modified sort_ard_hierarchical function

.Rhistory

@@ -0,0 +1,181 @@
+Sys.getenv()
+library(cards)
+library(gtsummary)
+ard <- ard_tabulate(
+data = cards::ADAE,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL
+)
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA
+)
+ard <- ard_tabulate(
+data = cards::ADAE,
+by = TRTA
+variables = c(AESOC, AEDECOD),
+ard <- ard_tabulate(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL
+)
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA
+)
+ae_tbl
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA,
+statistic = "{n} (p)}"
+)
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA,
+statistic = "{n} ({p})"
+)
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA,
+statistic = list(all_categorical() ~ "{n} ({p})")
+)
+ae_tbl
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA,
+statistic = list(all_categorical() ~ "{n} ({p})")
+) |>
+sort_ard_hierarchical()
+ard <- ard_tabulate(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL
+) |>
+sort_ard_hierarchical()
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+id = USUBJID
+) |>
+sort_ard_hierarchical()
+ae_tbl <- tbl_ard_summary(
+ard,
+by = TRTA,
+statistic = list(all_categorical() ~ "{n} ({p})")
+)
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+statistic = list(all_categorical() ~ "{n} ({p})")
+)
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+statistic = list(all_categorical() ~ "{n} ({p})")
+)
+ae_tbl
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+statistic = list(all_categorical() ~ "{n} ({p})"),
+id = USUBJID
+) |>
+sort_ard_hierarchical()
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+statistic = list(all_categorical() ~ "{n} ({p})")
+)
+ae_tbl
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+id = USUBJID
+) |>
+sort_ard_hierarchical()
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+variables = c(AESOC, AEDECOD)
+)
+ae_tbl
+devtools::load_all()
+getwd()
+setwd("D:/ARDs/cards")
+getwd()
+devtools::load_all()
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+statistic = list(all_categorical() ~ "{n} ({p})"),
+id = USUBJID
+) |>
+sort_ard_hierarchical()
+ADSL
+table(ADSL$TRTA)
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+statistic = list(all_categorical() ~ "{n} ({p})"),
+id = USUBJID
+) |>
+sort_ard_hierarchical(sort_col = Placebo)
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+statistic = list(all_categorical() ~ "{n} ({p})"),
+id = USUBJID
+) |>
+sort_ard_hierarchical(sort_col = 'Placebo')
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+variables = c(AESOC, AEDECOD)
+)
+ae_tbl
+ard <- ard_stack_hierarchical(
+data = cards::ADAE,
+by = TRTA,
+variables = c(AESOC, AEDECOD),
+denominator = cards::ADSL,
+statistic = list(all_categorical() ~ "{n} ({p})"),
+id = USUBJID
+) |>
+sort_ard_hierarchical(sort_col = 'Xanomeline High Dose')
+ae_tbl <- tbl_ard_hierarchical(
+ard,
+by = TRTA,
+variables = c(AESOC, AEDECOD)
+)
+ae_tbl
+devtools::check()
+devtools::install_dev_deps()
+devtools::check()
+devtools::test_coverage()
+devtools::install_dev_deps()
+devtools::check()
+devtools::check()
+styler::style_file("R/sort_ard_hierarchical.R")
+styler::style_file("R/sort_ard_hierarchical.R")
+spelling::update_wordlist()
+install.packages('spelling')
+spelling::update_wordlist()
+spelling::update_wordlist()
+spelling::update_wordlist()
+devtools::check()

.gitignore

@@ -1,6 +1,10 @@
 .Rproj.user
-docs
+.Rhistory
+.RData
+.Ruserdata
 .DS_Store
+docs
 tests/testthat/_snaps/**/*.new.md
 tests/testthat/_snaps/**/*.new.svg
 revdep
+

R/sort_ard_hierarchical.R

@@ -24,6 +24,8 @@
 #'     sums, otherwise `p` is used. If neither `n` nor `p` are present in `x` for the variable, an error will occur.
 #'
 #'   Defaults to `everything() ~ "descending"`.
+#' @param sort_col (`character`)\cr
+#'     name of the treatment column you want to sort by e.g "Placebo"; leave it blank if you to sort by the sum across all treatment columns.
 #'
 #' @return an ARD data frame of class 'card'
 #' @seealso [filter_ard_hierarchical()]
@@ -51,11 +53,19 @@
 #'   denominator = ADSL
 #' ) |>
 #'   sort_ard_hierarchical(sort = list(AESOC ~ "alphanumeric", AEDECOD ~ "descending"))
+#'
+#' ard_stack_hierarchical_count(
+#'   ADAE,
+#'   variables = c(AESOC, AEDECOD),
+#'   by = TRTA,
+#'   denominator = ADSL
+#' ) |>
+#'   sort_ard_hierarchical(sort_col = "Placebo")
 NULL
 
 #' @rdname sort_ard_hierarchical
 #' @export
-sort_ard_hierarchical <- function(x, sort = everything() ~ "descending") {
+sort_ard_hierarchical <- function(x, sort = everything() ~ "descending", sort_col = NULL) {
   set_cli_abort_call()
 
   # check and process inputs ---------------------------------------------------------------------
@@ -156,7 +166,7 @@ sort_ard_hierarchical <- function(x, sort = everything() ~ "descending") {
       # descending sort
       x_sort <- x_sort |>
         # calculate sums for each group at the current level, then get group indices
-        .append_hierarchy_sums(ard_args, cols, i)
+        .append_hierarchy_sums(ard_args, cols, i, sort_col)
     } else {
       # alphanumeric sort
       x_sort <- x_sort |>
@@ -248,7 +258,7 @@ sort_ard_hierarchical <- function(x, sort = everything() ~ "descending") {
 }
 
 # this function calculates and appends group sums/ordering for the current hierarchy level (across `by` variables)
-.append_hierarchy_sums <- function(x, ard_args, cols, i) {
+.append_hierarchy_sums <- function(x, ard_args, cols, i, sort_col = sort_col) {
   cur_var <- names(cols)[i] # get current grouping variable
   next_var <- names(cols)[i + 1] # get next grouping variable
 
@@ -275,6 +285,20 @@ sort_ard_hierarchical <- function(x, sort = everything() ~ "descending") {
   sort_stat <- if (n_stat) "n" else "p" # statistic used to calculate group sums
 
   # calculate group sums
+
+  # Introduced the ability to sort the ARD based on a particular treatment column
+
+  if (!is.null(sort_col)) {
+    x <- x |>
+      dplyr::mutate(stat = dplyr::case_when(
+        stat_name == sort_stat & variable == dplyr::last(ard_args$variables) & group1_level == sort_col ~ stat,
+        stat_name == sort_stat & variable == dplyr::last(ard_args$variables) & group1_level != sort_col ~ list(0),
+        TRUE ~ stat
+      ))
+  } else {
+    x <- x
+  }
+
   sum_i <- paste0("sum_group_", i) # sum column label
   x_sums <- x |>
     dplyr::filter(