Merge branch 'main' into 108-construct_model

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,6 +13,8 @@ Pre-review Checklist (if item does not apply, mark is as complete)
 - [ ] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()`
 - [ ] If a bug was fixed, a unit test was added.
 - [ ] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`.
+- [ ] If a new `ard_*()` function was added, `set_cli_abort_call()` has been set.
+- [ ] If a new `ard_*()` function was added and it depends on another package (such as, `broom`), `is_pkg_installed("broom", reference_pkg = "cardx")` has been set in the function call and the following added to the roxygen comments: `@examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"", reference_pkg = "cardx"))`
 - [ ] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()`
 
 Reviewer Checklist (if item does not apply, mark is as complete)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.1.0.9015
+Version: 0.1.0.9019
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),
@@ -31,6 +31,7 @@ Suggests:
     car (>= 3.0-11),
     effectsize (>= 0.6.0),
     geepack (>= 1.3.2),
+    ggsurvfit (>= 1.0.0),
     lme4 (>= 1.1-31),
     parameters (>= 0.20.2),
     smd (>= 0.6.6),

NAMESPACE

@@ -35,6 +35,7 @@ export(ard_survey_svychisq)
 export(ard_survey_svycontinuous)
 export(ard_survey_svyranktest)
 export(ard_survey_svyttest)
+export(ard_survival_survdiff)
 export(ard_survival_survfit)
 export(bt)
 export(bt_strip)

NEWS.md

@@ -1,4 +1,4 @@
-# cardx 0.1.0.9015
+# cardx 0.1.0.9019
 
 ### Breaking Changes
 
@@ -39,8 +39,9 @@ ard_moodtest()          -> ard_stats_mood_test()
 
 * Updated `ard_stats_t_test()` and `ard_stats_wilcox_test()` to no longer require the `by` argument, which yields central estimates with their confidence intervals. (#82)
 
-* Import cli call environment functions from `https://github.com/ddsjoberg/standalone/blob/main/R/standalone-cli_call_env.R` and implement `set_cli_abort_call` in user-facing functions. (#111, @edelarua)
+* Imported cli call environment functions from `https://github.com/ddsjoberg/standalone/blob/main/R/standalone-cli_call_env.R` and implemented `set_cli_abort_call` in user-facing functions. (#111)
 
+* Added `ard_survival_survdiff()` for creating results from `survival::survdiff()`. (#113)
 
 # cardx 0.1.0
 

R/ard_aod_wald_test.R

@@ -104,12 +104,10 @@ ard_aod_wald_test <- function(x, ...) {
 
 #' Extract data from wald.test object
 #'
-#'
 #' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()`
 #'
 #' @return a data frame containing the wald test results.
 #' @keywords internal
-
 .extract_wald_results <- function(wald_test) {
   df <- wald_test$result$chi2[("df")]
   statistic <- wald_test$result$chi2[("chi2")]

R/ard_car_vif.R

@@ -73,7 +73,7 @@ ard_car_vif <- function(x, ...) {
       values_to = "stat"
     ) |>
     dplyr::mutate(
-      context = "vif",
+      context = "car_vif",
       stat_label = ifelse(
         .data$stat_name == "aGVIF",
         "Adjusted GVIF",

R/ard_effectsize_cohens_d.R

@@ -159,7 +159,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
 #' cardx:::.format_cohens_d_results(
 #'   by = "ARM",
 #'   variable = "AGE",
@@ -181,7 +181,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
       fun_args_to_record = c("mu", "paired", "pooled_sd", "alternative"),
       formals = formals(asNamespace("effectsize")[["cohens_d"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "cohens_d")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "effectsize_cohens_d")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_effectsize_hedges_g.R

@@ -151,7 +151,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
 #' cardx:::.format_hedges_g_results(
 #'   by = "ARM",
 #'   variable = "AGE",
@@ -173,7 +173,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
       fun_args_to_record = c("mu", "paired", "pooled_sd", "alternative"),
       formals = formals(asNamespace("effectsize")[["hedges_g"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "hedges_g")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "effectsize_hedges_g")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_smd_smd.R

@@ -81,7 +81,7 @@ ard_smd_smd <- function(data, by, variables, ...) {
       formals = formals(smd::smd)["gref"],
       # removing the `std.error` ARGUMENT (not the result)
       passed_args = dots_list(...) |> utils::modifyList(list(std.error = NULL)),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "smd")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "smd_smd")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_stats_aov.R

@@ -49,7 +49,7 @@ ard_stats_aov <- function(formula, data, ...) {
           .data$stat_name %in% "meansq" ~ "Mean of Sum of Squares",
           TRUE ~ .data$stat_name
         ),
-      context = "aov",
+      context = "stats_aov",
       warning = aov["warning"],
       error = aov["error"]
     ) |>

R/ard_stats_chisq_test.R

@@ -53,7 +53,7 @@ ard_stats_chisq_test <- function(data, by, variables, ...) {
           c("correct", "p", "rescale.p", "simulate.p.value", "B"),
         formals = formals(stats::chisq.test),
         passed_args = dots_list(...),
-        lst_ard_columns = list(group1 = by, variable = variable, context = "chisqtest")
+        lst_ard_columns = list(group1 = by, variable = variable, context = "stats_chisq_test")
       ) |>
         dplyr::mutate(
           .after = "stat_name",

R/ard_stats_fisher_test.R

@@ -57,7 +57,7 @@ ard_stats_fisher_test <- function(data, by, variables, ...) {
           ),
         formals = formals(stats::fisher.test),
         passed_args = dots_list(...),
-        lst_ard_columns = list(group1 = by, variable = variable, context = "fishertest")
+        lst_ard_columns = list(group1 = by, variable = variable, context = "stats_fisher_test")
       ) |>
         dplyr::mutate(
           .after = "stat_name",

R/ard_stats_kruskal_test.R

@@ -48,7 +48,7 @@ ard_stats_kruskal_test <- function(data, by, variables) {
               broom::tidy()
           ),
         tidy_result_names = c("statistic", "p.value", "parameter", "method"),
-        lst_ard_columns = list(group1 = by, variable = variable, context = "kruskaltest")
+        lst_ard_columns = list(group1 = by, variable = variable, context = "stats_kruskal_test")
       ) |>
         dplyr::mutate(
           .after = "stat_name",

R/ard_stats_mcnemar_test.R

@@ -71,7 +71,7 @@ ard_stats_mcnemar_test <- function(data, by, variables, ...) {
 #'
 #' @return ARD data frame
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_mcnemartest_results(
 #'   by = "ARM",
 #'   variable = "AGE",
@@ -92,7 +92,7 @@ ard_stats_mcnemar_test <- function(data, by, variables, ...) {
       fun_args_to_record = c("correct"),
       formals = formals(asNamespace("stats")[["mcnemar.test"]]),
       passed_args = dots_list(...),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "mcnemartest")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "stats_mcnemar_test")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_stats_mood_test.R

@@ -73,7 +73,7 @@ ard_stats_mood_test <- function(data, by, variables, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_moodtest_results(
 #'   by = "SEX",
 #'   variable = "AGE",
@@ -91,7 +91,7 @@ ard_stats_mood_test <- function(data, by, variables, ...) {
       tidy_result_names = c("statistic", "p.value", "method", "alternative"),
       formals = formals(asNamespace("stats")[["mood.test.default"]]),
       passed_args = c(dots_list(...)),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "moodtest")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "stats_mood_test")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_stats_oneway_test.R

@@ -37,7 +37,7 @@ ard_stats_oneway_test <- function(formula, data, ...) {
       c("var.equal"),
     formals = formals(stats::oneway.test),
     passed_args = dots_list(...),
-    lst_ard_columns = list(context = "oneway.test")
+    lst_ard_columns = list(context = "stats_oneway_test")
   ) |>
     dplyr::mutate(
       .after = "stat_name",

R/ard_stats_prop_test.R

@@ -108,7 +108,7 @@ ard_stats_prop_test <- function(data, by, variables, ...) {
       fun_args_to_record = c("p", "conf.level", "correct"),
       formals = formals(stats::prop.test),
       passed_args = dots_list(...),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "proptest")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "stats_prop_test")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_stats_t_test.R

@@ -141,7 +141,7 @@ ard_stats_paired_t_test <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_ttest_results(
 #'   by = "ARM",
 #'   variable = "AGE",
@@ -168,7 +168,7 @@ ard_stats_paired_t_test <- function(data, by, variables, id, ...) {
       fun_args_to_record = c("mu", "paired", "var.equal", "conf.level"),
       formals = formals(asNamespace("stats")[["t.test.default"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
-      lst_ard_columns = list(variable = variable, context = "ttest")
+      lst_ard_columns = list(variable = variable, context = "stats_t_test")
     )
 
   if (!is_empty(by)) {

R/ard_stats_wilcox_test.R

@@ -148,7 +148,7 @@ ard_stats_paired_wilcox_test <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' # Pre-processing ADSL to have grouping factor (ARM here) with 2 levels
 #' ADSL <- cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
@@ -178,7 +178,7 @@ ard_stats_paired_wilcox_test <- function(data, by, variables, id, ...) {
       ),
       formals = formals(asNamespace("stats")[["wilcox.test.default"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
-      lst_ard_columns = list(variable = variable, context = "wilcoxtest")
+      lst_ard_columns = list(variable = variable, context = "stats_wilcox_test")
     )
 
   if (!is_empty(by)) {

R/ard_survey_svychisq.R

@@ -55,7 +55,7 @@ ard_survey_svychisq <- function(data, by, variables, statistic = "F", ...) {
           ),
         tidy_result_names = c("statistic", "p.value", "ndf", "ddf", "method"),
         passed_args = dots_list(...),
-        lst_ard_columns = list(group1 = by, variable = variable, context = "svychisq")
+        lst_ard_columns = list(group1 = by, variable = variable, context = "survey_svychisq")
       ) |>
         dplyr::mutate(
           .after = "stat_name",

R/ard_survey_svycontinuous.R

@@ -138,7 +138,7 @@ ard_survey_svycontinuous <- function(data, variables, by = NULL,
 
   # add class and return ARD object --------------------------------------------
   df_stats |>
-    dplyr::mutate(context = "continuous") |>
+    dplyr::mutate(context = "survey_svycontinuous") |>
     cards::tidy_ard_column_order() %>%
     {structure(., class = c("card", class(.)))} # styler: off
 }

R/ard_survey_svyranktest.R

@@ -68,7 +68,7 @@ ard_survey_svyranktest <- function(data, by, variables, test, ...) {
         "method", "alternative"
       ),
       passed_args = dots_list(...),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "svyranktest")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "survey_svyranktest")
     )
 
   # add the stat label ---------------------------------------------------------

R/ard_survey_svyttest.R

@@ -75,7 +75,7 @@ ard_survey_svyttest <- function(data, by, variables, conf.level = 0.95, ...) {
         "conf.level", "method", "alternative"
       ),
       passed_args = dots_list(...),
-      lst_ard_columns = list(group1 = by, variable = variable, context = "svyttest")
+      lst_ard_columns = list(group1 = by, variable = variable, context = "survey_svyttest")
     )
 
   # add the stat label ---------------------------------------------------------