Merged with devel

Merge branch 'devel' into 189-impute_dcutdtc-missing-dcutdtc

# Conflicts:
#	NEWS.md

.github/pull_request_template.md

@@ -1,11 +1,11 @@
-Thank you for your Pull Request! [admiraldev](https://pharmaverse.github.io/admiraldev/devel/index.html) have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the datacutr codebase remains robust and consistent.   
+Thank you for your Pull Request! [admiraldev](https://pharmaverse.github.io/admiraldev/index.html) have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the datacutr codebase remains robust and consistent.   
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html#writing-unit-tests-in-admiral-)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html#deprecation-1)?
+- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#writing-unit-tests-in-admiral-)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
 - [ ] Update to all relevant roxygen headers and examples 
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates

.lintr

@@ -1,4 +1,10 @@
-linters: linters_with_defaults(line_length_linter(100), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20))
+linters: linters_with_defaults(
+    line_length_linter(100),
+    object_usage_linter=NULL,
+    infix_spaces_linter=NULL,
+    indentation_linter=NULL,
+    cyclocomp_linter(complexity_limit = 22)
+  )
 exclusions: list(
-        "R/data.R",
-        "tests/testthat")
+    "R/data.R",
+    "tests/testthat")

NEWS.md

@@ -4,7 +4,10 @@
 - Added a "Report a bug" link to `{datacutr}` website (#182)
 
 ## Updates of Existing Functions
-- `impute_dcutdtc()` updated to allow missing data cutoff date (#189)
+- Update to `impute_dcutdtc()`, `date_cut()` and `special_dm_cut()` functions to allow for 
+datacut date to be null. In this case, all records for this patient 
+will be kept/left unchanged.
+- Warning added to `process_cut` if expected dataset `dm` is missing
 
 ## Breaking Changes
 - N/A
@@ -13,7 +16,7 @@
 - N/A
 
 ## Various
-- Minor documentation updates #171 #173 #177
+- Minor documentation updates #171 #173 #177 #184
 
 # datacutr 0.1.0
 

R/date_cut.R

@@ -64,20 +64,18 @@ date_cut <- function(dataset_sdtm,
     (length(get_duplicates(dataset_cut$USUBJID)) == 0),
     msg = "Duplicate patients in the DCUT (dataset_cut) dataset, please update."
   )
-  assert_that(
-    (any(is.na(mutate(dataset_cut, !!cut_var))) == FALSE),
-    msg = "At least one patient with missing datacut date (cut_var) in the DCUT
-    (dataset_cut) dataset, please update."
+  ifelse(any(is.na(mutate(dataset_cut, !!cut_var))) == TRUE,
+    print("At least 1 patient with missing datacut date, all records will be kept."), NA
   )
 
-
   dcut <- dataset_cut %>%
     mutate(DCUT_TEMP_DCUTDTM = !!cut_var) %>%
-    subset(select = c(USUBJID, DCUT_TEMP_DCUTDTM))
+    subset(select = c(USUBJID, DCUT_TEMP_DCUTDTM)) %>%
+    mutate(TEMP_DCUT_KEEP = "Y")
 
-  assert_that(is.POSIXt(dcut$DCUT_TEMP_DCUTDTM),
+  ifelse(!is.na(dcut$DCUT_TEMP_DCUTDTM), assert_that(is.POSIXt(dcut$DCUT_TEMP_DCUTDTM),
     msg = "cut_var is expected to be of date type POSIXt"
-  )
+  ), NA)
 
   attributes(dcut$USUBJID)$label <- attributes(dataset_sdtm$USUBJID)$label
 
@@ -92,7 +90,10 @@ date_cut <- function(dataset_sdtm,
   # Flag records to be removed - those occurring after cut date and patients not in dcut dataset
   dataset <- dataset_sdtm_pt %>%
     mutate(DCUT_TEMP_REMOVE = ifelse((DCUT_TEMP_SDTM_DATE > DCUT_TEMP_DCUTDTM) |
-      is.na(DCUT_TEMP_DCUTDTM), "Y", NA_character_))
+      is.na(TEMP_DCUT_KEEP), "Y", NA_character_))
+
+  # Ensure variable is character
+  dataset$DCUT_TEMP_REMOVE <- as.character(dataset$DCUT_TEMP_REMOVE)
 
   dataset <- drop_temp_vars(dsin = dataset, drop_dcut_temp = FALSE)
 

R/global.R

@@ -20,5 +20,6 @@ globalVariables(c(
   "DCUT_TEMP_DATE",
   "source_data",
   "DCUT_TEMP_REMOVE",
-  "DCUT_TEMP_DTHCHANGE"
+  "DCUT_TEMP_DTHCHANGE",
+  "TEMP_DCUT_KEEP"
 ))

R/process_cut.R

@@ -91,6 +91,9 @@ no_cut_v empty, in which case a default value of vector() will be used."
     msg = "special_dm must be either TRUE or FALSE"
   )
   if (special_dm) {
+    assert_that("dm" %in% names(source_sdtm_data),
+      msg = "dataset `dm` is missing but special_dm processing expects this"
+    )
     assert_that(
       setequal(names(source_sdtm_data), c(
         patient_cut_v, date_cut_m[, 1], no_cut_v,

R/special_dm_cut.R

@@ -48,10 +48,8 @@ special_dm_cut <- function(dataset_dm,
     (length(get_duplicates(dataset_cut$USUBJID)) == 0),
     msg = "Duplicate patients in the DCUT (dataset_cut) dataset, please update."
   )
-  assert_that(
-    (any(is.na(mutate(dataset_cut, !!cut_var))) == FALSE),
-    msg = "At least one patient with missing datacut date (cut_var) in the DCUT
-    (dataset_cut) dataset, please update."
+  ifelse(any(is.na(mutate(dataset_cut, !!cut_var))) == TRUE,
+    print("At least 1 patient with missing datacut date, all records will be kept."), NA
   )
   assert_data_frame(dataset_dm,
     required_vars = exprs(USUBJID, DTHDTC)
@@ -69,16 +67,19 @@ special_dm_cut <- function(dataset_dm,
       by = "USUBJID"
     )
 
-  assert_that(is.POSIXt(dm_temp$DCUT_TEMP_DCUTDTM),
+  ifelse(!is.na(dm_temp$DCUT_TEMP_DCUTDTM), assert_that(is.POSIXt(dm_temp$DCUT_TEMP_DCUTDTM),
     msg = "cut_var is expected to be of date type POSIXt"
-  )
+  ), NA)
 
   # Flag records with Death Date after Cut date
   dataset_updatedth <- dm_temp %>%
     mutate(DCUT_TEMP_DTHCHANGE = case_when(
-      DCUT_TEMP_DTHDT > DCUT_TEMP_DCUTDTM ~ "Y",
+      !is.na(DCUT_TEMP_DCUTDTM) & (DCUT_TEMP_DTHDT > DCUT_TEMP_DCUTDTM) ~ "Y",
       TRUE ~ as.character(NA)
     ))
 
+  # Ensure variable is character
+  dataset_updatedth$DCUT_TEMP_REMOVE <- as.character(dataset_updatedth$DCUT_TEMP_REMOVE)
+
   dataset_updatedth
 }

_pkgdown.yml

@@ -7,7 +7,7 @@ search:
 repo:
   url:
     home: https://github.com/pharmaverse/datacutr
-    source: https://github.com/pharmaverse/datacutr
+    source: https://github.com/pharmaverse/datacutr/blob/main/
     issue: https://github.com/pharmaverse/datacutr/issues/
     user: https://github.com/
 news:

tests/testthat/test-date_cut.R

@@ -178,3 +178,49 @@ test_that("All SDTMv dates are after datacut date", {
     expected_ae4
   )
 })
+
+# Test 5 - Datacut date is NA
+
+input_ae5 <- tibble::tribble(
+  ~STUDYID, ~USUBJID, ~AESEQ, ~AESTDTC,
+  "my_study", "subject1", 1, "2021-01-02",
+  "my_study", "subject1", 2, "2021-08-31",
+  "my_study", "subject1", 3, "2021-10-10",
+  "my_study", "subject2", 2, "2021-02-20",
+  "my_study", "subject3", 1, "2021-03-02"
+)
+
+input_dcut5 <- tibble::tribble(
+  ~STUDYID, ~USUBJID, ~DCUTDTM,
+  "my_study", "subject1", NA,
+  "my_study", "subject2", NA,
+  "my_study", "subject3", NA
+)
+
+
+expected_ae5 <- tibble::tribble(
+  ~STUDYID, ~USUBJID, ~AESEQ, ~AESTDTC, ~DCUT_TEMP_SDTM_DATE, ~DCUT_TEMP_DCUTDTM,
+  ~DCUT_TEMP_REMOVE,
+  "my_study", "subject1", 1, "2021-01-02", ymd_hms("2021-01-02T00:00:00"),
+  NA, NA_character_,
+  "my_study", "subject1", 2, "2021-08-31", ymd_hms("2021-08-31T00:00:00"),
+  NA, NA_character_,
+  "my_study", "subject1", 3, "2021-10-10", ymd_hms("2021-10-10T00:00:00"),
+  NA, NA_character_,
+  "my_study", "subject2", 2, "2021-02-20", ymd_hms("2021-02-20T00:00:00"),
+  NA, NA_character_,
+  "my_study", "subject3", 1, "2021-03-02", ymd_hms("2021-03-02T00:00:00"),
+  NA, NA_character_
+)
+
+test_that("DCUTDTM is NA", {
+  expect_equal(
+    date_cut(
+      dataset_sdtm = input_ae5,
+      sdtm_date_var = AESTDTC,
+      dataset_cut = input_dcut5,
+      cut_var = DCUTDTM
+    ),
+    expected_ae5
+  )
+})

tests/testthat/test-special_dm_cut.R

@@ -60,3 +60,53 @@ test_that("Error thrown if cut_var is not a POSIXt input", {
     regexp = "cut_var is expected to be of date type POSIXt"
   )
 })
+
+dcut_na <- tibble::tribble(
+  ~USUBJID, ~DCUTDTM,
+  "01-701-1015", NA,
+  "01-701-1023", NA,
+  "01-701-1028", NA,
+  "01-701-1033", NA,
+  "01-701-1047", NA,
+  "01-701-1057", NA,
+  "01-701-1097", NA,
+  "01-701-1111", NA,
+  "01-701-1115", NA,
+  "01-701-1118", NA
+)
+
+dm_expect_na <- tibble::tribble(
+  ~USUBJID, ~DTHDTC, ~DTHFL, ~DCUT_TEMP_REMOVE,
+  ~DCUT_TEMP_DTHDT, ~DCUT_TEMP_DCUTDTM, ~DCUT_TEMP_DTHCHANGE,
+  "01-701-1015", "", "", NA_character_,
+  NA, NA, NA_character_,
+  "01-701-1023", "2014-10-20", "Y", NA_character_,
+  ymd_hms("2014-10-20T00:00:00"), NA, NA_character_,
+  "01-701-1028", "2014-10-21", "Y", NA_character_,
+  ymd_hms("2014-10-21T00:00:00"), NA, NA_character_,
+  "01-701-1033", "2014-10-19", "Y", NA_character_,
+  ymd_hms("2014-10-19T00:00:00"), NA, NA_character_,
+  "01-701-1047", "2014-10-31", "Y", NA_character_,
+  ymd_hms("2014-10-31T00:00:00"), NA, NA_character_,
+  "01-701-1057", "2025-10-20", "Y", NA_character_,
+  ymd_hms("2025-10-20T00:00:00"), NA, NA_character_,
+  "01-701-1097", "2002-10-20", "Y", NA_character_,
+  ymd_hms("2002-10-20T00:00:00"), NA, NA_character_,
+  "01-701-1111", "", "Y", NA_character_,
+  NA, NA, NA_character_,
+  "01-701-1115", "", "Y", NA_character_,
+  NA, NA, NA_character_,
+  "01-701-1118", "2014-11-20", "", NA_character_,
+  ymd_hms("2014-11-20T00:00:00"), NA, NA_character_
+)
+
+test_that("Tests all expected outcomes when datacut date is NA", {
+  testthat::expect_equal(
+    special_dm_cut(
+      dataset_dm = dm,
+      dataset_cut = dcut_na,
+      cut_var = DCUTDTM
+    ),
+    dm_expect_na
+  )
+})