Decouple scda (#858)

closes #834 see also: - insightsengineering/scda#125 - insightsengineering/scda.2022#123 --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
insightsengineering · Jul 6, 2023 · fd79164 · fd79164
1 parent 603e041
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -49,8 +49,6 @@ Suggests:
     MultiAssayExperiment,
     R6,
     rmarkdown,
-    scda (>= 0.1.5),
-    scda.2022 (>= 0.1.3),
     shinyvalidate,
     testthat (>= 3.1.5),
     withr,
@@ -60,8 +58,6 @@ VignetteBuilder:
 RdMacros:
     lifecycle
 Remotes:
-    insightsengineering/scda.2022@*release,
-    insightsengineering/scda@*release,
     insightsengineering/teal.code@*release,
     insightsengineering/teal.data@*release,
     insightsengineering/teal.logger@*release,

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,8 @@
 # teal 0.13.0.9004
 
+### Miscellaneous
+
+* Removed `scda` package dependency from examples.
 # teal 0.13.0
 
 ### Breaking changes

diff --git a/R/dummy_functions.R b/R/dummy_functions.R
@@ -8,7 +8,7 @@
 #' @param data (`TealData`)
 #' @return dummy filter states
 #' @keywords internal
-get_dummy_filter <- function(data) { # nolint
+example_filter <- function(data) { # nolint
   ADSL <- teal.data::get_raw_data(x = data, dataname = "ADSL") # nolint
   ADLB <- teal.data::get_raw_data(x = data, dataname = "ADLB") # nolint
 
@@ -52,35 +52,50 @@ get_dummy_filter <- function(data) { # nolint
 #'
 #' @return `cdisc_data`
 #' @keywords internal
-get_dummy_cdisc_data <- function() { # nolint
-  teal_with_pkg <- function(pkg, code) {
-    pkg_name <- paste0("package:", pkg)
-    if (!pkg_name %in% search()) {
-      require(pkg, character.only = TRUE)
-      on.exit(detach(pkg_name, character.only = TRUE))
-    }
-    eval.parent(code)
-    return(invisible(NULL))
-  }
-
-  teal_with_pkg("scda", code = {
-    ADSL <- scda::synthetic_cdisc_data("latest")$adsl # nolint
-    ADAE <- scda::synthetic_cdisc_data("latest")$adae # nolint
-    ADLB <- scda::synthetic_cdisc_data("latest")$adlb # nolint
-  })
+example_cdisc_data <- function() { # nolint
+  ADSL <- data.frame( # nolint
+    STUDYID = "study",
+    USUBJID = 1:10,
+    SEX = sample(c("F", "M"), 10, replace = TRUE),
+    AGE = stats::rpois(10, 40)
+  )
+  ADTTE <- rbind(ADSL, ADSL, ADSL) # nolint
+  ADTTE$PARAMCD <- rep(c("OS", "EFS", "PFS"), each = 10) # nolint
+  ADTTE$AVAL <- c( # nolint
+    stats::rnorm(10, mean = 700, sd = 200), # dummy OS level
+    stats::rnorm(10, mean = 400, sd = 100), # dummy EFS level
+    stats::rnorm(10, mean = 450, sd = 200) # dummy PFS level
+  )
 
   ADSL$logical_test <- sample(c(TRUE, FALSE, NA), size = nrow(ADSL), replace = TRUE) # nolint
-  ADSL$SEX[1:150] <- NA # nolint
+  ADSL$SEX[c(2, 5)] <- NA # nolint
+
+  cdisc_data_obj <- teal.data::cdisc_data(
+    cdisc_dataset(dataname = "ADSL", x = ADSL),
+    cdisc_dataset(dataname = "ADTTE", x = ADTTE)
+  )
 
   res <- teal.data::cdisc_data(
     teal.data::cdisc_dataset(dataname = "ADSL", x = ADSL),
-    teal.data::cdisc_dataset(dataname = "ADAE", x = ADAE),
-    teal.data::cdisc_dataset(dataname = "ADLB", x = ADLB),
-    code = "
-      ADSL <- synthetic_cdisc_data(\"latest\")$adsl
-      ADAE <- synthetic_cdisc_data(\"latest\")$adae
-      ADLB <- synthetic_cdisc_data(\"latest\")$adlb
-    "
+    teal.data::cdisc_dataset(dataname = "ADTTE", x = ADTTE),
+    code = '
+      ADSL <- data.frame(
+        STUDYID = "study",
+        USUBJID = 1:10,
+        SEX = sample(c("F", "M"), 10, replace = TRUE),
+        AGE = rpois(10, 40)
+      )
+      ADTTE <- rbind(ADSL, ADSL, ADSL)
+      ADTTE$PARAMCD <- rep(c("OS", "EFS", "PFS"), each = 10)
+      ADTTE$AVAL <- c(
+        rnorm(10, mean = 700, sd = 200),
+        rnorm(10, mean = 400, sd = 100),
+        rnorm(10, mean = 450, sd = 200)
+      )
+
+      ADSL$logical_test <- sample(c(TRUE, FALSE, NA), size = nrow(ADSL), replace = TRUE)
+      ADSL$SEX[c(2, 5)] <- NA
+    '
   )
   return(res)
 }
@@ -90,8 +105,8 @@ get_dummy_cdisc_data <- function() { # nolint
 #' Returns a new `R6` object on each invocation, not a singleton.
 #' @return `FilteredData` with `ADSL` set
 #' @keywords internal
-get_dummy_datasets <- function() { # nolint
-  dummy_cdisc_data <- get_dummy_cdisc_data()
+example_datasets <- function() { # nolint
+  dummy_cdisc_data <- example_cdisc_data()
   return(teal.slice::init_filtered_data(dummy_cdisc_data))
 }
 
@@ -102,7 +117,7 @@ get_dummy_datasets <- function() { # nolint
 #'
 #' @return `teal_modules`
 #' @keywords internal
-get_dummy_modules <- function() {
+example_modules <- function() {
   mods <- modules(
     label = "d1",
     modules(

diff --git a/R/init.R b/R/init.R
@@ -111,41 +111,41 @@
 #' @include modules.R
 #'
 #' @examples
-#' library(scda)
-#'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
+#' new_iris <- transform(iris, id = seq_len(nrow(iris)))
+#' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL),
-#'     code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"
+#'   data = teal_data(
+#'     dataset("new_iris", new_iris),
+#'     dataset("new_mtcars", new_mtcars),
+#'     code = "
+#'       new_iris <- transform(iris, id = seq_len(nrow(iris)))
+#'       new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))
+#'     "
 #'   ),
 #'   modules = modules(
 #'     module(
-#'       "data source",
+#'       label = "data source",
 #'       server = function(input, output, session, data) {},
 #'       ui = function(id, ...) div(p("information about data source")),
 #'       filters = "all"
 #'     ),
-#'     example_module(),
+#'     example_module(label = "example teal module"),
 #'     module(
-#'       "ADSL AGE histogram",
+#'       "Iris Sepal.Length histogram",
 #'       server = function(input, output, session, data) {
 #'         output$hist <- renderPlot(
-#'           hist(data[["ADSL"]]()$AGE)
+#'           hist(data[["new_iris"]]()$Sepal.Length)
 #'         )
 #'       },
 #'       ui = function(id, ...) {
 #'         ns <- NS(id)
 #'         plotOutput(ns("hist"))
 #'       },
-#'       filters = "ADSL"
+#'       filters = "new_iris"
 #'     )
 #'   ),
-#'   title = "App title",
-#'   filter = list(ADSL = structure(list(AGE = list()), filterable = c("AGE", "SEX", "RACE"))),
-#'   header = tags$h1("Sample App"),
-#'   footer = tags$p("Copyright 2017 - 2020")
+#'   title = "App title"
 #' )
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)

diff --git a/R/module_nested_tabs.R b/R/module_nested_tabs.R
@@ -17,8 +17,8 @@
 #'   - `teal_modules`: `tabsetPanel` with each tab corresponding to recursively
 #'     calling this function on it.
 #' @examples
-#' mods <- teal:::get_dummy_modules()
-#' datasets <- teal:::get_dummy_datasets()
+#' mods <- teal:::example_modules()
+#' datasets <- teal:::example_datasets()
 #' app <- shinyApp(
 #'   ui = function() {
 #'     tagList(

diff --git a/R/module_tabs_with_filters.R b/R/module_tabs_with_filters.R
@@ -27,8 +27,8 @@
 #'
 #' @examples
 #'
-#' mods <- teal:::get_dummy_modules()
-#' datasets <- teal:::get_dummy_datasets()
+#' mods <- teal:::example_modules()
+#' datasets <- teal:::example_datasets()
 #'
 #' app <- shinyApp(
 #'   ui = function() {

diff --git a/R/module_teal.R b/R/module_teal.R
@@ -27,8 +27,8 @@
 #' @keywords internal
 #'
 #' @examples
-#' mods <- teal:::get_dummy_modules()
-#' raw_data <- reactive(teal:::get_dummy_cdisc_data())
+#' mods <- teal:::example_modules()
+#' raw_data <- reactive(teal:::example_cdisc_data())
 #' app <- shinyApp(
 #'   ui = function() {
 #'     teal:::ui_teal("dummy")

diff --git a/R/modules_debugging.R b/R/modules_debugging.R
@@ -13,20 +13,8 @@
 #' @keywords internal
 #'
 #' @examples
-#' library(scda)
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' # by testing with NA values, we will see whether the filtering really works when
-#' # we add and remove filters
-#' ADSL$SEX[1:150] <- NA
-#'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset(
-#'       dataname = "ADSL",
-#'       x = ADSL
-#'     ),
-#'     code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"
-#'   ),
+#'   data = list(iris = iris, mtcars = mtcars),
 #'   modules = teal:::filter_calls_module(),
 #'   header = "Simple teal app"
 #' )