Merge branch '126-ard_survfit_diff' of https://github.com/insightseng…

…ineering/cardx into 126-ard_survfit_diff

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.1.0.9025
+Version: 0.1.0.9027
 Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,4 @@
-# cardx 0.1.0.9025
+# cardx 0.1.0.9027
 
 ### Breaking Changes
 

R/ard_regression.R

@@ -49,6 +49,7 @@ ard_regression.default <- function(x, tidy_fun = broom.helpers::tidy_with_broom_
       values_to = "stat"
     ) |>
     dplyr::filter(map_lgl(.data$stat, Negate(is.na))) |>
+    dplyr::select(-(cards::all_ard_variables("levels") & dplyr::where(\(x) all(is.na(x))))) |>
     dplyr::mutate(
       fmt_fn =
         lapply(

R/ard_regression_basic.R

@@ -55,5 +55,6 @@ ard_regression_basic <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or
     utils::modifyList(val = rlang::dots_list(...))
 
   rlang::inject(ard_regression(x = x, tidy_fun = tidy_fun, !!!args)) |>
-    dplyr::filter(!.data$stat_name %in% stats_to_remove)
+    dplyr::filter(!.data$stat_name %in% stats_to_remove) |>
+    dplyr::select(-(cards::all_ard_variables("levels") & dplyr::where(\(x) all(is.na(x)))))
 }

R/construction_helpers.R

@@ -45,7 +45,7 @@
 #' @return depends on the calling function
 #' @name construction_helpers
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("withr", "lme4"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("withr", "lme4", "broom.helpers"), reference_pkg = "cardx"))
 #' construct_model(
 #'   x = mtcars,
 #'   formula = am ~ mpg + (1 | vs),

tests/testthat/_snaps/construction_helpers.md

@@ -5,11 +5,11 @@
         mtcars, `M P G` = mpg), formula = reformulate2(c("M P G", "cyl"), response = "hp"),
       method = "lm"))), stat_name %in% c("term", "estimate", "p.value"))
     Output
-        variable variable_level    context stat_name  stat_label        stat fmt_fn
-      1    M P G           <NA> regression      term        term     `M P G`   NULL
-      2    M P G           <NA> regression  estimate Coefficient   -2.774769      1
-      3    M P G           <NA> regression   p.value     p-value   0.2125285      1
-      4      cyl           <NA> regression      term        term         cyl   NULL
-      5      cyl           <NA> regression  estimate Coefficient    23.97863      1
-      6      cyl           <NA> regression   p.value     p-value 0.002814958      1
+        variable    context stat_name  stat_label        stat fmt_fn
+      1    M P G regression      term        term     `M P G`   NULL
+      2    M P G regression  estimate Coefficient   -2.774769      1
+      3    M P G regression   p.value     p-value   0.2125285      1
+      4      cyl regression      term        term         cyl   NULL
+      5      cyl regression  estimate Coefficient    23.97863      1
+      6      cyl regression   p.value     p-value 0.002814958      1
 

tests/testthat/test-ard_regression.R

@@ -20,3 +20,7 @@ test_that("ard_regression() works", {
     "Treatment Arm"
   )
 })
+
+test_that("ard_regression() does not produce `variable_level` column where not applicable", {
+  expect_true(!"variable_level" %in% names(lm(mpg ~ hp, mtcars) |> ard_regression()))
+})

tests/testthat/test-ard_regression_basic.R

@@ -9,3 +9,7 @@ test_that("ard_regression_basic() works", {
 
   expect_snapshot(as.data.frame(ard) |> dplyr::select(-fmt_fn))
 })
+
+test_that("ard_regression_basic() does not produce `variable_level` column where not applicable", {
+  expect_true(!"variable_level" %in% names(lm(mpg ~ hp, mtcars) |> ard_regression_basic()))
+})

tests/testthat/test-construction_helpers.R

@@ -1,4 +1,4 @@
-skip_if_not(is_pkg_installed(c("withr", "survey"), reference_pkg = "cardx"))
+skip_if_not(is_pkg_installed(c("broom.helpers", "withr", "survey"), reference_pkg = "cardx"))
 
 test_that("construct_model() works", {
   expect_snapshot(