replace usage of scda and scda.2022 with random.cdisc.data

insightsengineering · May 10, 2024 · 1fb2d9e · 1fb2d9e
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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", "scda", "scda.2022", "dplyr"]
+  packages: ["tern", "random.cdisc.data", "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
@@ -7,22 +7,20 @@ subtitle: Subgroup Analysis of Best Overall Response
 
 {{< include ../../_utils/envir_hook.qmd >}}
 
-:::: {.panel-tabset}
+::: panel-tabset
 ## Data Setup
 
 ```{r setup, message = FALSE}
 #| code-fold: show
 
-library(scda)
-library(scda.2022)
 library(dplyr)
 library(tern)
 library(nestcolor)
 
-adsl_f <- synthetic_cdisc_dataset("latest", "adsl") %>%
+adsl_f <- random.cdisc.data::cadsl %>%
   select(STUDYID, USUBJID, ARMCD, ARM, SEX, BMRKR2, STRATA1, STRATA2)
 
-adrs_f <- synthetic_cdisc_dataset("latest", "adrs") %>%
+adrs_f <- random.cdisc.data::cadrs %>%
   filter(PARAMCD == "INVET") %>%
   select(STUDYID, USUBJID, PARAMCD, AVISIT, AVALC)
 
@@ -49,7 +47,9 @@ 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(
@@ -69,8 +69,7 @@ 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
@@ -79,7 +78,9 @@ 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")) %>%
@@ -117,8 +118,7 @@ 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
@@ -127,7 +127,9 @@ 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(
@@ -147,8 +149,7 @@ 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
@@ -157,7 +158,9 @@ 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 plot4, test = list(plot_v4 = "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(
@@ -180,8 +183,7 @@ 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
@@ -190,7 +192,9 @@ 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") %>%
@@ -227,8 +231,7 @@ 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 >}}
@@ -244,11 +247,9 @@ library(teal.modules.clinical)
 ## Data reproducible code
 data <- teal_data()
 data <- within(data, {
-  library(scda)
-  library(scda.2022)
 
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-  ADRS <- synthetic_cdisc_dataset("latest", "adrs")
+  ADSL <- random.cdisc.data::cadsl
+  ADRS <- random.cdisc.data::cadrs
 })
 datanames <- c("ADSL", "ADRS")
 datanames(data) <- datanames
@@ -306,5 +307,4 @@ shinyApp(app$ui, app$server)
 :::
 
 {{< include ../../repro.qmd >}}
-
-::::
+:::
diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
@@ -7,7 +7,7 @@ subtitle: Subgroup Analysis of Survival Duration
 
 {{< include ../../_utils/envir_hook.qmd >}}
 
-:::: {.panel-tabset}
+::: panel-tabset
 ## Data Setup
 
 ```{r setup, message = FALSE}
@@ -17,8 +17,6 @@ library(tern)
 library(dplyr)
 library(forcats)
 library(nestcolor)
-library(scda)
-library(scda.2022)
 
 preprocess_adtte <- function(adtte) {
   # Save variable labels before data processing steps.
@@ -51,7 +49,7 @@ preprocess_adtte <- function(adtte) {
   adtte
 }
 
-anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
+anl <- random.cdisc.data::cadtte %>%
   preprocess_adtte()
 ```
 
@@ -61,6 +59,7 @@ anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
 ## {{< 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
 
@@ -82,8 +81,7 @@ 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
@@ -92,6 +90,7 @@ 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(
@@ -124,8 +123,7 @@ 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
@@ -134,6 +132,7 @@ 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
 
@@ -155,8 +154,7 @@ 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
@@ -165,6 +163,7 @@ 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
 
@@ -195,8 +194,7 @@ 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 >}}
@@ -212,19 +210,17 @@ library(teal.modules.clinical)
 ## Data reproducible code
 data <- teal_data()
 data <- within(data, {
-  library(scda)
-  library(scda.2022)
   library(dplyr)
   library(forcats)
 
-  ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+  ADSL <- random.cdisc.data::cadsl
   ADSL <- ADSL %>%
     filter(ARM %in% c("B: Placebo", "A: Drug X")) %>%
     mutate(ARM = droplevels(fct_relevel(ARM, "B: Placebo"))) %>%
     mutate(ARMCD = droplevels(fct_relevel(ARMCD, "ARM B")))
   ADSL$RACE <- droplevels(ADSL$RACE)
 
-  ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
+  ADTTE <- random.cdisc.data::cadtte
   adtte_labels <- col_labels(ADTTE)
 
   ADTTE <- ADTTE %>%
@@ -282,5 +278,4 @@ shinyApp(app$ui, app$server)
 :::
 
 {{< include ../../repro.qmd >}}
-
-::::
+:::