Replace $ reference with [[ in format_ae_listing() function

R/ae_listing.R

@@ -100,213 +100,209 @@ propercase <- function(x) paste0(toupper(substr(x, 1, 1)), tolower(substring(x,
 #'
 #' lapply(outdata, head, 20)
 format_ae_listing <- function(outdata, display_unique_records = FALSE) {
-  res <- outdata$ae_listing
-
-  obs_group <- metalite::collect_adam_mapping(outdata$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, 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", "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
-
-  res_columns <- lapply(names(res), function(x) {
-    if (toupper(x) %in% names(name_mapping)) {name_mapping[[toupper(x)]]}
-    else {x}
-  }) |> unlist()
-
-  # Site ID
-  if ("SITEID" %in% toupper(names(res))) {
-    res$Site_Number <- propercase(res$SITEID)
-  }
-
-  if ("SITENUM" %in% toupper(names(res))) {
-    res$Site_Number <- res$SITENUM
-  }
+  res <- outdata[["ae_listing"]]
+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, 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", "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
+
+res_columns <- lapply(names(res), function(x) {
+  if (toupper(x) %in% names(name_mapping)) {name_mapping[[toupper(x)]]}
+  else {x}
+}) |> unlist()
+
+# Site ID
+if ("SITEID" %in% toupper(names(res))) {
+  res[["Site_Number"]] <- propercase(res[["SITEID"]])
+}
 
-  # Participant ID
-  if ("USUBJID" %in% toupper(names(res))) {
-    res$Unique_Participant_ID <- res$USUBJID
-  }
-  if ("SUBJID" %in% toupper(names(res))) {
-    res$Participant_ID <- res$SUBJID
-  }
-  attr(res$Participant_ID, "label") <- NULL
+if ("SITENUM" %in% toupper(names(res))) {
+  res[["Site_Number"]] <- res[["SITENUM"]]
+}
 
-  res$Gender <- tools::toTitleCase(res$SEX)
+# Participant ID
+if ("USUBJID" %in% toupper(names(res))) {
+  res[["Unique_Participant_ID"]] <- res[["USUBJID"]]
+}
+if ("SUBJID" %in% toupper(names(res))) {
+  res[["Participant_ID"]] <- res[["SUBJID"]]
+}
+attr(res[["Participant_ID"]], "label") <- NULL
 
-  res$Race <- tools::toTitleCase(tolower(res$RACE))
+res[["Gender"]] <- tools::toTitleCase(res[["SEX"]])
 
-  res$Age <- res$AGE
+res[["Race"]] <- tools::toTitleCase(tolower(res[["RACE"]]))
 
-  res$Treatment_Group <- res[[obs_group]]
-  attr(res$Treatment_Group, "label") <- NULL
+res[["Age"]] <- res[["AGE"]]
 
-  # Onset epoch
-  if ("EPOCH" %in% toupper(names(res))) {
-    res$Onset_Epoch <- tools::toTitleCase(tolower(res$EPOCH)) # propcase the EPOCH
-  }
+res[["Treatment_Group"]] <- res[[obs_group]]
 
-  # Relative day of onset (ASTDY)
-  if ("ASTDY" %in% toupper(names(res))) {
-    res$Relative_Day_of_Onset <- res$ASTDY
-  }
+attr(res[["Treatment_Group"]], "label") <- NULL
 
-  # SOC
-  res$SOC_Name <- res[[par_var_soc]]
+# Onset epoch
+if ("EPOCH" %in% toupper(names(res))) {
+  res[["Onset_Epoch"]] <- tools::toTitleCase(tolower(res[["EPOCH"]])) # propcase the EPOCH
+}
 
-  # Adverse event
-  res$Adverse_Event <- propercase(res[[par_var]])
-  res <- res[, !(names(res) == par_var)]
 
-  # Duration
-  if ("ADURN" %in% toupper(names(res)) & "ADURU" %in% toupper(names(res))) {
-    res$Duration <- paste(ifelse(is.na(res$ADURN), "", as.character(res$ADURN)), tools::toTitleCase(tolower(res$ADURU)), sep = " ") # AE duration with unit
+# Relative day of onset (ASTDY)
+if ("ASTDY" %in% toupper(names(res))) {
+  res[["Relative_Day_of_Onset"]] <- res[["ASTDY"]]
+}
 
-    if (length(res$Duration > 0)){
-      for (i in 1:length(res$Duration)) {
-        if (is.na(res$ADURN[i])) {
-          res$Duration[i] <- ifelse(charmatch(toupper(res$AEOUT[i]), "RECOVERING/RESOLVING") > 0 |
-            charmatch(toupper(res$AEOUT[i]), "NOT RECOVERED/NOT RESOLVED") > 0, "Continuing", "Unknown")
-        }
+# SOC
+res[["SOC_Name"]] <- res[[par_var_soc]]
+
+# Adverse event
+res[["Adverse_Event"]] <- propercase(res[[par_var]])
+res <- res[, !(names(res) == par_var)]
+
+# Duration
+if ("ADURN" %in% toupper(names(res)) & "ADURU" %in% toupper(names(res))) {
+  res[["Duration"]] <- paste(ifelse(is.na(res[["ADURN"]]), "", as.character(res[["ADURN"]])),
+                             tools::toTitleCase(tolower(res[["ADURU"]])),
+                             sep = " ") # AE duration with unit
+
+  if (length(res[["Duration"]]) > 0) {
+    for (i in 1:length(res[["Duration"]])) {
+      if (is.na(res[["ADURN"]][i])) {
+        res[["Duration"]][i] <- ifelse(charmatch(toupper(res[["AEOUT"]][i]), "RECOVERING/RESOLVING") > 0 |
+                                         charmatch(toupper(res[["AEOUT"]][i]), "NOT RECOVERED/NOT RESOLVED") > 0,
+                                       "Continuing", "Unknown")
       }
     }
-    res <- res[,!(names(res) %in% "ADURU")]
-    res_columns <- res_columns[!(res_columns %in% "ADURU")]
   }
+res <- res[,!(names(res) %in% "ADURU")]
+res_columns <- res_columns[!(res_columns %in% "ADURU")]
+}
 
-  # Intensity
-  if ("AESEV" %in% toupper(names(res))) {
-    res$Intensity <- propercase(res$AESEV)
-  }
+# Intensity
+if ("AESEV" %in% toupper(names(res))) {
+  res[["Intensity"]] <- propercase(res[["AESEV"]])
+}
 
-  # Maximum toxicity grade
-  if ("ATOXGRN" %in% toupper(names(res))) {
-    res$Maximum_Toxicity_Grade <- res$ATOXGRN
-  }
+# Maximum toxicity grade
+if ("ATOXGRN" %in% toupper(names(res))) {
+  res[["Maximum_Toxicity_Grade"]] <- res[["ATOXGRN"]]
+}
 
-  # Serious
-  if ("AESER" %in% toupper(names(res))) {
-    res$Serious <- propercase(res$AESER)
-  }
+# Serious
+if ("AESER" %in% toupper(names(res))) {
+  res[["Serious"]] <- propercase(res[["AESER"]])
+}
 
-  # AE related
-  if ("AEREL" %in% toupper(names(res))) {
-    res$Related <- ifelse(res$AEREL == "RELATED", "Y", ifelse(
-      toupper(res$AEREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AEREL))
-    ))
-  }
+# AE related
+if ("AEREL" %in% toupper(names(res))) {
+  res[["Related"]] <- ifelse(res[["AEREL"]] == "RELATED", "Y", ifelse(
+    toupper(res[["AEREL"]]) == "NOT RELATED", "N", tools::toTitleCase(tolower(res[["AEREL"]]))
+  ))
+}
 
-  if ("AREL" %in% toupper(names(res))) {
-    res$Related <- ifelse(res$AREL == "RELATED", "Y", ifelse(
-      toupper(res$AREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AREL))
-    ))
+# Action taken
+if ("AEACN" %in% toupper(names(res))) {
+  if (length(res[["AEACN"]]) > 0) {
+    for (i in 1:length(res[["AEACN"]])) {
+      res[["Action_Taken"]][i] <- switch(res[["AEACN"]][i],
+                                         "DOSE NOT CHANGED" = "None",
+                                         "DOSE REDUCED" = "Reduced",
+                                         "DRUG INTERRUPTED" = "Interrupted",
+                                         "DOSE INCREASED" = "Increased",
+                                         "NOT APPLICABLE" = "N/A",
+                                         "UNKNOWN" = "Unknown",
+                                         tools::toTitleCase(tolower(res[["AEACN"]][i]))
+      )
+    }
+  } else {
+    res[["Action_Taken"]] <- res[["AEACN"]]
   }
+}
 
-  # Action taken
-  if ("AEACN" %in% toupper(names(res))) {
-    if (length(res$AEACN > 0)) {
-      for (i in 1:length(res$AEACN)) {
-        res$Action_Taken[i] <- switch(res$AEACN[i],
-          "DOSE NOT CHANGED" = "None",
-          "DOSE REDUCED" = "Reduced",
-          "DRUG INTERRUPTED" = "Interrupted",
-          "DOSE INCREASED" = "Increased",
-          "NOT APPLICABLE" = "N/A",
-          "UNKNOWN" = "Unknown",
-          tools::toTitleCase(tolower(res$AEACN[i]))
-        )
-      }
-    } else {
-      res$Action_Taken <- res$AEACN
+# Outcome
+if ("AEOUT" %in% toupper(names(res))) {
+  if (length(res[["AEOUT"]]) > 0) {
+    for (i in 1:length(res[["AEOUT"]])) {
+      res[["Outcome"]][i] <- switch(res[["AEOUT"]][i],
+                                    "RECOVERED/RESOLVED" = "Resolved",
+                                    "RECOVERING/RESOLVING" = "Resolving",
+                                    "RECOVERED/RESOLVED WITH SEQUELAE" = "Sequelae",
+                                    "NOT RECOVERED/NOT RESOLVED" = "Not Resolved",
+                                    tools::toTitleCase(tolower(res[["AEOUT"]][i]))
+      )
     }
+  } else {
+    res[["Outcome"]] <- res[["AEOUT"]]
   }
+}
+# Total dose on day of AE onset
+if ("AEDOSDUR" %in% toupper(names(res))) {
+  res[["ymd"]] <- substring(res[["AEDOSDUR"]], unlist(gregexpr("/P", res[["AEDOSDUR"]])) + 2)
+
+  res[["Total_Dose_on_Day_of_AE_Onset"]] <- ""
+
+  if (length(res[["AEDOSDUR"]]) > 0) {
+    for (i in 1:length(res[["AEDOSDUR"]])) {
+      if (unlist(gregexpr("Y", res[["ymd"]][i])) > 0) {
+        val_year <- substring(res[["ymd"]][i], 1, unlist(gregexpr("Y", res[["ymd"]][i])) - 1)
+        if (as.numeric(val_year) != 1) {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], val_year, " years")
+        } else {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], "1 year")
+        }
 
-  # Outcome
-  if ("AEOUT" %in% toupper(names(res))) {
-    if (length(res$AEOUT > 0)) {
-      for (i in 1:length(res$AEOUT)) {
-        res$Outcome[i] <- switch(res$AEOUT[i],
-          "RECOVERED/RESOLVED" = "Resolved",
-          "RECOVERING/RESOLVING" = "Resolving",
-          "RECOVERED/RESOLVED WITH SEQUELAE" = "Sequelae",
-          "NOT RECOVERED/NOT RESOLVED" = "Not Resolved",
-          tools::toTitleCase(tolower(res$AEOUT[i]))
-        )
+        res[["ymd"]][i] <- substring(res[["ymd"]][i], unlist(gregexpr("Y", res[["ymd"]][i])) + 1)
       }
-    } else {
-      res$Outcome <- res$AEOUT
-    }
-  }
+      if (unlist(gregexpr("M", res[["ymd"]][i])) > 0) {
+        val_month <- substring(res[["ymd"]][i], 1, unlist(gregexpr("M", res[["ymd"]][i])) - 1)
 
-  # Total dose on day of AE onset
-  if ("AEDOSDUR" %in% toupper(names(res))) {
-    res$ymd <- substring(res$AEDOSDUR, unlist(gregexpr("/P", res$AEDOSDUR)) + 2)
-
-    res$Total_Dose_on_Day_of_AE_Onset <- ""
-    print(length(res$AEDOSDUR))
-    print(nrow(res$AEDOSDUR))
-
-    if (length(res$AEDOSDUR) > 0){
-      for (i in 1:length(res$AEDOSDUR)) {
-        if (unlist(gregexpr("Y", res$ymd[i])) > 0) {
-          val_year <- substring(res$ymd[i], 1, unlist(gregexpr("Y", res$ymd[i])) - 1)
-          if (as.numeric(val_year) != 1) {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], val_year, " years")
-          } else {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], "1 year")
-          }
-
-          res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("Y", res$ymd[i])) + 1)
+        if (as.numeric(val_month) != 1) {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], " ", val_month, " months")
+        } else {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], " 1 month")
         }
-        if (unlist(gregexpr("M", res$ymd[i])) > 0) {
-          val_month <- substring(res$ymd[i], 1, unlist(gregexpr("M", res$ymd[i])) - 1)
 
-          if (as.numeric(val_month) != 1) {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_month, " months")
-          } else {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 month")
-          }
+        res[["ymd"]][i] <- substring(res[["ymd"]][i], unlist(gregexpr("M", res[["ymd"]][i])) + 1)
+      }
+      if (unlist(gregexpr("D", res[["ymd"]][i])) > 0) {
+        val_day <- substring(res[["ymd"]][i], 1, unlist(gregexpr("D", res[["ymd"]][i])) - 1)
 
-          res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("M", res$ymd[i])) + 1)
-        }
-        if (unlist(gregexpr("D", res$ymd[i])) > 0) {
-          val_day <- substring(res$ymd[i], 1, unlist(gregexpr("D", res$ymd[i])) - 1)
-
-          if (as.numeric(val_day) != 1) {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_day, " days")
-          } else {
-            res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 day")
-          }
+        if (as.numeric(val_day) != 1) {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], " ", val_day, " days")
+        } else {
+          res[["Total_Dose_on_Day_of_AE_Onset"]][i] <- paste0(res[["Total_Dose_on_Day_of_AE_Onset"]][i], " 1 day")
         }
       }
-    } else {
-      res$Total_Dose_on_Day_of_AE_Onset <- res$AEDOSDUR
     }
-    res <- res[, !(names(res) == "ymd"), drop = FALSE]
-  }
-
-  # Customized variable will use label as column header in
-  # drill down listing on interactive forest plot
-  if (!display_unique_records) {
-    outdata$ae_listing <- res[, res_columns]
   } else {
-    outdata$ae_listing <- res[, res_columns] |> unique()
+    res[["Total_Dose_on_Day_of_AE_Onset"]] <- res[["AEDOSDUR"]]
   }
+  res <- res[, !(names(res) == "ymd"), drop = FALSE]
+}
 
-  # Get all labels from the un-subset data
-  listing_label <- get_label(res)
-  listing_label <- gsub("_", " ", listing_label)
-  # Assign labels
-  outdata$ae_listing <- assign_label(
-    data = outdata$ae_listing,
-    var = names(outdata$ae_listing),
-    label = listing_label[match(names(outdata$ae_listing), names(listing_label))]
-  )
 
-  outdata
+# Customized variable will use label as column header in
+# drill down listing on interactive forest plot
+if (!display_unique_records) {
+  outdata[["ae_listing"]] <- res[, res_columns]
+} else {
+  outdata[["ae_listing"]] <- unique(res[, res_columns])
+}
+
+# Get all labels from the un-subset data
+listing_label <- get_label(res)
+listing_label <- gsub("_", " ", listing_label)
+# Assign labels
+outdata[["ae_listing"]] <- assign_label(
+  data = outdata[["ae_listing"]],
+  var = names(outdata[["ae_listing"]]),
+  label = listing_label[match(names(outdata[["ae_listing"]]), names(listing_label))]
+)
+
+outdata
 }