minor fix

Merge branch '59-question-can-users-customize-the-listing-columns' of https://github.com/Merck/metalite.sl into 59-question-can-users-customize-the-listing-columns

# Conflicts:
#	R/react_disposition.R

R/react_disposition.R

@@ -49,6 +49,7 @@
 #'     metadata_ae = metalite.ae::meta_ae_example()
 #'   )
 #' }
+
 react_disposition <- function(
      metadata_sl
     ,metadata_ae
@@ -66,19 +67,20 @@ react_disposition <- function(
     ,width           = 1200
     ) 
   {
+
   # ----------------------------------------- #
   #   default columns                         #
   # ----------------------------------------- #
   if (is.null(sl_col_selected)) {
     sl_col_selected <- c("trt01a", "siteid", "subjid", "sex", "age", "weightbl")
-    sl_col_names    <- c("Treatment", "Site", "Subject ID", "Sex", "Age (Year)", "Weight (kg)")
-  } 
-  
-  if (is.null(ae_col_selected)){
+    sl_col_names <- c("Treatment", "Site", "Subject ID", "Sex", "Age (Year)", "Weight (kg)")
+  }
+
+  if (is.null(ae_col_selected)) {
     ae_col_selected <- c("AESOC", "ASTDT", "AENDT", "AETERM", "duration", "AESEV", "AESER", "related", "AEACN", "AEOUT")
-    ae_col_names    <- c("SOC", "Onset Date", "End Date", "AE", "Duraion", "Intensity", "Serious", "Related", "Action Taken", "Outcome")
+    ae_col_names <- c("SOC", "Onset Date", "End Date", "AE", "Duraion", "Intensity", "Serious", "Related", "Action Taken", "Outcome")
   }
-  
+
   # ----------------------------------------- #
   #   total setting                           #
   # ----------------------------------------- #
@@ -90,7 +92,7 @@ react_disposition <- function(
   }
 
   # ----------------------------------------- #
-  #   prepare the baseline char table numbers #
+  #   prepare the disposition table numbers   #
   # ----------------------------------------- #
   x_sl <- metadata_sl |>
     prepare_disposition(
@@ -103,11 +105,6 @@ react_disposition <- function(
   tbl_sl <- x_sl$tbl
   tbl_sl$var_label[tbl_sl$name == "Participants in population"] <- "Participants in population"
 
-  # get AE listing
-  ae_listing_outdata <- 
-    metalite.ae::prepare_ae_listing(meta = metadata_ae, population = ae_population, analysis='ae_specific', observation = ae_observation, parameter = 'any')
-  ae_list <- ae_listing_outdata$meta$data_observation  
-
   # Define Column
   col_defs <- list()
   for (sl_name in names(tbl_sl)) {
@@ -144,17 +141,29 @@ react_disposition <- function(
 
   # Define columns for subject list
   sl_col_selected <- toupper(sl_col_selected)
-  if (!('USUBJID' %in% sl_col_selected)) u_sl_col_selected <- c('USUBJID', sl_col_selected)
+  if (!("USUBJID" %in% sl_col_selected)) u_sl_col_selected <- c("USUBJID", sl_col_selected)
   if (is.null(sl_col_names)) sl_col_names <- sl_col_selected
   sl_col_def <- list()
   for (i in 1:length(sl_col_selected)) sl_col_def[[sl_col_selected[i]]] <- reactable::colDef(sl_col_names[i])
-
+
+  # ----------------------------------------- #
+  #   get AE listing                          #
+  # ----------------------------------------- #
+  ae_listing_outdata <- 
+    metalite.ae::prepare_ae_listing(meta = metadata_ae, population = ae_population, analysis='ae_specific', observation = ae_observation, parameter = 'any')
+  ae_list <- ae_listing_outdata$meta$data_observation  
+
   # Define columns for AE list
   if (is.null(ae_col_names)) ae_col_names <- ae_col_selected
   ae_col_def <- list()
   for (i in 1:length(ae_col_selected)) ae_col_def[[ae_col_selected[i]]] <- reactable::colDef(ae_col_names[i])
 
+
+  # ----------------------------------------- #
+  #   making react table                      #
+  # ----------------------------------------- #
   trt_grp <- toupper(trtvar)
+  # show participant details when category not in "participants in population", "discontinued", "participants ongoing", "completed"
   details <- function(index) {
     dcsreas <- stringr::str_trim(tolower(tbl_sl$name[index]))
     if (!is.na(tbl_sl$name[index]) & !(dcsreas %in% c("participants in population", "discontinued", "participants ongoing", "completed"))) {
@@ -170,13 +179,13 @@ react_disposition <- function(
         subset = metadata_sl$data_population$USUBJID %in% usubjids,
         select = u_sl_col_selected
       )
-      subj_list[,sl_col_selected] |>
+      subj_list[, sl_col_selected] |>
         reactable::reactable(
           filterable = TRUE, defaultExpanded = FALSE, striped = TRUE, groupBy = trt_grp,
           columns = sl_col_def,
           details = function(index) {
             usubjid <- subj_list$USUBJID[index]
-            # get AE list of a subject
+            # get AE list of a subject if discontinued because of AE
             if (dcsreas %in% c("adverse event")) {
               sub_ae_listing <- ae_list |> subset(
                 subset = ae_list$USUBJID %in% usubjid,