Replace deprecated forcats::fct_explicit_na (#817)

Closes #811

DESCRIPTION

@@ -29,7 +29,7 @@ Imports:
     cowplot,
     dplyr,
     emmeans (>= 1.4.5),
-    forcats,
+    forcats (>= 1.0.0),
     formatters (>= 0.3.4.13),
     ggplot2,
     grid,

NEWS.md

@@ -49,7 +49,8 @@
 * Updated tests to use `testthat` 3rd edition.
 * Created separate documentation files for functions in different sections of pkgdown reference.
 * Created separate `.R` files for logistic regression and cox regression helper functions.
-* Removed all template tests from `tern`. These have been relocated to internal repo `scda.test`.
+* Removed all template tests from `tern`. These tests are in internal repo `scda.test`.
+* Replaced deprecated function `forcats::fct_explicit_na` with `forcats::fct_na_value_to_level`.
 
 # tern 0.7.10
 

R/missing_data.R

@@ -21,7 +21,8 @@ explicit_na <- function(x, label = "<Missing>") {
   checkmate::assert_string(label)
 
   if (is.factor(x)) {
-    forcats::fct_explicit_na(x, label)
+    x <- forcats::fct_na_value_to_level(x, label)
+    forcats::fct_drop(x, only = label)
   } else if (is.character(x)) {
     x[is.na(x)] <- label
     x
@@ -30,7 +31,6 @@ explicit_na <- function(x, label = "<Missing>") {
   }
 }
 
-
 #' Convert Strings to `NA`
 #'
 #' @description `r lifecycle::badge("stable")`

R/utils_factor.R

@@ -243,7 +243,7 @@ fct_discard <- function(x, discard) {
 #' @param na_level (`string`)\cr which level to use for missings.
 #'
 #' @return The modified factor with inserted and existing `NA` converted to `na_level`.
-#' @seealso [forcats::fct_explicit_na()] which is used internally.
+#' @seealso [forcats::fct_na_value_to_level()] which is used internally.
 #'
 #' @examples
 #' fct_explicit_na_if(factor(c("a", "b", NA)), c(TRUE, FALSE, FALSE))
@@ -253,7 +253,8 @@ fct_explicit_na_if <- function(x, condition, na_level = "<Missing>") {
   checkmate::assert_factor(x, len = length(condition))
   checkmate::assert_logical(condition)
   x[condition] <- NA
-  forcats::fct_explicit_na(x, na_level = na_level)
+  x <- forcats::fct_na_value_to_level(x, level = na_level)
+  forcats::fct_drop(x, only = na_level)
 }
 
 #' Collapsing of Factor Levels and Keeping Only Those New Group Levels

tests/testthat/_snaps/df_explicit_na.md

@@ -9,6 +9,36 @@
       3  A         A         A  F <Missing> <Missing>  3    NA
       4  B <Missing> <Missing>  E         C         C  4    NA
 
+---
+
+    Code
+      res
+    Output
+      $v1
+      [1] "B" "A"
+      
+      $v2
+      [1] "B"         "A"         "<Missing>"
+      
+      $v3
+      [1] "B"         "A"         "<Missing>"
+      
+      $v4
+      [1] "D" "E" "F"
+      
+      $v5
+      [1] "A"         "B"         "C"         "<Missing>"
+      
+      $v6
+      [1] "A"         "B"         "C"         "<Missing>"
+      
+      $v7
+      NULL
+      
+      $v8
+      NULL
+      
+
 # Default settings work when input data does not have labels
 
     Code

tests/testthat/_snaps/summarize_num_patients.md

@@ -92,7 +92,7 @@
       ——————————————————————————————————————————————————————————————————
       Number of patients with at least one event   3 (60.0%)   3 (75.0%)
       Number of events                                 4           4    
-       (n)                                             3           3    
+      (n)                                              3           3    
 
 ---
 
@@ -122,7 +122,7 @@
                A       B  
              (N=5)   (N=4)
       ————————————————————
-       (n)     3       3  
+      (n)      3       3  
 
 # s_num_patients count_by works as expected with healthy input
 
@@ -260,7 +260,7 @@
       ——————————————————————————————————————————————————————————————————
       Number of patients with at least one event   3 (60.0%)   3 (75.0%)
       Number of events                                 3           3    
-       (n)                                             3           3    
+      (n)                                              3           3    
 
 ---
 
@@ -290,7 +290,7 @@
                A       B  
              (N=5)   (N=4)
       ————————————————————
-       (n)     3       3  
+      (n)      3       3  
 
 # summarize_num_patients with count_by different combinations works as expected with healthy input
 
@@ -302,7 +302,7 @@
       ——————————————————————————————————————————————————————————————————
       Number of patients with at least one event   3 (60.0%)   3 (75.0%)
       Number of events                                 4           3    
-       (n)                                             3           3    
+      (n)                                              3           3    
 
 # analyze_num_patients works well for pagination
 

tests/testthat/test-df_explicit_na.R

@@ -20,6 +20,9 @@ testthat::test_that("Default fill in of missing values and conversion to factor
 
   res <- testthat::expect_silent(result)
   testthat::expect_snapshot(res)
+
+  res <- testthat::expect_silent(sapply(result, levels))
+  testthat::expect_snapshot(res)
 })
 
 testthat::test_that("Default settings work when input data does not have labels", {