update context after renaming ard_* functions (#123)

**What changes are proposed in this pull request?** update context after renaming `ard_*()` functions closes #117 -------------------------------------------------------------------------------- Pre-review Checklist (if item does not apply, mark is as complete) - [x] **All** GitHub Action workflows pass with a ✅ - [x] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()` - [x] If a bug was fixed, a unit test was added. - [x] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`. - [x] 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) - [ ] If a bug was fixed, a unit test was added. - [ ] 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 "`# 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 ✅ - [ ] Approve Pull Request - [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".
insightsengineering · Apr 16, 2024 · ca91444 · ca91444
1 parent ecd78dd
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diff --git a/R/ard_car_vif.R b/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",

diff --git a/R/ard_effectsize_cohens_d.R b/R/ard_effectsize_cohens_d.R
@@ -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 ---------------------------------------------------------

diff --git a/R/ard_effectsize_hedges_g.R b/R/ard_effectsize_hedges_g.R
@@ -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 ---------------------------------------------------------

diff --git a/R/ard_smd_smd.R b/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 ---------------------------------------------------------

diff --git a/R/ard_stats_aov.R b/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"]
     ) |>

diff --git a/R/ard_stats_chisq_test.R b/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",

diff --git a/R/ard_stats_fisher_test.R b/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",

diff --git a/R/ard_stats_kruskal_test.R b/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",

diff --git a/R/ard_stats_mcnemar_test.R b/R/ard_stats_mcnemar_test.R
@@ -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 ---------------------------------------------------------

diff --git a/R/ard_stats_mood_test.R b/R/ard_stats_mood_test.R
@@ -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 ---------------------------------------------------------

diff --git a/R/ard_stats_oneway_test.R b/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",

diff --git a/R/ard_stats_prop_test.R b/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 ---------------------------------------------------------

diff --git a/R/ard_stats_t_test.R b/R/ard_stats_t_test.R
@@ -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)) {

diff --git a/R/ard_stats_wilcox_test.R b/R/ard_stats_wilcox_test.R
@@ -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)) {

diff --git a/R/ard_survey_svychisq.R b/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",

diff --git a/R/ard_survey_svycontinuous.R b/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
 }

diff --git a/R/ard_survey_svyranktest.R b/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 ---------------------------------------------------------

diff --git a/R/ard_survey_svyttest.R b/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 ---------------------------------------------------------

diff --git a/R/ard_survival_survfit.R b/R/ard_survival_survfit.R
@@ -240,7 +240,7 @@ ard_survival_survfit <- function(x, times = NULL, probs = NULL, type = NULL) {
   ) %>%
     dplyr::bind_rows() %>%
     `rownames<-`(NULL) %>%
-    dplyr::mutate(context = "survival") %>%
+    dplyr::mutate(context = "survival_survfit") %>%
     dplyr::as_tibble()
 
   if (length(x$n) == 1) df_stat <- df_stat %>% dplyr::select(-"strata")

diff --git a/tests/testthat/_snaps/ard_car_vif.md b/tests/testthat/_snaps/ard_car_vif.md
@@ -4,32 +4,32 @@
       as.data.frame(ard_car_vif(lm(AGE ~ ARM + SEX, data = cards::ADSL)))
     Output
         variable context stat_name    stat_label     stat fmt_fn warning error
-      1      ARM     vif      GVIF          GVIF 1.015675      1    NULL  NULL
-      2      ARM     vif        df            df 2.000000      1    NULL  NULL
-      3      ARM     vif     aGVIF Adjusted GVIF 1.003896      1    NULL  NULL
-      4      SEX     vif      GVIF          GVIF 1.015675      1    NULL  NULL
-      5      SEX     vif        df            df 1.000000      1    NULL  NULL
-      6      SEX     vif     aGVIF Adjusted GVIF 1.007807      1    NULL  NULL
+      1      ARM car_vif      GVIF          GVIF 1.015675      1    NULL  NULL
+      2      ARM car_vif        df            df 2.000000      1    NULL  NULL
+      3      ARM car_vif     aGVIF Adjusted GVIF 1.003896      1    NULL  NULL
+      4      SEX car_vif      GVIF          GVIF 1.015675      1    NULL  NULL
+      5      SEX car_vif        df            df 1.000000      1    NULL  NULL
+      6      SEX car_vif     aGVIF Adjusted GVIF 1.007807      1    NULL  NULL
 
 ---
 
     Code
       as.data.frame(ard_car_vif(lm(AGE ~ BMIBL + EDUCLVL, data = cards::ADSL)))
     Output
         variable context stat_name stat_label     stat fmt_fn warning error
-      1    BMIBL     vif       VIF        VIF 1.010522      1    NULL  NULL
-      2  EDUCLVL     vif       VIF        VIF 1.010522      1    NULL  NULL
+      1    BMIBL car_vif       VIF        VIF 1.010522      1    NULL  NULL
+      2  EDUCLVL car_vif       VIF        VIF 1.010522      1    NULL  NULL
 
 # ard_car_vif() appropriate errors are given for model with only 1 term
 
     Code
       as.data.frame(ard_car_vif(lm(AGE ~ ARM, data = cards::ADSL)))
     Output
         variable context stat_name    stat_label stat fmt_fn warning
-      1      ARM     vif       VIF           VIF NULL   NULL    NULL
-      2      ARM     vif      GVIF          GVIF NULL   NULL    NULL
-      3      ARM     vif     aGVIF Adjusted GVIF NULL   NULL    NULL
-      4      ARM     vif        df            df NULL   NULL    NULL
+      1      ARM car_vif       VIF           VIF NULL   NULL    NULL
+      2      ARM car_vif      GVIF          GVIF NULL   NULL    NULL
+      3      ARM car_vif     aGVIF Adjusted GVIF NULL   NULL    NULL
+      4      ARM car_vif        df            df NULL   NULL    NULL
                                     error
       1 model contains fewer than 2 terms
       2 model contains fewer than 2 terms

diff --git a/tests/testthat/_snaps/ard_effectsize_cohens_d.md b/tests/testthat/_snaps/ard_effectsize_cohens_d.md
@@ -22,13 +22,13 @@
           "Xanomeline High Dose")), by = ARM, variables = c(BMIBL, HEIGHTBL)), c(1:3,
         5:6)), variable), n = 3))
     Output
-        group1 variable  context           stat_label      stat
-      1    ARM    BMIBL cohens_d Effect Size Estimate -0.436653
-      2    ARM    BMIBL cohens_d  CI Confidence Level      0.95
-      3    ARM    BMIBL cohens_d       CI Lower Bound -0.740282
-      4    ARM HEIGHTBL cohens_d Effect Size Estimate -0.299056
-      5    ARM HEIGHTBL cohens_d  CI Confidence Level      0.95
-      6    ARM HEIGHTBL cohens_d       CI Lower Bound -0.600975
+        group1 variable             context           stat_label      stat
+      1    ARM    BMIBL effectsize_cohens_d Effect Size Estimate -0.436653
+      2    ARM    BMIBL effectsize_cohens_d  CI Confidence Level      0.95
+      3    ARM    BMIBL effectsize_cohens_d       CI Lower Bound -0.740282
+      4    ARM HEIGHTBL effectsize_cohens_d Effect Size Estimate -0.299056
+      5    ARM HEIGHTBL effectsize_cohens_d  CI Confidence Level      0.95
+      6    ARM HEIGHTBL effectsize_cohens_d       CI Lower Bound -0.600975
 
 # ard_effectsize_paired_cohens_d() works
 

diff --git a/tests/testthat/_snaps/ard_effectsize_hedges_g.md b/tests/testthat/_snaps/ard_effectsize_hedges_g.md
@@ -22,13 +22,13 @@
           "Xanomeline High Dose")), by = ARM, variables = c(BMIBL, HEIGHTBL)), c(1:3,
         5:6)), variable), n = 3))
     Output
-        group1 variable  context           stat_label       stat
-      1    ARM    BMIBL hedges_g Effect Size Estimate -0.4347006
-      2    ARM    BMIBL hedges_g  CI Confidence Level       0.95
-      3    ARM    BMIBL hedges_g       CI Lower Bound -0.7369717
-      4    ARM HEIGHTBL hedges_g Effect Size Estimate -0.2977188
-      5    ARM HEIGHTBL hedges_g  CI Confidence Level       0.95
-      6    ARM HEIGHTBL hedges_g       CI Lower Bound -0.5982873
+        group1 variable             context           stat_label       stat
+      1    ARM    BMIBL effectsize_hedges_g Effect Size Estimate -0.4347006
+      2    ARM    BMIBL effectsize_hedges_g  CI Confidence Level       0.95
+      3    ARM    BMIBL effectsize_hedges_g       CI Lower Bound -0.7369717
+      4    ARM HEIGHTBL effectsize_hedges_g Effect Size Estimate -0.2977188
+      5    ARM HEIGHTBL effectsize_hedges_g  CI Confidence Level       0.95
+      6    ARM HEIGHTBL effectsize_hedges_g       CI Lower Bound -0.5982873
 
 # ard_effectsize_paired_hedges_g() works
 

diff --git a/tests/testthat/_snaps/ard_stats_aov.md b/tests/testthat/_snaps/ard_stats_aov.md
@@ -3,15 +3,15 @@
     Code
       as.data.frame(ard_stats_aov(AGE ~ ARM + SEX, data = cards::ADSL))
     Output
-         variable context stat_name             stat_label      stat warning error
-      1       ARM     aov     sumsq         Sum of Squares  71.38574    NULL  NULL
-      2       ARM     aov        df     Degrees of Freedom         2    NULL  NULL
-      3       ARM     aov    meansq Mean of Sum of Squares  35.69287    NULL  NULL
-      4       ARM     aov statistic              Statistic 0.5235002    NULL  NULL
-      5       ARM     aov   p.value                p-value 0.5930912    NULL  NULL
-      6       SEX     aov     sumsq         Sum of Squares  87.40947    NULL  NULL
-      7       SEX     aov        df     Degrees of Freedom         1    NULL  NULL
-      8       SEX     aov    meansq Mean of Sum of Squares  87.40947    NULL  NULL
-      9       SEX     aov statistic              Statistic  1.282017    NULL  NULL
-      10      SEX     aov   p.value                p-value 0.2586091    NULL  NULL
+         variable   context stat_name             stat_label      stat warning error
+      1       ARM stats_aov     sumsq         Sum of Squares  71.38574    NULL  NULL
+      2       ARM stats_aov        df     Degrees of Freedom         2    NULL  NULL
+      3       ARM stats_aov    meansq Mean of Sum of Squares  35.69287    NULL  NULL
+      4       ARM stats_aov statistic              Statistic 0.5235002    NULL  NULL
+      5       ARM stats_aov   p.value                p-value 0.5930912    NULL  NULL
+      6       SEX stats_aov     sumsq         Sum of Squares  87.40947    NULL  NULL
+      7       SEX stats_aov        df     Degrees of Freedom         1    NULL  NULL
+      8       SEX stats_aov    meansq Mean of Sum of Squares  87.40947    NULL  NULL
+      9       SEX stats_aov statistic              Statistic  1.282017    NULL  NULL
+      10      SEX stats_aov   p.value                p-value 0.2586091    NULL  NULL
 
diff --git a/tests/testthat/_snaps/ard_stats_chisq_test.md b/tests/testthat/_snaps/ard_stats_chisq_test.md
@@ -5,13 +5,13 @@
         by = "ARM", variables = "AGEGR1"), ard_stats_chisq_test(data = adsl_sub, by = "SEX",
         variables = "AGEGR1"))))
     Output
-                ARM         SEX variable   context stat_name         stat
-      1 Overall ARM        <NA>   AGEGR1 chisqtest statistic 5.079442e+00
-      2 Overall ARM        <NA>   AGEGR1 chisqtest   p.value 7.888842e-02
-      3 Overall ARM        <NA>   AGEGR1 chisqtest parameter 2.000000e+00
-      4 Overall ARM        <NA>   AGEGR1 chisqtest         B 2.000000e+03
-      5        <NA> Overall SEX   AGEGR1 chisqtest statistic 1.039442e+00
-      6        <NA> Overall SEX   AGEGR1 chisqtest   p.value 5.946864e-01
-      7        <NA> Overall SEX   AGEGR1 chisqtest parameter 2.000000e+00
-      8        <NA> Overall SEX   AGEGR1 chisqtest         B 2.000000e+03
+                ARM         SEX variable          context stat_name         stat
+      1 Overall ARM        <NA>   AGEGR1 stats_chisq_test statistic 5.079442e+00
+      2 Overall ARM        <NA>   AGEGR1 stats_chisq_test   p.value 7.888842e-02
+      3 Overall ARM        <NA>   AGEGR1 stats_chisq_test parameter 2.000000e+00
+      4 Overall ARM        <NA>   AGEGR1 stats_chisq_test         B 2.000000e+03
+      5        <NA> Overall SEX   AGEGR1 stats_chisq_test statistic 1.039442e+00
+      6        <NA> Overall SEX   AGEGR1 stats_chisq_test   p.value 5.946864e-01
+      7        <NA> Overall SEX   AGEGR1 stats_chisq_test parameter 2.000000e+00
+      8        <NA> Overall SEX   AGEGR1 stats_chisq_test         B 2.000000e+03
 
diff --git a/tests/testthat/_snaps/ard_stats_kruskal_test.md b/tests/testthat/_snaps/ard_stats_kruskal_test.md
@@ -3,14 +3,19 @@
     Code
       as.data.frame(ard_stats_kruskal_test(cards::ADSL, by = "ARM", variables = "AGE"))
     Output
-        group1 variable     context stat_name                           stat_label
-      1    ARM      AGE kruskaltest statistic Kruskal-Wallis chi-squared Statistic
-      2    ARM      AGE kruskaltest   p.value                              p-value
-      3    ARM      AGE kruskaltest parameter                   Degrees of Freedom
-      4    ARM      AGE kruskaltest    method                               method
-                                stat fmt_fn warning error
-      1                      1.63473      1    NULL  NULL
-      2                    0.4415937      1    NULL  NULL
-      3                            2      1    NULL  NULL
-      4 Kruskal-Wallis rank sum test   NULL    NULL  NULL
+        group1 variable            context stat_name
+      1    ARM      AGE stats_kruskal_test statistic
+      2    ARM      AGE stats_kruskal_test   p.value
+      3    ARM      AGE stats_kruskal_test parameter
+      4    ARM      AGE stats_kruskal_test    method
+                                  stat_label                         stat fmt_fn
+      1 Kruskal-Wallis chi-squared Statistic                      1.63473      1
+      2                              p-value                    0.4415937      1
+      3                   Degrees of Freedom                            2      1
+      4                               method Kruskal-Wallis rank sum test   NULL
+        warning error
+      1    NULL  NULL
+      2    NULL  NULL
+      3    NULL  NULL
+      4    NULL  NULL
 
diff --git a/tests/testthat/_snaps/ard_stats_mood_test.md b/tests/testthat/_snaps/ard_stats_mood_test.md
@@ -3,11 +3,11 @@
     Code
       as.data.frame(ard_stats_mood_test(cards::ADSL, by = SEX, variable = AGE))
     Output
-        group1 variable  context   stat_name             stat_label
-      1    SEX      AGE moodtest   statistic            Z-Statistic
-      2    SEX      AGE moodtest     p.value                p-value
-      3    SEX      AGE moodtest      method                 method
-      4    SEX      AGE moodtest alternative Alternative Hypothesis
+        group1 variable         context   stat_name             stat_label
+      1    SEX      AGE stats_mood_test   statistic            Z-Statistic
+      2    SEX      AGE stats_mood_test     p.value                p-value
+      3    SEX      AGE stats_mood_test      method                 method
+      4    SEX      AGE stats_mood_test alternative Alternative Hypothesis
                                  stat fmt_fn warning error
       1                     0.1292194      1    NULL  NULL
       2                     0.8971841      1    NULL  NULL