add new mode argument

DESCRIPTION

@@ -50,4 +50,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,5 +1,7 @@
 # dunlin 0.1.11.9000
 
+* New `mode` argument in `log_filter` determining whether all tables should be filtered to retain only the rows whose identifiers are present in the filtered data set selected with the `table` argument. (Previously, the behavior was triggered automatically when the `table` name was `adsl`)
+
 # dunlin 0.1.11
 
 * Added `subject_level_flag()` function.

R/filter.R

@@ -5,11 +5,10 @@
 #' @param ... further arguments to be passed to or from other methods.
 #' @returns a `data.frame` or `list` of `data.frame` filtered for the provided conditions.
 #' @details
-#' `log_filter` will filter the data/named list of data according to the `condition`.
+#' `log_filter` will filter the `data.frame` /named list of `data.frame` according to the `condition`.
 #' All the variables in `condition` must exist in the data (as variables) or in the parent
 #' frame(e.g., in global environment).
-#' For named list of data, if `ADSL` is available, `log_filter` will also try to subset all
-#' other datasets with `USUBJID`.
+#' For named list of `data.frame`,
 #' @export
 log_filter <- function(data, condition, ...) {
   UseMethod("log_filter")
@@ -44,29 +43,36 @@
 
 #' @rdname log_filter
 #' @param table (`string`) table name.
-#' @param by (`character`) variable names shared by `adsl` and other datasets for filtering.
+#' @param by (`character`) variable names shared by `table` and other datasets for filtering when `mode == "all"`.
 #' @param verbose (`flag`) whether to print a report about the filtering.
+#' @param mode (`string`) one of `all` or `unique` whether the other tables should be filtered based on the rows retained in `table`. Default value is `"all"` is `table == "adsl"` and `"unique"` otherwise.
 #' @export
 #' @examples
 #' log_filter(list(iris = iris), Sepal.Length >= 7, "iris", character(0))
-log_filter.list <- function(data, condition, table, by = c("USUBJID", "STUDYID"), suffix = NULL, verbose = FALSE, ...) {
+log_filter.list <- function(data, condition, table, by = c("USUBJID", "STUDYID"), suffix = NULL, verbose = FALSE, mode = ifelse(table == "adsl", "all", "unique"), ...) {
   checkmate::assert_list(data, types = "data.frame", names = "unique")
   assert_all_tablenames(data, table)
   checkmate::assert_names(colnames(data[[table]]), must.include = by)
+  checkmate::assert_character(by, null.ok = TRUE)
+  checkmate::assert_string(suffix, null.ok = TRUE)
+  checkmate::assert_flag(verbose)
+  checkmate::assert_subset(mode, c("all", "unique"))
+
   condition <- match.call()$condition
   data[[table]] <- eval(bquote(log_filter(data[[table]], .(condition), .(suffix))))
-  if (identical(table, "adsl")) {
-    for (k in setdiff(names(data), "adsl")) {
+
+  if (mode == "all") {
+    for (k in setdiff(names(data), table)) {
       if (all(by %in% names(data[[k]]))) {
-        if (length(by) == 0) by <- intersect(names(data[[k]]), names(data$adsl))
+        if (length(by) == 0) by <- intersect(names(data[[k]]), names(data[[table]]))
 
         ori_n <- nrow(data[[k]])
         ori_att <- attr(data[[k]], "rows")
 
-        data[[k]] <- dplyr::semi_join(data[[k]], data$adsl, by = by)
+        data[[k]] <- dplyr::semi_join(data[[k]], data[[table]], by = by)
 
         rows <- list(list(init = ori_n, final = nrow(data[[k]]), suffix = suffix))
-        names(rows) <- paste0("Filtered by adsl: ", deparse(condition), collapse = "")
+        names(rows) <- paste0(sprintf("Filtered by %s: ", table), deparse(condition), collapse = "")
         attr(data[[k]], "rows") <- c(ori_att, rows)
       }
     }

R/reformat.R

@@ -1,4 +1,8 @@
 #' Reformat Values
+#'
+#' Replaces substitute values in `vectors` or `list` of `data.frame` using used defined [`rule`].
+#' See `vignette("Reformatting", package = "dunlin")` for a detailed guide on using this function.
+#'
 #' @param obj (`character`, `factor` or `list of data.frame`) to reformat.
 #' @param format (`rule`) or (`list`) of `rule` depending on the class of obj.
 #' @param ... for compatibility between methods and pass additional special mapping to transform rules.

tests/testthat/test-filter.R

@@ -145,6 +145,23 @@ test_that("log_filter works with long conditions", {
   expect_identical(df1, df2, ignore_attr = TRUE)
 })
 
+test_that("log_filters works with custom `mode` argument", {
+  dfa <- data.frame(USUBJID = letters[5:14], b = 1:10)
+  dfb <- data.frame(USUBJID = letters[1:10], c = 1:10)
+
+  attr(dfa$USUBJID, "label") <- "usubjid_dfa"
+  attr(dfb$USUBJID, "label") <- "usubjid_dfb"
+
+  df_raw <- list(adsl = dfa, dfb = dfb)
+  res <- expect_silent(log_filter(df_raw, c >= 7, "dfb", by = "USUBJID", mode = "all"))
+  expect_equal(nrow(res$dfb), 4)
+  expect_equal(nrow(res$adsl), 4)
+
+  res <- expect_silent(log_filter(df_raw, c >= 7, "dfb", by = "USUBJID", mode = "unique"))
+  expect_equal(nrow(res$dfb), 4)
+  expect_equal(nrow(res$adsl), 10)
+})
+
 # get_log ----
 
 test_that("get_log works as expected", {