update the calculation

R/avg.R

@@ -56,7 +56,7 @@ avg_event <- function(id, group, par = NULL) {
       FUN.VALUE = numeric(1)
     )
     count <- vapply(split(res, res$Var2),
-      nrow,
+      function(x) sum(x$Freq, na.rm = TRUE),
       FUN.VALUE = numeric(1)
     )
   } else {
@@ -79,7 +79,7 @@ avg_event <- function(id, group, par = NULL) {
           par = unique(X$par),
           avg = mean(X$n, na.rm = TRUE),
           se = sd(X$n, na.rm = TRUE) / sqrt(nrow(X)),
-          count = nrow(X)
+          count = sum(X$n)
         )
       }) |>
       do.call(what = rbind) |>

R/extend_ae_specific.R

@@ -240,7 +240,7 @@ extend_ae_specific_duration <- function(outdata,
 #'   parameter = "rel"
 #' ) |>
 #'   extend_ae_specific_events() |>
-#'   format_ae_specific(display = c("n", "prop", "events"))
+#'   format_ae_specific(display = c("n", "prop", "events_avg"))
 #' head(tbl$tbl)
 extend_ae_specific_events <- function(outdata) {
   meta <- outdata$meta
@@ -338,9 +338,11 @@ extend_ae_specific_events <- function(outdata) {
   count <- rbind(count, blank_row)[order(index), ]
   names(count) <- paste0("eventscount_", seq_len(ncol(count)))
 
+  # fill NA value with zero
   outdata$events_avg <- avg
   outdata$events_se <- se
-  outdata$events_count <- count
+  # fill NA value with zero
+  outdata$events_count <- replace(count, is.na(count), 0)
   outdata$extend_call <- c(outdata$extend_call, match.call())
 
   outdata

tests/testthat/test-independent-testing-avg_event.R

@@ -23,7 +23,7 @@ test_that("if par = NULL, return the average number of events in each group (tak
 
   count <- vapply(
     split(res, res$Var2),
-    function(x) nrow(x),
+    function(x) sum(x$Freq, na.rm = TRUE),
     FUN.VALUE = numeric(1)
   )
 
@@ -33,7 +33,7 @@ test_that("if par = NULL, return the average number of events in each group (tak
   expect_equal(avg1, avg2)
 })
 
-test_that("if par = NULL, return the average number of events in each group (take the r2rtf::r2rtf_adae dataset as an example)", {
+test_that("if par not NULL, return the average number of events in each group (take the r2rtf::r2rtf_adae dataset as an example)", {
   r2rtf_adae <- r2rtf::r2rtf_adae
   r2rtf_adae$TRTA <- factor(r2rtf_adae$TRTA)
 
@@ -49,7 +49,7 @@ test_that("if par = NULL, return the average number of events in each group (tak
     dplyr::summarise(
       avg = mean(n, na.rm = TRUE),
       se = sd(n, na.rm = TRUE) / sqrt(dplyr::n()),
-      count = dplyr::n(),
+      count = sum(n),
       .groups = "keep"
     ) |>
     tidyr::pivot_wider(id_cols = par, names_from = group, values_from = c("avg", "se", "count"))