Add Documentation Landing Page

_quarto.yml

@@ -68,6 +68,7 @@ website:
       collapse-level: 2
       contents:
         - documentation/index.qmd
+        - auto: documentation/*.qmd  
         - section: Version 7.1
           contents:
             - section: User Guides

docs/concepts/facts/LinearRegressionLMPriors.html

@@ -394,7 +394,7 @@ <h3 class="anchored" data-anchor-id="interpretation-of-parameters">Interpretatio
 The standard deviation around the expectation of the final visit response. This dictates how close the imputed final endpoint responses are to the mean response for a subject given <span class="math inline">\(\alpha\)</span> and <span class="math inline">\(\beta\)</span>. Lower <span class="math inline">\(\lambda_t\)</span> implies higher correlation between the early visit response and final visit response.
 </dd>
 </dl>
-<p>```tpptxlgagaafd #| standalone: true #| viewerHeight: 1000</p>
+<p>```ddqkfmcfhjlyc #| standalone: true #| viewerHeight: 1000</p>
 <p>library(shiny) library(DT) library(ggplot2) library(htmltools)</p>
 <p>alignCenter &lt;- function(el) { htmltools::tagAppendAttributes(el, style=“margin-left:auto;margin-right:auto;” ) }</p>
 <p>sketch = htmltools::withTags(table( class = ‘display’, thead( tr( th(rowspan = 2, ’‘), th(rowspan = 2, style = “border-right: solid 1px;”,’Observed Visit Data’), th(colspan = 2, class=” dt-center”, style = “border-right: solid 1px;”,‘B1 priors’), th(colspan = 2, class=” dt-center”, style = “border-right: solid 1px;”,‘B2 priors’), th(colspan = 2, class=” dt-center”, style = “border-right: solid 1px;”,‘BB priors’) ), tr( th(“mean”), th(style = “border-right: solid 1px;”, “SD”), th(“mean”), th(style = “border-right: solid 1px;”, “SD”), th(“center”), th(style = “border-right: solid 1px;”, “weight”), ) ) ))</p>

docs/documentation/index.html

@@ -152,6 +152,12 @@
   <a href="../documentation/index.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
@@ -255,21 +261,28 @@
 </nav>
 <div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+
+  <ul>
+  <li><a href="#what-youll-find-here" id="toc-what-youll-find-here" class="nav-link active" data-scroll-target="#what-youll-find-here">What You’ll Find Here</a></li>
+  <li><a href="#how-to-get-the-most-out-of-this-section" id="toc-how-to-get-the-most-out-of-this-section" class="nav-link" data-scroll-target="#how-to-get-the-most-out-of-this-section">How to Get the Most Out of This Section</a></li>
+  </ul>
+</nav>
     </div>
 <!-- main -->
-<main class="content column-page-right" id="quarto-document-content">
+<main class="content column-body" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Documentation</h1>
-<p class="subtitle lead">FACTS 7.1.1</p>
+<p class="subtitle lead">Your Comprehensive Resource for Understanding and Using Our Software</p>
 </div>
 
 
 
-<div class="quarto-title-meta column-page-right">
+<div class="quarto-title-meta column-body">
 
 
 
@@ -281,125 +294,21 @@ <h1 class="title">Documentation</h1>
 </header>
 
 
-<p>Home page for Documentation.</p>
-<p><a href="#tbl-crmterms" class="quarto-xref">Table&nbsp;1</a> gives an overview of the acronyms and abbreviations used in the documentation.</p>
-<div id="tbl-crmterms" class="striped hover quarto-float quarto-figure quarto-figure-center anchored" data-tbl-colwidths="[15,85]">
-<figure class="quarto-float quarto-float-tbl figure">
-<figcaption class="quarto-float-caption-top quarto-float-caption quarto-float-tbl" id="tbl-crmterms-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-Table&nbsp;1: List of terms used in the user guides
-</figcaption>
-<div aria-describedby="tbl-crmterms-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<table class="table-striped table-hover caption-top table">
-<colgroup>
-<col style="width: 15%">
-<col style="width: 85%">
-</colgroup>
-<thead>
-<tr class="header">
-<th style="text-align: left;">Name</th>
-<th style="text-align: left;">Definition</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td style="text-align: left;">Cap</td>
-<td style="text-align: left;">A limit on the number of subjects recruited. In FACTS N-CRM users can specify a cap on the overall number of subjects to be recruited in the trial (the ‘Overall Cap’) and specify stopping rules to define when the trial should stop before it reaches cap.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Control</td>
-<td style="text-align: left;">Is the treatment arm with which the novel treatment(s) are principally being compared. Control may be placebo, or some existing standard of care, or therapy, against which the novel treatment has to be benchmarked in order to determine its likely usefulness.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Core</td>
-<td style="text-align: left;">FACTS Core: A mode of FACTS for designing trials where multiple treatments, (possibly different doses of a novel treatment) are tested against a control and optionally an active comparator.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">CRM</td>
-<td style="text-align: left;">Continual Reassessment Method – a dose escalation design where the dose-toxicity is estimated using a simple Bayesian model, and the resulting estimates used to control the dose escalation and estimate the Maximum Tolerated Dose (MTD).</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">DE</td>
-<td style="text-align: left;">Dose Escalation: a mode of FACTS where subjects are treated in cohorts and dose escalation is determined by the number of toxicities observed.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">ED</td>
-<td style="text-align: left;">Enrichment Designs: a mode of FACTS for designing trials where the same treatment is testing in different settings for example different sub-populations or different but related indications.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">FACTS</td>
-<td style="text-align: left;">Fixed and Adaptive Clinical Trial Simulator.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Final Endpoint</td>
-<td style="text-align: left;">The final value, or state, of a subject’s endpoint.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">GUI</td>
-<td style="text-align: left;">Graphical User Interface, the part of the FACTS application that the user interacts with.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Method</td>
-<td style="text-align: left;">In the FACTS documentation we try to reserve the term ‘method’ for the algorithms used in the simulation (as opposed to the analysis) part of the program. In the analysis part we use the term ‘Model’, see below.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Model</td>
-<td style="text-align: left;">In the FACTS documentation we try to reserve the term ‘model’ for the statistical models used in the analysis of the trial data (in the ‘design’ section of the FACTS user interface). Where mathematical algorithms are used for other purposes in FACTS (for instance in the generation of the simulated data) we try to use the term ‘method’. We have found that initially it is very easy for users to be confused between these two parts of FACTS and we feel that using distinct terminology may help to reduce this.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">MTD</td>
-<td style="text-align: left;">The dose most likely to be the Maximum Tolerated Dose (MTD) – the dose with the highest Pr(MTD).</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">MTD+</td>
-<td style="text-align: left;">The dose most likely to be the MTD+ – the dose with the highest Pr(MTD+).</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Pr(MTD)</td>
-<td style="text-align: left;">A dose’s probability of being MTD is the probability that it is the dose with the highest probability of having a toxicity rate in the acceptable toxicity band, and (if a threshold has been specified) does not have a probability of excess or unacceptable toxicity above the threshold. This estimate of MTD is constrained to select one of the available doses.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Pr(MTD+)</td>
-<td style="text-align: left;">A dose’s probability of being the MTD+ is the probability that it is the dose with the highest probability of having a toxicity rate in the acceptable band, and (if a threshold has been specified) does not have a probability of excess or unacceptable toxicity above the threshold. Unlike Pr(MTD), Pr(MTD+) includes estimating whether a dose below or a dose above the range of those being tested is more likely to have a toxicity in the acceptable band than any of the doses in the range.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Profile</td>
-<td style="text-align: left;">A profile is a specification of one aspect of a scenario. A scenario is made up of one profile of each of the required types for the type of trial being simulated. FACTS allows the user to specify multiple profiles of each type and then presents all the possible combinations of profiles as scenarios that can be used to drive simulations.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Response</td>
-<td style="text-align: left;">The change in a subject’s endpoint compared to their baseline state.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Scenario</td>
-<td style="text-align: left;">A scenario is the complete specification of the unknown external factors that determine the data observed on the trial and its timing. The exact factors depend on the type of trial being simulated but typically include: <br> -) the distribution of the final change from base line, or probability of response or rate of events in the different treatment groups <br> -) the properties of subjects’ early responses and the correlation with their final outcome <br> -) the rate at which subjects are recruited into the trial <br> -) the rate at which subjects drop out of the trial.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">SPEC</td>
-<td style="text-align: left;">The Design Engine Specification, describes the system algorithms, and meaning of parameters.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Response</td>
-<td style="text-align: left;">The change in a subject’s endpoint compared to their baseline state.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Subject</td>
-<td style="text-align: left;">Someone recruited onto a clinical trial for the purposes of learning about the properties of a treatment. Depending on the type of trial they might be patients or they might be healthy volunteers.</td>
-</tr>
-<tr class="even">
-<td style="text-align: left;">Treatment Arm</td>
-<td style="text-align: left;">Subjects on entering the study are randomized to different ‘treatment arms’. Subjects randomized to the same arm receive the same treatment and the responses of the subjects in the arm analyzed to determine the expected response to that treatment, allowing the expected responses to the different treatments to be compared.</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">UG</td>
-<td style="text-align: left;">The User Guide; describes how to use the system.</td>
-</tr>
-</tbody>
-</table>
-</div>
-</figure>
-</div>
+<p>Welcome to the Documentation section — your go-to repository of in-depth user guides and practical examples that illuminate every aspect of FACTS. Whether you’re just getting started or delving into advanced functionalities, these resources are designed to help you navigate our software with confidence and ease.</p>
+<section id="what-youll-find-here" class="level2">
+<h2 class="anchored" data-anchor-id="what-youll-find-here">What You’ll Find Here</h2>
+<ul>
+<li>User Guides: Access detailed manuals covering the full range of our engines. From foundations to advanced features, learn how to set up your desired trial design, learn about best practices and obtain focused understanding of the subject matter, and troubleshoot common issues.</li>
+<li>Installation Instructions: Get up and running quickly with clear guidance. Our installation resources walk you through every phase—downloading the software, deploying it in various environments, and start FACTSing!</li>
+<li>Examples: Explore a range of constructed and real-world studies that demonstrate our software’s capabilities in action and discover strategies to optimize performance.</li>
+</ul>
+</section>
+<section id="how-to-get-the-most-out-of-this-section" class="level2">
+<h2 class="anchored" data-anchor-id="how-to-get-the-most-out-of-this-section">How to Get the Most Out of This Section</h2>
+<p>This section contains resources for the current and past versions of FACTS, which you can choose in the sidebar. If necessary, begin by reviewing the installation guides. Later, you may consult engine-specific user manuals for deeper insights, and explore our curated examples to bring theory into practice. With these resources at your fingertips, you’ll gain a richer, more informed understanding of FACTS and maximize your potential for success.</p>
 
 
+</section>
 
 </main> <!-- /main -->
 <!-- footer.html -->

docs/documentation/v71/examples/CRM/example1.html

@@ -152,6 +152,12 @@
   <a href="../../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/examples/CRM/example2.html

@@ -152,6 +152,12 @@
   <a href="../../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/examples/Staged/example1.html

@@ -152,6 +152,12 @@
   <a href="../../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/examples/Staged/example2.html

@@ -152,6 +152,12 @@
   <a href="../../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/userguides/core.html

@@ -181,6 +181,12 @@
   <a href="../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/userguides/crm.html

@@ -235,6 +235,12 @@
   <a href="../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

docs/documentation/v71/userguides/installation.html

@@ -152,6 +152,12 @@
   <a href="../../../documentation/index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Documentation</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../../documentation/glossary.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Glossary</span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container">