diff --git a/book/test-utils/envir_hook.qmd b/book/_utils/envir_hook.qmd
similarity index 100%
rename from book/test-utils/envir_hook.qmd
rename to book/_utils/envir_hook.qmd
diff --git a/book/test-utils/save_results.qmd b/book/_utils/save_results.qmd
similarity index 100%
rename from book/test-utils/save_results.qmd
rename to book/_utils/save_results.qmd
diff --git a/book/webr-utils/shinylive.qmd b/book/_utils/shinylive.qmd
similarity index 100%
rename from book/webr-utils/shinylive.qmd
rename to book/_utils/shinylive.qmd
diff --git a/book/webr-utils/webr.qmd b/book/_utils/webr.qmd
similarity index 100%
rename from book/webr-utils/webr.qmd
rename to book/_utils/webr.qmd
diff --git a/book/appendix/reproducibility.qmd b/book/appendix/reproducibility.qmd
index 54d4b5b664..ae3ff89c15 100644
--- a/book/appendix/reproducibility.qmd
+++ b/book/appendix/reproducibility.qmd
@@ -4,7 +4,7 @@ title: Reproducibility
------------------------------------------------------------------------
-{{< include ../test-utils/envir_hook.qmd >}}
+{{< include ../_utils/envir_hook.qmd >}}
## Session Info
diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd
index 875f9796dd..02ef1d0e99 100644
--- a/book/graphs/efficacy/fstg01.qmd
+++ b/book/graphs/efficacy/fstg01.qmd
@@ -5,7 +5,7 @@ subtitle: Subgroup Analysis of Best Overall Response
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,7 +70,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Specifying Class Variables and
Options for the Treatment Variable
@@ -118,7 +118,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Selecting Columns and
Changing the Alpha Level
@@ -148,7 +148,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Fixed
Symbol Size
@@ -181,7 +181,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of CR Only, Setting
Values Indicating Response
@@ -228,10 +228,10 @@ height <- 5
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -302,7 +302,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
index 672c23e86d..f7042212f2 100644
--- a/book/graphs/efficacy/fstg02.qmd
+++ b/book/graphs/efficacy/fstg02.qmd
@@ -5,7 +5,7 @@ subtitle: Subgroup Analysis of Survival Duration
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -83,7 +83,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Specifying Class Variables and
Options for the Treatment Variable
@@ -125,7 +125,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Selecting Columns and
Changing the Alpha Level
@@ -156,7 +156,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Fixed
Symbol Size
@@ -196,10 +196,10 @@ plot_v3.width <- 8 # nolint: object_name.
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -278,7 +278,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd
index 058380dbe6..b978e8ab1f 100644
--- a/book/graphs/efficacy/kmg01.qmd
+++ b/book/graphs/efficacy/kmg01.qmd
@@ -5,7 +5,7 @@ subtitle: Kaplan-Meier Plot
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -44,7 +44,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Failures
@@ -67,7 +67,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Without
Comparative Statistics
@@ -87,7 +87,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Without
Censoring Marks
@@ -109,7 +109,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Modifying
Censoring Marks
@@ -132,7 +132,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Modifying Options for Statistics,
Tie Handling, Stratification, etc.
@@ -160,7 +160,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
::: {.content-visible when-profile="development"}
@@ -170,7 +170,7 @@ height <- 6
```
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -240,7 +240,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd
index d6741aec55..7a5884d1f0 100644
--- a/book/graphs/efficacy/mmrmg01.qmd
+++ b/book/graphs/efficacy/mmrmg01.qmd
@@ -5,7 +5,7 @@ subtitle: Plots for Mixed-Effect Model Repeated Measures Analysis
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
Given an MMRM fitted with `s_mmrm`, `g_mmrm_lsmeans` displays for each visit the adjusted means within group and/or difference in adjusted means between groups.
`g_mmrm_diagnostic` displays marginal residual plots for evaluating model fit.
@@ -114,7 +114,7 @@ plot <- g_mmrm_diagnostic(mmrm_results, type = "q-q-residual")
plot
```
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/efficacy/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd
index be80ba1ec7..d2d52917fb 100644
--- a/book/graphs/efficacy/mmrmg02.qmd
+++ b/book/graphs/efficacy/mmrmg02.qmd
@@ -5,7 +5,7 @@ subtitle: Forest Plot for Mixed-Effect Model Repeated Measures
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -136,7 +136,7 @@ width <- 15
height <- 4
```
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/other/brg01.qmd b/book/graphs/other/brg01.qmd
index 1f85df0d13..b78d6d52fd 100644
--- a/book/graphs/other/brg01.qmd
+++ b/book/graphs/other/brg01.qmd
@@ -5,7 +5,7 @@ subtitle: Bar Chart
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -61,7 +61,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Percentage
@@ -92,7 +92,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Frequency with
Total Number of Subjects
@@ -120,7 +120,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Frequency
with Horizontal Bars
@@ -144,7 +144,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Percentage
and Confidence Intervals
@@ -196,7 +196,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Percentage by
Treatment and Covariate
@@ -229,7 +229,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Percentage by
Covariate and Treatment
@@ -261,7 +261,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot7")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Percentage
with Mean and Median
@@ -331,7 +331,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot8")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Categorical
Variable
@@ -368,10 +368,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot9")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/other/bwg01.qmd b/book/graphs/other/bwg01.qmd
index 782c2a689f..7164f02ba0 100644
--- a/book/graphs/other/bwg01.qmd
+++ b/book/graphs/other/bwg01.qmd
@@ -5,7 +5,7 @@ subtitle: Box Plot
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -108,7 +108,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Changing
Whiskers
@@ -137,7 +137,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Adding
Outliers
@@ -167,7 +167,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Specifying Marker
for Outliers and
Adding Patient ID
@@ -208,7 +208,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot Specifying
Marker for Mean
@@ -234,7 +234,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot by Treatment
and Timepoint
@@ -278,7 +278,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot by Timepoint
and Treatment
@@ -316,7 +316,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot7")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with
Table Section
@@ -390,7 +390,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot8")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Number of Patients
only in Table Section
@@ -417,10 +417,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot8", "plot9")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -527,7 +527,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/other/cig01.qmd b/book/graphs/other/cig01.qmd
index c27bff57e8..0f1f34df26 100644
--- a/book/graphs/other/cig01.qmd
+++ b/book/graphs/other/cig01.qmd
@@ -5,7 +5,7 @@ subtitle: Confidence Interval Plot
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -61,7 +61,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1and2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Confidence Interval Using
a Different Stratification Variable
@@ -99,7 +99,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Median and
95% CIs for Median
@@ -139,7 +139,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Median and 95% CIs for
Median Using Different Alpha Level
@@ -179,7 +179,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of Mean
and Median
@@ -198,10 +198,10 @@ table
```
`r webr_code_labels <- c("setup", "table6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -289,7 +289,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd
index 6c00435519..8881478c4d 100644
--- a/book/graphs/other/ippg01.qmd
+++ b/book/graphs/other/ippg01.qmd
@@ -5,7 +5,7 @@ subtitle: Individual Patient Plot Over Time
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
For illustration purposes, we will subset the `adlb` dataset for safety population in treatment arm A and a specific lab parameter (`ALT`).
@@ -65,7 +65,7 @@ plots
```
`r webr_code_labels <- c("setup", "plots1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Patient Baselines as Reference
@@ -97,10 +97,10 @@ plots
```
`r webr_code_labels <- c("setup", "plots2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -180,7 +180,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/other/ltg01.qmd b/book/graphs/other/ltg01.qmd
index 9db5cec6a1..81e191870a 100644
--- a/book/graphs/other/ltg01.qmd
+++ b/book/graphs/other/ltg01.qmd
@@ -5,7 +5,7 @@ subtitle: Lattice Plot of Laboratory Tests by Treatment Group Over Time
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
Lattice plots are natively handled by R, the examples below rely mostly on the package `ggplot2`.
@@ -75,7 +75,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Modifying Facets
@@ -98,7 +98,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Modifying X-Axis
@@ -121,7 +121,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1", "plot2", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Liver Function Tests
Including Mean, Median, and 95% CIs
@@ -192,7 +192,7 @@ plot
```
`r webr_code_labels <- c("setup", "pre-processing", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Adding Mean
@@ -216,7 +216,7 @@ plot
```
`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Adding Median
@@ -240,7 +240,7 @@ plot
```
`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot51", "plot52")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Changing Confidence Level
@@ -265,10 +265,10 @@ plot
```
`r webr_code_labels <- c("setup", "pre-processing", "plot4", "plot53")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd
index af11f08142..23b2bef627 100644
--- a/book/graphs/other/mng01.qmd
+++ b/book/graphs/other/mng01.qmd
@@ -5,7 +5,7 @@ subtitle: Mean Plot
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -67,7 +67,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Mean and CIs of Change
from Baseline (Changing the Input
Analysis Data Set and Analysis Variable)
@@ -88,7 +88,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Mean (+/-SD)
(Changing the Statistics)
@@ -110,7 +110,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Mean and CI
(Modify Alpha Level)
@@ -131,7 +131,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Mean and CI (with Number
of Patients only in Table Section)
@@ -151,7 +151,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Mean and CI
(with Table Section)
@@ -171,7 +171,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot of Median and CI (Visits
Condensed in Table Section)
@@ -195,10 +195,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot7")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -254,7 +254,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/pharmacokinetic/pkcg01.qmd b/book/graphs/pharmacokinetic/pkcg01.qmd
index c0d0c550ee..15b1842d62 100644
--- a/book/graphs/pharmacokinetic/pkcg01.qmd
+++ b/book/graphs/pharmacokinetic/pkcg01.qmd
@@ -5,7 +5,7 @@ subtitle: Plot of PK Concentration Over Time by Subject
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -60,7 +60,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot in Log Scale
@@ -101,10 +101,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/pharmacokinetic/pkcg02.qmd b/book/graphs/pharmacokinetic/pkcg02.qmd
index 92a002f750..e9ffa4b2f9 100644
--- a/book/graphs/pharmacokinetic/pkcg02.qmd
+++ b/book/graphs/pharmacokinetic/pkcg02.qmd
@@ -5,7 +5,7 @@ subtitle: Plot of PK Concentration Over Time by Cohort/Treatment Group/Dose
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -60,7 +60,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot in Log Scale
@@ -102,10 +102,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd
index f83ccc84a0..8768a79beb 100644
--- a/book/graphs/pharmacokinetic/pkcg03.qmd
+++ b/book/graphs/pharmacokinetic/pkcg03.qmd
@@ -5,7 +5,7 @@ subtitle: Plot of Mean PK Concentration Over Time by Cohort
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -69,7 +69,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot in Log Scale
@@ -114,10 +114,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd
index 52291e3f15..3a2447ea4b 100644
--- a/book/graphs/pharmacokinetic/pkpg01.qmd
+++ b/book/graphs/pharmacokinetic/pkpg01.qmd
@@ -5,7 +5,7 @@ subtitle: Plot of Mean Cumulative Percentage (%) of Recovered Drug in Urine
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -85,7 +85,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Six Cohorts
@@ -149,10 +149,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/pharmacokinetic/pkpg02.qmd b/book/graphs/pharmacokinetic/pkpg02.qmd
index a5b5d19e4a..87c348bcf9 100644
--- a/book/graphs/pharmacokinetic/pkpg02.qmd
+++ b/book/graphs/pharmacokinetic/pkpg02.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary of Serum PK Parameters by Treatment
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -117,7 +117,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Summary of Plasma Pharmacokinetic
Parameters with Median Points
@@ -165,10 +165,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/graphs/pharmacokinetic/pkpg03.qmd b/book/graphs/pharmacokinetic/pkpg03.qmd
index 9f281765e5..ecf90046fd 100644
--- a/book/graphs/pharmacokinetic/pkpg03.qmd
+++ b/book/graphs/pharmacokinetic/pkpg03.qmd
@@ -5,7 +5,7 @@ subtitle: Box Plot of Pharmacokinetic Parameters by Visit -- Plasma
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -66,10 +66,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/pharmacokinetic/pkpg04.qmd b/book/graphs/pharmacokinetic/pkpg04.qmd
index 1fedd4a9bb..8477ee9d0f 100644
--- a/book/graphs/pharmacokinetic/pkpg04.qmd
+++ b/book/graphs/pharmacokinetic/pkpg04.qmd
@@ -5,7 +5,7 @@ subtitle: Box Plot of Pharmacokinetic Parameters by Visit -- Plasma
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -68,10 +68,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/graphs/pharmacokinetic/pkpg06.qmd b/book/graphs/pharmacokinetic/pkpg06.qmd
index eda138f6fe..b747bd3f7d 100644
--- a/book/graphs/pharmacokinetic/pkpg06.qmd
+++ b/book/graphs/pharmacokinetic/pkpg06.qmd
@@ -5,7 +5,7 @@ subtitle: Boxplot of Metabolite to Parent Ratios by Treatment
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -110,7 +110,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Drug Y Boxplot
@@ -160,7 +160,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Whiskers at
Minimum and Maximum Values
@@ -196,7 +196,7 @@ plot
```
`r webr_code_labels <- c("setup", "plot3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Plot with Whiskers at
5th and 95th Percentiles
@@ -265,10 +265,10 @@ plot
```
`r webr_code_labels <- c("setup", "plot4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/listings/ADA/adal02.qmd b/book/listings/ADA/adal02.qmd
index a35769fa75..8c3c740e08 100644
--- a/book/listings/ADA/adal02.qmd
+++ b/book/listings/ADA/adal02.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Anti-Drug Antibody Data for Treatment Emergent ADA Positive
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -132,10 +132,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/ECG/egl01.qmd b/book/listings/ECG/egl01.qmd
index 2ded459bb0..13dddd91a7 100644
--- a/book/listings/ECG/egl01.qmd
+++ b/book/listings/ECG/egl01.qmd
@@ -5,7 +5,7 @@ subtitle: 'Listing of ECG Data: Safety-Evaluable Patients'
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -99,10 +99,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael01.qmd b/book/listings/adverse-events/ael01.qmd
index d4a8689c39..3b407ed324 100644
--- a/book/listings/adverse-events/ael01.qmd
+++ b/book/listings/adverse-events/ael01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Preferred Terms, Lowest Level Terms, and Investigator-Speci
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -49,10 +49,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael01_nollt.qmd b/book/listings/adverse-events/ael01_nollt.qmd
index 0e3abbfeb2..2d69881016 100644
--- a/book/listings/adverse-events/ael01_nollt.qmd
+++ b/book/listings/adverse-events/ael01_nollt.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Preferred Terms and Investigator-Specified Adverse Event Te
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -48,10 +48,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael02.qmd b/book/listings/adverse-events/ael02.qmd
index 248f1fda00..166cb605cd 100644
--- a/book/listings/adverse-events/ael02.qmd
+++ b/book/listings/adverse-events/ael02.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Adverse Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -91,10 +91,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael02_ed.qmd b/book/listings/adverse-events/ael02_ed.qmd
index a6574ed9ac..623606a41e 100644
--- a/book/listings/adverse-events/ael02_ed.qmd
+++ b/book/listings/adverse-events/ael02_ed.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Adverse Events (for Early Development Studies)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -109,10 +109,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael03.qmd b/book/listings/adverse-events/ael03.qmd
index 3e68bde13c..6917f7655a 100644
--- a/book/listings/adverse-events/ael03.qmd
+++ b/book/listings/adverse-events/ael03.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Serious Adverse Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -105,10 +105,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/adverse-events/ael04.qmd b/book/listings/adverse-events/ael04.qmd
index b997a4270a..23c887c7d6 100644
--- a/book/listings/adverse-events/ael04.qmd
+++ b/book/listings/adverse-events/ael04.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Patient Deaths
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -59,10 +59,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/concomitant-medications/cml01.qmd b/book/listings/concomitant-medications/cml01.qmd
index b2ffcc6132..65e7ed40eb 100644
--- a/book/listings/concomitant-medications/cml01.qmd
+++ b/book/listings/concomitant-medications/cml01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Previous and Concomitant Medications
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,10 +70,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/concomitant-medications/cml02a_gl.qmd b/book/listings/concomitant-medications/cml02a_gl.qmd
index d0df99d432..9df1ec3533 100644
--- a/book/listings/concomitant-medications/cml02a_gl.qmd
+++ b/book/listings/concomitant-medications/cml02a_gl.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Concomitant Medication Class Level 2, Preferred Name, and I
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -48,10 +48,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/concomitant-medications/cml02b_gl.qmd b/book/listings/concomitant-medications/cml02b_gl.qmd
index b47fdee1d0..d047d9b72a 100644
--- a/book/listings/concomitant-medications/cml02b_gl.qmd
+++ b/book/listings/concomitant-medications/cml02b_gl.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Concomitant Medication Class, Preferred Name, and Investiga
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -51,10 +51,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/development-safety-update-report/dsur4.qmd b/book/listings/development-safety-update-report/dsur4.qmd
index 97b07b9fa9..d5ad418f94 100644
--- a/book/listings/development-safety-update-report/dsur4.qmd
+++ b/book/listings/development-safety-update-report/dsur4.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Patients Who Died During Reporting Period
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -50,10 +50,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/disposition/dsl01.qmd b/book/listings/disposition/dsl01.qmd
index 9c43fe0ec7..5fe113e61d 100644
--- a/book/listings/disposition/dsl01.qmd
+++ b/book/listings/disposition/dsl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Patients with Study Drug Withdrawn Due to Adverse Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -58,10 +58,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/disposition/dsl02.qmd b/book/listings/disposition/dsl02.qmd
index 01fad5c063..67a11e97d5 100644
--- a/book/listings/disposition/dsl02.qmd
+++ b/book/listings/disposition/dsl02.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Patients Who Discontinued Early from Study
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -66,10 +66,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/efficacy/oncl01.qmd b/book/listings/efficacy/oncl01.qmd
index a2d43a3f86..032bebaa89 100644
--- a/book/listings/efficacy/oncl01.qmd
+++ b/book/listings/efficacy/oncl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Individual Efficacy Data
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -110,10 +110,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/exposure/exl01.qmd b/book/listings/exposure/exl01.qmd
index 816a7bbe84..76d9850d5e 100644
--- a/book/listings/exposure/exl01.qmd
+++ b/book/listings/exposure/exl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Exposure to Study Drug
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -58,10 +58,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/lab-results/lbl01.qmd b/book/listings/lab-results/lbl01.qmd
index 0e4f3efbee..8edc48dffd 100644
--- a/book/listings/lab-results/lbl01.qmd
+++ b/book/listings/lab-results/lbl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Laboratory Test Results
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -83,10 +83,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/lab-results/lbl01_rls.qmd b/book/listings/lab-results/lbl01_rls.qmd
index ba2c970d55..b1601eb34a 100644
--- a/book/listings/lab-results/lbl01_rls.qmd
+++ b/book/listings/lab-results/lbl01_rls.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Laboratory Test Results Using Roche Safety Lab Standardizat
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -88,10 +88,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/lab-results/lbl02a.qmd b/book/listings/lab-results/lbl02a.qmd
index 49c2fa106b..d4ffd25287 100644
--- a/book/listings/lab-results/lbl02a.qmd
+++ b/book/listings/lab-results/lbl02a.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Laboratory Abnormalities (constant units)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -83,10 +83,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/lab-results/lbl02a_rls.qmd b/book/listings/lab-results/lbl02a_rls.qmd
index ff2c52809d..61e1aa523f 100644
--- a/book/listings/lab-results/lbl02a_rls.qmd
+++ b/book/listings/lab-results/lbl02a_rls.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Laboratory Abnormalities Defined by Roche Safety Lab Standa
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -103,10 +103,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/lab-results/lbl02b.qmd b/book/listings/lab-results/lbl02b.qmd
index 095007ecdd..141c5d935b 100644
--- a/book/listings/lab-results/lbl02b.qmd
+++ b/book/listings/lab-results/lbl02b.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Laboratory Abnormalities (variable units)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -84,10 +84,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/medical-history/mhl01.qmd b/book/listings/medical-history/mhl01.qmd
index dac3900878..b57f603b52 100644
--- a/book/listings/medical-history/mhl01.qmd
+++ b/book/listings/medical-history/mhl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Medical History and Concurrent Diseases
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -62,10 +62,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/pharmacokinetic/pkcl01.qmd b/book/listings/pharmacokinetic/pkcl01.qmd
index 49c9524441..e24972fc40 100644
--- a/book/listings/pharmacokinetic/pkcl01.qmd
+++ b/book/listings/pharmacokinetic/pkcl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Drug A Concentration by Treatment Group, Patient and Nomina
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -58,10 +58,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/pharmacokinetic/pkcl02.qmd b/book/listings/pharmacokinetic/pkcl02.qmd
index c0a0c95f50..238164a630 100644
--- a/book/listings/pharmacokinetic/pkcl02.qmd
+++ b/book/listings/pharmacokinetic/pkcl02.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Drug A Urine Concentration and Volumes
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -91,10 +91,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/pharmacokinetic/pkpl01.qmd b/book/listings/pharmacokinetic/pkpl01.qmd
index dc9eb417b8..7bfa1418f6 100644
--- a/book/listings/pharmacokinetic/pkpl01.qmd
+++ b/book/listings/pharmacokinetic/pkpl01.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Drug A Plasma PK Parameters
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -62,10 +62,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/pharmacokinetic/pkpl02.qmd b/book/listings/pharmacokinetic/pkpl02.qmd
index 3674664213..48e9ec5393 100644
--- a/book/listings/pharmacokinetic/pkpl02.qmd
+++ b/book/listings/pharmacokinetic/pkpl02.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Drug A Urine PK Parameters
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -63,10 +63,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/pharmacokinetic/pkpl04.qmd b/book/listings/pharmacokinetic/pkpl04.qmd
index dd3889450c..8c0ec70255 100644
--- a/book/listings/pharmacokinetic/pkpl04.qmd
+++ b/book/listings/pharmacokinetic/pkpl04.qmd
@@ -5,7 +5,7 @@ subtitle: Listing of Individual Drug A AUCIFO and CMAX Ratios Following Drug A o
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -78,10 +78,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/listings/vital-signs/vsl01.qmd b/book/listings/vital-signs/vsl01.qmd
index 267deee097..a8bce52275 100644
--- a/book/listings/vital-signs/vsl01.qmd
+++ b/book/listings/vital-signs/vsl01.qmd
@@ -5,7 +5,7 @@ subtitle: 'Listing of Vital Signs: Safety-Evaluable Patients'
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -132,10 +132,10 @@ head(lsting, 20)
```
`r webr_code_labels <- c("setup", "lsting")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/tables/ADA/adat01.qmd b/book/tables/ADA/adat01.qmd
index 04d733e8cf..cd9f87b356 100644
--- a/book/tables/ADA/adat01.qmd
+++ b/book/tables/ADA/adat01.qmd
@@ -5,7 +5,7 @@ subtitle: Baseline Prevalence and Incidence of Treatment Emergent ADA
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -242,10 +242,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ADA/adat02.qmd b/book/tables/ADA/adat02.qmd
index 881238dbc7..4daf4c1892 100644
--- a/book/tables/ADA/adat02.qmd
+++ b/book/tables/ADA/adat02.qmd
@@ -5,7 +5,7 @@ subtitle: Summary of Patients with Treatment-Induced ADA
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -142,10 +142,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ADA/adat03.qmd b/book/tables/ADA/adat03.qmd
index 5b429cba17..8a5b762ae8 100644
--- a/book/tables/ADA/adat03.qmd
+++ b/book/tables/ADA/adat03.qmd
@@ -5,7 +5,7 @@ subtitle: Summary of Serum Concentrations at Timepoints Where ADA Samples Were C
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -119,10 +119,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ADA/adat04a.qmd b/book/tables/ADA/adat04a.qmd
index a4cb29c1aa..ee8edc7188 100644
--- a/book/tables/ADA/adat04a.qmd
+++ b/book/tables/ADA/adat04a.qmd
@@ -5,7 +5,7 @@ subtitle: Baseline Prevalence and Incidence of Treatment Emergent NAbs
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -268,10 +268,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ADA/adat04b.qmd b/book/tables/ADA/adat04b.qmd
index aff0936747..5fc4dc1f42 100644
--- a/book/tables/ADA/adat04b.qmd
+++ b/book/tables/ADA/adat04b.qmd
@@ -5,7 +5,7 @@ subtitle: Baseline Prevalence and Incidence of NAbs
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -227,10 +227,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd
index 12328c363a..66202265cd 100644
--- a/book/tables/ECG/egt01.qmd
+++ b/book/tables/ECG/egt01.qmd
@@ -5,7 +5,7 @@ subtitle: ECG Results and Change from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -84,10 +84,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -152,7 +152,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd
index 8ac1122724..92e2e3a204 100644
--- a/book/tables/ECG/egt02.qmd
+++ b/book/tables/ECG/egt02.qmd
@@ -5,7 +5,7 @@ subtitle: ECG Abnormalities (EGT02_1 & EGT02_2)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -60,7 +60,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## ECG Abnormalities Among Subjects
Without Abnormality at Baseline
@@ -87,10 +87,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -147,7 +147,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd
index 2fdf817040..0e5475fe53 100644
--- a/book/tables/ECG/egt03.qmd
+++ b/book/tables/ECG/egt03.qmd
@@ -5,7 +5,7 @@ subtitle: Shift Table of ECG Interval Data -- Baseline Versus Minimum/Maximum Po
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -96,7 +96,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of Baseline Versus
Maximum Post-Baseline
@@ -150,10 +150,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -223,7 +223,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/ECG/egt04.qmd b/book/tables/ECG/egt04.qmd
index c9ee6a145f..5b7d4a98bb 100644
--- a/book/tables/ECG/egt04.qmd
+++ b/book/tables/ECG/egt04.qmd
@@ -5,7 +5,7 @@ subtitle: Shift Table of Qualitative ECG Assessments
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -90,10 +90,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd
index fec40eb085..9e7b066933 100644
--- a/book/tables/ECG/egt05_qtcat.qmd
+++ b/book/tables/ECG/egt05_qtcat.qmd
@@ -5,7 +5,7 @@ subtitle: ECG Actual Values and Changes from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -108,10 +108,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -221,7 +221,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd
index 286a34c51e..9fdc2a8ee8 100644
--- a/book/tables/adverse-events/aet01.qmd
+++ b/book/tables/adverse-events/aet01.qmd
@@ -5,7 +5,7 @@ subtitle: Safety Summary
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -139,7 +139,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Medical
Concepts Section
@@ -213,7 +213,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Modified Rows
@@ -282,7 +282,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Rows Counting
Events & Additional Sections
@@ -367,10 +367,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -454,7 +454,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd
index 0d2d017970..66f13cfbd8 100644
--- a/book/tables/adverse-events/aet01_aesi.qmd
+++ b/book/tables/adverse-events/aet01_aesi.qmd
@@ -5,7 +5,7 @@ subtitle: Safety Summary (Adverse Events of Special Interest)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
@@ -173,7 +173,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Optional Lines
@@ -246,7 +246,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table For Studies
with Multiple Drugs
@@ -534,7 +534,7 @@ result
`r webr_code_labels <- c("variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs
by SMQ
@@ -715,10 +715,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -844,7 +844,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd
index 627223615f..4afdde78f7 100644
--- a/book/tables/adverse-events/aet02.qmd
+++ b/book/tables/adverse-events/aet02.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
::::: {.panel-tabset}
## Data Setup
@@ -78,7 +78,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
The variable `result` corresponds to the adverse events table.
@@ -104,7 +104,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Event Totals
@@ -164,7 +164,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
High-Level Term
@@ -238,7 +238,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Preferred
Terms Only
@@ -271,7 +271,7 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In of
Treatment Groups
@@ -326,7 +326,7 @@ result
```
`r webr_code_labels <- c("setup", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with an Incidence Rate
$\geq$ 5% in Any Treatment Group (subsetting
preferred terms based on frequency)
@@ -381,7 +381,7 @@ result
```
`r webr_code_labels <- c("setup", "variant7")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with an Incidence Rate $\geq$ 5% in
Any Treatment Group (subsetting preferred terms
based on frequency with high-level terms)
@@ -452,7 +452,7 @@ result
```
`r webr_code_labels <- c("setup", "variant8")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with an Incidence Rate $\geq$ 10%
in Any Treatment Group (subsetting
preferred terms based on frequency)
@@ -507,7 +507,7 @@ result
```
`r webr_code_labels <- c("setup", "variant9")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with an Incidence Rate $\geq$ 3
Patients in Any Treatment Group (subsetting
preferred terms based on number of patients)
@@ -562,7 +562,7 @@ result
```
`r webr_code_labels <- c("setup", "variant10")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with a Difference in Incidence Rate $\geq$ 5%
Between Any Treatment (subsetting preferred terms based
on difference in percentage between treatment groups)
@@ -617,7 +617,7 @@ result
```
`r webr_code_labels <- c("setup", "variant11")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with an Incidence Rate $\geq$ 5%
in B: Placebo (subsetting preferred terms based
on frequency for a particular treatment group)
@@ -672,7 +672,7 @@ result
```
`r webr_code_labels <- c("setup", "variant12")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of AEs with a Difference in Incidence Rate $\geq$ 5% Between
Arm A and Arm B or Arm C (displaying preferred terms with a
difference of at least x% between selected treatment groups)
@@ -726,10 +726,10 @@ result
```
`r webr_code_labels <- c("setup", "variant13")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -784,7 +784,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd
index 9e01315c2c..be1423b7a0 100644
--- a/book/tables/adverse-events/aet02_smq.qmd
+++ b/book/tables/adverse-events/aet02_smq.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events by Standardized MedDRA Query
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -122,7 +122,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Customized Queries
@@ -185,10 +185,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -252,7 +252,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd
index c7611a3ce9..4f9e670c26 100644
--- a/book/tables/adverse-events/aet03.qmd
+++ b/book/tables/adverse-events/aet03.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events by Greatest Intensity
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -108,10 +108,10 @@ result
`r webr_code_labels <- c("setup", "pre-processing", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -164,7 +164,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd
index 58ce49039d..54e9356b49 100644
--- a/book/tables/adverse-events/aet04.qmd
+++ b/book/tables/adverse-events/aet04.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events by Highest NCI CTCAE Grade
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -193,7 +193,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In
of Treatment Groups
@@ -269,7 +269,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In
of Grades
@@ -342,7 +342,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Collapsing
of Grades
@@ -421,7 +421,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Using Worst Grade
Flags from ADAE
@@ -538,7 +538,7 @@ result
```
`r webr_code_labels <- c("setup", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with an Incidence Rate
$\geq$ X%, Totals Unrestricted
@@ -561,7 +561,7 @@ result
```
`r webr_code_labels <- c("setup", "variant8")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with a Difference in
Incidence Rate $\geq$ 10%
@@ -579,7 +579,7 @@ result
```
`r webr_code_labels <- c("setup", "variant9")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with an Incidence Rate
$\geq$ 5%, SOCs \< 5% Removed
@@ -602,10 +602,10 @@ result
```
`r webr_code_labels <- c("setup", "variant11")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -658,7 +658,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet04_pi.qmd b/book/tables/adverse-events/aet04_pi.qmd
index e109badd00..ee3863e21a 100644
--- a/book/tables/adverse-events/aet04_pi.qmd
+++ b/book/tables/adverse-events/aet04_pi.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events Reported in $\geq$ 10% of Patients by Highest NCI CTCAE
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -102,7 +102,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Patients Treated with a Particular Treatment by Highest NCI
CTCAE Grade (specifying a treatment for selecting preferred terms)
@@ -137,7 +137,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events Reported in $\geq$ 5% of Patients by
Highest NCI CTCAE Grade (changing the threshold)
@@ -172,7 +172,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events Reported in $\geq$ 5% of Patients and
$\geq$ 2% Difference Between Treatments by Highest
NCI CTCAE Grade (using more than one condition)
@@ -208,7 +208,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events Reported in $\geq$ 10% of Patients for Any Grade
or $\geq$ 5% of Patients for Grade 3-4 by Highest NCI CTCAE
Grade (using different condition depending on the grade)
@@ -245,7 +245,7 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table with
Modified Grade Grouping
@@ -310,7 +310,7 @@ result
```
`r webr_code_labels <- c("setup", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table with
Overlapping Grade Groupings
@@ -374,7 +374,7 @@ result
```
`r webr_code_labels <- c("setup", "variant7")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table without SOCs
@@ -422,10 +422,10 @@ result
```
`r webr_code_labels <- c("setup", "variant8")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -485,7 +485,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet05.qmd b/book/tables/adverse-events/aet05.qmd
index e367519c97..fd1aa547e0 100644
--- a/book/tables/adverse-events/aet05.qmd
+++ b/book/tables/adverse-events/aet05.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Event Rate Adjusted for Patient-Years at Risk -- First Occurre
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -51,7 +51,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Setting Type of Confidence Interval
@@ -80,10 +80,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -147,7 +147,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet05_all.qmd b/book/tables/adverse-events/aet05_all.qmd
index 0224c847b5..c0ece0e99c 100644
--- a/book/tables/adverse-events/aet05_all.qmd
+++ b/book/tables/adverse-events/aet05_all.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Event Rate Adjusted for Patient-Years at Risk -- All Occurrenc
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -57,7 +57,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Setting Type of Confidence Interval
@@ -81,10 +81,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -155,7 +155,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet06.qmd b/book/tables/adverse-events/aet06.qmd
index 0bd2c28d56..5a9c6e9bfd 100644
--- a/book/tables/adverse-events/aet06.qmd
+++ b/book/tables/adverse-events/aet06.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events by Baseline Characteristic
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -129,7 +129,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Other Baseline
Characteristics (e.g. Biomarker Group)
@@ -190,7 +190,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Baseline Characteristic
from ADSUB (e.g. BMI Category)
@@ -251,7 +251,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Regrouped Baseline
Characteristics (e.g. Race)
@@ -313,7 +313,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Baseline Characteristics
(e.g. Sex) Including High-Level Terms
@@ -394,10 +394,10 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -452,7 +452,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet06_smq.qmd b/book/tables/adverse-events/aet06_smq.qmd
index 19821323c4..dd539e5240 100644
--- a/book/tables/adverse-events/aet06_smq.qmd
+++ b/book/tables/adverse-events/aet06_smq.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events by Baseline Characteristic, by SMQ and Preferred Term
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -144,7 +144,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Sex, by SMQ and
Preferred Term (with Customized Queries)
@@ -203,7 +203,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Adverse Events by Other Baseline
Characteristics (e.g. Age Group)
@@ -254,10 +254,10 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -343,7 +343,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet07.qmd b/book/tables/adverse-events/aet07.qmd
index 17c6be1da1..917b1465ec 100644
--- a/book/tables/adverse-events/aet07.qmd
+++ b/book/tables/adverse-events/aet07.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events Resulting in Death
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -79,7 +79,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In of Treatment Groups without Deaths
@@ -117,10 +117,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -201,7 +201,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet09.qmd b/book/tables/adverse-events/aet09.qmd
index dd081fd3f7..b21eef9b85 100644
--- a/book/tables/adverse-events/aet09.qmd
+++ b/book/tables/adverse-events/aet09.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events Related to Study Drug
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -97,7 +97,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Including High-Level Terms
@@ -181,10 +181,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -240,7 +240,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet09_smq.qmd b/book/tables/adverse-events/aet09_smq.qmd
index b5f0a8d8bc..e30063dc31 100644
--- a/book/tables/adverse-events/aet09_smq.qmd
+++ b/book/tables/adverse-events/aet09_smq.qmd
@@ -5,7 +5,7 @@ subtitle: Adverse Events Related to Study Drug by Standardized MedDRA Query
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -126,7 +126,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Customized Queries
@@ -189,10 +189,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -262,7 +262,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/adverse-events/aet10.qmd b/book/tables/adverse-events/aet10.qmd
index 89f4663982..d5e7bcd518 100644
--- a/book/tables/adverse-events/aet10.qmd
+++ b/book/tables/adverse-events/aet10.qmd
@@ -5,7 +5,7 @@ subtitle: Most Common ($\geq$ 5%) Adverse Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -67,7 +67,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Most Common ($\geq$ 35%) Adverse Events (setting threshold)
@@ -109,10 +109,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -171,7 +171,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/concomitant-medications/cmt01.qmd b/book/tables/concomitant-medications/cmt01.qmd
index 928cb30eb3..aa9420a4b1 100644
--- a/book/tables/concomitant-medications/cmt01.qmd
+++ b/book/tables/concomitant-medications/cmt01.qmd
@@ -5,7 +5,7 @@ subtitle: Concomitant Medications (GNEDrug Legacy Coding)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -92,7 +92,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Showing Medications Prior
to the Start of the Study
@@ -144,7 +144,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Subtotal Per
Medication Class Suppressed
@@ -192,7 +192,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Sorted by Total Column Showing
Additional "All Patients" Column
@@ -252,10 +252,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -318,7 +318,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/concomitant-medications/cmt01a.qmd b/book/tables/concomitant-medications/cmt01a.qmd
index 09de04d15c..be7b5e7501 100644
--- a/book/tables/concomitant-medications/cmt01a.qmd
+++ b/book/tables/concomitant-medications/cmt01a.qmd
@@ -5,7 +5,7 @@ subtitle: Concomitant Medications by Medication Class and Preferred Name
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -86,7 +86,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Changing
ATC Class Level
@@ -140,7 +140,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Classes
Sorted by Frequency
@@ -191,7 +191,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Total Number of Treatments
per Medication Class Suppressed
@@ -244,10 +244,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -310,7 +310,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/concomitant-medications/cmt01b.qmd b/book/tables/concomitant-medications/cmt01b.qmd
index 91f8c79c49..9996b2c2e2 100644
--- a/book/tables/concomitant-medications/cmt01b.qmd
+++ b/book/tables/concomitant-medications/cmt01b.qmd
@@ -5,7 +5,7 @@ subtitle: Concomitant Medications by Medication Class and Preferred Name
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -113,7 +113,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Changing
Class Levels
@@ -179,7 +179,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Classes
Sorted by Frequency
@@ -268,10 +268,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -333,7 +333,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/concomitant-medications/cmt02_pt.qmd b/book/tables/concomitant-medications/cmt02_pt.qmd
index 0007b38f0a..34681f53aa 100644
--- a/book/tables/concomitant-medications/cmt02_pt.qmd
+++ b/book/tables/concomitant-medications/cmt02_pt.qmd
@@ -5,7 +5,7 @@ subtitle: Concomitant Medications by Preferred Name (WHODrug Coding)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,10 +70,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -136,7 +136,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/deaths/dtht01.qmd b/book/tables/deaths/dtht01.qmd
index 759e196718..c09d889b34 100644
--- a/book/tables/deaths/dtht01.qmd
+++ b/book/tables/deaths/dtht01.qmd
@@ -5,7 +5,7 @@ subtitle: Deaths
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -48,7 +48,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting
Sections to Display
@@ -93,7 +93,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table for Studies Collecting Death
Information from Public Records
@@ -145,7 +145,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Adding Details for "All other causes"
Category for Studies Collecting Death
Information from Public Records
@@ -207,10 +207,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/demography/dmt01.qmd b/book/tables/demography/dmt01.qmd
index f9ba403aca..773f379e52 100644
--- a/book/tables/demography/dmt01.qmd
+++ b/book/tables/demography/dmt01.qmd
@@ -5,7 +5,7 @@ subtitle: Demographics and Baseline Characteristics
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -115,7 +115,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with an Additional
Study-Specific Categorical Variable
@@ -146,7 +146,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Subgrouping
for Some Analyses
@@ -173,7 +173,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Additional Vital
Signs Baseline Values
@@ -200,7 +200,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Additional
Values from ADSUB
@@ -226,10 +226,10 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -277,7 +277,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/disclosures/disclosurest01.qmd b/book/tables/disclosures/disclosurest01.qmd
index 67e41b6e67..baca277361 100644
--- a/book/tables/disclosures/disclosurest01.qmd
+++ b/book/tables/disclosures/disclosurest01.qmd
@@ -5,7 +5,7 @@ subtitle: Disclosures Outputs
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Patient Disposition Table
(CTgov & EudraCT)
@@ -128,7 +128,7 @@ result
```
`r webr_code_labels <- c("setup1", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Demographic Table
(CTgov & EudraCT)
@@ -188,7 +188,7 @@ result
```
`r webr_code_labels <- c("setup2", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Enrollment by Country
Table (EudraCT only)
@@ -231,7 +231,7 @@ result
```
`r webr_code_labels <- c("setup3", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Non-Serious Adverse Events
Reported in $\geq$ 5% of Patients in Any
Treatment Group (CTgov & EudraCT)
@@ -321,7 +321,7 @@ result
```
`r webr_code_labels <- c("setup4", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Serious Adverse Events, Fatal SAEs
and SAEs Related to Study Medication,
by Treatment Group (CTgov & EudraCT)
@@ -388,7 +388,7 @@ result
```
`r webr_code_labels <- c("setup5", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Death Table
(EudraCT only)
@@ -425,10 +425,10 @@ result
```
`r webr_code_labels <- c("setup6", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/tables/disclosures/eudrat01.qmd b/book/tables/disclosures/eudrat01.qmd
index a081bc1cef..60bdc3f53e 100644
--- a/book/tables/disclosures/eudrat01.qmd
+++ b/book/tables/disclosures/eudrat01.qmd
@@ -5,7 +5,7 @@ subtitle: Non-Serious Adverse Events Reported in $\geq$ 5% of Patients in Any Tr
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -95,10 +95,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/disclosures/eudrat02.qmd b/book/tables/disclosures/eudrat02.qmd
index 10fdca44e3..498c1c6b40 100644
--- a/book/tables/disclosures/eudrat02.qmd
+++ b/book/tables/disclosures/eudrat02.qmd
@@ -5,7 +5,7 @@ subtitle: Serious Adverse Events, Fatal Serious Adverse Events, and Serious Adve
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -72,10 +72,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/disposition/dst01.qmd b/book/tables/disposition/dst01.qmd
index 671adbf22b..da6c08e7b0 100644
--- a/book/tables/disposition/dst01.qmd
+++ b/book/tables/disposition/dst01.qmd
@@ -5,7 +5,7 @@ subtitle: Patient Disposition
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,7 +70,7 @@ result1
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Grouping of Reasons
@@ -103,7 +103,7 @@ result2
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Adding Optional Rows
@@ -133,10 +133,10 @@ result3
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -204,7 +204,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/disposition/pdt01.qmd b/book/tables/disposition/pdt01.qmd
index 7dc909c5bb..22ae587327 100644
--- a/book/tables/disposition/pdt01.qmd
+++ b/book/tables/disposition/pdt01.qmd
@@ -5,7 +5,7 @@ subtitle: Major Protocol Deviations
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -67,10 +67,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -125,7 +125,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/disposition/pdt02.qmd b/book/tables/disposition/pdt02.qmd
index 7242f9b4e9..3ab4ee01ca 100644
--- a/book/tables/disposition/pdt02.qmd
+++ b/book/tables/disposition/pdt02.qmd
@@ -5,7 +5,7 @@ subtitle: Major Protocol Deviations Related to Epidemic/Pandemic
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -68,10 +68,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/efficacy/aovt01.qmd b/book/tables/efficacy/aovt01.qmd
index bf5ee986ff..eb3cc8854d 100644
--- a/book/tables/efficacy/aovt01.qmd
+++ b/book/tables/efficacy/aovt01.qmd
@@ -5,7 +5,7 @@ subtitle: ANCOVA for Multiple End Points
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -64,10 +64,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -143,7 +143,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/aovt02.qmd b/book/tables/efficacy/aovt02.qmd
index 5a3879e911..23d6093672 100644
--- a/book/tables/efficacy/aovt02.qmd
+++ b/book/tables/efficacy/aovt02.qmd
@@ -5,7 +5,7 @@ subtitle: ANCOVA with Single End Point and Customized Table
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
This example will focus on data from a single visit "WEEK 1 DAY 8" and a single endpoint "FKSI-FWB".
Only evaluable populations will be analyzed.
@@ -71,10 +71,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -149,7 +149,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/aovt03.qmd b/book/tables/efficacy/aovt03.qmd
index 00c9cded25..310e379eef 100644
--- a/book/tables/efficacy/aovt03.qmd
+++ b/book/tables/efficacy/aovt03.qmd
@@ -5,7 +5,7 @@ subtitle: ANCOVA with Consideration of Interaction
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
This example will focus on data from multiple visits and take the interaction between visits and arms into consideration.
@@ -72,10 +72,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/efficacy/cfbt01.qmd b/book/tables/efficacy/cfbt01.qmd
index cb993816e0..15c2ca985f 100644
--- a/book/tables/efficacy/cfbt01.qmd
+++ b/book/tables/efficacy/cfbt01.qmd
@@ -5,7 +5,7 @@ subtitle: Efficacy Data and Change from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -92,10 +92,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -163,7 +163,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/cmht01.qmd b/book/tables/efficacy/cmht01.qmd
index ecf861b770..875aa2a542 100644
--- a/book/tables/efficacy/cmht01.qmd
+++ b/book/tables/efficacy/cmht01.qmd
@@ -5,7 +5,7 @@ subtitle: Cochran-Mantel-Haenszel (CMH) Summary
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -80,7 +80,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of Multiple Parameters
@@ -148,10 +148,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -208,7 +208,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/coxt01.qmd b/book/tables/efficacy/coxt01.qmd
index 68d3e259aa..bf00cafdf0 100644
--- a/book/tables/efficacy/coxt01.qmd
+++ b/book/tables/efficacy/coxt01.qmd
@@ -5,7 +5,7 @@ subtitle: Cox Regression
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
Cox models are the most commonly used methods to estimate the magnitude of the effect in survival analyses.
It assumes proportional hazards; that is, it assumes that the ratio of the hazards of the two groups (e.g. two arms) is constant over time.
@@ -78,7 +78,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Cox Regression
with Interaction Term
@@ -111,7 +111,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Cox Regression
Specifying Covariates
@@ -146,7 +146,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Cox Regression Setting
Strata, Ties, Alpha Level
@@ -187,10 +187,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -256,7 +256,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/coxt02.qmd b/book/tables/efficacy/coxt02.qmd
index ed87afaa92..2692540660 100644
--- a/book/tables/efficacy/coxt02.qmd
+++ b/book/tables/efficacy/coxt02.qmd
@@ -5,7 +5,7 @@ subtitle: Multivariable Cox Regression
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
Analysis based on multivariable Cox models is usually not performed for the Clinical Study Report (CSR) or regulatory documents, serving exploratory purposes only (e.g. for publication).
In practice, the model usually includes only the main effects (without interaction terms).
@@ -79,7 +79,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Multivariable Cox Regression
with Interaction Term
@@ -140,14 +140,14 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Multivariable Cox Regression
with Selection Process for Covariates
See the *Multivariable Cox Regression with Interaction Term* tab.
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -208,7 +208,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/dort01.qmd b/book/tables/efficacy/dort01.qmd
index a071e86c66..2d4ab97b2f 100644
--- a/book/tables/efficacy/dort01.qmd
+++ b/book/tables/efficacy/dort01.qmd
@@ -5,7 +5,7 @@ subtitle: Duration of Response
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -99,7 +99,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting
Sections to Display
@@ -161,7 +161,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Analysis Details
like Conf. Type and Alpha Level
@@ -223,7 +223,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Time Point for
the "XX Months duration" Analysis
@@ -283,10 +283,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -360,7 +360,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/lgrt02.qmd b/book/tables/efficacy/lgrt02.qmd
index 44bfa32a23..1023f52fbd 100644
--- a/book/tables/efficacy/lgrt02.qmd
+++ b/book/tables/efficacy/lgrt02.qmd
@@ -5,7 +5,7 @@ subtitle: Multi-Variable Logistic Regression
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -71,7 +71,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Multi-Variable Logistic Regression
with Interaction Term
@@ -106,7 +106,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Multi-Variable Logistic Regression
Specifying Covariates
@@ -140,7 +140,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Multi-Variable Logistic Regression Setting
an Event, Alpha Level, and Level for Interaction
@@ -176,10 +176,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -244,7 +244,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/mmrmt01.qmd b/book/tables/efficacy/mmrmt01.qmd
index 823cb63749..44ed9bf83d 100644
--- a/book/tables/efficacy/mmrmt01.qmd
+++ b/book/tables/efficacy/mmrmt01.qmd
@@ -5,7 +5,7 @@ subtitle: Tables for Mixed-Effect Model Repeated Measures Analysis
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -211,7 +211,7 @@ Statistics to evaluate choice of covariance structure are being investigated and
as.rtable(mmrm_results, type = "diagnostic")
```
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/efficacy/onct05.qmd b/book/tables/efficacy/onct05.qmd
index 093382cf2f..f568ffd8e3 100644
--- a/book/tables/efficacy/onct05.qmd
+++ b/book/tables/efficacy/onct05.qmd
@@ -5,7 +5,7 @@ subtitle: Objective Response Rate by Subgroup
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -71,7 +71,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Specifying
Class Variables
@@ -102,7 +102,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting Columns
and Changing the Alpha Level
@@ -130,7 +130,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Setting Values
Indicating Response
@@ -161,10 +161,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -238,7 +238,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/ratet01.qmd b/book/tables/efficacy/ratet01.qmd
index 13cb19b42f..44bc468d63 100644
--- a/book/tables/efficacy/ratet01.qmd
+++ b/book/tables/efficacy/ratet01.qmd
@@ -5,7 +5,7 @@ subtitle: Event Rate Summary for Recurrent Events
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
This example will focus on data from a single visit "WEEK 1 DAY 8" and a single endpoint "FKSI-FWB".
Only evaluable populations will be analyzed.
@@ -92,10 +92,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/efficacy/rbmit01.qmd b/book/tables/efficacy/rbmit01.qmd
index 54220c2fd8..10de92de4b 100644
--- a/book/tables/efficacy/rbmit01.qmd
+++ b/book/tables/efficacy/rbmit01.qmd
@@ -5,7 +5,7 @@ subtitle: Tables for RBMI
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -212,7 +212,7 @@ result <- basic_table() %>%
result
```
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/rspt01.qmd b/book/tables/efficacy/rspt01.qmd
index 6b24d366eb..fafa971171 100644
--- a/book/tables/efficacy/rspt01.qmd
+++ b/book/tables/efficacy/rspt01.qmd
@@ -5,7 +5,7 @@ subtitle: Best Overall Response
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -84,7 +84,7 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting
Sections to Display
@@ -119,7 +119,7 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Analysis Details like Type of
Confidence Interval, Alpha Level, Test Statistic
@@ -169,7 +169,7 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Stratified Analysis
@@ -228,7 +228,7 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying the Definition
of Overall Response
@@ -252,7 +252,7 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Defining New
Sections to Display
@@ -283,10 +283,10 @@ result
```
`r webr_code_labels <- c("setup", "pre-processing", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -360,7 +360,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/efficacy/ttet01.qmd b/book/tables/efficacy/ttet01.qmd
index a6439944ac..db9999beda 100644
--- a/book/tables/efficacy/ttet01.qmd
+++ b/book/tables/efficacy/ttet01.qmd
@@ -5,7 +5,7 @@ subtitle: Time-To-Event Summary
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::::: {.panel-tabset}
## Data Setup
@@ -102,7 +102,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting
Sections to Display
@@ -151,7 +151,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Analysis Details
like Conf. Type, Ties, Alpha Level
@@ -226,7 +226,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Stratified Analysis
@@ -292,7 +292,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Time Point for
the "XX Months" Analysis
@@ -352,7 +352,7 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Requesting
\> 1 p-value
@@ -430,10 +430,10 @@ result
```
`r webr_code_labels <- c("setup", "variant6")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -507,7 +507,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/exposure/ext01.qmd b/book/tables/exposure/ext01.qmd
index 438f6d8008..da0f71e625 100644
--- a/book/tables/exposure/ext01.qmd
+++ b/book/tables/exposure/ext01.qmd
@@ -5,7 +5,7 @@ subtitle: Study Drug Exposure Table
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -101,7 +101,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Optional Analyses
@@ -155,7 +155,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with User-Specified
Categories for Missed Doses
@@ -214,10 +214,10 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -294,7 +294,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt01.qmd b/book/tables/lab-results/lbt01.qmd
index 199a1f24d1..b1520b4403 100644
--- a/book/tables/lab-results/lbt01.qmd
+++ b/book/tables/lab-results/lbt01.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results and Change from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -88,10 +88,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -156,7 +156,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt02.qmd b/book/tables/lab-results/lbt02.qmd
index da1de0f8b8..7a686daaae 100644
--- a/book/tables/lab-results/lbt02.qmd
+++ b/book/tables/lab-results/lbt02.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -63,10 +63,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -129,7 +129,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt03.qmd b/book/tables/lab-results/lbt03.qmd
index 6dfc9dc9d0..9339774f1f 100644
--- a/book/tables/lab-results/lbt03.qmd
+++ b/book/tables/lab-results/lbt03.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results Change from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -74,7 +74,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
In the final step, a new variable is derived from `AVISIT` that can specify the method of estimation of the evaluated change.
@@ -118,10 +118,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -208,7 +208,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt04.qmd b/book/tables/lab-results/lbt04.qmd
index f2613cee95..ad250b5b3c 100644
--- a/book/tables/lab-results/lbt04.qmd
+++ b/book/tables/lab-results/lbt04.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Abnormalities Not Present at Baseline
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -59,10 +59,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -120,7 +120,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt05.qmd b/book/tables/lab-results/lbt05.qmd
index 533c25754a..10938e0654 100644
--- a/book/tables/lab-results/lbt05.qmd
+++ b/book/tables/lab-results/lbt05.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Abnormalities with Single and Replicated Marked
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -111,7 +111,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Showing
All Categories
@@ -141,7 +141,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with
Study-Specific
MLAs
@@ -187,10 +187,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt06.qmd b/book/tables/lab-results/lbt06.qmd
index 6847c4cd16..01fc760e42 100644
--- a/book/tables/lab-results/lbt06.qmd
+++ b/book/tables/lab-results/lbt06.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Abnormalities by Visit and Baseline Status
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -67,7 +67,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table for
Multiple Lab Tests
@@ -102,10 +102,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt07.qmd b/book/tables/lab-results/lbt07.qmd
index fbce805638..c4a33ebba8 100644
--- a/book/tables/lab-results/lbt07.qmd
+++ b/book/tables/lab-results/lbt07.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -108,10 +108,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -169,7 +169,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt08.qmd b/book/tables/lab-results/lbt08.qmd
index fbd6edd352..cc6168c44e 100644
--- a/book/tables/lab-results/lbt08.qmd
+++ b/book/tables/lab-results/lbt08.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results with Highest NCI CTCAE Grade at Any Time
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -74,10 +74,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt09.qmd b/book/tables/lab-results/lbt09.qmd
index 4a4a522a44..c07f6b10f7 100644
--- a/book/tables/lab-results/lbt09.qmd
+++ b/book/tables/lab-results/lbt09.qmd
@@ -5,7 +5,7 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -135,7 +135,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting Sections
@@ -176,10 +176,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt10.qmd b/book/tables/lab-results/lbt10.qmd
index 7dcd79cde0..e95869e190 100644
--- a/book/tables/lab-results/lbt10.qmd
+++ b/book/tables/lab-results/lbt10.qmd
@@ -5,7 +5,7 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,7 +70,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting Sections
@@ -101,10 +101,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt10_bl.qmd b/book/tables/lab-results/lbt10_bl.qmd
index f3b7bd2c12..bb10a0451c 100644
--- a/book/tables/lab-results/lbt10_bl.qmd
+++ b/book/tables/lab-results/lbt10_bl.qmd
@@ -5,7 +5,7 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -70,7 +70,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting Sections
@@ -101,10 +101,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt11.qmd b/book/tables/lab-results/lbt11.qmd
index f02295e817..e41ab5fc41 100644
--- a/book/tables/lab-results/lbt11.qmd
+++ b/book/tables/lab-results/lbt11.qmd
@@ -5,7 +5,7 @@ subtitle: Time to First Increase in Liver Laboratory Test Result Meeting Hy's La
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -85,7 +85,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Time-To-Event Summary
Selecting Sections to Display
@@ -109,7 +109,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Time-To-Event Summary
with Stratified Analysis
@@ -149,10 +149,10 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -226,7 +226,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt11_bl.qmd b/book/tables/lab-results/lbt11_bl.qmd
index 5521fc60c3..24a0876d0c 100644
--- a/book/tables/lab-results/lbt11_bl.qmd
+++ b/book/tables/lab-results/lbt11_bl.qmd
@@ -5,7 +5,7 @@ subtitle: Time to First Increase in Liver Laboratory Test Result Meeting Hy's La
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -85,7 +85,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Time-To-Event Summary
Selecting Sections to Display
@@ -109,7 +109,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Time-To-Event Summary
with Stratified Analysis
@@ -149,10 +149,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -226,7 +226,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt12.qmd b/book/tables/lab-results/lbt12.qmd
index 5fbe559b4c..dd72221bac 100644
--- a/book/tables/lab-results/lbt12.qmd
+++ b/book/tables/lab-results/lbt12.qmd
@@ -5,7 +5,7 @@ subtitle: Liver Laboratory Tests by Time on Treatment -- Patients with Elevated
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -75,10 +75,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt12_bl.qmd b/book/tables/lab-results/lbt12_bl.qmd
index 8961405f89..45ad964c79 100644
--- a/book/tables/lab-results/lbt12_bl.qmd
+++ b/book/tables/lab-results/lbt12_bl.qmd
@@ -5,7 +5,7 @@ subtitle: Liver Laboratory Tests by Time on Treatment -- Patients with Elevated
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -75,10 +75,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/lab-results/lbt13.qmd b/book/tables/lab-results/lbt13.qmd
index cb28aa2917..e6e6a549e3 100644
--- a/book/tables/lab-results/lbt13.qmd
+++ b/book/tables/lab-results/lbt13.qmd
@@ -5,7 +5,7 @@ subtitle: NCI CTCAE Grade Laboratory Abnormalities by Visit and Baseline Grade
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -115,7 +115,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table (High)
@@ -198,7 +198,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Without Patients with
Missing Baseline (Low)
@@ -280,7 +280,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Missing Baseline
Considered as Grade 0 (High)
@@ -361,7 +361,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In
of Grades (High)
@@ -445,10 +445,10 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -517,7 +517,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt14.qmd b/book/tables/lab-results/lbt14.qmd
index e30bfc332c..d9c6c7b8ff 100644
--- a/book/tables/lab-results/lbt14.qmd
+++ b/book/tables/lab-results/lbt14.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Results Shift Table -- Highest NCI CTCAE Grade Post-Ba
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -96,7 +96,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Standard Table (Low)
@@ -160,7 +160,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Without Patients with
Missing Baseline (High)
@@ -223,7 +223,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Missing Baseline
Considered as Grade 0 (Low)
@@ -285,7 +285,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Fill-In of Grades
@@ -347,10 +347,10 @@ result
```
`r webr_code_labels <- c("setup", "variant5")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -419,7 +419,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/lab-results/lbt15.qmd b/book/tables/lab-results/lbt15.qmd
index 2ccf0ac349..a78095b34e 100644
--- a/book/tables/lab-results/lbt15.qmd
+++ b/book/tables/lab-results/lbt15.qmd
@@ -5,7 +5,7 @@ subtitle: Laboratory Test Shifts to NCI CTCAE Grade 3-4 Post-Baseline
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -103,7 +103,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Cut Point
@@ -117,10 +117,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -200,7 +200,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/medical-history/mht01.qmd b/book/tables/medical-history/mht01.qmd
index 163d85e9cf..9451aae426 100644
--- a/book/tables/medical-history/mht01.qmd
+++ b/book/tables/medical-history/mht01.qmd
@@ -5,7 +5,7 @@ subtitle: Medical History
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -74,7 +74,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table of History
Prior to Study
@@ -93,7 +93,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Total Number
of Conditions Suppressed
@@ -133,7 +133,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Total Number of Conditions Per Body
System After The Summary of Patients
@@ -186,10 +186,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -243,7 +243,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/pharmacokinetic/pkct01.qmd b/book/tables/pharmacokinetic/pkct01.qmd
index 9e6ea369f0..5e8ed8a624 100644
--- a/book/tables/pharmacokinetic/pkct01.qmd
+++ b/book/tables/pharmacokinetic/pkct01.qmd
@@ -5,7 +5,7 @@ subtitle: Summary Concentration Table
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -98,7 +98,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Implementing 1/3 Imputation Rule
@@ -138,7 +138,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Implementing 1/2 Imputation Rule
@@ -178,10 +178,10 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt02.qmd b/book/tables/pharmacokinetic/pkpt02.qmd
index b60724be1e..ea6df8e170 100644
--- a/book/tables/pharmacokinetic/pkpt02.qmd
+++ b/book/tables/pharmacokinetic/pkpt02.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary -- Plasma/Serum/Blood PK Parameters
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -72,7 +72,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -95,10 +95,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt03.qmd b/book/tables/pharmacokinetic/pkpt03.qmd
index 75246e36e1..9fde0c177c 100644
--- a/book/tables/pharmacokinetic/pkpt03.qmd
+++ b/book/tables/pharmacokinetic/pkpt03.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary of Plasma by Treatment (Stats in Col
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -144,7 +144,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug X: Remove Rows with 0s
@@ -163,7 +163,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -180,10 +180,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt04.qmd b/book/tables/pharmacokinetic/pkpt04.qmd
index e559b04dbe..91a7b483e2 100644
--- a/book/tables/pharmacokinetic/pkpt04.qmd
+++ b/book/tables/pharmacokinetic/pkpt04.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary -- Urine PK Parameters (Stats in Row
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -72,7 +72,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -95,10 +95,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt05.qmd b/book/tables/pharmacokinetic/pkpt05.qmd
index 62abdf024d..767e293f29 100644
--- a/book/tables/pharmacokinetic/pkpt05.qmd
+++ b/book/tables/pharmacokinetic/pkpt05.qmd
@@ -5,7 +5,7 @@ subtitle: Summary of Urinary PK Parameters by Treatment Arm (Stats in Columns)
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -91,7 +91,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -114,10 +114,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt06.qmd b/book/tables/pharmacokinetic/pkpt06.qmd
index b2dee8a45c..d970631d9f 100644
--- a/book/tables/pharmacokinetic/pkpt06.qmd
+++ b/book/tables/pharmacokinetic/pkpt06.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary -- Dose-Normalized PK Parameters (St
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -74,7 +74,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -97,10 +97,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt07.qmd b/book/tables/pharmacokinetic/pkpt07.qmd
index c039cdd789..908d18ea64 100644
--- a/book/tables/pharmacokinetic/pkpt07.qmd
+++ b/book/tables/pharmacokinetic/pkpt07.qmd
@@ -5,7 +5,7 @@ subtitle: Table of Mean Dose-Normalized Selected Pharmacokinetic Parameters (Sta
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -93,7 +93,7 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
#### Plasma Drug Y
@@ -116,10 +116,10 @@ result
```
`r webr_code_labels <- c("setup", "lyt", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt08.qmd b/book/tables/pharmacokinetic/pkpt08.qmd
index 3d88f6d5d6..9e73b5067a 100644
--- a/book/tables/pharmacokinetic/pkpt08.qmd
+++ b/book/tables/pharmacokinetic/pkpt08.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Summary of Cumulative Amount of Drug Elimina
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -91,10 +91,10 @@ cat(rtables::toString(result, indent_size = 10))
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/pharmacokinetic/pkpt11.qmd b/book/tables/pharmacokinetic/pkpt11.qmd
index 260f781ab8..f45e262449 100644
--- a/book/tables/pharmacokinetic/pkpt11.qmd
+++ b/book/tables/pharmacokinetic/pkpt11.qmd
@@ -5,7 +5,7 @@ subtitle: Pharmacokinetic Parameter Estimated Ratios of Geometric Means and 90%
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -164,10 +164,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/risk-management-plan/rmpt01.qmd b/book/tables/risk-management-plan/rmpt01.qmd
index db43a6fd20..1fcd7fcb94 100644
--- a/book/tables/risk-management-plan/rmpt01.qmd
+++ b/book/tables/risk-management-plan/rmpt01.qmd
@@ -5,7 +5,7 @@ subtitle: Duration of Exposure for Risk Management Plan
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -83,10 +83,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -169,7 +169,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/risk-management-plan/rmpt03.qmd b/book/tables/risk-management-plan/rmpt03.qmd
index c1de4fa870..dea5539d88 100644
--- a/book/tables/risk-management-plan/rmpt03.qmd
+++ b/book/tables/risk-management-plan/rmpt03.qmd
@@ -5,7 +5,7 @@ subtitle: Extent of Exposure by Age Group and Gender for Risk Management Plan
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -92,7 +92,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Excluding Empty Age Groups
@@ -123,10 +123,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -222,7 +222,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/risk-management-plan/rmpt04.qmd b/book/tables/risk-management-plan/rmpt04.qmd
index 142411c9fd..eb24a9851d 100644
--- a/book/tables/risk-management-plan/rmpt04.qmd
+++ b/book/tables/risk-management-plan/rmpt04.qmd
@@ -5,7 +5,7 @@ subtitle: Extent of Exposure by Ethnic Origin for Risk Management Plan
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -72,10 +72,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -150,7 +150,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/risk-management-plan/rmpt05.qmd b/book/tables/risk-management-plan/rmpt05.qmd
index 2925c18a8f..1774e556cf 100644
--- a/book/tables/risk-management-plan/rmpt05.qmd
+++ b/book/tables/risk-management-plan/rmpt05.qmd
@@ -5,7 +5,7 @@ subtitle: Extent of Exposure by Race for Risk Management Plan
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -74,10 +74,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -152,7 +152,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/risk-management-plan/rmpt06.qmd b/book/tables/risk-management-plan/rmpt06.qmd
index b34ba59522..eb9dc3a08a 100644
--- a/book/tables/risk-management-plan/rmpt06.qmd
+++ b/book/tables/risk-management-plan/rmpt06.qmd
@@ -5,7 +5,7 @@ subtitle: Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Manage
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -132,7 +132,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Selecting
Sections to Display
@@ -189,7 +189,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table with Differences
@@ -262,7 +262,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table Modifying Alpha Level and
Type of Confidence Interval
@@ -338,7 +338,7 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## Table by SMQ
@@ -349,7 +349,7 @@ result
# In progress
```
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
diff --git a/book/tables/safety/enrollment01.qmd b/book/tables/safety/enrollment01.qmd
index 694857a83f..ae2200d10d 100644
--- a/book/tables/safety/enrollment01.qmd
+++ b/book/tables/safety/enrollment01.qmd
@@ -5,7 +5,7 @@ subtitle: Enrollment Variants
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -71,7 +71,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## ENT01A -- Enrollment by Country
and Investigator Number
@@ -95,7 +95,7 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## ENT02 -- Enrollment by Region, Country,
and Investigator Number/Name
@@ -121,7 +121,7 @@ result
```
`r webr_code_labels <- c("setup", "variant3")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## ENT02A -- Enrollment by Country
and Investigator Number/Name
@@ -145,10 +145,10 @@ result
```
`r webr_code_labels <- c("setup", "variant4")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -232,7 +232,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/vital-signs/vst01.qmd b/book/tables/vital-signs/vst01.qmd
index cd49c55957..b795a7c048 100644
--- a/book/tables/vital-signs/vst01.qmd
+++ b/book/tables/vital-signs/vst01.qmd
@@ -5,7 +5,7 @@ subtitle: Vital Sign Results and Change from Baseline by Visit
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -125,10 +125,10 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -229,7 +229,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/book/tables/vital-signs/vst02.qmd b/book/tables/vital-signs/vst02.qmd
index 425455a550..192f8639ad 100644
--- a/book/tables/vital-signs/vst02.qmd
+++ b/book/tables/vital-signs/vst02.qmd
@@ -5,7 +5,7 @@ subtitle: Vital Sign Abnormalities
------------------------------------------------------------------------
-{{< include ../../test-utils/envir_hook.qmd >}}
+{{< include ../../_utils/envir_hook.qmd >}}
:::: {.panel-tabset}
## Data Setup
@@ -60,7 +60,7 @@ result
```
`r webr_code_labels <- c("setup", "variant1")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
## VST02_2 -- Table of Abnormalities Among
Subjects Without Abnormality at Baseline
@@ -86,10 +86,10 @@ result
```
`r webr_code_labels <- c("setup", "variant2")`
-{{< include ../../webr-utils/webr.qmd >}}
+{{< include ../../_utils/webr.qmd >}}
:::
-{{< include ../../test-utils/save_results.qmd >}}
+{{< include ../../_utils/save_results.qmd >}}
## `teal` App
@@ -149,7 +149,7 @@ app <- init(
shinyApp(app$ui, app$server)
```
-{{< include ../../webr-utils/shinylive.qmd >}}
+{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
diff --git a/package/README.md b/package/README.md
index 375095bf66..7d67ffa967 100644
--- a/package/README.md
+++ b/package/README.md
@@ -23,7 +23,7 @@ As an article author, you need to (i) register the hooks, (ii) use them where ap
(i) Register the hooks
-* At the beggining of the article, add the following: `{{< include ../../test-utils/envir_hook.qmd >}}`.
+* At the beggining of the article, add the following: `{{< include ../../_utils/envir_hook.qmd >}}`.
It will register the `knitr` hooks for further use and will not produce any visible changes to the content.
(ii) Use the hooks
@@ -41,7 +41,7 @@ It will register the `knitr` hooks for further use and will not produce any visi
(iii) Save the results
-* At the end of the article (after all chunks with outputs), add `{{< include ../../test-utils/save_results.qmd >}}` to save all objects as `.Rds` files.
+* At the end of the article (after all chunks with outputs), add `{{< include ../../_utils/save_results.qmd >}}` to save all objects as `.Rds` files.
This logic has been implemented in many articles already. Please refer to the existing ones for examples.