(Closes issue #131) Make cal_min_max_date (and by extension oak_cal_ref_dates) work with Date objects and hms time objects (not just character date and time strings)

NEWS.md

@@ -1,3 +1,7 @@
+# sdtm.oak V0.2.1
+
+Cal_min_max_date (and by extension oak_cal_ref_dates) now works with raw data containing Date objects and hms time objects (not just character date and time strings).
+
 # sdtm.oak V0.2.0
 
 - DM Domain: New functions `calc_min_max_date()` and `oak_calc_ref_dates()` to support DM domain programming.

R/cal_min_max_date.R

@@ -73,7 +73,7 @@ cal_min_max_date <- function(raw_dataset,
 
   # Time is not used in reference date then use only date
   if (is.na(time_variable)) {
-    fin_df$datetime <- create_iso8601(raw_dataset[[date_variable]],
+    fin_df$datetime <- create_iso8601(as.character(raw_dataset[[date_variable]]),
       .format = date_format
     )
   } else {

tests/testthat/test-cal_min_max_date.R

@@ -24,7 +24,7 @@ test_that("Warn if date variable parameter is NULL", {
   expect_identical(observed, expected)
 })
 
-test_that("cal_min_max_date works as expected", {
+test_that("cal_min_max_date works with date and time strings", {
   EX <- tibble::tribble(
     ~patient_number,    ~EX_ST_DT, ~EX_ST_TM,
     "001",           "26-04-2022", "10:20",
@@ -93,3 +93,70 @@ test_that("Warning is displayed if date or time variables parameters passed are
 
   expect_identical(observed, expected)
 })
+
+test_that("cal_min_max_date works with Date and hms (time) objects", {
+  EX <- tibble::tribble(
+    ~patient_number,    ~EX_ST_DT,            ~EX_ST_TM,
+    "001",           as.Date("2022-04-26"), hms::hms(seconds = NULL, minutes = 20L, hours = 10L),
+    "001",           as.Date("2022-04-25"), hms::hms(seconds = NULL, minutes = 15L, hours = 10L),
+    "001",           as.Date("2022-04-25"), hms::hms(seconds = NULL, minutes = 19L, hours = 10L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 23L, hours = 6L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 59L, hours = 4L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 59L, hours = 5L)
+  )
+  expected_min <- tibble::tribble(
+    ~patient_number,          ~datetime,
+    "001",           "2022-04-25T10:15:00",
+    "002",           "2022-05-26T04:59:00"
+  )
+
+  expected_max <- tibble::tribble(
+    ~patient_number,           ~datetime,
+    "002",            "2022-05-26T06:23:00",
+    "001",            "2022-04-26T10:20:00"
+  )
+
+  observed_min <- cal_min_max_date(EX,
+    date_variable = "EX_ST_DT",
+    time_variable = "EX_ST_TM",
+    val_type = "min",
+    date_format = "y-m-d",
+    time_format = "H:M:S"
+  )
+
+  expect_identical(observed_min, expected_min)
+
+  observed_max <- cal_min_max_date(EX,
+    date_variable = "EX_ST_DT",
+    time_variable = "EX_ST_TM",
+    val_type = "max",
+    date_format = "y-m-d",
+    time_format = "H:M:S"
+  )
+
+  expect_identical(observed_max, expected_max)
+})
+
+test_that("cal_min_max_date works with Date objects (no time)", {
+  EX <- tibble::tribble(
+    ~patient_number,    ~EX_ST_DT,
+    "001",           as.Date("04-25-22", "%m-%d-%y"),
+    "001",           as.Date("04-25-22", "%m-%d-%y"),
+    "002",           as.Date("05-26-22", "%m-%d-%y")
+  )
+  expected_min <- tibble::tribble(
+    ~patient_number,    ~datetime,
+    "001",           create_iso8601("04-25-22", .format = "m-d-y"),
+    "002",           create_iso8601("05-26-22", .format = "m-d-y")
+  )
+
+  observed_min <- cal_min_max_date(EX,
+    date_variable = "EX_ST_DT",
+    time_variable = NA,
+    val_type = "min",
+    date_format = "y-m-d",
+    time_format = NA
+  )
+
+  expect_identical(observed_min, expected_min)
+})

tests/testthat/test-oak_cal_ref_dates.R

@@ -63,3 +63,100 @@ test_that("Calculate the Reference dates :RFENDTC", {
   expected_rfendtc <- expected |> dplyr::select(-"RFSTDTC")
   expect_identical(observed_rfendtc, expected_rfendtc)
 })
+
+test_that("oak_cal_ref_dates works with Date and hms (time) objects", {
+  dm <- tibble::tribble(
+    ~patient_number,
+    "001",
+    "002"
+  )
+
+  EX <- tibble::tribble(
+    ~patient_number, ~EX_ST_DT,             ~EX_ST_TM,
+    "001",           as.Date("2022-04-26"), hms::hms(seconds = NULL, minutes = 20L, hours = 10L),
+    "001",           as.Date("2022-04-25"), hms::hms(seconds = NULL, minutes = 15L, hours = 10L),
+    "001",           as.Date("2022-04-25"), hms::hms(seconds = NULL, minutes = 19L, hours = 10L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 23L, hours = 6L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 59L, hours = 4L),
+    "002",           as.Date("2022-05-26"), hms::hms(seconds = NULL, minutes = 59L, hours = 5L)
+  )
+
+  ref_date_conf_df <- tibble::tribble(
+    ~raw_dataset_name, ~date_var, ~time_var, ~dformat, ~tformat, ~sdtm_var_name,
+    "EX", "EX_ST_DT", "EX_ST_TM", "y-m-d", "H:M:S", "RFSTDTC"
+  )
+
+  raw_source <- list(EX = EX)
+
+  observed_min <- oak_cal_ref_dates(dm,
+    der_var = "RFSTDTC",
+    min_max = "min",
+    ref_date_config_df = ref_date_conf_df,
+    raw_source = raw_source
+  )
+
+  expected_min <- tibble::tribble(
+    ~patient_number, ~RFSTDTC,
+    "001",           "2022-04-25T10:15:00",
+    "002",           "2022-05-26T04:59:00"
+  )
+
+  expect_identical(observed_min, expected_min)
+
+  ref_date_conf_df_max <- tibble::tribble(
+    ~raw_dataset_name, ~date_var, ~time_var, ~dformat, ~tformat, ~sdtm_var_name,
+    "EX", "EX_ST_DT", "EX_ST_TM", "y-m-d", "H:M:S", "RFENDTC"
+  )
+
+  observed_max <- oak_cal_ref_dates(dm,
+    der_var = "RFENDTC",
+    min_max = "max",
+    ref_date_config_df = ref_date_conf_df_max,
+    raw_source = raw_source
+  )
+
+  expected_max <- tibble::tribble(
+    ~patient_number, ~RFENDTC,
+    "001",           "2022-04-26T10:20:00",
+    "002",           "2022-05-26T06:23:00"
+  )
+
+  expect_identical(observed_max, expected_max)
+})
+
+test_that("oak_cal_ref_dates works with Date objects (no time)", {
+  dm <- tibble::tribble(
+    ~patient_number,
+    "001",
+    "002"
+  )
+
+  EX <- tibble::tribble(
+    ~patient_number, ~EX_ST_DT,
+    "001",           as.Date("04-25-22", "%m-%d-%y"),
+    "001",           as.Date("04-25-22", "%m-%d-%y"),
+    "002",           as.Date("05-26-22", "%m-%d-%y")
+  )
+
+  ref_date_conf_df <- tibble::tribble(
+    ~raw_dataset_name, ~date_var, ~time_var, ~dformat, ~tformat, ~sdtm_var_name,
+    "EX", "EX_ST_DT", NA_character_, "y-m-d", NA_character_, "RFSTDTC"
+  )
+
+  raw_source <- list(EX = EX)
+
+  observed_min <- oak_cal_ref_dates(dm,
+    der_var = "RFSTDTC",
+    min_max = "min",
+    ref_date_config_df = ref_date_conf_df,
+    raw_source = raw_source
+  )
+
+  expected_min <- tibble::tribble(
+    ~patient_number,    ~RFSTDTC,
+    "001",           create_iso8601("04-25-22", .format = "m-d-y"),
+    "002",           create_iso8601("05-26-22", .format = "m-d-y")
+  )
+
+  expect_identical(observed_min, expected_min)
+})