1012 substitute {assertthat} with {checkmate} in a couple of functions

.pre-commit-config.yaml

@@ -21,7 +21,6 @@ repos:
           - insightsengineering/teal
           - insightsengineering/teal.transform
           - tern
-          - assertthat
           - broom
           - checkmate
           - dplyr

DESCRIPTION

@@ -30,7 +30,6 @@ Depends:
     teal.transform (>= 0.4.0.9011),
     tern (>= 0.9.3)
 Imports:
-    assertthat,
     broom (>= 0.7.10),
     checkmate (>= 2.1.0),
     dplyr (>= 1.0.5),
@@ -71,7 +70,7 @@ VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: insightsengineering/teal,
     insightsengineering/teal.transform, insightsengineering/tern,
-    cran/assertthat, tidymodels/broom, mllg/checkmate, tidyverse/dplyr,
+    tidymodels/broom, mllg/checkmate, tidyverse/dplyr,
     rstudio/DT, insightsengineering/formatters, tidyverse/ggplot2,
     slowkow/ggrepel, r-lib/lifecycle, daroczig/logger, tidyverse/magrittr,
     r-lib/rlang, insightsengineering/rlistings, rstudio/rmarkdown,

NAMESPACE

@@ -65,7 +65,6 @@ export(tm_t_smq)
 export(tm_t_summary)
 export(tm_t_summary_by)
 export(tm_t_tte)
-import(assertthat)
 import(teal)
 import(teal.transform)
 import(tern)

R/dynamic_assertions.R

@@ -15,9 +15,8 @@ NULL
 #'
 #' @examples
 #'
-#' library(assertthat)
 #' library(testthat)
-#' expect_error(assertthat::assert_that(teal_enough_rows(data = iris, min_nrow = 1500)))
+#' expect_error(stopifnot(teal_enough_rows(data = iris, min_nrow = 1500)))
 teal_enough_rows <- function(data, min_nrow) nrow(data) >= min_nrow
 assertthat::on_failure(teal_enough_rows) <- function(call, env) {
   call[[1]] <- validate_enough_rows
@@ -45,7 +44,7 @@ validate_enough_rows <- function(data, min_nrow) {
 #' @examples
 #'
 #' armcd <- NULL
-#' expect_error(assertthat::assert_that(teal_has_element(str = armcd, "ARMCD")))
+#' expect_error(stopifnot(teal_has_element(str = armcd, "ARMCD")))
 teal_has_element <- function(str, ...) length(str) > 0
 assertthat::on_failure(teal_has_element) <- function(call, env) {
   call[[1]] <- validate_has_elements

R/tm_g_forest_rsp.R

@@ -34,14 +34,13 @@ template_forest_rsp <- function(dataname = "ANL",
                                 conf_level = 0.95,
                                 col_symbol_size = NULL,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(parentname),
-    assertthat::is.string(arm_var),
-    assertthat::is.string(aval_var),
-    assertthat::is.string(obj_var_name),
-    is.null(subgroup_var) || is.character(subgroup_var)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(parentname)
+  checkmate::assert_string(arm_var)
+  checkmate::assert_string(aval_var)
+  checkmate::assert_string(obj_var_name)
+  checkmate::assert_character(subgroup_var, null.ok = TRUE)
 
   y <- list()
   ref_arm_val <- paste(ref_arm, collapse = "/")
@@ -312,10 +311,7 @@ tm_g_forest_rsp <- function(label,
   checkmate::assert_string(parentname)
   checkmate::assert_flag(fixed_symbol_size)
   checkmate::assert_class(conf_level, "choices_selected")
-  assertthat::assert_that(
-    inherits(default_responses, c("list", "character", "numeric", "NULL")),
-    msg = "`default_responses` must be a named list or an array."
-  )
+  checkmate::assert_multi_class(default_responses, c("list", "character", "numeric"), null.ok = TRUE)
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")
   checkmate::assert_numeric(plot_width, len = 3, any.missing = FALSE, null.ok = TRUE, finite = TRUE)

R/tm_g_forest_tte.R

@@ -24,12 +24,11 @@ template_forest_tte <- function(dataname = "ANL",
                                 col_symbol_size = NULL,
                                 time_unit_var = "AVALU",
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(arm_var),
-    assertthat::is.string(obj_var_name),
-    is.character(subgroup_var) || is.null(subgroup_var)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(arm_var)
+  checkmate::assert_string(obj_var_name)
+  checkmate::assert_character(subgroup_va, null.ok = TRUE)
 
   y <- list()
   ref_arm_val <- paste(ref_arm, collapse = "/")

R/tm_g_ipp.R

@@ -51,20 +51,18 @@ template_g_ipp <- function(dataname = "ANL",
     )
   }
 
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(paramcd),
-    assertthat::is.string(arm_var),
-    assertthat::is.string(aval_var),
-    assertthat::is.string(avalu_var),
-    assertthat::is.string(id_var),
-    assertthat::is.string(visit_var),
-    assertthat::is.string(baseline_var),
-    assertthat::is.flag(add_baseline_hline),
-    assertthat::is.flag(separate_by_obs),
-    assertthat::is.flag(suppress_legend),
-    assertthat::is.flag(add_avalu)
-  )
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(paramcd)
+  checkmate::assert_string(arm_var)
+  checkmate::assert_string(aval_var)
+  checkmate::assert_string(avalu_var)
+  checkmate::assert_string(id_var)
+  checkmate::assert_string(visit_var)
+  checkmate::assert_string(baseline_var)
+  checkmate::assert_flag(add_baseline_hline)
+  checkmate::assert_flag(separate_by_obs)
+  checkmate::assert_flag(suppress_legend)
+  checkmate::assert_flag(add_avalu)
 
   y <- list()
   # Data preprocessing

R/tm_g_km.R

@@ -37,17 +37,16 @@ template_g_km <- function(dataname = "ANL",
                           width_annots = list(surv_med = grid::unit(0.45, "npc"), coxph = grid::unit(0.6, "npc")),
                           ci_ribbon = FALSE,
                           title = "KM Plot") {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(arm_var),
-    assertthat::is.string(aval_var),
-    assertthat::is.string(cnsr_var),
-    assertthat::is.string(time_unit_var),
-    assertthat::is.flag(compare_arm),
-    assertthat::is.flag(combine_comp_arms),
-    is.null(xticks) | is.numeric(xticks),
-    assertthat::is.string(title)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(arm_var)
+  checkmate::assert_string(aval_var)
+  checkmate::assert_string(cnsr_var)
+  checkmate::assert_string(time_unit_var)
+  checkmate::assert_flag(compare_arm)
+  checkmate::assert_flag(combine_comp_arms)
+  checkmate::assert_numeric(xticks, null.ok = TRUE)
+  checkmate::assert_string(title)
 
   ref_arm_val <- paste(ref_arm, collapse = "/")
   y <- list()

R/tm_g_lineplot.R

@@ -39,16 +39,16 @@ template_g_lineplot <- function(dataname = "ANL",
                                 title = "Line Plot",
                                 y_lab = "",
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(strata),
-    assertthat::is.string(x),
-    assertthat::is.string(y),
-    assertthat::is.string(y_unit),
-    assertthat::is.string(paramcd),
-    assertthat::is.string(title),
-    assertthat::is.string(y_lab)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(strata)
+  checkmate::assert_string(x)
+  checkmate::assert_string(y)
+  checkmate::assert_string(y_unit)
+  checkmate::assert_string(paramcd)
+  checkmate::assert_string(title)
+  checkmate::assert_string(y_lab)
+
   z <- list()
 
   data_list <- list()

R/tm_g_pp_adverse_events.R

@@ -27,18 +27,17 @@ template_adverse_events <- function(dataname = "ANL",
                                     patient_id,
                                     font_size = 12L,
                                     ggplot2_args = teal.widgets::ggplot2_args()) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(aeterm),
-    assertthat::is.string(tox_grade),
-    assertthat::is.string(causality),
-    assertthat::is.string(outcome),
-    assertthat::is.string(action),
-    assertthat::is.string(time) || is.null(time),
-    assertthat::is.string(decod) || is.null(decod),
-    assertthat::is.string(patient_id),
-    is.numeric(font_size)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(aeterm)
+  checkmate::assert_string(tox_grade)
+  checkmate::assert_string(causality)
+  checkmate::assert_string(outcome)
+  checkmate::assert_string(action)
+  checkmate::assert_string(time, null.ok = TRUE)
+  checkmate::assert_string(decod, null.ok = TRUE)
+  checkmate::assert_string(patient_id)
+  checkmate::assert_numeric(font_size)
 
   y <- list()
 

R/tm_g_pp_patient_timeline.R

@@ -36,20 +36,19 @@ template_patient_timeline <- function(dataname = "ANL",
                                       ggplot2_args = teal.widgets::ggplot2_args()) {
   # Note: The variables used for aetime_start, aetime_end, dstime_start and dstime_end are to be
   # updated after random.cdisc.data updates.
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(aeterm) || is.null(aeterm),
-    assertthat::is.string(aetime_start) || is.null(aetime_start),
-    assertthat::is.string(aetime_end) || is.null(aetime_end),
-    assertthat::is.string(dstime_start) || is.null(dstime_start),
-    assertthat::is.string(dstime_end) || is.null(dstime_end),
-    assertthat::is.string(cmdecod) || is.null(cmdecod),
-    assertthat::is.string(aerelday_start) || is.null(aerelday_start),
-    assertthat::is.string(dsrelday_start) || is.null(dsrelday_start),
-    is.numeric(font_size),
-    is.logical(relative_day),
-    assertthat::is.string(patient_id)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(aeterm, null.ok = TRUE)
+  checkmate::assert_string(aetime_start, null.ok = TRUE)
+  checkmate::assert_string(aetime_end, null.ok = TRUE)
+  checkmate::assert_string(dstime_start, null.ok = TRUE)
+  checkmate::assert_string(dstime_end, null.ok = TRUE)
+  checkmate::assert_string(cmdecod, null.ok = TRUE)
+  checkmate::assert_string(aerelday_start, null.ok = TRUE)
+  checkmate::assert_string(dsrelday_start, null.ok = TRUE)
+  checkmate::assert_numeric(font_size)
+  checkmate::assert_logical(relative_day)
+  checkmate::assert_string(patient_id)
 
   chart_list <- list()
   if (!relative_day) {
@@ -471,11 +470,11 @@ tm_g_pp_patient_timeline <- function(label,
     plot_width[1],
     lower = plot_width[2], upper = plot_width[3], null.ok = TRUE, .var.name = "plot_width"
   )
-  assertthat::assert_that(!xor(is.null(aetime_start), is.null(aetime_end)))
-  assertthat::assert_that(!xor(is.null(dstime_start), is.null(dstime_end)))
-  assertthat::assert_that(!xor(is.null(aerelday_start), is.null(aerelday_end)))
-  assertthat::assert_that(!xor(is.null(dsrelday_start), is.null(dsrelday_end)))
-  assertthat::assert_that(
+  stopifnot(!xor(is.null(aetime_start), is.null(aetime_end)))
+  stopifnot(!xor(is.null(dstime_start), is.null(dstime_end)))
+  stopifnot(!xor(is.null(aerelday_start), is.null(aerelday_end)))
+  stopifnot(!xor(is.null(dsrelday_start), is.null(dsrelday_end)))
+  stopifnot(
     (!is.null(aeterm) && (!is.null(aetime_start) || !is.null(aerelday_start))) ||
       (!is.null(cmdecod) && (!is.null(dstime_start) || !is.null(dsrelday_start)))
   )

R/tm_g_pp_therapy.R

@@ -30,21 +30,20 @@ template_therapy <- function(dataname = "ANL",
                              patient_id,
                              font_size = 12L,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(atirel),
-    assertthat::is.string(cmdecod),
-    assertthat::is.string(cmindc),
-    assertthat::is.string(cmdose),
-    assertthat::is.string(cmtrt),
-    assertthat::is.string(cmdosu),
-    assertthat::is.string(cmroute),
-    assertthat::is.string(cmdosfrq),
-    assertthat::is.string(cmstdy),
-    assertthat::is.string(cmendy),
-    assertthat::is.string(patient_id),
-    is.numeric(font_size)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(atirel)
+  checkmate::assert_string(cmdecod)
+  checkmate::assert_string(cmindc)
+  checkmate::assert_string(cmdose)
+  checkmate::assert_string(cmtrt)
+  checkmate::assert_string(cmdosu)
+  checkmate::assert_string(cmroute)
+  checkmate::assert_string(cmdosfrq)
+  checkmate::assert_string(cmstdy)
+  checkmate::assert_string(cmendy)
+  checkmate::assert_string(patient_id)
+  is.numeric(font_size)
 
   y <- list()
   y$table_list <- list()

R/tm_g_pp_vitals.R

@@ -29,14 +29,12 @@ template_vitals <- function(dataname = "ANL",
     )
   }
 
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(paramcd),
-    assertthat::is.string(xaxis),
-    assertthat::is.string(aval_var),
-    assertthat::is.string(patient_id),
-    is.numeric(font_size)
-  )
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(paramcd)
+  checkmate::assert_string(xaxis)
+  checkmate::assert_string(aval_var)
+  checkmate::assert_string(patient_id)
+  checkmate::assert_numeric(font_size)
 
   # Note: VSDY (study day of vital signs) was replaced with ADY (analysis day)
   y <- list()

R/tm_t_abnormality.R

@@ -34,23 +34,22 @@ template_abnormality <- function(parentname,
                                  na_level = default_na_str(),
                                  basic_table_args = teal.widgets::basic_table_args(),
                                  tbl_title) {
-  assertthat::assert_that(
-    assertthat::is.string(dataname),
-    assertthat::is.string(id_var),
-    assertthat::is.string(parentname),
-    assertthat::is.string(arm_var),
-    is.character(by_vars),
-    is.list(abnormal),
-    assertthat::is.string(grade),
-    assertthat::is.string(baseline_var),
-    assertthat::is.string(treatment_flag_var),
-    assertthat::is.string(treatment_flag),
-    assertthat::is.flag(add_total),
-    assertthat::is.string(total_label),
-    assertthat::is.flag(exclude_base_abn),
-    assertthat::is.flag(drop_arm_levels),
-    assertthat::is.string(tbl_title)
-  )
+
+  checkmate::assert_string(dataname)
+  checkmate::assert_string(id_var)
+  checkmate::assert_string(parentname)
+  checkmate::assert_string(arm_var)
+  checkmate::check_character(by_vars)
+  checkmate::check_list(abnormal)
+  checkmate::assert_string(grade)
+  checkmate::assert_string(baseline_var)
+  checkmate::assert_string(treatment_flag_var)
+  checkmate::assert_string(treatment_flag)
+  checkmate::assert_flag(add_total)
+  checkmate::assert_string(total_label)
+  checkmate::assert_flag(exclude_base_abn)
+  checkmate::assert_flag(drop_arm_levels)
+  checkmate::assert_string(tbl_title)
 
   y <- list()