Default category setting for extend_exp_duration()

R/extend_exp_duration.R

@@ -43,9 +43,9 @@
 #'     duration_category_labels = c(">=1 day", ">=7 days", ">=28 days", ">=12 weeks", ">=24 weeks")
 #'   )
 extend_exp_duration <- function(outdata,
-                                category_section_label = NULL,
-                                duration_category_list = NULL,
-                                duration_category_labels = NULL) {
+                                category_section_label = paste0(metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$label, " (extend)"),
+                                duration_category_list = extract_duration_category_ranges(duration_category_labels),
+                                duration_category_labels = levels(outdata$meta$data_population[[metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$vargroup]])) {
   res <- outdata
   meta <- res$meta
   analysis <- res$analysis
@@ -191,10 +191,6 @@ extend_exp_duration <- function(outdata,
       pop_subset <- metalite::collect_adam_mapping(meta, population)$subset
       pop_subset <- rlang::quo(TRTDURGR == !!label & !!pop_subset)
 
-      if (is.null(category_section_label)) {
-        category_section_label <- paste0(metalite::collect_adam_mapping(meta, parameter)$label, " (cumulative)")
-      }
-
       meta_cum <- meta_sl(
         data_population,
         dataset_observation = NULL,

R/meta_sl_example.R

@@ -180,14 +180,14 @@ meta_sl_exposure_example <- function() {
   adexsum$APERIOD <- 1
 
   adexsum$AVAL <- sample(x = 1:(24 * 7), size = length(adexsum$USUBJID), replace = TRUE)
-  adexsum$EXDURGR[adexsum$AVAL >= 1] <- ">=1 day and <7days"
+  adexsum$EXDURGR[adexsum$AVAL >= 1] <- ">=1 day and <7 days"
   adexsum$EXDURGR[adexsum$AVAL >= 7] <- ">=7 days and <28 days"
   adexsum$EXDURGR[adexsum$AVAL >= 28] <- ">=28 days and <12 weeks"
   adexsum$EXDURGR[adexsum$AVAL >= 12 * 7] <- ">=12 weeks and <24 weeks"
   adexsum$EXDURGR[adexsum$AVAL >= 24 * 7] <- ">=24 weeks"
 
   adexsum$EXDURGR <- factor(adexsum$EXDURGR,
-    levels = c(">=1 day and <7days", ">=7 days and <28 days", ">=28 days and <12 weeks", ">=12 weeks and <24 weeks", ">=24 weeks")
+    levels = c(">=1 day and <7 days", ">=7 days and <28 days", ">=28 days and <12 weeks", ">=12 weeks and <24 weeks", ">=24 weeks")
   )
 
   plan <- metalite::plan(

R/plotly_exp_duration.R

@@ -354,7 +354,7 @@ plotly_exp_duration <- function(outdata,
     stop("No plot is available. Please check the input data.")
   }
 
-  histograms <- names(p)
+  histograms <- plot_type_label
   histograms_ids <- paste0("histogram_type_", uuid::UUIDgenerate(), "|", histograms)
   plot_divs <- lapply(histograms_ids, function(x) {
     element <- unlist(strsplit(x, "\\|"))[2]

R/utils.R

@@ -55,3 +55,62 @@ rtf_output <- function(
 
   invisible(outdata)
 }
+
+#' Obtain a list of category ranges from a character label for exposure duration analysis
+#'
+#' @param labels A character vector of a category label
+#'
+#' @noRd
+extract_duration_category_ranges <- function(labels) {
+  times <- labels |>
+    stringr::str_extract_all(pattern = "\\d+") |>
+    lapply(function(x) {
+      if (length(x) == 0) {
+        stop("A real number for duration category is not recognized. Please rename the category label in the input data, or use `duration_category_list` and `duration_category_labels`.")
+      }
+      as.numeric(x)
+    })
+
+  factors <- labels |>
+    stringr::str_extract_all(pattern = "\\d+ ?([a-zA-Z]+)") |>
+    lapply(
+      function(x) {
+        unit <- stringr::str_extract(x, pattern = "\\d+ ?([a-zA-Z])", group = 1)
+        factor <- sapply(unit, USE.NAMES = FALSE, function(y) {
+          if (toupper(y) == "D") {
+            1
+          } else if (toupper(y) == "W") {
+            7
+          } else if (toupper(y) == "M") {
+            30.4367
+          } else if (toupper(y) == "Y") {
+            365.24
+          } else {
+            warning("The unit of duration category is not recognized. The unit is handled as day(s).")
+            1
+          }
+        })
+        return(factor)
+      }
+    )
+
+  list <- lapply(
+    seq_along(times),
+    function(x) {
+      if (length(times[[x]]) < 2) {
+        time <- c(times[[x]], rep(NA, 2 - length(times[[x]])))
+      } else {
+        time <- times[[x]]
+      }
+      if (length(factors[[x]]) == 1) {
+        factor <- rep(factors[[x]], 2)
+      } else if (length(factors[[x]]) == 0) {
+        factor <- rep(1, 2)
+      } else {
+        factor <- factors[[x]]
+      }
+      return(time * factor)
+    }
+  )
+  return(list)
+}