Fix tests - deprecate pairwise and add another test for `format_cou…

…nt_fraction` (#987) Closes #984
insightsengineering · Jun 26, 2023 · 7071f31 · 7071f31
1 parent 800fc42
commit 7071f31
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Showing 6 changed files with 6 additions and 56 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -221,7 +221,6 @@ export(logistic_summary_by_flag)
 export(month2day)
 export(or_clogit)
 export(or_glm)
-export(pairwise)
 export(prop_agresti_coull)
 export(prop_clopper_pearson)
 export(prop_diff_cmh)

diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@
 
 ### Miscellaneous
 * Began deprecation of `time_unit_input` and `time_unit_output` arguments and replaced them with the `input_time_unit` and `num_pt_year`, respectively, in `control_incidence_rate`.
+* Removed deprecated `pairwise` function.
 
 # tern 0.8.3
 

diff --git a/R/coxph.R b/R/coxph.R
@@ -1,25 +1,3 @@
-#' Pairwise Formula Special Term
-#'
-#' @description `r lifecycle::badge("deprecated")`
-#'
-#' The special term `pairwise` indicate that the model should be fitted individually for
-#' every tested level in comparison to the reference level.
-#'
-#' @param x the variable for which pairwise result is expected.
-#'
-#' @return Variable "paired".
-#'
-#' @details Let's `ARM` being a factor with level A, B, C; let's be B the reference level,
-#'   a model calling the formula including `pairwise(ARM)` will result in two models:
-#'   * A model including only levels A and B, and effect of A estimated in reference to B.
-#'   * A model including only levels C and B, the effect of C estimated in reference to B.
-#'
-#' @export
-pairwise <- function(x) {
-  lifecycle::deprecate_warn("0.8.1.9013", "pairwise()", "univariate()")
-  structure(x, varname = deparse(substitute(x)))
-}
-
 #' Univariate Formula Special Term
 #'
 #' @description `r lifecycle::badge("stable")`

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -173,8 +173,3 @@ reference:
     desc: Data included in the package.
     contents:
       - starts_with("ex_")
-
-  - title: Deprecated Functions
-    desc: Functions that are currently deprecated within `tern`.
-    contents:
-      - pairwise
diff --git a/man/pairwise.Rd b/man/pairwise.Rd
diff --git a/tests/testthat/test-formats.R b/tests/testthat/test-formats.R
@@ -47,6 +47,11 @@ testthat::test_that("format_count_fraction works with count of 0", {
   testthat::expect_snapshot(res)
 })
 
+testthat::test_that("format_count_fraction works with NA input", {
+  result <- format_count_fraction(NA)
+  testthat::expect_identical(result, "NA")
+})
+
 testthat::test_that("format_count_fraction_fixed_dp works with healthy inputs", {
   result <- format_count_fraction_fixed_dp(c(2, 0.5))