enhancements after overall code review

.Rbuildignore

@@ -1,5 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.pre-commit-config\.yaml$
 ^temp$
 ^.github$
 ^staged_dependencies.yaml$

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.2.2.9009
+    rev: v0.2.2.9013
     hooks:
       - id: style-files
         name: Style code with `styler`

NAMESPACE

@@ -14,7 +14,6 @@ export(aet03_1)
 export(aet03_1_lyt)
 export(aet04_1)
 export(aet04_1_lyt)
-export(append_to_pmap)
 export(assert_colnames)
 export(bol_YN)
 export(cmt01a_1)

R/aet01.R

@@ -11,14 +11,10 @@
 #' @param safety_var (`character`) the safety variables to be summarized.
 #' @param lbl_safety_var (`character`) the labels of the safety variables to be summarized.
 #'
-#' @importFrom magrittr %>%
-#'
-#' @return
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("aet01_1")
@@ -66,7 +62,7 @@ aet01_1 <- function(adam_db,
   tbl <- set_decoration(tbl, deco)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl
@@ -80,9 +76,6 @@ aet01_1 <- function(adam_db,
 #' @param safety_var (`character`) the safety variables to be summarized.
 #' @param lbl_safety_var (`character`) the labels of the safety variables to be summarized.
 #'
-#' @importFrom magrittr %>%
-#'
-#' @return
 #' @export
 #'
 #' @examples
@@ -110,8 +103,7 @@ aet01_1_lyt <- function(armvar = .study$actualarm,
                         )) {
   names(lbl_safety_var) <- safety_var
 
-  lyt_adae <-
-    basic_table_deco(deco) %>%
+  lyt_adae <- basic_table_deco(deco) %>%
     split_cols_by(var = armvar) %>%
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
@@ -133,8 +125,7 @@ aet01_1_lyt <- function(armvar = .study$actualarm,
       .indent_mods = 0L
     )
 
-  lyt_adsl <-
-    basic_table_deco(deco) %>%
+  lyt_adsl <- basic_table_deco(deco) %>%
     split_cols_by(var = armvar) %>%
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
@@ -172,9 +163,6 @@ aet01_1_lyt <- function(armvar = .study$actualarm,
 #' @param medconcept_var (`character`) the medical concept variables to be summarized.
 #' @param lbl_medconcept_var (`character`) the label of the medical concept variables to be summarized.
 #'
-#' @importFrom magrittr %>%
-#'
-#' @return
 #' @export
 #'
 #' @examples
@@ -231,7 +219,7 @@ aet01_2 <- function(adam_db,
   tbl <- set_decoration(tbl, deco)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl
@@ -247,7 +235,6 @@ aet01_2 <- function(adam_db,
 #' @param medconcept_var (`character`) the medical concept variables to be summarized.
 #' @param lbl_medconcept_var (`character`) the label of the medical concept variables to be summarized.
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -280,8 +267,7 @@ aet01_2_lyt <- function(armvar = .study$actualarm,
   names(lbl_safety_var) <- safety_var
   names(lbl_medconcept_var) <- medconcept_var
 
-  lyt_adae <-
-    basic_table_deco(deco) %>%
+  lyt_adae <- basic_table_deco(deco) %>%
     split_cols_by(var = armvar) %>%
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%
@@ -312,8 +298,7 @@ aet01_2_lyt <- function(armvar = .study$actualarm,
       .indent_mods = 0L
     )
 
-  lyt_adsl <-
-    basic_table_deco(deco) %>%
+  lyt_adsl <- basic_table_deco(deco) %>%
     split_cols_by(var = armvar) %>%
     add_colcounts() %>%
     ifneeded_add_overall_col(lbl_overall) %>%

R/aet02.R

@@ -13,13 +13,11 @@
 #'  * Sort Dictionary-Derived Code (`AEDECOD`) by highest overall frequencies.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(rtables)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("aet02_1")
@@ -39,7 +37,7 @@
 #'
 #' db_m <- db %>%
 #'   dm_zoom_to(adae) %>%
-#'   mutate(AEBODSYS = with_label(AEBODSYS, "Medra System Organ Class")) %>%
+#'   mutate(AEBODSYS = formatters::with_label(AEBODSYS, "Medra System Organ Class")) %>%
 #'   dm_update_zoomed()
 #'
 #' aet02_1(db_m) %>% head()
@@ -65,7 +63,7 @@ aet02_1 <- function(adam_db,
   tbl <- build_table(lyt, dbsel$adae, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%
@@ -167,22 +165,19 @@ aet02_1_lyt <- function(armvar = .study$actualarm,
 #' @export
 #'
 #' @examples
-#'
 #' library(dm)
-#' library(rtables)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("aet02_2")
 #'
-#'
 #' aet02_2(db) %>% head(15)
 #'
 #' # Additional Examples
 #' aet02_2(db, lbl_overall = "All Patients") %>% head()
 #'
 #' db_m <- db %>%
 #'   dm_zoom_to(adae) %>%
-#'   mutate(AEBODSYS = with_label(AEBODSYS, "MedDRA System Organ Class")) %>%
+#'   mutate(AEBODSYS = formatters::with_label(AEBODSYS, "MedDRA System Organ Class")) %>%
 #'   dm_update_zoomed()
 #'
 #' aet02_2(db_m) %>% head()
@@ -210,7 +205,7 @@ aet02_2 <- function(adam_db,
   tbl <- build_table(lyt, adae, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%
@@ -364,7 +359,7 @@ aet02_3 <- function(adam_db,
   tbl <- build_table(lyt, adam_db$adae, alt_counts_df = adam_db$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%

R/aet03.R

@@ -14,14 +14,11 @@
 #'  * Sort by Body System or Organ Class (`SOC`) and Dictionary-Derived Term (`PT`).
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
-#'
 #' library(dm)
-#' library(rtables)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("aet03_1")

R/aet04.R

@@ -14,13 +14,11 @@
 #'  Grade is sorted by severity.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(rtables)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("aet03_1")

R/assertions.R

@@ -17,7 +17,6 @@
 #' my_colnames <- NULL
 #' assert_colnames(mtcars, my_colnames, null_ok = FALSE)
 #' }
-#'
 assert_colnames <- function(df, x, null_ok = TRUE) {
   if (!null_ok && is.null(x)) {
     stop(

R/cmt01a.R

@@ -21,13 +21,11 @@
 #'  the specific medication.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   dm_zoom_to(adcm) %>%
@@ -64,7 +62,7 @@ cmt01a_1 <- function(adam_db,
   tbl <- build_table(lyt, dbsel$adcm, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%
@@ -168,13 +166,11 @@ cmt01a_1_lyt <- function(armvar = .study$planarm,
 #'  the specific medication.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   dm_zoom_to(adcm) %>%
@@ -212,7 +208,7 @@ cmt01a_2 <- function(adam_db,
   tbl <- build_table(lyt, dbsel$adcm, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%
@@ -254,13 +250,11 @@ cmt01a_2 <- function(adam_db,
 #'  the specific medication.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   dm_zoom_to(adcm) %>%
@@ -297,7 +291,7 @@ cmt01a_3 <- function(adam_db,
   tbl <- build_table(lyt, dbsel$adcm, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl_sorted <- tbl %>%

R/cmt02_pt.R

@@ -10,12 +10,10 @@
 #'  * Order by decreasing total number of patients with the specific medication.
 #'  * Does not include a total column by default.
 #'
-#' @return
 #' @export
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   dm_zoom_to(adcm) %>%
@@ -44,7 +42,7 @@ cmt02_pt_1 <- function(adam_db,
   tbl <- build_table(lyt, dbsel$adcm, alt_counts_df = dbsel$adsl)
 
   if (prune_0) {
-    tbl <- tbl %>% prune_table()
+    tbl <- prune_table(tbl)
   }
 
   tbl %>%

R/dm_explicit_na.R

@@ -14,7 +14,6 @@
 #' @importFrom checkmate assert_class assert_character assert_logical
 #' @importFrom dm dm_zoom_to dm_update_zoomed
 #' @importFrom dplyr mutate across
-#' @importFrom magrittr %>%
 #' @importFrom tern explicit_na sas_na
 #'
 #' @return `dm` object with explicit missing levels
@@ -89,7 +88,7 @@ dm_explicit_na <- function(data,
     if (length(names_fact_col) > 0L) {
       data <- data %>%
         dm_zoom_to(!!tab_sym) %>%
-        mutate(across(names_fact_col, function(x) explicit_na(sas_na(x), label = na_level))) %>%
+        mutate(across(names_fact_col, function(x) tern::explicit_na(sas_na(x), label = na_level))) %>%
         dm_update_zoomed()
     }
   }
@@ -106,16 +105,13 @@ dm_explicit_na <- function(data,
 #'
 #' @importFrom checkmate assert_true
 #' @importFrom tern explicit_na sas_na
-#'
-#' @return
-#'
 h_as_factor <- function(x, na_label) {
   assert_true(is.character(x) || is.logical(x))
 
   init_lab <- attr(x, "label")
 
   x_chr <- as.character(x)
-  res <- explicit_na(sas_na(x_chr), label = na_label)
+  res <- tern::explicit_na(sas_na(x_chr), label = na_label)
 
   lvl_x <- setdiff(sort(unique(res)), na_label)
 

R/dmt01.R

@@ -16,14 +16,10 @@
 #'  * Split columns by arm (planned or actual / code or description)
 #'  * Include a total column by default
 #'
-#' @importFrom magrittr %>%
-#'
 #' @export
 #'
 #' @examples
-#'
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
 #'   preprocess_data("dmt01_1")

R/dst01.R

@@ -39,12 +39,10 @@ check_dst01_1_args <- function(reason, status, status_treatment) {
 #'  * Sort withdrawal reasons by alphabetic order.
 #'
 #' @importFrom dplyr filter
-#' @importFrom magrittr %>%
 #'
 #' @export
 #'
 #' @examples
-#'
 #' library(dm)
 #'
 #' db <- syn_test_data() %>%
@@ -480,7 +478,7 @@ dst01_3 <- function(adam_db,
 
   col_info(tbl) <- col_info(tbl2)
 
-  if (prune_0) tbl <- tbl %>% prune_table()
+  if (prune_0) tbl <- prune_table(tbl)
 
   tbl <- rbind(tbl2, tbl)