Merge pull request #87 from OxfordIHTM/dev

add tests for new functions

R/cod_check_dod.R

@@ -18,7 +18,7 @@ cod_check_dod <- function(dod) {
   dod_check <- ifelse(is.na(dod), 1L, 0L)
 
   dod_check <- ifelse(
-    stringr::str_detect(string = dod, pattern = "[0-9]{4}", negate = TRUE),
+    nchar(dod) > 4 | stringr::str_detect(dod, pattern = "[a-zA-Z]"),
     1L, 0L
   )
 

R/cod_check_input.R

@@ -53,7 +53,7 @@ cod_check_codedit_input <- function(df) {
   ## Return tibble of check results ----
   tibble::tibble(
     sex_check, age_check,
-    code_check = tibble::tibble(code_check, code_check_note),
+    code_check, code_check_note,
     dod_check
   )
 }

R/cod_structure_input.R

@@ -19,7 +19,7 @@
 #'   record identifiers. Default to NULL. If NULL, unique record identifiers
 #'   will be generated.
 #'
-#' @returns A data.frame with 6 columns and number of rows equal to `df` with
+#' @returns A tibble with 6 columns and number of rows equal to `df` with
 #'   names `"FreeId"`, `"Sex"`, `"Age Value"`, `"Age Type"`, `"Code"`, and
 #'   `"Death Date"`.
 #'

tests/testthat/test-cod_check_dod.R

@@ -0,0 +1,22 @@
+# Tets for cod_check_dod -------------------------------------------------------
+
+testthat::test_that(
+  "cod_check_dod outputs appropriate results", {
+    expect_s3_class(cod_check_dod("2024"), "tbl")
+
+    expect_identical(
+      cod_check_dod("2024"),
+      tibble::tibble(
+        dod_check = 0L,
+        dod_check_note = "No issues with date of death value"
+      )
+    )
+
+    expect_identical(
+      cod_check_dod("2024-06-01"),
+      tibble::tibble(
+        dod_check = 1L,
+        dod_check_note = "Date of death value is not in year format"
+      )
+    )
+})

tests/testthat/test-cod_check_input.R

@@ -0,0 +1,18 @@
+# Tests for cod_check_input ----------------------------------------------------
+
+testthat::test_that(
+  "cod_check_input outputs appropriate results", {
+    expect_s3_class(cod_check_codedit_input(icd10_example), "tbl")
+
+    expect_named(
+      cod_check_codedit_input(icd10_example),
+      c("sex_check", "sex_check_note",
+        "age_check", "age_check_note",
+        "code_check", "code_check_note",
+        "dod_check", "dod_check_note")
+    )
+
+    expect_warning(
+      cod_check_codedit_input(icd10_example |> dplyr::select(-FreeId))
+    )
+})

tests/testthat/test-cod_structure_input.R

@@ -0,0 +1,27 @@
+# Tests for cod_structure_input ------------------------------------------------
+
+df <- data.frame(
+  id = 1:3,
+  sex = c(1, 1, 2),
+  dob = c("1977-11-05", "1971-04-04", "2012-08-13"),
+  dod = c("2024-06-28", "2023-10-11", "2023-09-25"),
+  code = c("P219", "O230", "Q913")
+)
+
+
+testthat::test_that(
+  "cod_structure_input outputs appropriate results", {
+    expect_s3_class(
+      cod_structure_input(
+        df, sex = "sex", dob = "dob", dod = "dod", code = "code"
+      ),
+      "tbl"
+    )
+
+    expect_s3_class(
+      cod_structure_input(
+        df = df, sex = "sex", dob = "dob", dod = "dod", code = "code", id = "id"
+      ),
+      "tbl"
+    )
+})