rework for generalization

DESCRIPTION

@@ -133,7 +133,6 @@ Collate:
     'prop_diff.R'
     'prop_diff_test.R'
     'prune_occurrences.R'
-    'reflast.R'
     'response_biomarkers_subgroups.R'
     'response_subgroups.R'
     'riskdiff.R'
@@ -160,3 +159,4 @@ Collate:
     'utils_factor.R'
     'utils_grid.R'
     'utils_rtables.R'
+    'utils_split_funs.R'

NAMESPACE

@@ -217,6 +217,7 @@ export(has_fraction_in_cols)
 export(has_fractions_difference)
 export(imputation_rule)
 export(keep_content_rows)
+export(keep_level_order)
 export(keep_rows)
 export(logistic_regression_cols)
 export(logistic_summary_by_flag)

R/utils_split_funs.R

@@ -0,0 +1,108 @@
+#' Custom Split Functions
+#'
+#' @description
+#' Collection of useful functions that are expanding on the core list of functions
+#' provided by `rtables`. See `?rtables::custom_split_funs` and [rtables::make_split_fun()]
+#' for more information on how to make a custom split function. All these functions
+#' work with [split_rows_by()] argument `split_fun` to modify the way the split
+#' happens.
+#'
+#' @seealso [rtables::make_split_fun()]
+#'
+#' @name utils_split_funs
+NULL
+
+#' @describeIn utils_split_funs split function to place reference group facet last
+#'  during post-processing stage.
+#'
+#' @return
+#' * `ref_group_last` returns an utility function that puts the reference group
+#'  as last and needs to be assigned to `split_fun`.
+#'
+#' @examples
+#' library(dplyr)
+#'
+#' dat <- data.frame(
+#'   x = factor(letters[1:5], levels = letters[5:1]),
+#'   y = 1:5
+#' )
+#' # ref_group_last
+#'
+#' # With rtables layout functions
+#' basic_table() %>%
+#'   split_cols_by("x", ref_group = "c", split_fun = ref_group_last) %>%
+#'   analyze("y") %>%
+#'   build_table(dat)
+#'
+#' # With tern layout funcitons
+#' adtte_f <- tern_ex_adtte %>%
+#'   filter(PARAMCD == "OS") %>%
+#'   mutate(
+#'     AVAL = day2month(AVAL),
+#'     is_event = CNSR == 0
+#'   )
+#'
+#' basic_table() %>%
+#'   split_cols_by(var = "ARMCD", ref_group = "ARM B", split_fun = ref_group_last) %>%
+#'   add_colcounts() %>%
+#'   surv_time(
+#'     vars = "AVAL",
+#'     var_labels = "Survival Time (Months)",
+#'     is_event = "is_event",
+#'   ) %>%
+#'   build_table(df = adtte_f)
+#'
+#' @export
+ref_group_last <- make_split_fun(
+  post = list(
+    function(splret, spl, fulldf) {
+      if (!"ref_group_value" %in% slotNames(spl)) {
+        stop("Reference group is undefined.")
+      }
+
+      spl_var <- spl@payload # can be substituted by splret$labels
+      init_lvls <- levels(fulldf[[spl_var]])
+
+      if (!all(names(splret$values) %in% init_lvls)) {
+        stop("This split function does not work with combination facets.")
+      }
+
+      ref_group_pos <- which(init_lvls == spl@ref_group_value)
+      reord_lvls <- c(init_lvls[-ref_group_pos], init_lvls[ref_group_pos])
+      ord <- match(reord_lvls, names(splret$values))
+
+      make_split_result(
+        splret$values[ord],
+        splret$datasplit[ord],
+        splret$labels[ord]
+      )
+    }
+  )
+)
+#' @describeIn utils_split_funs split function to keep original order of factor
+#'  levels in the split.
+#'
+#' @return
+#' * `keep_level_order` returns an utility function that keeps the original levels'.
+#'  It needs to be assigned to `split_fun`.
+#'
+#' @examples
+#' # keep_level_order --------
+#' # Even if default would bring ref_group first, the original order puts it last
+#' basic_table() %>%
+#'   split_cols_by("Species", ref_group = "virginica", split_fun = keep_level_order) %>%
+#'   analyze("Sepal.Length") %>%
+#'   build_table(iris)
+#'
+#' @export
+keep_level_order <- make_split_fun(
+  post = list(
+    function(splret, spl, fulldf, ...) {
+      # browser() if you enter here the order of splret seems already correct
+      ord <- order(names(splret$values))
+      make_split_result(splret$values[ord],
+                        splret$datasplit[ord],
+                        splret$labels[ord])
+    }
+  )
+)