Merge pull request #3 from Boehringer-Ingelheim/2-align-basic-info-pa…

…rameter-with-api-conventions 2 align basic info parameter with api conventions
Boehringer-Ingelheim · Sep 2, 2024 · 76be84e · 76be84e
2 parents 82d3e78 + deca33a
commit 76be84e
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diff --git a/.lintr b/.lintr
@@ -0,0 +1,6 @@
+linters: linters_with_defaults(
+  line_length_linter(120),
+  object_usage_linter = NULL,
+  indentation_linter = NULL,
+  trailing_whitespace_linter = NULL
+  )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dv.clinlines
 Title: DaVinci's Clinical Timelines
-Version: 1.0.3
+Version: 1.0.4
 Authors@R:
     c(
       person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# dv.clinlines 1.0.4
+
+* Adapt basic_info parameter to adhere module standard
+
 # dv.clinlines 1.0.3
 
 * Initial release of dv.clinlines package to GitHub.

diff --git a/R/data_prep.R b/R/data_prep.R
@@ -176,21 +176,21 @@ add_ids <- function(data_list) {
 #' @keywords internal
 set_basics <- function(data_list, basic_info = default_basic_info(), subjid_var) {
   # Extract subject level dataset from data_list
-  data <- data_list[[basic_info$data]]
+  data <- data_list[[basic_info$subject_level_dataset_name]]
 
   check_names(
     data,
-    var_names = c(basic_info$trt_start, basic_info$trt_end, basic_info$icf_date),
+    var_names = c(basic_info$trt_start_var, basic_info$trt_end_var, basic_info$icf_date_var),
     subjid_var = subjid_var
   )
-  check_date_type(data, c(basic_info$trt_start, basic_info$trt_end, basic_info$icf_date))
+  check_date_type(data, c(basic_info$trt_start_var, basic_info$trt_end_var, basic_info$icf_date_var))
 
   return(
     list(
       data = dplyr::rename(data, dplyr::all_of(c(subject_id = subjid_var))),
-      trt_start = basic_info$trt_start,
-      trt_end = basic_info$trt_end,
-      icf_date = basic_info$icf_date
+      trt_start = basic_info$trt_start_var,
+      trt_end = basic_info$trt_end_var,
+      icf_date = basic_info$icf_date_var
     )
   )
 }

diff --git a/R/helpers.R b/R/helpers.R
@@ -2,22 +2,27 @@
 #'
 #' Helper function to support configuration of a Clinical Timelines module.
 #'
-#' @param data Character name of the subject level analysis dataset (e.g. "adsl", "dm")
+#' @param subject_level_dataset_name Character name of the subject level analysis dataset (e.g. "adsl", "dm")
 #'   as it is called in the \code{data_list} parameter.
-#' @param trt_start Character name of the variable that contains treatment start dates.
-#'   Must be present in the data frame mentioned in the \code{data} element.
-#' @param trt_end Character name of the variable that contains treatment end dates.
-#'   Must be present in the data frame mentioned in the \code{data} element.
-#' @param icf_date Character name of the variable that contains informed consent dates.
-#'   Must be present in the data frame mentioned in the \code{data} element.
+#' @param trt_start_var Character name of the variable that contains treatment start dates.
+#'   Must be present in the data frame mentioned in the \code{subject_level_dataset_name} element.
+#' @param trt_end_var Character name of the variable that contains treatment end dates.
+#'   Must be present in the data frame mentioned in the \code{subject_level_dataset_name} element.
+#' @param icf_date_var Character name of the variable that contains informed consent dates.
+#'   Must be present in the data frame mentioned in the \code{subject_level_dataset_name} element.
 #'
 #' @return A list that could directly be used as input for the \code{basic_info} parameter
 #'   of \code{mod_clinical_timelines()} and \code{mod_clinical_timelines_server()}.
 #' @export
 #'
-set_basic_info <- function(data, trt_start, trt_end, icf_date) {
+set_basic_info <- function(subject_level_dataset_name, trt_start_var, trt_end_var, icf_date_var) {
   return(
-    list(data = data, trt_start = trt_start, trt_end = trt_end, icf_date = icf_date)
+    list(
+      subject_level_dataset_name = subject_level_dataset_name,
+      trt_start_var = trt_start_var,
+      trt_end_var = trt_end_var,
+      icf_date_var = icf_date_var
+      )
   )
 }
 

diff --git a/R/mock_clinical_timelines.R b/R/mock_clinical_timelines.R
@@ -35,10 +35,10 @@ mock_clinical_timelines_server <- function(input, output, session) {
     data_name = shiny::reactive("dummyData"),
     data_list,
     basic_info = list(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     ),
     mapping = list(
       adsl = list(

diff --git a/R/mock_with_mm.R b/R/mock_with_mm.R
@@ -19,10 +19,10 @@ mock_with_mm_app <- function() {
     "Clinical Timelines" = mod_clinical_timelines(
       module_id = "mod1",
       basic_info = list(
-        data = "adsl",
-        trt_start = "TRTSDT",
-        trt_end = "TRTEDT",
-        icf_date = "RFICDT"
+        subject_level_dataset_name = "adsl",
+        trt_start_var = "TRTSDT",
+        trt_end_var = "TRTEDT",
+        icf_date_var = "RFICDT"
       ),
       mapping = list(
         adsl = list(

diff --git a/R/mod_clinical_timelines.R b/R/mod_clinical_timelines.R
@@ -110,7 +110,15 @@ mod_clinical_timelines_server <- function(module_id,
   checkmate::assert_multi_class(data_name, c("reactive", "shinymeta_reactive"), add = ac)
   checkmate::assert_multi_class(dataset_list, c("reactive", "shinymeta_reactive"), add = ac)
   checkmate::assert_list(basic_info, types = "character", add = ac)
-  checkmate::assert_subset(names(basic_info), choices = c("data", "trt_start", "trt_end", "icf_date"), add = ac)
+  checkmate::assert_subset(
+    names(basic_info),
+    choices = c(
+      "subject_level_dataset_name",
+      "trt_start_var",
+      "trt_end_var",
+      "icf_date_var"),
+    add = ac
+  )
   checkmate::assert_list(mapping, types = "list", add = ac)
   checkmate::assert_character(unlist(mapping), add = ac)
   lapply(mapping, function(x) {
@@ -250,8 +258,8 @@ mod_clinical_timelines_server <- function(module_id,
 #' A character string that serves as unique identifier for the module.
 #' @param basic_info `[list(character(1)+)]`
 #'
-#' A list of four elements: \code{data}, \code{trt_start},
-#'   \code{trt_end}, and \code{icf_date}. Assigns the name
+#' A list of four elements: \code{subject_level_dataset_name}, \code{trt_start_var},
+#'   \code{trt_end_var}, and \code{icf_date_var}. Assigns the name
 #'   of a subject level dataset and column names of treatment start and end, and informed
 #'   consent variables.
 #' @param mapping `[list(list(list(character(1)+)))]`
@@ -459,7 +467,7 @@ mod_clinical_timelines <- function(module_id,
         # afmm$dataset_metadata$name holds the name of the currently selected set of dataset (dv.manager)
         data_name = afmm$dataset_metadata$name,
         dataset_list = shiny::reactive({
-          afmm$filtered_dataset()[unique(c(basic_info$data, names(mapping), drug_admin$name))]
+          afmm$filtered_dataset()[unique(c(basic_info$subject_level_dataset_name, names(mapping), drug_admin$name))]
         }),
         basic_info = basic_info,
         mapping = mapping,

diff --git a/R/prep_dummy_data.R b/R/prep_dummy_data.R
@@ -76,10 +76,10 @@ prep_dummy_data <- function(n = 200) {
 default_basic_info <- function() {
   return(
     set_basic_info(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     )
   )
 }

diff --git a/README.md b/README.md
@@ -56,10 +56,10 @@ module_list <- list(
   "Clinical Timelines" = dv.clinlines::mod_clinical_timelines(
     module_id = "mod1",
     basic_info = list(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     ),
     mapping = list(
       adsl = list(

diff --git a/man/mod_clinical_timelines.Rd b/man/mod_clinical_timelines.Rd
diff --git a/man/mod_clinical_timelines_server.Rd b/man/mod_clinical_timelines_server.Rd
diff --git a/man/prep_data.Rd b/man/prep_data.Rd
diff --git a/man/set_basic_info.Rd b/man/set_basic_info.Rd
diff --git a/man/set_basics.Rd b/man/set_basics.Rd
diff --git a/tests/testthat/apps/bmk_app/app.R b/tests/testthat/apps/bmk_app/app.R
@@ -29,10 +29,10 @@ bmk_server <- function(input, output, session) {
     data_name = shiny::reactive("dummyData"),
     data_list,
     basic_info = list(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     ),
     mapping = list(
       adsl = list(

diff --git a/tests/testthat/apps/large_app/app.R b/tests/testthat/apps/large_app/app.R
@@ -54,10 +54,10 @@ data_list <- list(adsl = adsl, adae = adae, exp = exp)
 clinlines <- dv.clinlines::mod_clinical_timelines(
   module_id = "mod",
   basic_info = list(
-    data = "adsl",
-    trt_start = "TRTSDT",
-    trt_end = "TRTEDT",
-    icf_date = "RFICDT"
+    subject_level_dataset_name = "adsl",
+    trt_start_var = "TRTSDT",
+    trt_end_var = "TRTEDT",
+    icf_date_var = "RFICDT"
   ),
   mapping = list(
     adsl = list(

diff --git a/tests/testthat/apps/mm_app/app.R b/tests/testthat/apps/mm_app/app.R
@@ -13,10 +13,10 @@ dummyData2 <- dv.clinlines:::prep_dummy_data(200) # nolint
 clinlines <- dv.clinlines::mod_clinical_timelines(
   module_id = "mod",
   basic_info = list(
-    data = "adsl",
-    trt_start = "TRTSDT",
-    trt_end = "TRTEDT",
-    icf_date = "RFICDT"
+    subject_level_dataset_name = "adsl",
+    trt_start_var = "TRTSDT",
+    trt_end_var = "TRTEDT",
+    icf_date_var = "RFICDT"
   ),
   mapping = list(
     adsl = list(

diff --git a/tests/testthat/test-data_prep.R b/tests/testthat/test-data_prep.R
@@ -134,10 +134,10 @@ test_that("set_basics() returns a list with fixed names", {
   basic_list <- set_basics(
     data_list = list(adsl = df),
     basic_info = list(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     ),
     subjid_var = "USUBJID"
   )

diff --git a/tests/testthat/test-helpers.R b/tests/testthat/test-helpers.R
@@ -1,7 +1,17 @@
 # Tests for set_basic_info() ----
 test_that("set_basic_info() returns a named list", {
-  outcome <- set_basic_info(data = "adsl", trt_start = "start", trt_end = "end", icf_date = "consent")
-  expected <- list(data = "adsl", trt_start = "start", trt_end = "end", icf_date = "consent")
+  outcome <- set_basic_info(
+    subject_level_dataset_name = "adsl",
+    trt_start_var = "start",
+    trt_end_var = "end",
+    icf_date_var = "consent"
+  )
+  expected <- list(
+    subject_level_dataset_name = "adsl",
+    trt_start_var = "start",
+    trt_end_var = "end",
+    icf_date_var = "consent"
+  )
   expect_equal(outcome, expected)
 })
 

diff --git a/tests/testthat/test-prep_dummy_data.R b/tests/testthat/test-prep_dummy_data.R
@@ -20,7 +20,12 @@ test_that("prep_dummy_data() adds a flag for AEREL", {
 # Tests for default_basic_info() ----
 test_that("default_basic_info() returns a named list with default settings ", {
   outcome <- default_basic_info()
-  expected <- list(data = "adsl", trt_start = "TRTSDT", trt_end = "TRTEDT", icf_date = "RFICDT")
+  expected <- list(
+    subject_level_dataset_name = "adsl",
+    trt_start_var = "TRTSDT",
+    trt_end_var = "TRTEDT",
+    icf_date_var = "RFICDT"
+  )
 
   expect_equal(outcome, expected)
 })

diff --git a/vignettes/ae-filter.Rmd b/vignettes/ae-filter.Rmd
@@ -64,10 +64,10 @@ module_list <- list(
   "Clinical Timelines" = mod_clinical_timelines(
     module_id = "mod1",
     basic_info = list(
-      data = "adsl",
-      trt_start = "TRTSDT",
-      trt_end = "TRTEDT",
-      icf_date = "RFICDT"
+      subject_level_dataset_name = "adsl",
+      trt_start_var = "TRTSDT",
+      trt_end_var = "TRTEDT",
+      icf_date_var = "RFICDT"
     ),
     mapping = list(
       adsl = list(