reverse any layout changes

insightsengineering · May 14, 2024 · 1d51d3f · 1d51d3f
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diff --git a/book/_quarto.yml b/book/_quarto.yml
@@ -43,7 +43,7 @@ execute:
 engine: knitr
 webr:
   channel-type: "post-message"
-  packages: ["tern", "random.cdisc.data", "dplyr"]
+  packages: ["tern", "scda", "scda.2022", "dplyr"]
   show-startup-message: false
   autoload-packages: false
 
@@ -118,4 +118,4 @@ website:
 profile:
   group:
     - [stable, development]
-  default: stable
+  default: stable
diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd
@@ -47,9 +47,7 @@ var_labels(anl_rsp_arms_ab) <- c(anl_labels, is_rsp = "Is Responder")
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
-
 <!-- skip strict because of https://github.com/insightsengineering/tern/issues/1186 -->
-
 ```{r plot1, test = list(plot_v1 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
 df <- extract_rsp_subgroups(
   variables = list(
@@ -69,7 +67,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot1")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
@@ -78,9 +77,7 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
-
 <!-- skip strict because of https://github.com/insightsengineering/tern/issues/1186 -->
-
 ```{r plot2, test = list(plot_v2 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
 anl_rsp_comb_arms_ac <- anl %>%
   mutate(is_rsp = AVALC %in% c("CR", "PR")) %>%
@@ -118,7 +115,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot2")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Selecting Columns and <br/> Changing the Alpha Level
@@ -127,9 +125,7 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
-
 <!-- skip strict because of https://github.com/insightsengineering/tern/issues/1186 -->
-
 ```{r plot3, test = list(plot_v3 = "plot"), fig.width = 10, fig.height = 4, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
 df <- extract_rsp_subgroups(
   variables = list(
@@ -149,7 +145,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot3")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot with Fixed <br/> Symbol Size
@@ -183,7 +180,8 @@ plot <- g_forest(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot4")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot of CR Only, Setting <br/> Values Indicating Response
@@ -192,9 +190,7 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
-
 <!-- skip strict because of https://github.com/insightsengineering/tern/issues/1186 -->
-
 ```{r plot5, test = list(plot_v5 = "plot"), fig.width = 20, fig.height = 5, opts.label = ifelse(packageVersion("survival") < "3.5-8" || packageVersion("tern") < "0.9.3.9018", "skip_test_strict", "")}
 anl_cr_arms_ab <- anl %>%
   mutate(is_rsp = AVALC == "CR") %>%
@@ -231,7 +227,8 @@ width <- 20
 height <- 5
 ```
 
-`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot5")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 {{< include ../../_utils/save_results.qmd >}}
@@ -306,4 +303,5 @@ shinyApp(app$ui, app$server)
 :::
 
 {{< include ../../repro.qmd >}}
+
 ::::
diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
@@ -1,8 +1,6 @@
 ---
 title: FSTG02
 subtitle: Subgroup Analysis of Survival Duration
-editor_options: 
-  chunk_output_type: console
 ---
 
 ------------------------------------------------------------------------
@@ -61,7 +59,6 @@ anl <- random.cdisc.data::cadtte %>%
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->
-
 ```{r plot1, test = list(plot_v1 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
 anl1 <- anl
 
@@ -83,7 +80,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot1")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
@@ -92,7 +90,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->
-
 ```{r plot2, test = list(plot_v2 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
 anl2 <- anl %>%
   mutate(
@@ -125,7 +122,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot2")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Selecting Columns and <br/> Changing the Alpha Level
@@ -134,7 +132,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->
-
 ```{r plot3, test = list(plot_v3 = "plot"), fig.width = 8, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
 anl3 <- anl
 
@@ -156,7 +153,8 @@ plot <- g_forest(tbl = result)
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot3")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot with Fixed <br/> Symbol Size
@@ -165,7 +163,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/insightsengineering/rtables/issues/830 -->
-
 ```{r plot4, test = list(plot_v4 = "plot"), fig.width = 15, fig.height = 4, opts.label = ifelse(packageVersion("rtables") < "0.6.6.9011", "skip_test_strict", "")}
 anl4 <- anl
 
@@ -196,7 +193,8 @@ height <- 4
 plot_v3.width <- 8 # nolint: object_name.
 ```
 
-`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot4")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 {{< include ../../_utils/save_results.qmd >}}
@@ -280,4 +278,5 @@ shinyApp(app$ui, app$server)
 :::
 
 {{< include ../../repro.qmd >}}
+
 ::::
diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd
@@ -30,7 +30,6 @@ variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD")
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot1, fig.width = 9, fig.height = 6, test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
@@ -42,7 +41,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot1")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot1")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot of Failures
@@ -51,7 +51,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot2, fig.width = 9, fig.height = 6, test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
@@ -65,7 +64,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot2")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot2")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Without <br/> Comparative Statistics
@@ -74,7 +74,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot3, fig.width = 9, fig.height = 6, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
@@ -85,7 +84,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot3")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot3")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Without <br/> Censoring Marks
@@ -94,7 +94,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot4, fig.width = 9, fig.height = 6, test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
@@ -107,7 +106,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot4")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot4")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Modifying <br/> Censoring Marks
@@ -116,7 +116,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot5, fig.width = 9, fig.height = 6, test = list(plot_v5 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_km(
   df = anl,
@@ -130,7 +129,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot5")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot5")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ## Plot Modifying Options for Statistics, <br/> Tie Handling, Stratification, etc.
@@ -139,7 +139,6 @@ plot
 ## {{< fa regular file-lines sm fw >}} Preview
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot6, fig.width = 9, fig.height = 6, test = list(plot_v6 = "plot"), opts.label = "skip_test_strict"}
 variables$strata <- c("STRATA1", "STRATA2")
 plot <- g_km(
@@ -158,7 +157,8 @@ plot <- g_km(
 plot
 ```
 
-`r webr_code_labels <- c("setup", "plot6")` {{< include ../../_utils/webr.qmd >}}
+`r webr_code_labels <- c("setup", "plot6")` 
+{{< include ../../_utils/webr.qmd >}}
 :::
 
 ::: {.content-visible when-profile="development"}
@@ -239,4 +239,5 @@ shinyApp(app$ui, app$server)
 :::
 
 {{< include ../../repro.qmd >}}
+
 ::::
diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd
@@ -46,7 +46,6 @@ mmrm_results <- fit_mmrm(
 ### Considering the treatment variable in the model
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot1, dev.args = list(pointsize = 6), test = list(plot_v1 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
@@ -59,7 +58,6 @@ plot
 ### Considering the treatment variable in the model, with lines
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot2, dev.args = list(pointsize = 6), test = list(plot_v2 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
@@ -73,7 +71,6 @@ plot
 ### Considering the treatment variable in the model, with statistics table
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot3, dev.args = list(pointsize = 6), fig.height = 7, test = list(plot_v3 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
@@ -91,7 +88,6 @@ plot
 Users can choose to display both estimates and contrasts together by running `g_mmrm_lsmeans(mmrm_results)`.
 
 <!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
-
 ```{r plot4, dev.args = list(pointsize = 6), test = list(plot_v4 = "plot"), opts.label = "skip_test_strict"}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
@@ -180,4 +176,5 @@ shinyApp(app$ui, app$server)
 ```
 
 {{< include ../../repro.qmd >}}
+
 ::::
diff --git a/book/graphs/efficacy/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd
@@ -137,4 +137,5 @@ height <- 4
 {{< include ../../_utils/save_results.qmd >}}
 
 {{< include ../../repro.qmd >}}
+
 ::::
Original file line number	Diff line number	Diff line change
Expand Up		@@ -137,4 +137,5 @@ height <- 4
		{{< include ../../_utils/save_results.qmd >}}

		{{< include ../../repro.qmd >}}

		::::