Merge pull request #4 from Boehringer-Ingelheim/rc/1.0.4

Rc/1.0.4
Boehringer-Ingelheim · Oct 11, 2024 · 5ba3d1c · 5ba3d1c
2 parents 82d3e78 + 932d217
commit 5ba3d1c
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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, filter, and drug_admin 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
@@ -33,13 +33,13 @@ prep_data <- function(data_list,
     data_list <- append(data_list, list(no_da = empty_drug_admin))
 
     drug_admin <- list(
-      name = "no_da",
+      dataset_name = "no_da",
       start_var = "start",
       end_var = "end",
       detail_var = "details",
       label = "",
-      exp_dose = "dose",
-      exp_dose_unit = "unit"
+      dose_var = "dose",
+      dose_unit_var = "unit"
     )
   }
 
@@ -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
     )
   )
 }
@@ -299,9 +299,9 @@ set_events_intern <- function(data_list, mapping = default_mapping(), subjid_var
 #'   \item{\code{detail_var}: Character name of the variable that contains the treatment
 #'     information. Must exist in the dataset mentioned in the \code{name} element.}
 #'   \item{\code{label}: Free-text character label for the drug administration event.}
-#'   \item{\code{exp_dose}: Character name of the variable that contains the dosis level
+#'   \item{\code{dose_var}: Character name of the variable that contains the dosis level
 #'     information. Must exist in the dataset mentioned in the \code{name} element.}
-#'   \item{\code{exp_dose_unit}: Character name of the variable that contains the dosis
+#'   \item{\code{dose_unit_var}: Character name of the variable that contains the dosis
 #'     unit. Must exist in the dataset mentioned in the \code{name} element.}
 #' }
 #'
@@ -314,27 +314,27 @@ set_events_intern <- function(data_list, mapping = default_mapping(), subjid_var
 #' \item{\code{detail_var}: Information about drug name and dosage.}
 #' \item{\code{set}: Name of the dataset the data origins from.}
 #' \item{\code{set_id}: Row ID's of the related dataset.}
-#' \item{\code{exp_dose}: Indicates whether the dose of the treatment has increased,
+#' \item{\code{dose_var}: Indicates whether the dose of the treatment has increased,
 #' decreased or stayed the same compared to the last dose at the same subject.}
 #'  \item{\code{group}: Label for the event types.}
 #' }
 #'
 #' @keywords internal
 #'
 set_exp_intervals <- function(data_list, mapping = default_drug_admin(), subjid_var) {
-  col_list <- mapping[!names(mapping) %in% c("name")]
+  col_list <- mapping[!names(mapping) %in% c("dataset_name")]
 
   cols <- c(col_list$start_var, col_list$end_var, col_list$detail_var)
-  data <- data_list[[mapping$name]]
+  data <- data_list[[mapping$dataset_name]]
 
   data <- data %>%
     dplyr::group_by(get(subjid_var)) %>%
     dplyr::mutate(
       exp_dose = dplyr::case_when(
-        is.na(dplyr::lag(get(col_list$exp_dose))) ~ "start/equal",
-        dplyr::lag(get(col_list$exp_dose)) == get(col_list$exp_dose) ~ "start/equal",
-        dplyr::lag(get(col_list$exp_dose)) < get(col_list$exp_dose) ~ "increase",
-        dplyr::lag(get(col_list$exp_dose)) > get(col_list$exp_dose) ~ "decrease"
+        is.na(dplyr::lag(get(col_list$dose_var))) ~ "start/equal",
+        dplyr::lag(get(col_list$dose_var)) == get(col_list$dose_var) ~ "start/equal",
+        dplyr::lag(get(col_list$dose_var)) < get(col_list$dose_var) ~ "increase",
+        dplyr::lag(get(col_list$dose_var)) > get(col_list$dose_var) ~ "decrease"
       )
     ) %>%
     dplyr::ungroup()
@@ -346,8 +346,8 @@ set_exp_intervals <- function(data_list, mapping = default_drug_admin(), subjid_
     dplyr::mutate(
       detail_var = paste(
         .data[[col_list$detail_var]], "-",
-        .data[[col_list$exp_dose]],
-        .data[[col_list$exp_dose_unit]]
+        .data[[col_list$dose_var]],
+        .data[[col_list$dose_unit_var]]
       )
     ) %>%
     dplyr::select(
@@ -358,10 +358,9 @@ set_exp_intervals <- function(data_list, mapping = default_drug_admin(), subjid_
       start_exp = tidyselect::all_of(col_list$start_var),
       end_exp = tidyselect::all_of(col_list$end_var)
     ) %>%
-    dplyr::mutate(set = mapping$name) %>%
+    dplyr::mutate(set = mapping$dataset_name) %>%
     dplyr::rename(dplyr::all_of(c(subject_id = subjid_var)))
 
-
   return(interval_df)
 }
 
@@ -578,26 +577,26 @@ complete_events <- function(combined_data, trt_start, trt_end) {
 set_filter_dataset <- function(filter, data_list, mapping, subjid_var) {
   # Check for inconsistencies on modul definition side
   if (length(filter$ae_filter) < 3) stop("No ae_filter defined for Clinical Timelines!")
-  if (!filter$ae_filter$data_name %in% names(data_list)) {
+  if (!filter$ae_filter$dataset_name %in% names(data_list)) {
     msg <- paste0(
       "Clinical Timelines (dv.clinlines) cannot find ",
-      filter$ae_filter$data_name,
+      filter$ae_filter$dataset_name,
       " in your data list."
     )
 
     stop(msg)
   }
 
-  only_filters <- filter$ae_filter[!names(filter$ae_filter) %in% c("data_name", "label")]
+  only_filters <- filter$ae_filter[!names(filter$ae_filter) %in% c("dataset_name", "label")]
 
-  check_names(data_list[[filter$ae_filter$data_name]],
-    unlist(only_filters), # drop data_name
+  check_names(data_list[[filter$ae_filter$dataset_name]],
+    unlist(only_filters), # drop dataset_name
     subjid_var = subjid_var
   )
 
-  ae_info <- mapping[[filter$ae_filter$data_name]][[filter$ae_filter$label]]
+  ae_info <- mapping[[filter$ae_filter$dataset_name]][[filter$ae_filter$label]]
 
-  filter_dataset <- data_list[[filter$ae_filter$data_name]] %>%
+  filter_dataset <- data_list[[filter$ae_filter$dataset_name]] %>%
     dplyr::select(
       dplyr::all_of(
         c(

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
+    )
   )
 }
 
@@ -70,7 +75,7 @@ set_event <- function(start_dt_var,
 #'
 #' Helper function to support configuration of a Clinical Timelines module.
 #'
-#' @param name Character name of the data frame that holds drug administration data
+#' @param dataset_name Character name of the data frame that holds drug administration data
 #'   (e.g. ex domain) as it is called in the \code{data_list} parameter.
 #' @param start_var Character name of the variable that contains the start dates
 #'   (e.g. exposure start dates). Must be present in the data frame mentioned in the name
@@ -81,31 +86,31 @@ set_event <- function(start_dt_var,
 #' @param detail_var Character name of the variable that contains the treatment
 #' information. Must exist in the dataset mentioned in the name element.
 #' @param label Free-text character label for the drug administration event.
-#' @param exp_dose Character name of the variable that contains the dosis level
+#' @param dose_var Character name of the variable that contains the dosis level
 #' information. Must exist in the dataset mentioned in the name element.
-#' @param exp_dose_unit Character name of the variable that contains the dosis unit.
+#' @param dose_unit_var Character name of the variable that contains the dosis unit.
 #' Must exist in the dataset mentioned in the name element.
 #'
 #' @return A list that could directly be used as input for the \code{drug_admin} parameter
 #'   of \code{mod_clinical_timelines()} and \code{mod_clinical_timelines_server()}.
 #' @export
 #'
-set_drug_admin <- function(name,
+set_drug_admin <- function(dataset_name,
                            start_var,
                            end_var,
                            detail_var,
                            label,
-                           exp_dose,
-                           exp_dose_unit) {
+                           dose_var,
+                           dose_unit_var) {
   return(
     list(
-      name = name,
+      dataset_name = dataset_name,
       start_var = start_var,
       end_var = end_var,
       detail_var = detail_var,
       label = label,
-      exp_dose = exp_dose,
-      exp_dose_unit = exp_dose_unit
+      dose_var = dose_var,
+      dose_unit_var = dose_unit_var
     )
   )
 }
diff --git a/R/local_filter_setup.R b/R/local_filter_setup.R
@@ -7,8 +7,8 @@
 #'
 local_filters <- function(ns) {
   ui_list <- list(
-    serious_AE = shiny::radioButtons(
-      ns("serious_AE"),
+    serious_ae = shiny::radioButtons(
+      ns("serious_ae"),
       label = "Serious Adverse Events?",
       choices = c("Yes" = "Y", "No" = "N", "All" = "all"),
       selected = "all"
@@ -27,8 +27,8 @@ local_filters <- function(ns) {
       multiple = TRUE,
       options = list(placeholder = "All PT's selected")
     ),
-    drug_rel_AE = shiny::radioButtons(
-      ns("drug_rel_AE"),
+    drug_rel_ae = shiny::radioButtons(
+      ns("drug_rel_ae"),
       label = "Drug related Adverse Events?",
       choices = c("Yes" = "Y", "No" = "N", "All" = "all"),
       selected = "all"

diff --git a/R/mock_clinical_timelines.R b/R/mock_clinical_timelines.R
@@ -13,7 +13,7 @@ mock_clinical_timelines_UI <- function(id = NULL) { # nolint
     shiny::tags$h1("BI Clinical Timelines", class = "mod-title"),
     mod_clinical_timelines_UI(
       ns("clin_tl"),
-      list("serious_AE", "soc", "pref_term", "drug_rel_AE")
+      list("serious_ae_var", "soc_var", "pref_term_var", "drug_rel_ae_var")
     )
   )
 
@@ -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(
@@ -68,23 +68,23 @@ mock_clinical_timelines_server <- function(input, output, session) {
       )
     ),
     drug_admin = list(
-      name = "exp",
+      dataset_name = "exp",
       start_var = "EXSTDTC",
       end_var = "EXENDTC",
       detail_var = "EXTRT",
       label = "Drug Administration",
-      exp_dose = "EXDOSE",
-      exp_dose_unit = "EXDOSU"
+      dose_var = "EXDOSE",
+      dose_unit_var = "EXDOSU"
     ),
     subjid_var = "USUBJID",
     filter = list(
       ae_filter = list(
-        data_name = "adae",
+        dataset_name = "adae",
         label = "Adverse Events",
-        soc = "AESOC",
-        serious_AE = "AESER",
-        pref_term = "AEDECOD",
-        drug_rel_AE = "AEREL"
+        soc_var = "AESOC",
+        serious_ae_var = "AESER",
+        pref_term_var = "AEDECOD",
+        drug_rel_ae_var = "AEREL"
       )
     ),
     ms = 50

diff --git a/R/mock_local_filter.R b/R/mock_local_filter.R
@@ -9,7 +9,7 @@ mock_local_filter_UI <- function(request) { # nolint
     shiny::bookmarkButton(),
     mod_local_filter_UI(
       "filter",
-      list("soc", "pref_term", "drug_rel_AE", "serious_AE")
+      list("soc_var", "pref_term_var", "drug_rel_ae_var", "serious_ae_var")
     ),
     shiny::tableOutput("table")
   )
@@ -69,7 +69,8 @@ mock_local_filter_server <- function(input, output, session) {
   filtered_data <- mod_local_filter_server(
     "filter",
     filter = list(ae_filter = list(
-      data_name = "adae", soc = "AESOC", pref_term = "AEDECOD", drug_rel_AE = "AEREL", serious_AE = "AESER"
+      dataset_name = "adae", soc_var = "AESOC", pref_term_var = "AEDECOD", drug_rel_ae_var = "AEREL",
+      serious_ae_var = "AESER"
     )),
     joined_data = initial_data,
     changed = shiny::reactive(1)