyzing ADSL variables. Updated tm_t_coxreg can work covariate selected. Updated tm_a_mmrm can work treatment variable selected. Updated tm_g_forest_tte total number events also shown table. Updated tm_t_events_summary work pooled studies. Updated validation level tm_t_coxreg. Updated validation level tm_t_logistic. Added validation tm_t_binary_outcome tm_t_rsp ensure strata variable contains one level selecting one strata variable. Updated warning message deselecting statistics tm_t_summary tm_t_summary_by explain need select least one statistic.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.8","text":"Added option download expand tables. tm_g_km added support downloading images updated x-axis label show title case. Added slider font size plots. Added persistence selected table lengths. timeline plot now supports edge cases. vitals tab, removed unused label text legend, updated plot display stable colors per levels, cleared x-axis limit fixed legend update filtering. Also added note clarify supported horizontal lines cases. Updated adverse events tab show warning message instead empty plot data empty. Fixed PARAMCD selected levels current patient. Updated pre-processing code inside template_tte dataset without events still produces table. Updated code use correct denominator duration response endpoints. Modified parameter arm_var accept one column. selecting two columns arm_var, second variable nest first one. Added argument show_labels template_summary show label single summary variable table. Added new parameter conf_arg tm_t_rsp consistent efficacy modules. Added validation statement tm_g_ipp module print message deselecting Timepoint Variable drop-. Removed header definition tm_g_forest_rsp tm_g_forest_tte now default header g_forest. Fixed validation statement tm_t_coxreg models without strata using likelihood tests return result. Clarified functionality drop_arm_levels tm_t_summary tm_t_summary_by. encodings panel, checkbox show parent dataset analysis dataset different.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.8","text":"Replaced remaining two observe function calls observeEvent optimize performance. Fixed grammar “Select patient’s id” error message tm_g_patient_profile. Fixed font_size default templates 12L instead vector 3 integers cleaned associated unnecessary code. Fixed deprecated function warning tm_g_barchart_simple. Fixed subgroup_var definition truncation tm_g_forest_rsp tm_g_forest_tte. Clarified labeling related regression type encoding panel tm_t_coxreg.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-8","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.8","text":"Added validation case filtering rows therapy tab tm_g_patient_profile. Updated internals modules read data correct field filter_spec objects. Fixed reactivity filter panel PARAMCD variable levels input tm_g_patient_profile vitals tab plot get reset filtering. Updated vitals plot tab tm_g_patient_profile drop NA entries plot. Updated tm_t_coxreg take values account. Added check tm_t_coxreg interactions univariate models multivariate models. Updated tm_t_events_summary work pooled studies.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-module-0-8-7","dir":"Changelog","previous_headings":"","what":"New Module","title":"teal.modules.clinical 0.8.7","text":"Added new module tm_g_patient_profile profile patients based predefined categories. Added new module tm_g_ipp individual patient plots.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.7","text":"Added argument drop_arm_levels safety modules. allows removal columns based factor levels found filtered data. Updated tm_g_km allow plot failure probability y-axis, tick interval selection x-axis option create plot without confidence interval ribbon (new default). Added argument time_unit_var template_g_km add time unit x-axis label.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.7","text":"Removed redundant Analysis Data: label Encodings Panel. Removed limit requiring 15 fewer columns tabulation modules. New upper threshold 100 columns. Decreased lower limit number observations required modules. Safety tables require least one record. Requirements efficacy outputs per treatment group: tm_a_mmrm requires five records, tm_t_logistic tm_t_coxreg require two records, remaining modules require least one record per treatment group. graphs, lower threshold two records. Removed argument cnsr_val tm_t_events_patyear added new argument events_var. arm_ref_comp_observer include parentname argument. Show R code include datasets retrieved data_extract_spec objects. Refactored stringr dependency patient profile module. Added missing table calls chunks tm_t_events tm_t_events_by_grade.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"new-features-0-8-6","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.clinical 0.8.6","text":"Added new module tm_g_ci confidence interval plots. Added new module tm_t_ancova analysis variance summary tables. Added new module tm_t_mult_events multi-event tables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"enhancements-0-8-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.clinical 0.8.6","text":"Refactored modules using redesigned rtables tern packages. Enhanced modules. now take advantage data_extract_spec data_merge_module functionality teal. Reduced clutter repeated datasets encodings panels. Updated modules use OptionalSelectInput conf_level.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"miscellaneous-0-8-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.clinical 0.8.6","text":"Added vignette substitute can helpful developing analysis template functions teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"bug-fixes-0-8-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.modules.clinical 0.8.6","text":"Updated tm_t_events module use user’s non-default choices prune_freq prune_diff.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-085","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.5","title":"teal.modules.clinical 0.8.5","text":"graph modules now accept plot_width argument specifies plot width renders slider adjust width interactively module. FilteredData object now passed arm_ref_comp_observer modules now support nested lists containing delayed_data objects. Replace plot_with_height module new plot_with_settings module. Update examples use code argument inside cdisc_dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-084","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.4","title":"teal.modules.clinical 0.8.4","text":"Extend tm_t_coxreg optionally produce univariate Cox regressions. Updated tm_t_binary_outcome display Odds Ratio estimates, include new methods CIs p-values display summary individual response categories. Updated tm_t_tte optionally compare arms, removed conf_level argument. Updated tm_g_km optionally compare arms. Extend tm_g_km optionally scale X axis range case one plot. New tm_a_mmrm MMRM analysis. Deprecated tm_t_mmrm (superseded tm_a_mmrm).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-083","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.3","title":"teal.modules.clinical 0.8.3","text":"New tm_t_coxreg module multi-variable Cox regressions. New tm_t_binary_outcome module. New tm_t_events_patyear module: events rate adjusted patient-year risk table. Remove grade_levels argument tm_t_events_by_grade. Updated response table single arm. New tm_t_abnormality module. Removed get_relabel_call get_relabel_call2 favor teal.devel::get_relabel_call teal.devel::get_anl_relabel_call.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-082","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.2","title":"teal.modules.clinical 0.8.2","text":"Add confidence level survfit, coxph, ztest; add confidence type, ties, percentiles tm_t_tte. Optionally use single term tm_t_events tm_t_events_by_grade modules. New tm_t_logistic module. New tm_t_mmrm module. New modules tm_t_summary_by tm_t_events_summary. Add stratified analysis tm_g_forest_tte tm_g_forest_rsp. Add confidence level plotting symbol size options tm_g_forest_rsp tm_g_forest_tte.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-081","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.1","title":"teal.modules.clinical 0.8.1","text":"New tm_t_events tm_t_events_by_grade modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-080","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.8.0","title":"teal.modules.clinical 0.8.0","text":"Optionally show KM CoxPH table tm_g_km.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-070","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.7.0","title":"teal.modules.clinical 0.7.0","text":"Use teal.devel.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.clinical/main/news/index.html","id":"tealmodulesclinical-060","dir":"Changelog","previous_headings":"","what":"teal.modules.clinical 0.6.0","title":"teal.modules.clinical 0.6.0","text":"Package renamed teal.modules.clinical. Rename tm_t_summarize_variables tm_t_summary. Usage teal::choices_selected() function instead *_var *_var_choices arguments.","code":""}]