Resolving Merge Conflicts for #112

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,16 +14,14 @@ Pre-review Checklist (if item does not apply, mark is as complete)
 - [ ] 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()`.
 - [ ] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()`
-- [ ] Request a reviewer
 
 Reviewer Checklist (if item does not apply, mark is as complete)
 
 - [ ] If a bug was fixed, a unit test was added.
-- [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website.
 - [ ] Code coverage is suitable for any new functions/features: `devtools::test_coverage()`
 
 When the branch is ready to be merged:
-- [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# cards (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
+- [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# cardx (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
 - [ ] **All** GitHub Action workflows pass with a :white_check_mark:
 - [ ] Approve Pull Request
 - [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".

.github/workflows/R-CMD-check.yaml

@@ -8,7 +8,6 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
 name: R-CMD-check
 

.github/workflows/check.yaml

@@ -8,8 +8,6 @@ on:
       - synchronize
       - reopened
       - ready_for_review
-    branches:
-      - main
   push:
     branches:
       - main

.github/workflows/test-coverage.yaml

@@ -4,7 +4,6 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
 name: test-coverage
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.1.0.9011
+Version: 0.1.0.9014
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),
@@ -25,17 +25,20 @@ Imports:
     rlang (>= 1.1.1),
     tidyr (>= 1.3.0)
 Suggests:
+    aod (>= 1.3.3),
     broom (>= 1.0.5),
     broom.helpers (>= 1.13.0),
     car (>= 3.0-11),
     effectsize (>= 0.6.0),
+    geepack (>= 1.3.2),
+    lme4 (>= 1.1-31),
     parameters (>= 0.20.2),
     smd (>= 0.6.6),
     spelling,
     survey (>= 4.1),
     survival (>= 3.2-11),
     testthat (>= 3.2.0),
-    withr
+    withr (>= 2.5.0)
 Remotes: 
     insightsengineering/cards
 Config/Needs/website: insightsengineering/nesttemplate

NAMESPACE

@@ -1,36 +1,40 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(ard_regression,default)
+S3method(ard_stats_anova,anova)
+S3method(ard_stats_anova,data.frame)
 export("%>%")
 export(all_of)
 export(any_of)
-export(ard_aov)
+export(ard_aod_wald_test)
 export(ard_car_anova)
-export(ard_chisqtest)
-export(ard_cohens_d)
-export(ard_fishertest)
-export(ard_hedges_g)
-export(ard_kruskaltest)
-export(ard_mcnemartest)
-export(ard_moodtest)
-export(ard_onewaytest)
-export(ard_paired_cohens_d)
-export(ard_paired_hedges_g)
-export(ard_paired_ttest)
-export(ard_paired_wilcoxtest)
+export(ard_car_vif)
+export(ard_effectsize_cohens_d)
+export(ard_effectsize_hedges_g)
+export(ard_effectsize_paired_cohens_d)
+export(ard_effectsize_paired_hedges_g)
 export(ard_proportion_ci)
-export(ard_proptest)
 export(ard_regression)
 export(ard_regression_basic)
-export(ard_smd)
-export(ard_survfit)
-export(ard_svychisq)
-export(ard_svycontinuous)
-export(ard_svyranktest)
-export(ard_svyttest)
-export(ard_ttest)
-export(ard_vif)
-export(ard_wilcoxtest)
+export(ard_smd_smd)
+export(ard_stats_anova)
+export(ard_stats_aov)
+export(ard_stats_chisq_test)
+export(ard_stats_fisher_test)
+export(ard_stats_kruskal_test)
+export(ard_stats_mcnemar_test)
+export(ard_stats_mood_test)
+export(ard_stats_oneway_test)
+export(ard_stats_paired_t_test)
+export(ard_stats_paired_wilcox_test)
+export(ard_stats_prop_test)
+export(ard_stats_t_test)
+export(ard_stats_wilcox_test)
+export(ard_survey_svychisq)
+export(ard_survey_svycontinuous)
+export(ard_survey_svyranktest)
+export(ard_survey_svyttest)
+export(ard_survival_survfit)
 export(contains)
 export(ends_with)
 export(everything)
@@ -48,6 +52,7 @@ export(starts_with)
 export(where)
 import(rlang)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
 importFrom(dplyr,contains)

NEWS.md

@@ -1,23 +1,43 @@
-# cardx 0.1.0.9011
+# cardx 0.1.0.9014
+
+### Breaking Changes
+
+* Updated function names to follow the pattern `ard_<pkgname>_<fnname>()`. Former functions names have _not_ been deprecated. (#106)
+
+```r
+ard_ttest()             -> ard_stats_t_test()
+ard_paired_ttest()      -> ard_stats_paired_t_test()
+ard_wilcoxtest()        -> ard_stats_wilcox_test()
+ard_paired_wilcoxtest() -> ard_stats_paired_wilcox_test()
+ard_chisqtest()         -> ard_stats_chisq_test()
+ard_fishertest()        -> ard_stats_fisher_test()
+ard_kruskaltest()       -> ard_stats_kruskal_test()
+ard_mcnemartest()       -> ard_stats_mcnemar_test()
+ard_moodtest()          -> ard_stats_mood_test()
+```
+
+### New Features
 
 * Added the following functions for calculating Analysis Results Data (ARD).
-  - `ard_aov()` for calculating ANOVA results using `stats::aov()`. (#3)
+  - `ard_stats_aov()` for calculating ANOVA results using `stats::aov()`. (#3)
+  - `ard_stats_anova()` for calculating ANOVA results using `stats::anova()`. (#12) 
+  - `ard_aod_wald_test()` for calculating Wald Tests for regression models using `aod::wald.test()`. (#84)
   - `ard_car_anova()` for calculating ANOVA results using `car::Anova()`. (#3)
-  - `ard_onewaytest()` for calculating ANOVA results using `stats::oneway.test()`. (#3)
-  - `ard_cohens_d()`, `ard_paired_cohens_d()`, `ard_hedges_g()`, and `ard_paired_hedges_g()` for standardized differences using `effectsize::cohens_d()` and `effectsize::hedges_g()`. (#50)
-  - `ard_proptest()` for tests of proportions using `stats::prop.test()`. (#64)
+  - `ard_stats_oneway_test()` for calculating ANOVA results using `stats::oneway.test()`. (#3)
+  - `ard_effectsize_cohens_d()`, `ard_effectsize_paired_cohens_d()`, `ard_effectsize_hedges_g()`, and `ard_effectsize_paired_hedges_g()` for standardized differences using `effectsize::cohens_d()` and `effectsize::hedges_g()`. (#50)
+  - `ard_stats_prop_test()` for tests of proportions using `stats::prop.test()`. (#64)
   - `ard_regression_basic()` for basic regression models. The function focuses on matching terms to underlying variables names. (#46)
-  - `ard_smd()` for calculating standardized mean differences using `smd::smd()`. (#4)
-  - `ard_survfit()` for survival analyses using `survival::survfit()`. (#43)
-  - `ard_svycontinuous()` for calculating univariate summary statistics from weighted/survey data using many functions from the {survey} package. (#68)
-  - `ard_svychisq()` for weighted/survey chi-squared test using `survey::svychisq()`. (#72)
-  - `ard_svyttest()` for weighted/survey t-tests using `survey::svyttest()`. (#70)
-  - `ard_svyranktest()` for weighted/survey rank tests using `survey::svyranktest()`. (#71)
-  - `ard_vif()` for calculating the variance inflation factor using `car::vif()`. (#10)
+  - `ard_smd_smd()` for calculating standardized mean differences using `smd::smd()`. (#4)
+  - `ard_survival_survfit()` for survival analyses using `survival::survfit()`. (#43)
+  - `ard_survey_svycontinuous()` for calculating univariate summary statistics from weighted/survey data using many functions from the {survey} package. (#68)
+  - `ard_survey_svychisq()` for weighted/survey chi-squared test using `survey::svychisq()`. (#72)
+  - `ard_survey_svyttest()` for weighted/survey t-tests using `survey::svyttest()`. (#70)
+  - `ard_survey_svyranktest()` for weighted/survey rank tests using `survey::svyranktest()`. (#71)
+  - `ard_car_vif()` for calculating the variance inflation factor using `car::vif()`. (#10)
 
-* Updated functions `ard_ttest()`, `ard_paired_ttest()`, `ard_wilcoxtest()`, `ard_paired_wilcoxtest()`, `ard_chisqtest()`, `ard_fishertest()`, `ard_kruskaltest()`, `ard_mcnemartest()`, and `ard_moodtest()` to accept multiple variables at once. Independent tests are calculated for each variable. The `variable` argument is renamed to `variables`. (#77)
+* Updated functions `ard_stats_t_test()`, `ard_stats_paired_t_test()`, `ard_stats_wilcox_test()`, `ard_stats_paired_wilcox_test()`, `ard_stats_chisq_test()`, `ard_stats_fisher_test()`, `ard_stats_kruskal_test()`, `ard_stats_mcnemar_test()`, and `ard_stats_mood_test()` to accept multiple variables at once. Independent tests are calculated for each variable. The `variable` argument is renamed to `variables`. (#77)
 
-* Updated `ard_ttest()` and `ard_wilcoxtest()` to no longer require the `by` argument, which yields central estimates with their confidence intervals. (#82)
+* 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)
 
 # cardx 0.1.0
 

R/ard_aod_wald_test.R

@@ -0,0 +1,118 @@
+#' ARD Wald Test
+#'
+#' @description
+#' Function takes a regression model object and calculates Wald
+#' statistical test using [`aod::wald.test()`].
+#'
+#' @param x regression model object
+#' @param ... arguments passed to `aod::wald.test(...)`
+#'
+#' @return data frame
+#' @export
+#'
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "aod", reference_pkg = "cardx"))
+#' lm(AGE ~ ARM, data = cards::ADSL) |>
+#'   ard_aod_wald_test()
+ard_aod_wald_test <- function(x, ...) {
+  set_cli_abort_call()
+  # check installed packages ---------------------------------------------------
+  check_pkg_installed("aod", reference_pkg = "cardx")
+
+  # check inputs ---------------------------------------------------------------
+  check_not_missing(x)
+
+  # run regression() -----------------------------------------------------------
+  reg_model <- cards::eval_capture_conditions(
+    ard_regression_basic(x, intercept = TRUE, stats_to_remove = c(
+      "var_type",
+      "var_label",
+      "var_class", "label",
+      "contrasts_type", "contrasts", "var_nlevels", "std.error",
+      "conf.low", "conf.high", "statistic", "p.value", "estimate"
+    ))
+  )
+
+  if (!is.null(reg_model[["error"]])) {
+    cli::cli_abort(
+      c("Unable to identify underlying variable names in regression model.",
+        i = "Is this model type supported by {.fun broom.helpers::tidy_plus_plus}, which is the function used to identify variable names?"
+      ),
+      call = get_cli_abort_call()
+    )
+  }
+  aod <-
+    reg_model[["result"]] %>%
+    dplyr::select(c(
+      variable = "variable",
+      model_terms = "stat"
+    )) %>%
+    dplyr::mutate(term_id = dplyr::row_number()) %>%
+    tidyr::nest(data = -"variable") %>%
+    dplyr::rowwise() %>%
+    dplyr::mutate(
+      model_terms = unlist(.data$data[["model_terms"]]) %>% list(),
+      model_terms_id = rlang::set_names(.data$data[["term_id"]]) %>% list()
+    )
+  # run wald.test() -----------------------------------------------------------
+  wald_test <-
+    cards::eval_capture_conditions(lapply(seq_len(length(aod$model_terms_id)), function(terms_id) {
+      aod::wald.test(
+        Sigma = stats::vcov(x),
+        b = stats::coef(x), Terms = aod$model_terms_id[[terms_id]]
+      )
+    }))
+
+
+  df_list <- do.call(rbind, lapply(wald_test$result, .extract_wald_results))
+
+  cbind(aod$variable, df_list) %>%
+    tidyr::pivot_longer(
+      cols = !"aod$variable",
+      names_to = "stat_name",
+      values_to = "stat"
+    ) %>%
+    dplyr::rename(
+      "variable" = "aod$variable"
+    ) |>
+    dplyr::mutate(
+      stat = as.list(.data$stat),
+      stat_label =
+        dplyr::case_when(
+          .data$stat_name %in% "statistic" ~ "Statistic",
+          .data$stat_name %in% "df" ~ "Degrees of Freedom",
+          .data$stat_name %in% "p.value" ~ "p-value",
+          TRUE ~ .data$stat_name
+        ),
+      fmt_fn =
+        map(
+          .data$stat,
+          function(.x) {
+            # styler: off
+            if (is.integer(.x)) return(0L)
+            if (is.numeric(.x)) return(1L)
+            # styler: on
+            NULL
+          }
+        ),
+      context = "aod_wald_test",
+      warning = wald_test["warning"],
+      error = wald_test["error"]
+    ) |>
+    cards::tidy_ard_column_order() %>%
+      {structure(., class = c("card", class(.)))} # styler: off
+}
+
+#' Extract data from wald.test object
+#'
+#'
+#' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()`
+#'
+#' @return a data frame containing the wald test results.
+#' @keywords internal
+
+.extract_wald_results <- function(wald_test) {
+  df <- wald_test$result$chi2[("df")]
+  statistic <- wald_test$result$chi2[("chi2")]
+  p.value <- wald_test$result$chi2[("P")]
+  data.frame(df, statistic, p.value)
+}

R/ard_car_anova.R

@@ -27,10 +27,13 @@ ard_car_anova <- function(x, ...) {
   car_anova <- cards::eval_capture_conditions(car::Anova(x, ...))
 
   if (!is.null(car_anova[["error"]])) {
-    cli::cli_abort(c(
-      "There was an error running {.fun car::Anova}. See error message below.",
-      x = car_anova[["error"]]
-    ))
+    cli::cli_abort(
+      c(
+        "There was an error running {.fun car::Anova}. See error message below.",
+        x = car_anova[["error"]]
+      ),
+      call = get_cli_abort_call()
+    )
   }
 
   car_anova[["result"]] |>

R/ard_vif.R → R/ard_car_vif.R

@@ -10,14 +10,16 @@
 #' @param ... arguments passed to `car::vif(...)`
 #'
 #' @return data frame
-#' @name ard_vif
-#' @rdname ard_vif
+#' @name ard_car_vif
+#' @rdname ard_car_vif
 #' @export
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "car", reference_pkg = "cardx"))
 #' lm(AGE ~ ARM + SEX, data = cards::ADSL) |>
-#'   ard_vif()
-ard_vif <- function(x, ...) {
+#'   ard_car_vif()
+ard_car_vif <- function(x, ...) {
+  set_cli_abort_call()
+  check_pkg_installed("car", reference_pkg = "cardx")
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)
 
@@ -30,7 +32,8 @@ ard_vif <- function(x, ...) {
     # we cannot get variable names, error out
     if (!is.null(lst_terms[["error"]])) {
       cli::cli_abort(
-        c("There was an error running {.fun car::vif}. See below.", x = vif[["error"]])
+        c("There was an error running {.fun car::vif}. See below.", x = vif[["error"]]),
+        call = get_cli_abort_call()
       )
     }
     vif$result <- dplyr::tibble(