Merge branch 'main' into 104_reformulate_for_nonsyntactic

insightsengineering · Apr 26, 2024 · db701a1 · db701a1
2 parents 2f5cc89 + 07689a2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.1.0.9027
+Version: 0.1.0.9028
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# cardx 0.1.0.9027
+# cardx 0.1.0.9028
 
 ### Breaking Changes
 

diff --git a/tests/testthat/_snaps/ard_car_vif.md b/tests/testthat/_snaps/ard_car_vif.md
@@ -20,27 +20,12 @@
       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 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
-      3 model contains fewer than 2 terms
-      4 model contains fewer than 2 terms
-
 # ard_vif() issues friendly messaging for incorrect object passed in/can't get terms of model
 
     Code
-      ard_vif(cards::ADSL)
+      ard_car_vif(cards::ADSL)
     Condition
-      Error in `ard_vif()`:
-      ! could not find function "ard_vif"
+      Error in `ard_car_vif()`:
+      ! There was an error running `car::vif()`. See below.
+      x no applicable method for 'vcov' applied to an object of class "c('tbl_df', 'tbl', 'data.frame')"
 
diff --git a/tests/testthat/_snaps/ard_effectsize_cohens_d.md b/tests/testthat/_snaps/ard_effectsize_cohens_d.md
@@ -1,21 +1,5 @@
 # ard_effectsize_cohens_d() works
 
-    Code
-      as.data.frame(dplyr::select(ard_effectsize_cohens_d(cards::ADSL, by = ARM,
-      variables = AGE), c("variable", "stat_name", "error")))
-    Output
-        variable   stat_name                                           error
-      1      AGE    estimate Grouping variable y must have exactly 2 levels.
-      2      AGE  conf.level Grouping variable y must have exactly 2 levels.
-      3      AGE    conf.low Grouping variable y must have exactly 2 levels.
-      4      AGE   conf.high Grouping variable y must have exactly 2 levels.
-      5      AGE          mu Grouping variable y must have exactly 2 levels.
-      6      AGE      paired Grouping variable y must have exactly 2 levels.
-      7      AGE   pooled_sd Grouping variable y must have exactly 2 levels.
-      8      AGE alternative Grouping variable y must have exactly 2 levels.
-
----
-
     Code
       as.data.frame(dplyr::slice_head(dplyr::group_by(dplyr::select(
         ard_effectsize_cohens_d(dplyr::filter(cards::ADSL, ARM %in% c("Placebo",
@@ -30,20 +14,3 @@
       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
-
-    Code
-      as.data.frame(dplyr::select(ard_effectsize_paired_cohens_d(dplyr::mutate(
-        ADSL_paired, ARM = ifelse(dplyr::row_number() == 1L, "3rd ARM", ARM)), by = ARM,
-      variable = AGE, id = USUBJID), c("variable", "stat_name", "error")))
-    Output
-        variable   stat_name                                                error
-      1      AGE    estimate The `by` argument must have two and only two levels.
-      2      AGE  conf.level The `by` argument must have two and only two levels.
-      3      AGE    conf.low The `by` argument must have two and only two levels.
-      4      AGE   conf.high The `by` argument must have two and only two levels.
-      5      AGE          mu The `by` argument must have two and only two levels.
-      6      AGE      paired The `by` argument must have two and only two levels.
-      7      AGE   pooled_sd The `by` argument must have two and only two levels.
-      8      AGE alternative The `by` argument must have two and only two levels.
-
diff --git a/tests/testthat/_snaps/ard_effectsize_hedges_g.md b/tests/testthat/_snaps/ard_effectsize_hedges_g.md
@@ -1,21 +1,5 @@
 # ard_effectsize_hedges_g() works
 
-    Code
-      as.data.frame(dplyr::select(ard_effectsize_hedges_g(cards::ADSL, by = ARM,
-      variable = AGE), c("variable", "stat_name", "error")))
-    Output
-        variable   stat_name                                           error
-      1      AGE    estimate Grouping variable y must have exactly 2 levels.
-      2      AGE  conf.level Grouping variable y must have exactly 2 levels.
-      3      AGE    conf.low Grouping variable y must have exactly 2 levels.
-      4      AGE   conf.high Grouping variable y must have exactly 2 levels.
-      5      AGE          mu Grouping variable y must have exactly 2 levels.
-      6      AGE      paired Grouping variable y must have exactly 2 levels.
-      7      AGE   pooled_sd Grouping variable y must have exactly 2 levels.
-      8      AGE alternative Grouping variable y must have exactly 2 levels.
-
----
-
     Code
       as.data.frame(dplyr::slice_head(dplyr::group_by(dplyr::select(
         ard_effectsize_hedges_g(dplyr::filter(cards::ADSL, ARM %in% c("Placebo",
@@ -30,20 +14,3 @@
       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
-
-    Code
-      as.data.frame(dplyr::select(ard_effectsize_paired_hedges_g(dplyr::mutate(
-        ADSL_paired, ARM = ifelse(dplyr::row_number() == 1L, "3rd ARM", ARM)), by = ARM,
-      variable = AGE, id = USUBJID), c("variable", "stat_name", "error")))
-    Output
-        variable   stat_name                                                error
-      1      AGE    estimate The `by` argument must have two and only two levels.
-      2      AGE  conf.level The `by` argument must have two and only two levels.
-      3      AGE    conf.low The `by` argument must have two and only two levels.
-      4      AGE   conf.high The `by` argument must have two and only two levels.
-      5      AGE          mu The `by` argument must have two and only two levels.
-      6      AGE      paired The `by` argument must have two and only two levels.
-      7      AGE   pooled_sd The `by` argument must have two and only two levels.
-      8      AGE alternative The `by` argument must have two and only two levels.
-
diff --git a/tests/testthat/_snaps/ard_stats_t_test.md b/tests/testthat/_snaps/ard_stats_t_test.md
diff --git a/tests/testthat/test-ard_car_vif.R b/tests/testthat/test-ard_car_vif.R
@@ -15,25 +15,19 @@ test_that("ard_car_vif() works", {
 })
 
 test_that("ard_car_vif() appropriate errors are given for model with only 1 term", {
-  expect_snapshot(
-    lm(AGE ~ ARM, data = cards::ADSL) |>
-      ard_car_vif() |>
-      as.data.frame()
-  )
   expect_equal(
     lm(AGE ~ ARM, data = cards::ADSL) |>
       ard_car_vif() |>
-      dplyr::select(error) |>
-      unlist() |>
-      unique(),
-    "model contains fewer than 2 terms"
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 })
 
 
 test_that("ard_vif() issues friendly messaging for incorrect object passed in/can't get terms of model", {
   expect_snapshot(
     error = TRUE,
-    cards::ADSL |> ard_vif()
+    cards::ADSL |> ard_car_vif()
   )
 })
diff --git a/tests/testthat/test-ard_effectsize_cohens_d.R b/tests/testthat/test-ard_effectsize_cohens_d.R
@@ -26,11 +26,12 @@ test_that("ard_effectsize_cohens_d() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     cards::ADSL |>
       ard_effectsize_cohens_d(by = ARM, variables = AGE) |>
-      dplyr::select(c("variable", "stat_name", "error")) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 
   # test that the function works with multiple variables
@@ -83,13 +84,14 @@ test_that("ard_effectsize_paired_cohens_d() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     ADSL_paired |>
       dplyr::mutate(
         ARM = ifelse(dplyr::row_number() == 1L, "3rd ARM", ARM)
       ) |>
       ard_effectsize_paired_cohens_d(by = ARM, variable = AGE, id = USUBJID) |>
-      dplyr::select(c("variable", "stat_name", "error")) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 })
diff --git a/tests/testthat/test-ard_effectsize_hedges_g.R b/tests/testthat/test-ard_effectsize_hedges_g.R
@@ -24,11 +24,12 @@ test_that("ard_effectsize_hedges_g() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     cards::ADSL |>
       ard_effectsize_hedges_g(by = ARM, variable = AGE) |>
-      dplyr::select(c("variable", "stat_name", "error")) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 
   # test that the function works with multiple variables as once
@@ -83,13 +84,14 @@ test_that("ard_effectsize_paired_hedges_g() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     ADSL_paired |>
       dplyr::mutate(
         ARM = ifelse(dplyr::row_number() == 1L, "3rd ARM", ARM)
       ) |>
       ard_effectsize_paired_hedges_g(by = ARM, variable = AGE, id = USUBJID) |>
-      dplyr::select(c("variable", "stat_name", "error")) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 })
diff --git a/tests/testthat/test-ard_stats_t_test.R b/tests/testthat/test-ard_stats_t_test.R
@@ -44,10 +44,12 @@ test_that("ard_stats_t_test() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     cards::ADSL |>
       ard_stats_t_test(by = ARM, variable = AGE, var.equal = TRUE) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 
   # test that the function works with multiple variables at once
@@ -102,12 +104,14 @@ test_that("ard_stats_paired_t_test() works", {
   )
 
   # errors are properly handled
-  expect_snapshot(
+  expect_equal(
     ADSL_paired |>
       dplyr::mutate(
         ARM = ifelse(dplyr::row_number() == 1L, "3rd ARM", ARM)
       ) |>
       ard_stats_paired_t_test(by = ARM, variable = AGE, id = USUBJID, var.equal = TRUE) |>
-      as.data.frame()
+      dplyr::select(error) %>%
+      is.null(),
+    FALSE
   )
 })