diff --git a/book/_utils/shinylive.qmd b/book/_utils/shinylive.qmd index 683216dfd7..5eb33529b5 100644 --- a/book/_utils/shinylive.qmd +++ b/book/_utils/shinylive.qmd @@ -13,11 +13,6 @@ Global shinylive configuration is available in the `_quarto.yaml` file. The performance is slighly worse and some of the features (e.g. downloading) might not work at all. ::: - - ```{r shinylive-constructor, echo = FALSE, results = "asis", opts.label = "skip_if_testing"} repo_url <- ifelse(identical(Sys.getenv("QUARTO_PROFILE"), "stable"), "https://insightsengineering.r-universe.dev", "https://pharmaverse.r-universe.dev") options(webr_pkg_repos = c("r-universe" = repo_url, getOption("webr_pkg_repos"))) diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd index ae1786849e..835a11d4ae 100644 --- a/book/graphs/efficacy/fstg01.qmd +++ b/book/graphs/efficacy/fstg01.qmd @@ -8,11 +8,8 @@ subtitle: Subgroup Analysis of Best Overall Response {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(nestcolor) @@ -229,6 +226,14 @@ height <- 5 {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -301,5 +306,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd index 07d9c1923c..5d84f1acf2 100644 --- a/book/graphs/efficacy/fstg02.qmd +++ b/book/graphs/efficacy/fstg02.qmd @@ -8,11 +8,8 @@ subtitle: Subgroup Analysis of Survival Duration {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(forcats) @@ -197,6 +194,14 @@ plot_v3.width <- 8 # nolint: object_name. {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -278,5 +283,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd index 4316e498bb..d1dad1149d 100644 --- a/book/graphs/efficacy/kmg01.qmd +++ b/book/graphs/efficacy/kmg01.qmd @@ -8,11 +8,8 @@ subtitle: Kaplan-Meier Plot {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(nestcolor) @@ -168,6 +165,14 @@ height <- 6 ``` ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -239,5 +244,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd index fdca815b70..bde4f6afd8 100644 --- a/book/graphs/efficacy/mmrmg01.qmd +++ b/book/graphs/efficacy/mmrmg01.qmd @@ -10,12 +10,9 @@ subtitle: Plots for Mixed-Effect Model Repeated Measures Analysis 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. -:::: {.panel-tabset} -## Data Setup and
Model Fitting - -```{r setup, message = FALSE} -#| code-fold: show +:::: {.panel-tabset} and
Model Fitting +```{r setup, echo = FALSE} library(dplyr) library(tern.mmrm) library(nestcolor) @@ -112,6 +109,14 @@ plot <- g_mmrm_diagnostic(mmrm_results, type = "q-q-residual") plot ``` +## Data Setup and
Model Fitting + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -176,5 +181,3 @@ shinyApp(app$ui, app$server) ``` {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/efficacy/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd index ffee055d0d..76d66a4f08 100644 --- a/book/graphs/efficacy/mmrmg02.qmd +++ b/book/graphs/efficacy/mmrmg02.qmd @@ -8,11 +8,8 @@ subtitle: Forest Plot for Mixed-Effect Model Repeated Measures {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern.mmrm) library(nestcolor) @@ -134,8 +131,14 @@ width <- 15 height <- 4 ``` -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/other/brg01.qmd b/book/graphs/other/brg01.qmd index d8745da8c4..e4c98f172b 100644 --- a/book/graphs/other/brg01.qmd +++ b/book/graphs/other/brg01.qmd @@ -8,11 +8,8 @@ subtitle: Bar Chart {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(binom) library(dplyr) library(ggplot2) @@ -368,16 +365,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/other/bwg01.qmd b/book/graphs/other/bwg01.qmd index 063e885cc9..49d0577998 100644 --- a/book/graphs/other/bwg01.qmd +++ b/book/graphs/other/bwg01.qmd @@ -8,12 +8,8 @@ subtitle: Box Plot {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show -# generic code for all plots +```{r setup, echo = FALSE} library(dplyr) library(ggplot2) library(nestcolor) @@ -418,6 +414,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -527,5 +531,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/other/cig01.qmd b/book/graphs/other/cig01.qmd index a99349a476..c72fdd3b31 100644 --- a/book/graphs/other/cig01.qmd +++ b/book/graphs/other/cig01.qmd @@ -8,11 +8,8 @@ subtitle: Confidence Interval Plot {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(ggplot2) library(dplyr) @@ -199,6 +196,14 @@ table {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -288,5 +293,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd index cb2d311ccb..41fa6da3f7 100644 --- a/book/graphs/other/ippg01.qmd +++ b/book/graphs/other/ippg01.qmd @@ -10,11 +10,8 @@ subtitle: Individual Patient Plot Over Time For illustration purposes, we will subset the `adlb` dataset for safety population in treatment arm A and a specific lab parameter (`ALT`). :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -98,6 +95,14 @@ plots {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -180,5 +185,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/other/ltg01.qmd b/book/graphs/other/ltg01.qmd index f3380a54dd..aee3996000 100644 --- a/book/graphs/other/ltg01.qmd +++ b/book/graphs/other/ltg01.qmd @@ -10,11 +10,8 @@ subtitle: Lattice Plot of Laboratory Tests by Treatment Group Over Time Lattice plots are natively handled by R, the examples below rely mostly on the package `ggplot2`. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(teal.modules.clinical) library(ggplot2) @@ -266,16 +263,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd index 34bdd06998..5e71ad7e29 100644 --- a/book/graphs/other/mng01.qmd +++ b/book/graphs/other/mng01.qmd @@ -8,11 +8,8 @@ subtitle: Mean Plot {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(nestcolor) @@ -196,6 +193,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -254,5 +259,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/graphs/pharmacokinetic/pkcg01.qmd b/book/graphs/pharmacokinetic/pkcg01.qmd index ae95cbf64d..9898c88252 100644 --- a/book/graphs/pharmacokinetic/pkcg01.qmd +++ b/book/graphs/pharmacokinetic/pkcg01.qmd @@ -8,11 +8,8 @@ subtitle: Plot of PK Concentration Over Time by Subject {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -102,16 +99,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkcg02.qmd b/book/graphs/pharmacokinetic/pkcg02.qmd index 0389fa6a4e..6616c2abfd 100644 --- a/book/graphs/pharmacokinetic/pkcg02.qmd +++ b/book/graphs/pharmacokinetic/pkcg02.qmd @@ -8,11 +8,8 @@ subtitle: Plot of PK Concentration Over Time by Cohort/Treatment Group/Dose {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -103,16 +100,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd index 357ae99df9..9d5d49a48e 100644 --- a/book/graphs/pharmacokinetic/pkcg03.qmd +++ b/book/graphs/pharmacokinetic/pkcg03.qmd @@ -8,11 +8,8 @@ subtitle: Plot of Mean PK Concentration Over Time by Cohort {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -115,16 +112,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd index aabc87e721..54367195a8 100644 --- a/book/graphs/pharmacokinetic/pkpg01.qmd +++ b/book/graphs/pharmacokinetic/pkpg01.qmd @@ -8,11 +8,8 @@ subtitle: Plot of Mean Cumulative Percentage (%) of Recovered Drug in Urine {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -150,16 +147,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkpg02.qmd b/book/graphs/pharmacokinetic/pkpg02.qmd index 1436a372e2..bfa98ab7f5 100644 --- a/book/graphs/pharmacokinetic/pkpg02.qmd +++ b/book/graphs/pharmacokinetic/pkpg02.qmd @@ -8,11 +8,8 @@ subtitle: Pharmacokinetic Parameter Summary of Serum PK Parameters by Treatment {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -166,16 +163,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkpg03.qmd b/book/graphs/pharmacokinetic/pkpg03.qmd index 1522c87bed..10afa556b1 100644 --- a/book/graphs/pharmacokinetic/pkpg03.qmd +++ b/book/graphs/pharmacokinetic/pkpg03.qmd @@ -8,11 +8,8 @@ subtitle: Box Plot of Pharmacokinetic Parameters by Visit -- Plasma {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -67,8 +64,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkpg04.qmd b/book/graphs/pharmacokinetic/pkpg04.qmd index 357a6f0ee1..a9cc364dd9 100644 --- a/book/graphs/pharmacokinetic/pkpg04.qmd +++ b/book/graphs/pharmacokinetic/pkpg04.qmd @@ -8,11 +8,8 @@ subtitle: Box Plot of Pharmacokinetic Parameters by Visit -- Plasma {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(ggplot2) @@ -69,8 +66,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/graphs/pharmacokinetic/pkpg06.qmd b/book/graphs/pharmacokinetic/pkpg06.qmd index d4ff113d1c..150b584e24 100644 --- a/book/graphs/pharmacokinetic/pkpg06.qmd +++ b/book/graphs/pharmacokinetic/pkpg06.qmd @@ -8,11 +8,8 @@ subtitle: Boxplot of Metabolite to Parent Ratios by Treatment {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(ggplot2) library(tidyr) @@ -266,16 +263,14 @@ plot {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/ADA/adal02.qmd b/book/listings/ADA/adal02.qmd index 33e9b1cc9f..07f92b81ef 100644 --- a/book/listings/ADA/adal02.qmd +++ b/book/listings/ADA/adal02.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Anti-Drug Antibody Data for Treatment Emergent ADA Positive {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -133,8 +130,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/ECG/egl01.qmd b/book/listings/ECG/egl01.qmd index ab67169bb0..980d0380ac 100644 --- a/book/listings/ECG/egl01.qmd +++ b/book/listings/ECG/egl01.qmd @@ -8,11 +8,8 @@ subtitle: 'Listing of ECG Data: Safety-Evaluable Patients' {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -100,8 +97,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 5112035378..c3598856dc 100644 --- a/book/listings/adverse-events/ael01.qmd +++ b/book/listings/adverse-events/ael01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Preferred Terms, Lowest Level Terms, and Investigator-Speci {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -50,8 +47,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 0153bc8b90..70e7c6eca8 100644 --- a/book/listings/adverse-events/ael01_nollt.qmd +++ b/book/listings/adverse-events/ael01_nollt.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Preferred Terms and Investigator-Specified Adverse Event Te {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -49,8 +46,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 0f466aa1db..cf0b46820f 100644 --- a/book/listings/adverse-events/ael02.qmd +++ b/book/listings/adverse-events/ael02.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Adverse Events {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -92,8 +89,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 8637b1cad0..6c18dcdebc 100644 --- a/book/listings/adverse-events/ael02_ed.qmd +++ b/book/listings/adverse-events/ael02_ed.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Adverse Events (for Early Development Studies) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) library(lubridate) @@ -110,8 +107,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 f1a690a3f4..ec6cbec0da 100644 --- a/book/listings/adverse-events/ael03.qmd +++ b/book/listings/adverse-events/ael03.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Serious Adverse Events {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -106,8 +103,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 e1f1a2f1d2..2ecc423a60 100644 --- a/book/listings/adverse-events/ael04.qmd +++ b/book/listings/adverse-events/ael04.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Patient Deaths {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -60,8 +57,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 75b14e5d47..2e628f7235 100644 --- a/book/listings/concomitant-medications/cml01.qmd +++ b/book/listings/concomitant-medications/cml01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Previous and Concomitant Medications {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -71,8 +68,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 14d6aa3883..b8b97465d3 100644 --- a/book/listings/concomitant-medications/cml02a_gl.qmd +++ b/book/listings/concomitant-medications/cml02a_gl.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Concomitant Medication Class Level 2, Preferred Name, and I {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -49,8 +46,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 3c283a6e9d..773c1735c7 100644 --- a/book/listings/concomitant-medications/cml02b_gl.qmd +++ b/book/listings/concomitant-medications/cml02b_gl.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Concomitant Medication Class, Preferred Name, and Investiga {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -52,8 +49,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 76b377f449..68fd97a91e 100644 --- a/book/listings/development-safety-update-report/dsur4.qmd +++ b/book/listings/development-safety-update-report/dsur4.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Patients Who Died During Reporting Period {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -51,8 +48,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/disposition/dsl01.qmd b/book/listings/disposition/dsl01.qmd index 632f2ba14a..eb3032e860 100644 --- a/book/listings/disposition/dsl01.qmd +++ b/book/listings/disposition/dsl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Patients with Study Drug Withdrawn Due to Adverse Events {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -59,8 +56,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/disposition/dsl02.qmd b/book/listings/disposition/dsl02.qmd index 5e1b256aba..a8ef9e40c4 100644 --- a/book/listings/disposition/dsl02.qmd +++ b/book/listings/disposition/dsl02.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Patients Who Discontinued Early from Study {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -67,8 +64,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/efficacy/oncl01.qmd b/book/listings/efficacy/oncl01.qmd index 73fe222078..8dd8e2c6c3 100644 --- a/book/listings/efficacy/oncl01.qmd +++ b/book/listings/efficacy/oncl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Individual Efficacy Data {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -111,8 +108,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/exposure/exl01.qmd b/book/listings/exposure/exl01.qmd index b6f1d958af..efafdb13a2 100644 --- a/book/listings/exposure/exl01.qmd +++ b/book/listings/exposure/exl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Exposure to Study Drug {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -59,8 +56,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 d08c567033..0725eff14b 100644 --- a/book/listings/lab-results/lbl01.qmd +++ b/book/listings/lab-results/lbl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Laboratory Test Results {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -84,8 +81,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 a3fcf1a17e..a779e9863b 100644 --- a/book/listings/lab-results/lbl01_rls.qmd +++ b/book/listings/lab-results/lbl01_rls.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Laboratory Test Results Using Roche Safety Lab Standardizat {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -89,8 +86,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 04b9a40a6d..681fde0a51 100644 --- a/book/listings/lab-results/lbl02a.qmd +++ b/book/listings/lab-results/lbl02a.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Laboratory Abnormalities (constant units) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -84,8 +81,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 0536e3a430..690955f890 100644 --- a/book/listings/lab-results/lbl02a_rls.qmd +++ b/book/listings/lab-results/lbl02a_rls.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Laboratory Abnormalities Defined by Roche Safety Lab Standa {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -104,8 +101,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 726da32aab..e51b9408f6 100644 --- a/book/listings/lab-results/lbl02b.qmd +++ b/book/listings/lab-results/lbl02b.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Laboratory Abnormalities (variable units) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -85,8 +82,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 132856e8d2..570a9f2b44 100644 --- a/book/listings/medical-history/mhl01.qmd +++ b/book/listings/medical-history/mhl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Medical History and Concurrent Diseases {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -63,8 +60,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/pharmacokinetic/pkcl01.qmd b/book/listings/pharmacokinetic/pkcl01.qmd index 8eaa8ea9ff..2217e7a466 100644 --- a/book/listings/pharmacokinetic/pkcl01.qmd +++ b/book/listings/pharmacokinetic/pkcl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Drug A Concentration by Treatment Group, Patient and Nomina {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(rlistings) library(dplyr) @@ -59,8 +56,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/pharmacokinetic/pkcl02.qmd b/book/listings/pharmacokinetic/pkcl02.qmd index f041982f88..10582c9a8d 100644 --- a/book/listings/pharmacokinetic/pkcl02.qmd +++ b/book/listings/pharmacokinetic/pkcl02.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Drug A Urine Concentration and Volumes {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -92,8 +89,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/pharmacokinetic/pkpl01.qmd b/book/listings/pharmacokinetic/pkpl01.qmd index 7de39e998a..40e5173690 100644 --- a/book/listings/pharmacokinetic/pkpl01.qmd +++ b/book/listings/pharmacokinetic/pkpl01.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Drug A Plasma PK Parameters {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -63,8 +60,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/pharmacokinetic/pkpl02.qmd b/book/listings/pharmacokinetic/pkpl02.qmd index f2defbcb36..f55073430b 100644 --- a/book/listings/pharmacokinetic/pkpl02.qmd +++ b/book/listings/pharmacokinetic/pkpl02.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Drug A Urine PK Parameters {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -64,8 +61,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/listings/pharmacokinetic/pkpl04.qmd b/book/listings/pharmacokinetic/pkpl04.qmd index 85a8c96a97..36be382a6e 100644 --- a/book/listings/pharmacokinetic/pkpl04.qmd +++ b/book/listings/pharmacokinetic/pkpl04.qmd @@ -8,11 +8,8 @@ subtitle: Listing of Individual Drug A AUCIFO and CMAX Ratios Following Drug A o {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -79,8 +76,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 3110463cc6..d0d9fbcbe1 100644 --- a/book/listings/vital-signs/vsl01.qmd +++ b/book/listings/vital-signs/vsl01.qmd @@ -8,11 +8,8 @@ subtitle: 'Listing of Vital Signs: Safety-Evaluable Patients' {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(rlistings) @@ -133,8 +130,14 @@ head(lsting, 20) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/repro.qmd b/book/repro.qmd index d5ccfd7052..bb332e9aed 100644 --- a/book/repro.qmd +++ b/book/repro.qmd @@ -2,28 +2,27 @@ ### Timestamp -```{r systime, message = FALSE} -#| code-fold: show -#| renv.ignore: TRUE +```{r systime} +#| echo: FALSE Sys.time() ``` ### Session Info -```{r sessioninfo, message = FALSE} -#| code-fold: show +```{r sessioninfo} +#| echo: FALSE #| renv.ignore: TRUE -sessionInfo() +sessioninfo::session_info() ``` ### `.lock` file Download the `.lock` file and use [`renv::restore()`](https://rstudio.github.io/renv/reference/restore.html) on it to recreate environment used to generate this website. -```{r snapshot, message = FALSE, opts.label = "skip_if_testing"} -#| code-fold: true +```{r snapshot, opts.label = "skip_if_testing"} +#| echo: FALSE #| renv.ignore: TRUE parent_file_path <- knitr::current_input(dir = TRUE) diff --git a/book/tables/ADA/adat01.qmd b/book/tables/ADA/adat01.qmd index aac96b31c5..9f3f549b2d 100644 --- a/book/tables/ADA/adat01.qmd +++ b/book/tables/ADA/adat01.qmd @@ -8,11 +8,7 @@ subtitle: Baseline Prevalence and Incidence of Treatment Emergent ADA {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show - +```{r setup, echo = FALSE} library(tern) library(dplyr) library(tibble) @@ -258,16 +254,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ADA/adat02.qmd b/book/tables/ADA/adat02.qmd index 1e96d6549c..8cd90776f4 100644 --- a/book/tables/ADA/adat02.qmd +++ b/book/tables/ADA/adat02.qmd @@ -8,11 +8,8 @@ subtitle: Summary of Patients with Treatment-Induced ADA {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -143,16 +140,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ADA/adat03.qmd b/book/tables/ADA/adat03.qmd index dbfeba7646..a26c67006e 100644 --- a/book/tables/ADA/adat03.qmd +++ b/book/tables/ADA/adat03.qmd @@ -8,11 +8,8 @@ subtitle: Summary of Serum Concentrations at Timepoints Where ADA Samples Were C {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -120,16 +117,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ADA/adat04a.qmd b/book/tables/ADA/adat04a.qmd index ea8f44ea9f..21ba43bbc3 100644 --- a/book/tables/ADA/adat04a.qmd +++ b/book/tables/ADA/adat04a.qmd @@ -8,11 +8,8 @@ subtitle: Baseline Prevalence and Incidence of Treatment Emergent NAbs {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(tibble) @@ -284,16 +281,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ADA/adat04b.qmd b/book/tables/ADA/adat04b.qmd index d8974f4bcc..841e3b06c9 100644 --- a/book/tables/ADA/adat04b.qmd +++ b/book/tables/ADA/adat04b.qmd @@ -8,11 +8,8 @@ subtitle: Baseline Prevalence and Incidence of NAbs {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(tibble) @@ -242,16 +239,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd index c49e4d3631..795d971d98 100644 --- a/book/tables/ECG/egt01.qmd +++ b/book/tables/ECG/egt01.qmd @@ -8,11 +8,8 @@ subtitle: ECG Results and Change from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -85,6 +82,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -152,5 +157,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd index 6495542bd6..83cdbf7ab0 100644 --- a/book/tables/ECG/egt02.qmd +++ b/book/tables/ECG/egt02.qmd @@ -8,11 +8,8 @@ subtitle: ECG Abnormalities (EGT02_1 & EGT02_2) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -88,6 +85,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -146,5 +151,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd index a19975836f..1750494620 100644 --- a/book/tables/ECG/egt03.qmd +++ b/book/tables/ECG/egt03.qmd @@ -8,11 +8,8 @@ subtitle: Shift Table of ECG Interval Data -- Baseline Versus Minimum/Maximum Po {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -151,6 +148,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -222,5 +227,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/ECG/egt04.qmd b/book/tables/ECG/egt04.qmd index 8ea98251c4..7e1e744021 100644 --- a/book/tables/ECG/egt04.qmd +++ b/book/tables/ECG/egt04.qmd @@ -8,14 +8,8 @@ subtitle: Shift Table of Qualitative ECG Assessments {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -For the EGT04 template, data imputation should be avoided, and missing data explicit and accounted for, so the contingency table sum adds up to the group N. -For illustration purposes, missing data are added to the example dataset. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) set.seed(123) @@ -91,16 +85,17 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -## `teal` App +For the EGT04 template, data imputation should be avoided, and missing data explicit and accounted for, so the contingency table sum adds up to the group N. +For illustration purposes, missing data are added to the example dataset. -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd index 89eed5f375..66b3873150 100644 --- a/book/tables/ECG/egt05_qtcat.qmd +++ b/book/tables/ECG/egt05_qtcat.qmd @@ -8,11 +8,8 @@ subtitle: ECG Actual Values and Changes from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -109,6 +106,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -221,5 +226,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd index a34f8ed074..7caada42fa 100644 --- a/book/tables/adverse-events/aet01.qmd +++ b/book/tables/adverse-events/aet01.qmd @@ -8,13 +8,8 @@ subtitle: Safety Summary {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -To illustrate, additional variables such as flags (TRUE/FALSE) for select AEs of interest and select AE baskets are added to the `adae` dataset. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -368,6 +363,23 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +To illustrate, additional variables such as flags (TRUE/FALSE) for select AEs of interest and select AE baskets are added to the `adae` dataset. + +```{r setup} +#| code-fold: show +``` + + +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -454,5 +466,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd index 5690c6556f..55304e8bf8 100644 --- a/book/tables/adverse-events/aet01_aesi.qmd +++ b/book/tables/adverse-events/aet01_aesi.qmd @@ -8,14 +8,8 @@ subtitle: Safety Summary (Adverse Events of Special Interest) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -To illustrate, additional variables such as flags (TRUE/FALSE) for selected AEs of interest. -Please consult your SAP on how to handle missing AE grades. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -716,6 +710,17 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +To illustrate, additional variables such as flags (TRUE/FALSE) for selected AEs of interest. +Please consult your SAP on how to handle missing AE grades. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -844,5 +849,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd index f82d99b111..dc60575841 100644 --- a/book/tables/adverse-events/aet02.qmd +++ b/book/tables/adverse-events/aet02.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -727,6 +724,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -783,5 +788,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd index f7a9b1db38..5c89750535 100644 --- a/book/tables/adverse-events/aet02_smq.qmd +++ b/book/tables/adverse-events/aet02_smq.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events by Standardized MedDRA Query {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(stringr) @@ -186,6 +183,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -251,5 +256,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd index 9f1249a57e..259c0c2bd8 100644 --- a/book/tables/adverse-events/aet03.qmd +++ b/book/tables/adverse-events/aet03.qmd @@ -8,10 +8,8 @@ subtitle: Adverse Events by Greatest Intensity {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -110,6 +108,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -164,5 +170,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd index 8db38216b6..f38082d6ef 100644 --- a/book/tables/adverse-events/aet04.qmd +++ b/book/tables/adverse-events/aet04.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events by Highest NCI CTCAE Grade {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -602,6 +599,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -656,5 +661,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet04_pi.qmd b/book/tables/adverse-events/aet04_pi.qmd index 20a7fddb27..26103c7e0c 100644 --- a/book/tables/adverse-events/aet04_pi.qmd +++ b/book/tables/adverse-events/aet04_pi.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events Reported in $\geq$ 10% of Patients by Highest NCI CTCAE {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -423,6 +420,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -484,5 +489,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet05.qmd b/book/tables/adverse-events/aet05.qmd index 75d193417b..486d9e19b4 100644 --- a/book/tables/adverse-events/aet05.qmd +++ b/book/tables/adverse-events/aet05.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Event Rate Adjusted for Patient-Years at Risk -- First Occurre {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -81,6 +78,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -147,5 +152,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet05_all.qmd b/book/tables/adverse-events/aet05_all.qmd index 58a77f8793..d57bca053a 100644 --- a/book/tables/adverse-events/aet05_all.qmd +++ b/book/tables/adverse-events/aet05_all.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Event Rate Adjusted for Patient-Years at Risk -- All Occurrenc {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -82,6 +79,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -155,5 +160,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet06.qmd b/book/tables/adverse-events/aet06.qmd index 94b1eb74a8..c2d0bc3676 100644 --- a/book/tables/adverse-events/aet06.qmd +++ b/book/tables/adverse-events/aet06.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events by Baseline Characteristic {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -395,6 +392,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -451,5 +456,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet06_smq.qmd b/book/tables/adverse-events/aet06_smq.qmd index b5b9deb3a3..59d1cf956f 100644 --- a/book/tables/adverse-events/aet06_smq.qmd +++ b/book/tables/adverse-events/aet06_smq.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events by Baseline Characteristic, by SMQ and Preferred Term {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(stringr) @@ -255,6 +252,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -343,5 +348,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet07.qmd b/book/tables/adverse-events/aet07.qmd index f804e8925a..313e0cb2ca 100644 --- a/book/tables/adverse-events/aet07.qmd +++ b/book/tables/adverse-events/aet07.qmd @@ -8,13 +8,8 @@ subtitle: Adverse Events Resulting in Death {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -For illustrative purposes, we will pre-process `AESDTH` in ADAE so there are no deaths in arm A and concatenate `AEBODSYS` and `AEDECOD` as per GDSR output standards for AET07. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -118,6 +113,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +For illustrative purposes, we will pre-process `AESDTH` in ADAE so there are no deaths in arm A and concatenate `AEBODSYS` and `AEDECOD` as per GDSR output standards for AET07. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -201,5 +206,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet09.qmd b/book/tables/adverse-events/aet09.qmd index c85cddc51f..fbfa1ec8c9 100644 --- a/book/tables/adverse-events/aet09.qmd +++ b/book/tables/adverse-events/aet09.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events Related to Study Drug {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -182,6 +179,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -239,5 +244,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet09_smq.qmd b/book/tables/adverse-events/aet09_smq.qmd index 632341d025..36726a591f 100644 --- a/book/tables/adverse-events/aet09_smq.qmd +++ b/book/tables/adverse-events/aet09_smq.qmd @@ -8,11 +8,8 @@ subtitle: Adverse Events Related to Study Drug by Standardized MedDRA Query {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(stringr) @@ -190,6 +187,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -261,5 +266,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/adverse-events/aet10.qmd b/book/tables/adverse-events/aet10.qmd index 11bd173ee9..3c2b6f29c8 100644 --- a/book/tables/adverse-events/aet10.qmd +++ b/book/tables/adverse-events/aet10.qmd @@ -8,11 +8,8 @@ subtitle: Most Common ($\geq$ 5%) Adverse Events {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -110,6 +107,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -170,5 +175,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/concomitant-medications/cmt01.qmd b/book/tables/concomitant-medications/cmt01.qmd index 3d97ad3cf0..cd67b6d3c0 100644 --- a/book/tables/concomitant-medications/cmt01.qmd +++ b/book/tables/concomitant-medications/cmt01.qmd @@ -8,11 +8,8 @@ subtitle: Concomitant Medications (GNEDrug Legacy Coding) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -253,6 +250,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -318,5 +323,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/concomitant-medications/cmt01a.qmd b/book/tables/concomitant-medications/cmt01a.qmd index 2b6e7b2875..7b57d4d00a 100644 --- a/book/tables/concomitant-medications/cmt01a.qmd +++ b/book/tables/concomitant-medications/cmt01a.qmd @@ -8,11 +8,8 @@ subtitle: Concomitant Medications by Medication Class and Preferred Name {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -245,6 +242,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -309,5 +314,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/concomitant-medications/cmt01b.qmd b/book/tables/concomitant-medications/cmt01b.qmd index f7afde4196..5bf303781a 100644 --- a/book/tables/concomitant-medications/cmt01b.qmd +++ b/book/tables/concomitant-medications/cmt01b.qmd @@ -8,11 +8,8 @@ subtitle: Concomitant Medications by Medication Class and Preferred Name {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -269,6 +266,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -332,5 +337,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/concomitant-medications/cmt02_pt.qmd b/book/tables/concomitant-medications/cmt02_pt.qmd index f5ebfbe064..b2dc1e73e0 100644 --- a/book/tables/concomitant-medications/cmt02_pt.qmd +++ b/book/tables/concomitant-medications/cmt02_pt.qmd @@ -8,11 +8,8 @@ subtitle: Concomitant Medications by Preferred Name (WHODrug Coding) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -71,6 +68,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -135,5 +140,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/deaths/dtht01.qmd b/book/tables/deaths/dtht01.qmd index 31d338d72e..3fc1e690fb 100644 --- a/book/tables/deaths/dtht01.qmd +++ b/book/tables/deaths/dtht01.qmd @@ -8,11 +8,8 @@ subtitle: Deaths {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -208,16 +205,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/demography/dmt01.qmd b/book/tables/demography/dmt01.qmd index 9c37020786..74ac32d306 100644 --- a/book/tables/demography/dmt01.qmd +++ b/book/tables/demography/dmt01.qmd @@ -8,11 +8,8 @@ subtitle: Demographics and Baseline Characteristics {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(tidyr) @@ -227,6 +224,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -276,5 +281,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/disclosures/disclosurest01.qmd b/book/tables/disclosures/disclosurest01.qmd index 1c5a6c397d..6643615e08 100644 --- a/book/tables/disclosures/disclosurest01.qmd +++ b/book/tables/disclosures/disclosurest01.qmd @@ -416,8 +416,8 @@ result {{< include ../../_utils/webr.qmd >}} ::: +:::: + {{< include ../../_utils/save_results.qmd >}} {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/disclosures/eudrat01.qmd b/book/tables/disclosures/eudrat01.qmd index 54761b235e..bb7b5eda8d 100644 --- a/book/tables/disclosures/eudrat01.qmd +++ b/book/tables/disclosures/eudrat01.qmd @@ -8,13 +8,8 @@ subtitle: Non-Serious Adverse Events Reported in $\geq$ 5% of Patients in Any Tr {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -Define a trimming function `get_adae_trimmed` to filter for AEs of greater than 5% incidence rate. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -96,16 +91,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -## `teal` App +Define a trimming function `get_adae_trimmed` to filter for AEs of greater than 5% incidence rate. -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/disclosures/eudrat02.qmd b/book/tables/disclosures/eudrat02.qmd index 64edb7fc2c..af82edbea6 100644 --- a/book/tables/disclosures/eudrat02.qmd +++ b/book/tables/disclosures/eudrat02.qmd @@ -8,13 +8,8 @@ subtitle: Serious Adverse Events, Fatal Serious Adverse Events, and Serious Adve {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -For illustrative purposes, the `adae` data is filtered by arm `A: Drug X` here. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -73,16 +68,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -## `teal` App +For illustrative purposes, the `adae` data is filtered by arm `A: Drug X` here. -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/disposition/dst01.qmd b/book/tables/disposition/dst01.qmd index a1fef5fc32..bac5d2c664 100644 --- a/book/tables/disposition/dst01.qmd +++ b/book/tables/disposition/dst01.qmd @@ -8,11 +8,8 @@ subtitle: Patient Disposition {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -134,6 +131,14 @@ result3 {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -204,5 +209,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/disposition/pdt01.qmd b/book/tables/disposition/pdt01.qmd index 4173eb1779..faa6aa0ff8 100644 --- a/book/tables/disposition/pdt01.qmd +++ b/book/tables/disposition/pdt01.qmd @@ -8,11 +8,8 @@ subtitle: Major Protocol Deviations {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -68,6 +65,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -124,5 +129,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/disposition/pdt02.qmd b/book/tables/disposition/pdt02.qmd index 60e7769c95..22a8e3318b 100644 --- a/book/tables/disposition/pdt02.qmd +++ b/book/tables/disposition/pdt02.qmd @@ -8,11 +8,8 @@ subtitle: Major Protocol Deviations Related to Epidemic/Pandemic {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -69,16 +66,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/efficacy/aovt01.qmd b/book/tables/efficacy/aovt01.qmd index febe738dc7..b418053147 100644 --- a/book/tables/efficacy/aovt01.qmd +++ b/book/tables/efficacy/aovt01.qmd @@ -8,11 +8,8 @@ subtitle: ANCOVA for Multiple End Points {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -65,6 +62,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -142,5 +147,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/aovt02.qmd b/book/tables/efficacy/aovt02.qmd index 375ab530c5..a43f4c8a97 100644 --- a/book/tables/efficacy/aovt02.qmd +++ b/book/tables/efficacy/aovt02.qmd @@ -11,11 +11,8 @@ This example will focus on data from a single visit "WEEK 1 DAY 8" and a single Only evaluable populations will be analyzed. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -72,6 +69,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -148,5 +153,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/aovt03.qmd b/book/tables/efficacy/aovt03.qmd index e964e4b9ac..1d2c547fd2 100644 --- a/book/tables/efficacy/aovt03.qmd +++ b/book/tables/efficacy/aovt03.qmd @@ -10,11 +10,8 @@ subtitle: ANCOVA with Consideration of Interaction This example will focus on data from multiple visits and take the interaction between visits and arms into consideration. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -73,16 +70,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/efficacy/cfbt01.qmd b/book/tables/efficacy/cfbt01.qmd index 3eec178b76..17bb26b8b7 100644 --- a/book/tables/efficacy/cfbt01.qmd +++ b/book/tables/efficacy/cfbt01.qmd @@ -8,11 +8,8 @@ subtitle: Efficacy Data and Change from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -93,6 +90,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -162,5 +167,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/cmht01.qmd b/book/tables/efficacy/cmht01.qmd index 4418de4fa5..21553ade12 100644 --- a/book/tables/efficacy/cmht01.qmd +++ b/book/tables/efficacy/cmht01.qmd @@ -8,11 +8,8 @@ subtitle: Cochran-Mantel-Haenszel (CMH) Summary {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -145,10 +142,18 @@ result <- build_table( result ``` -`r webr_code_labels <- c("setup", "variant2")` +`r webr_code_labels <- c("setup", "variant2")` {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -207,5 +212,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/coxt01.qmd b/book/tables/efficacy/coxt01.qmd index 126eb8cae2..413dbbe757 100644 --- a/book/tables/efficacy/coxt01.qmd +++ b/book/tables/efficacy/coxt01.qmd @@ -12,11 +12,8 @@ It assumes proportional hazards; that is, it assumes that the ratio of the hazar This ratio is referred to as the "hazard ratio" and is one of the most commonly reported metrics to describe the effect size in survival analysis. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -188,6 +185,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -255,5 +260,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/coxt02.qmd b/book/tables/efficacy/coxt02.qmd index 8541443fca..1eb6506aeb 100644 --- a/book/tables/efficacy/coxt02.qmd +++ b/book/tables/efficacy/coxt02.qmd @@ -14,11 +14,8 @@ The analysis follows the same principles (i.e. stratified vs. unstratified analy Since there is usually no pre-specified hypothesis testing for such analysis, the p-values must be interpreted with caution. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(broom) @@ -145,6 +142,14 @@ result See the *Multivariable Cox Regression with Interaction Term* tab. +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -207,5 +212,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/dort01.qmd b/book/tables/efficacy/dort01.qmd index 45903b6401..be826970d0 100644 --- a/book/tables/efficacy/dort01.qmd +++ b/book/tables/efficacy/dort01.qmd @@ -8,11 +8,8 @@ subtitle: Duration of Response {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -284,6 +281,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -359,5 +364,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/lgrt02.qmd b/book/tables/efficacy/lgrt02.qmd index 7626413e06..63ed42f787 100644 --- a/book/tables/efficacy/lgrt02.qmd +++ b/book/tables/efficacy/lgrt02.qmd @@ -8,11 +8,8 @@ subtitle: Multi-Variable Logistic Regression {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -177,6 +174,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -244,5 +249,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/mmrmt01.qmd b/book/tables/efficacy/mmrmt01.qmd index e60ab4fd5a..c9f62e5bb4 100644 --- a/book/tables/efficacy/mmrmt01.qmd +++ b/book/tables/efficacy/mmrmt01.qmd @@ -8,11 +8,8 @@ subtitle: Tables for Mixed-Effect Model Repeated Measures Analysis {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern.mmrm) library(broom) @@ -209,6 +206,14 @@ Statistics to evaluate choice of covariance structure are being investigated and as.rtable(mmrm_results, type = "diagnostic") ``` +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -272,5 +277,3 @@ shinyApp(app$ui, app$server) ``` {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/onct05.qmd b/book/tables/efficacy/onct05.qmd index 38d629389e..e14571522d 100644 --- a/book/tables/efficacy/onct05.qmd +++ b/book/tables/efficacy/onct05.qmd @@ -8,11 +8,8 @@ subtitle: Objective Response Rate by Subgroup {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -162,6 +159,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -237,5 +242,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/ratet01.qmd b/book/tables/efficacy/ratet01.qmd index a247f45115..31c7a64802 100644 --- a/book/tables/efficacy/ratet01.qmd +++ b/book/tables/efficacy/ratet01.qmd @@ -11,11 +11,8 @@ This example will focus on data from a single visit "WEEK 1 DAY 8" and a single Only evaluable populations will be analyzed. :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -94,16 +91,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In Progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/efficacy/rbmit01.qmd b/book/tables/efficacy/rbmit01.qmd index c605d0de26..345024794c 100644 --- a/book/tables/efficacy/rbmit01.qmd +++ b/book/tables/efficacy/rbmit01.qmd @@ -8,16 +8,8 @@ subtitle: Tables for RBMI {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -We use a publicly available example dataset from an antidepressant clinical trial of an active drug versus placebo from the `rbmi` package. -The relevant endpoint is the Hamilton 17-item depression rating scale (`HAMD17`) which was assessed at baseline and at weeks 1, 2, 4, and 6. -Study drug discontinuation occurred in 24% of subjects from the active drug and 26% of subjects from placebo. -All data after study drug discontinuation are missing and there is a single additional intermittent missing observation. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern.rbmi) library(dplyr) set.seed(123) @@ -215,8 +207,19 @@ result <- basic_table() %>% result ``` -{{< include ../../_utils/save_results.qmd >}} +## Data Setup + +We use a publicly available example dataset from an antidepressant clinical trial of an active drug versus placebo from the `rbmi` package. +The relevant endpoint is the Hamilton 17-item depression rating scale (`HAMD17`) which was assessed at baseline and at weeks 1, 2, 4, and 6. +Study drug discontinuation occurred in 24% of subjects from the active drug and 26% of subjects from placebo. +All data after study drug discontinuation are missing and there is a single additional intermittent missing observation. + +```{r setup} +#| code-fold: show +``` -{{< include ../../repro.qmd >}} :::: +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/efficacy/rspt01.qmd b/book/tables/efficacy/rspt01.qmd index 95efe12f81..a28741ef93 100644 --- a/book/tables/efficacy/rspt01.qmd +++ b/book/tables/efficacy/rspt01.qmd @@ -8,11 +8,8 @@ subtitle: Best Overall Response {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -284,6 +281,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -360,5 +365,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/efficacy/ttet01.qmd b/book/tables/efficacy/ttet01.qmd index f41730d1a1..1da2c85d5d 100644 --- a/book/tables/efficacy/ttet01.qmd +++ b/book/tables/efficacy/ttet01.qmd @@ -8,11 +8,8 @@ subtitle: Time-To-Event Summary {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -431,6 +428,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -506,5 +511,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/exposure/ext01.qmd b/book/tables/exposure/ext01.qmd index 9cfd7e987a..2551252ceb 100644 --- a/book/tables/exposure/ext01.qmd +++ b/book/tables/exposure/ext01.qmd @@ -8,11 +8,8 @@ subtitle: Study Drug Exposure Table {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(tidyr) @@ -215,6 +212,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -294,5 +299,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt01.qmd b/book/tables/lab-results/lbt01.qmd index c9ca5205f2..e5e3bdb8af 100644 --- a/book/tables/lab-results/lbt01.qmd +++ b/book/tables/lab-results/lbt01.qmd @@ -8,13 +8,8 @@ subtitle: Laboratory Test Results and Change from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -In order to generate the `LBT01` standard tabulation, the `adlb` dataset may be pre-processed so as to discriminate baseline from follow-up visits. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -89,6 +84,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +In order to generate the `LBT01` standard tabulation, the `adlb` dataset may be pre-processed so as to discriminate baseline from follow-up visits. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -156,5 +161,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt02.qmd b/book/tables/lab-results/lbt02.qmd index dfe63d25f1..6912289923 100644 --- a/book/tables/lab-results/lbt02.qmd +++ b/book/tables/lab-results/lbt02.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Test Results by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} # Preparation of an illustrative dataset library(tern) @@ -64,6 +61,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -128,5 +133,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt03.qmd b/book/tables/lab-results/lbt03.qmd index af4d6eb7f2..e25542a7c8 100644 --- a/book/tables/lab-results/lbt03.qmd +++ b/book/tables/lab-results/lbt03.qmd @@ -8,13 +8,8 @@ subtitle: Laboratory Test Results Change from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -For illustration purposes, this example focuses on "C-Reactive Protein Measurement" starting from baseline, while excluding visit at week 1 for subjects who were randomized to the placebo group. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -119,6 +114,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +For illustration purposes, this example focuses on "C-Reactive Protein Measurement" starting from baseline, while excluding visit at week 1 for subjects who were randomized to the placebo group. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -207,5 +212,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt04.qmd b/book/tables/lab-results/lbt04.qmd index 6c654d406e..7ec2565979 100644 --- a/book/tables/lab-results/lbt04.qmd +++ b/book/tables/lab-results/lbt04.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Abnormalities Not Present at Baseline {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -60,6 +57,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -119,5 +124,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt05.qmd b/book/tables/lab-results/lbt05.qmd index 80b769cbf7..25623484c6 100644 --- a/book/tables/lab-results/lbt05.qmd +++ b/book/tables/lab-results/lbt05.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Abnormalities with Single and Replicated Marked {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -188,8 +185,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -{{< include ../../repro.qmd >}} +```{r setup} +#| code-fold: show +``` :::: + +{{< 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 a1a49c9dc1..d23241a68c 100644 --- a/book/tables/lab-results/lbt06.qmd +++ b/book/tables/lab-results/lbt06.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Abnormalities by Visit and Baseline Status {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -103,16 +100,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt07.qmd b/book/tables/lab-results/lbt07.qmd index 20561c2e9d..2098c0dac8 100644 --- a/book/tables/lab-results/lbt07.qmd +++ b/book/tables/lab-results/lbt07.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(forcats) @@ -109,6 +106,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -169,5 +174,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt08.qmd b/book/tables/lab-results/lbt08.qmd index 7464ee0ccc..1a8a23db89 100644 --- a/book/tables/lab-results/lbt08.qmd +++ b/book/tables/lab-results/lbt08.qmd @@ -8,11 +8,8 @@ subtitle: Laboratory Test Results with Highest NCI CTCAE Grade at Any Time {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -75,16 +72,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt09.qmd b/book/tables/lab-results/lbt09.qmd index 88aa292f19..c27c9764d2 100644 --- a/book/tables/lab-results/lbt09.qmd +++ b/book/tables/lab-results/lbt09.qmd @@ -8,11 +8,8 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -177,16 +174,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt10.qmd b/book/tables/lab-results/lbt10.qmd index 7415bfca0e..84a6b94a9b 100644 --- a/book/tables/lab-results/lbt10.qmd +++ b/book/tables/lab-results/lbt10.qmd @@ -8,11 +8,8 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -102,16 +99,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt10_bl.qmd b/book/tables/lab-results/lbt10_bl.qmd index ef44deb999..73fd78b114 100644 --- a/book/tables/lab-results/lbt10_bl.qmd +++ b/book/tables/lab-results/lbt10_bl.qmd @@ -8,11 +8,8 @@ subtitle: Liver Laboratory Tests -- Patients with Elevated Post-Baseline AST or {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -102,16 +99,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt11.qmd b/book/tables/lab-results/lbt11.qmd index 19e5087de9..fd12276c46 100644 --- a/book/tables/lab-results/lbt11.qmd +++ b/book/tables/lab-results/lbt11.qmd @@ -8,11 +8,8 @@ subtitle: Time to First Increase in Liver Laboratory Test Result Meeting Hy's La {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -150,6 +147,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -226,5 +231,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt11_bl.qmd b/book/tables/lab-results/lbt11_bl.qmd index bc8bafa594..24d3515ccb 100644 --- a/book/tables/lab-results/lbt11_bl.qmd +++ b/book/tables/lab-results/lbt11_bl.qmd @@ -8,11 +8,8 @@ subtitle: Time to First Increase in Liver Laboratory Test Result Meeting Hy's La {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -150,6 +147,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -226,5 +231,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt12.qmd b/book/tables/lab-results/lbt12.qmd index d6053435ec..bbd97eed36 100644 --- a/book/tables/lab-results/lbt12.qmd +++ b/book/tables/lab-results/lbt12.qmd @@ -8,11 +8,8 @@ subtitle: Liver Laboratory Tests by Time on Treatment -- Patients with Elevated {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -76,16 +73,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt12_bl.qmd b/book/tables/lab-results/lbt12_bl.qmd index 42929fcdcc..4e1720e7bd 100644 --- a/book/tables/lab-results/lbt12_bl.qmd +++ b/book/tables/lab-results/lbt12_bl.qmd @@ -8,11 +8,8 @@ subtitle: Liver Laboratory Tests by Time on Treatment -- Patients with Elevated {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -76,16 +73,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/lab-results/lbt13.qmd b/book/tables/lab-results/lbt13.qmd index eaa79b4fc7..02fafe64fd 100644 --- a/book/tables/lab-results/lbt13.qmd +++ b/book/tables/lab-results/lbt13.qmd @@ -8,16 +8,8 @@ subtitle: NCI CTCAE Grade Laboratory Abnormalities by Visit and Baseline Grade {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -Please note that for each variant, the `adlb` dataset needs to be filtered on correct flags like `WGRLOVFL`, `WGRHIVFL`, et al., otherwise the layout function will not return the correct counts. -There is an option to create a record for a lab test where no record is found at that visit. -If you specified `add_derived_type = "PHANTOM"` & `dtype_phantom_cond`, you don't have to use the `h_adsl_adlb_merge_using_worst_flag` function to preprocess your `adlb` dataset. -Otherwise please follow the pre-processing steps below before applying the layout functions. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -446,6 +438,19 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +Please note that for each variant, the `adlb` dataset needs to be filtered on correct flags like `WGRLOVFL`, `WGRHIVFL`, et al., otherwise the layout function will not return the correct counts. +There is an option to create a record for a lab test where no record is found at that visit. +If you specified `add_derived_type = "PHANTOM"` & `dtype_phantom_cond`, you don't have to use the `h_adsl_adlb_merge_using_worst_flag` function to preprocess your `adlb` dataset. +Otherwise please follow the pre-processing steps below before applying the layout functions. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -516,5 +521,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt14.qmd b/book/tables/lab-results/lbt14.qmd index 0abe5fadd6..514393ca5c 100644 --- a/book/tables/lab-results/lbt14.qmd +++ b/book/tables/lab-results/lbt14.qmd @@ -8,16 +8,8 @@ subtitle: Laboratory Test Results Shift Table -- Highest NCI CTCAE Grade Post-Ba {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -Please note that for each variant, the `adlb` dataset needs to be filtered on correct flags like `WGRLOFL`, `WGRHIFL`, et al., otherwise the layout function will not return the correct counts. -There is an option to create a record for a lab test where no record is found at that visit. -If you specified `add_derived_type = "PHANTOM"` & `dtype_phantom_cond`, you don't have to use the `h_adsl_adlb_merge_using_worst_flag` function to preprocess your `adlb` dataset. -Otherwise please follow the pre-processing steps below before applying the layout functions. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -348,6 +340,19 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +Please note that for each variant, the `adlb` dataset needs to be filtered on correct flags like `WGRLOFL`, `WGRHIFL`, et al., otherwise the layout function will not return the correct counts. +There is an option to create a record for a lab test where no record is found at that visit. +If you specified `add_derived_type = "PHANTOM"` & `dtype_phantom_cond`, you don't have to use the `h_adsl_adlb_merge_using_worst_flag` function to preprocess your `adlb` dataset. +Otherwise please follow the pre-processing steps below before applying the layout functions. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -418,5 +423,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/lab-results/lbt15.qmd b/book/tables/lab-results/lbt15.qmd index 8c5f45daf5..80d655df1f 100644 --- a/book/tables/lab-results/lbt15.qmd +++ b/book/tables/lab-results/lbt15.qmd @@ -8,13 +8,8 @@ subtitle: Laboratory Test Shifts to NCI CTCAE Grade 3-4 Post-Baseline {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -Because the `random.cdisc.data` dataset `adlb` doesn't have the `PARCAT1` variable, this variable is created from `LBCAT` in pre-processing. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) library(forcats) @@ -118,6 +113,16 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +Because the `random.cdisc.data` dataset `adlb` doesn't have the `PARCAT1` variable, this variable is created from `LBCAT` in pre-processing. + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -200,5 +205,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/medical-history/mht01.qmd b/book/tables/medical-history/mht01.qmd index fbadb10c68..6e670d1705 100644 --- a/book/tables/medical-history/mht01.qmd +++ b/book/tables/medical-history/mht01.qmd @@ -8,11 +8,8 @@ subtitle: Medical History {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -187,6 +184,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -243,5 +248,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/pharmacokinetic/pkct01.qmd b/book/tables/pharmacokinetic/pkct01.qmd index bbf5551545..b16a174cbb 100644 --- a/book/tables/pharmacokinetic/pkct01.qmd +++ b/book/tables/pharmacokinetic/pkct01.qmd @@ -8,11 +8,8 @@ subtitle: Summary Concentration Table {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -179,16 +176,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt02.qmd b/book/tables/pharmacokinetic/pkpt02.qmd index ec5c816387..6a2ad43368 100644 --- a/book/tables/pharmacokinetic/pkpt02.qmd +++ b/book/tables/pharmacokinetic/pkpt02.qmd @@ -8,11 +8,8 @@ subtitle: Pharmacokinetic Parameter Summary -- Plasma/Serum/Blood PK Parameters {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -96,16 +93,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt03.qmd b/book/tables/pharmacokinetic/pkpt03.qmd index da9a5dd618..968c65f317 100644 --- a/book/tables/pharmacokinetic/pkpt03.qmd +++ b/book/tables/pharmacokinetic/pkpt03.qmd @@ -8,12 +8,9 @@ subtitle: Pharmacokinetic Parameter Summary of Plasma by Treatment (Stats in Col {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup -```{r setup, message = FALSE, opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} -#| code-fold: show - +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -181,16 +178,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt04.qmd b/book/tables/pharmacokinetic/pkpt04.qmd index 84af4786e1..47698822af 100644 --- a/book/tables/pharmacokinetic/pkpt04.qmd +++ b/book/tables/pharmacokinetic/pkpt04.qmd @@ -8,11 +8,8 @@ subtitle: Pharmacokinetic Parameter Summary -- Urine PK Parameters (Stats in Row {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -96,16 +93,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt05.qmd b/book/tables/pharmacokinetic/pkpt05.qmd index 0d10a1a196..7b146e9d10 100644 --- a/book/tables/pharmacokinetic/pkpt05.qmd +++ b/book/tables/pharmacokinetic/pkpt05.qmd @@ -8,11 +8,8 @@ subtitle: Summary of Urinary PK Parameters by Treatment Arm (Stats in Columns) {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -115,16 +112,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt06.qmd b/book/tables/pharmacokinetic/pkpt06.qmd index 6840d6bb81..f42bc821a0 100644 --- a/book/tables/pharmacokinetic/pkpt06.qmd +++ b/book/tables/pharmacokinetic/pkpt06.qmd @@ -8,11 +8,8 @@ subtitle: Pharmacokinetic Parameter Summary -- Dose-Normalized PK Parameters (St {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(stringr) @@ -98,16 +95,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt07.qmd b/book/tables/pharmacokinetic/pkpt07.qmd index 6cf5b4b5e6..3ce7158435 100644 --- a/book/tables/pharmacokinetic/pkpt07.qmd +++ b/book/tables/pharmacokinetic/pkpt07.qmd @@ -8,11 +8,8 @@ subtitle: Table of Mean Dose-Normalized Selected Pharmacokinetic Parameters (Sta {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) library(stringr) @@ -117,16 +114,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt08.qmd b/book/tables/pharmacokinetic/pkpt08.qmd index 6ff86a0ab5..2464f2164f 100644 --- a/book/tables/pharmacokinetic/pkpt08.qmd +++ b/book/tables/pharmacokinetic/pkpt08.qmd @@ -8,11 +8,8 @@ subtitle: Pharmacokinetic Parameter Summary of Cumulative Amount of Drug Elimina {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -92,16 +89,14 @@ cat(rtables::toString(result, indent_size = 10)) {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/pharmacokinetic/pkpt11.qmd b/book/tables/pharmacokinetic/pkpt11.qmd index 963aa8302a..4b5a9620ac 100644 --- a/book/tables/pharmacokinetic/pkpt11.qmd +++ b/book/tables/pharmacokinetic/pkpt11.qmd @@ -8,12 +8,9 @@ subtitle: Pharmacokinetic Parameter Estimated Ratios of Geometric Means and 90% {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup -```{r setup, message = FALSE, opts.label = ifelse(packageVersion("tern") < "0.9.3.9020", "skip_test_strict", "")} -#| code-fold: show - +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -165,16 +162,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: -{{< include ../../_utils/save_results.qmd >}} - -## `teal` App +## Data Setup -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/risk-management-plan/rmpt01.qmd b/book/tables/risk-management-plan/rmpt01.qmd index 5e5ab5b890..9964f721b3 100644 --- a/book/tables/risk-management-plan/rmpt01.qmd +++ b/book/tables/risk-management-plan/rmpt01.qmd @@ -8,11 +8,8 @@ subtitle: Duration of Exposure for Risk Management Plan {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -84,6 +81,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -169,5 +174,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/risk-management-plan/rmpt03.qmd b/book/tables/risk-management-plan/rmpt03.qmd index 5e044d4835..08ecacbe7f 100644 --- a/book/tables/risk-management-plan/rmpt03.qmd +++ b/book/tables/risk-management-plan/rmpt03.qmd @@ -8,11 +8,8 @@ subtitle: Extent of Exposure by Age Group and Gender for Risk Management Plan {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -124,6 +121,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -222,5 +227,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/risk-management-plan/rmpt04.qmd b/book/tables/risk-management-plan/rmpt04.qmd index 19794c6477..d54ab43349 100644 --- a/book/tables/risk-management-plan/rmpt04.qmd +++ b/book/tables/risk-management-plan/rmpt04.qmd @@ -8,11 +8,8 @@ subtitle: Extent of Exposure by Ethnic Origin for Risk Management Plan {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -73,6 +70,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -150,5 +155,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/risk-management-plan/rmpt05.qmd b/book/tables/risk-management-plan/rmpt05.qmd index 464ceb1e14..45287ecbcc 100644 --- a/book/tables/risk-management-plan/rmpt05.qmd +++ b/book/tables/risk-management-plan/rmpt05.qmd @@ -8,11 +8,8 @@ subtitle: Extent of Exposure by Race for Risk Management Plan {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -75,6 +72,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -152,5 +157,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/risk-management-plan/rmpt06.qmd b/book/tables/risk-management-plan/rmpt06.qmd index ab4dccff63..dbe6801fd2 100644 --- a/book/tables/risk-management-plan/rmpt06.qmd +++ b/book/tables/risk-management-plan/rmpt06.qmd @@ -8,14 +8,8 @@ subtitle: Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Manage {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -The `adae` and `adsl` datasets need to undergo data processing before table production. -Some new variables are added to these datasets to create the desired tables. - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -347,16 +341,17 @@ result # In progress ``` -{{< include ../../_utils/save_results.qmd >}} +## Data Setup -## `teal` App +The `adae` and `adsl` datasets need to undergo data processing before table production. +Some new variables are added to these datasets to create the desired tables. -```{r teal, opts.label = c("skip_if_testing", "app")} +```{r setup} #| code-fold: show - -# In progress ``` -{{< include ../../repro.qmd >}} - :::: + +{{< include ../../_utils/save_results.qmd >}} + +{{< include ../../repro.qmd >}} diff --git a/book/tables/safety/enrollment01.qmd b/book/tables/safety/enrollment01.qmd index d1139b9fa9..44eff69f6a 100644 --- a/book/tables/safety/enrollment01.qmd +++ b/book/tables/safety/enrollment01.qmd @@ -8,11 +8,8 @@ subtitle: Enrollment Variants {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(forcats) library(tern) @@ -146,6 +143,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -233,5 +238,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/vital-signs/vst01.qmd b/book/tables/vital-signs/vst01.qmd index 1d43af0da3..70bcf3c6f5 100644 --- a/book/tables/vital-signs/vst01.qmd +++ b/book/tables/vital-signs/vst01.qmd @@ -8,11 +8,8 @@ subtitle: Vital Sign Results and Change from Baseline by Visit {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(tern) library(dplyr) @@ -126,6 +123,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -230,5 +235,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/book/tables/vital-signs/vst02.qmd b/book/tables/vital-signs/vst02.qmd index 0601b9aba0..80ae32b905 100644 --- a/book/tables/vital-signs/vst02.qmd +++ b/book/tables/vital-signs/vst02.qmd @@ -8,11 +8,8 @@ subtitle: Vital Sign Abnormalities {{< include ../../_utils/envir_hook.qmd >}} :::: {.panel-tabset} -## Data Setup - -```{r setup, message = FALSE} -#| code-fold: show +```{r setup, echo = FALSE} library(dplyr) library(tern) @@ -87,6 +84,14 @@ result {{< include ../../_utils/webr.qmd >}} ::: +## Data Setup + +```{r setup} +#| code-fold: show +``` + +:::: + {{< include ../../_utils/save_results.qmd >}} ## `teal` App @@ -149,5 +154,3 @@ shinyApp(app$ui, app$server) ::: {{< include ../../repro.qmd >}} - -:::: diff --git a/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md b/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md index 7efad52641..bea886c4e9 100644 --- a/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md +++ b/package/tests/testthat/_snaps/development/tables-efficacy-mmrmt01.md @@ -13,7 +13,7 @@ Difference in Adjusted Means (SE) 0.759 (0.973) -0.325 (0.976) 95% CI (-1.155, 2.672) (-2.243, 1.593) Relative Increase (%) 21.8% -9.3% - p-value (MMRM) 0.4362 0.7393 + p-value (MMRM) 0.4362 0.7394 WEEK 2 DAY 15 n 134 134 132 Adjusted Mean (SE) 9.135 (0.768) 9.018 (0.767) 8.509 (0.773) @@ -21,7 +21,7 @@ Difference in Adjusted Means (SE) -0.117 (1.087) -0.626 (1.090) 95% CI (-2.253, 2.020) (-2.768, 1.517) Relative Increase (%) -1.3% -6.8% - p-value (MMRM) 0.9147 0.5662 + p-value (MMRM) 0.9146 0.5662 WEEK 3 DAY 22 n 134 134 132 Adjusted Mean (SE) 13.547 (0.871) 16.014 (0.871) 15.789 (0.877) diff --git a/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md b/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md index 138240e761..b197682aed 100644 --- a/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md +++ b/package/tests/testthat/_snaps/stable/tables-efficacy-mmrmt01.md @@ -13,7 +13,7 @@ Difference in Adjusted Means (SE) 0.759 (0.973) -0.325 (0.976) 95% CI (-1.155, 2.672) (-2.243, 1.593) Relative Increase (%) 21.8% -9.3% - p-value (MMRM) 0.4362 0.7393 + p-value (MMRM) 0.4362 0.7394 WEEK 2 DAY 15 n 134 134 132 Adjusted Mean (SE) 9.135 (0.768) 9.018 (0.767) 8.509 (0.773) @@ -21,7 +21,7 @@ Difference in Adjusted Means (SE) -0.117 (1.087) -0.626 (1.090) 95% CI (-2.253, 2.020) (-2.768, 1.517) Relative Increase (%) -1.3% -6.8% - p-value (MMRM) 0.9147 0.5662 + p-value (MMRM) 0.9146 0.5662 WEEK 3 DAY 22 n 134 134 132 Adjusted Mean (SE) 13.547 (0.871) 16.014 (0.871) 15.789 (0.877)