Merge pull request #55 from Merck/fix-soc-display-in-listing

Fix a bug not to display any AE lsiting for a SOC in forestly table.
Merck · Jun 11, 2024 · 62e0447 · 62e0447
2 parents acbf106 + 648b361
commit 62e0447
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Showing 2 changed files with 14 additions and 7 deletions.
diff --git a/R/ae_forestly.R b/R/ae_forestly.R
@@ -145,12 +145,14 @@ ae_forestly <- function(outdata,
 
       t_details <- subset(
         outdata$ae_listing,
-        (toupper(outdata$ae_listing$Adverse_Event) %in% toupper(t_row)) &
-          (outdata$ae_listing$param == t_param)
+        ((toupper(outdata$ae_listing$Adverse_Event) %in% toupper(t_row)) &
+          (outdata$ae_listing$param == t_param)) |
+        ((toupper(outdata$ae_listing$SOC_Name) %in% toupper(t_row)) &
+           (outdata$ae_listing$param == t_param))
       )
 
       # Exclude 'param' column from t_details
-      t_details <- t_details[, !(names(t_details) == "param")]
+      t_details <- t_details[, !(names(t_details) %in% c("param", "SOC_Name"))]
 
       # Get all labels from the un-subset data
       listing_label <- get_label(outdata$ae_listing)

diff --git a/R/ae_listing.R b/R/ae_listing.R
@@ -40,17 +40,18 @@ collect_ae_listing <- function(
     )) {
   obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
   par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
+  par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
 
   obs <- metalite::collect_observation_record(
     outdata$meta,
     outdata$population,
     outdata$observation,
     outdata$parameter,
-    var = c(par_var, obs_group, display)
+    var = c(par_var, par_var_soc, obs_group, display)
   )
 
   # Keep variable used to display only
-  outdata$ae_listing <- obs[, c(par_var, obs_group, display)]
+  outdata$ae_listing <- obs[, c(par_var, par_var_soc, obs_group, display)]
 
   # Get all labels from the un-subset data
   listing_label <- get_label(obs)
@@ -103,12 +104,13 @@ format_ae_listing <- function(outdata, display_unique_records = FALSE) {
 
   obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
   par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
+  par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
 
   new_name <- c("SITEID", "SITENUM", "USUBJID", "SUBJID", "SEX", "RACE", "AGE", obs_group, "EPOCH",
-                "ASTDY", par_var, "ADURN", "AESEV", "AESER", "AEREL", "AREL", "AEACN",
+                "ASTDY", par_var, par_var_soc, "ADURN", "AESEV", "AESER", "AEREL", "AREL", "AEACN",
                 "AEOUT", "AEDOSDUR", "ATOXGRN")
   name_mapping <- c("Site_Number", "Site_Number", "Unique_Participant_ID", "Participant_ID", "Gender", "Race", "Age", "Treatment_Group", "Onset_Epoch",
-                    "Relative_Day_of_Onset", "Adverse_Event", "Duration", "Intensity", "Serious", "Related", "Related", "Action_Taken",
+                    "Relative_Day_of_Onset", "Adverse_Event", "SOC_Name", "Duration", "Intensity", "Serious", "Related", "Related", "Action_Taken",
                     "Outcome", "Total_Dose_on_Day_of_AE_Onset", "Maximum_Toxicity_Grade")
   names(name_mapping) <- new_name
 
@@ -154,6 +156,9 @@ format_ae_listing <- function(outdata, display_unique_records = FALSE) {
     res$Relative_Day_of_Onset <- res$ASTDY
   }
 
+  # SOC
+  res$SOC_Name <- res[[par_var_soc]]
+
   # Adverse event
   res$Adverse_Event <- propercase(res[[par_var]])
   res <- res[, !(names(res) == par_var)]