Closes #1966 address derive_vars_joined bugs

NEWS.md

@@ -38,6 +38,8 @@ the `filter_add` using the next phase of the deprecation process. (#1950)
 
 - The list of package authors/contributors has been reformatted so that those who are actively maintaining the code base are now marked as *authors*, whereas those who made a significant contribution in the past are now down as *contributors*. All other acknowledgements have been moved to README section (#1941).
 
+- `derive_vars_joined()` had two bugs with regards to duplicates messaging and when `new_vars` was set to `NULL` that have now been addressed (#1966). 
+
 # admiral 0.11.1
 
 - Fix bug in `derive_param_tte()`. (#1962)

R/derive_joined.R

@@ -349,7 +349,7 @@ derive_vars_joined <- function(dataset,
 
   filter_add <- assert_filter_cond(enexpr(filter_add), optional = TRUE)
   filter_join <- assert_filter_cond(enexpr(filter_join), optional = TRUE)
-
+  original_new_vars <- new_vars
   if (is.null(new_vars)) {
     new_vars <- chr2vars(colnames(dataset_add))
   }
@@ -399,17 +399,18 @@ derive_vars_joined <- function(dataset,
         suffix = ".join"
       ),
       mode = mode,
-      check_type = check_type
+      check_type = "none"
     )
   }
 
   # merge new variables to the input dataset and rename them
-  data %>%
+  data_final <- data %>%
     derive_vars_merged(
       dataset_add = data_return,
       by_vars = exprs(!!!by_vars_left, !!tmp_obs_nr),
       new_vars = add_suffix_to_vars(new_vars, vars = common_vars, suffix = ".join"),
       missing_values = missing_values,
+      check_type = check_type,
       duplicate_msg = paste(
         paste(
           "After applying `filter_join` the joined dataset contains more",
@@ -423,4 +424,10 @@ derive_vars_joined <- function(dataset,
       )
     ) %>%
     remove_tmp_vars()
+
+  if (is.null(original_new_vars)) {
+    data_final <- data_final %>%
+      select(-ends_with("join"))
+  }
+  return(data_final)
 }

tests/testthat/test-derive_joined.R

@@ -242,3 +242,65 @@ test_that("derive_vars_joined Test 7: new_vars expressions using variables from
     keys = c("USUBJID", "AESEQ")
   )
 })
+## Test 8: NULL new_vars will still remove .join columns ----
+test_that("derive_vars_joined Test 8: NULL new_vars will still remove .join columns", {
+  myd <- data.frame(day = c(1, 2, 3), val = c(0, 17, 21))
+  expect_dfs_equal(
+    base = myd,
+    compare = derive_vars_joined(
+      myd,
+      dataset_add = myd,
+      order = exprs(day),
+      mode = "last",
+      filter_join = day < day.join
+    ),
+    keys = c("day", "val")
+  )
+})
+## Test 9: check_type suppressed until the final derive_vars_merged() chunk ----
+test_that("derive_vars_joined Test 9: check_type suppressed until the final derive_vars_merged() chunk", { # nolint
+  adlb_ast <- tribble(
+    ~ADT,         ~ASEQ,
+    "2002-01-01", 1,
+    "2002-02-02", 2,
+    "2002-02-02", 3
+  ) %>%
+    mutate(
+      STUDYID = "ABC",
+      USUBJID = "1",
+      ADT = ymd(ADT),
+      ADTM = as_datetime(ADT)
+    )
+
+  adlb_tbili_pbl <- tribble(
+    ~ADT,         ~ASEQ,
+    "2002-01-01", 4,
+    "2002-02-02", 5,
+    "2002-02-02", 6
+  ) %>%
+    mutate(
+      STUDYID = "ABC",
+      USUBJID = "1",
+      ADT = ymd(ADT),
+      ADTM = as_datetime(ADT)
+    )
+
+  adlb_joined <- derive_vars_joined(
+    adlb_ast,
+    dataset_add = adlb_tbili_pbl,
+    by_vars = exprs(STUDYID, USUBJID),
+    order = exprs(ADTM, ASEQ),
+    new_vars = exprs(TBILI_ADT = ADT),
+    filter_join = ADT <= ADT.join,
+    mode = "first"
+  )
+
+  expected <- adlb_ast %>%
+    mutate(TBILI_ADT = as.Date(c("2002-01-01", "2002-02-02", "2002-02-02"), "%Y-%m-%d"))
+
+  expect_dfs_equal(
+    base = expected,
+    compare = adlb_joined,
+    keys = c("ADT", "ASEQ", "STUDYID", "USUBJID", "ADTM", "TBILI_ADT")
+  )
+})