put table first (#266)

an attempt to fix #265 currently one table only but if this is ok I can go for other tables as well ![Sep-20-2024 11-56-05](https://github.com/user-attachments/assets/9a18f7fe-be42-42d7-bf42-a121ed13f659) Changes: - move "Data Setup" at the very end of the tabset - move "teal App" as a section below tabset - move "Reproducibility" as a section below tabset - hide code in there - use `session_info::session_info()` for better readability
insightsengineering · Sep 23, 2024 · 6762c02 · 6762c02
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diff --git 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.
 :::
 
-<!--
-we have to put some code upfront
-- need to setup repos on r-universe - currently it's not possible to setup this elsewhere (e.g. shinylive config or chunk attribute)
--->
-
 ```{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
@@ -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
@@ -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
@@ -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
@@ -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 <br/> Model Fitting
-
-```{r setup, message = FALSE}
-#| code-fold: show
+:::: {.panel-tabset} and <br/> 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 <br/> 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 >}}
-
-::::