remove dm_domain default

R/calculate_study_day.R

@@ -7,13 +7,13 @@
 #' NA will be returned for those records.
 #'
 #' @param sdtm_in Input data frame that contains the target date.
+#' @param dm_domain Reference date frame that contains the reference date.
 #' @param tgdt Target date from `sdtm_in` that will be used to calculate the study
 #' day.
-#' @param study_day_var New study day variable name in the output. For
-#' example, AESTDY for AE domain and CMSTDY for CM domain.
-#' @param dm_domain Reference date frame that contains the reference date.
 #' @param refdt Reference date from `dm_domain` that will be used as reference to
 #' calculate the study day.
+#' @param study_day_var New study day variable name in the output. For
+#' example, AESTDY for AE domain and CMSTDY for CM domain.
 #' @param merge_key Character to represents the merging key between `sdtm_in` and
 #' `dm_domain`.
 #'
@@ -33,16 +33,15 @@
 #' )
 #' ae$AESTDTC <- as.Date(ae$AESTDTC)
 #' dm$RFSTDTC <- as.Date(dm$RFSTDTC)
-#' calculate_study_day(ae, "AESTDTC", "AESTDY", "dm", "RFSTDTC")
+#' calculate_study_day(ae, dm, "AESTDTC", "RFSTDTC", "AESTDY")
 #'
 calculate_study_day <- function(sdtm_in,
+                                dm_domain,
                                 tgdt,
+                                refdt,
                                 study_day_var,
-                                dm_domain = "DM",
-                                refdt = "RFSTDTC",
                                 merge_key = "USUBJID") {
   assertthat::assert_that(is.data.frame(sdtm_in))
-  dm_domain <- eval(parse(text = dm_domain))
   assertthat::assert_that(is.data.frame(dm_domain))
   assertthat::assert_that(
     utils::hasName(dm_domain, refdt),

tests/testthat/test-calculate_study_day.R

@@ -19,23 +19,23 @@ test_that("`calculate_study_day()` works as expected for invalid input", {
     "dm_domain is not a data frame"
   )
   expect_error(
-    calculate_study_day(iris, "d", "e", "iris", "b"),
+    calculate_study_day(iris, iris, "d", "e", "b"),
     "dm_domain needs to have the variable of refdt"
   )
   expect_error(
-    calculate_study_day(iris, "e", "d", "iris", "Species"),
+    calculate_study_day(iris, iris, "d", "Species"),
     "sdtm_in needs to have the variable of tgdt"
   )
   expect_error(
-    calculate_study_day(iris, "Petal.Length", "e", "iris", "Species"),
+    calculate_study_day(iris, iris, "Petal.Length", "Species", "e"),
     "needs to have the variable of merge_key"
   )
   expect_error(
-    calculate_study_day(iris, "Petal.Length", 123L, "iris", "Species", "Species"),
+    calculate_study_day(iris, iris, "Petal.Length", "Species", 123L, "Species"),
     "study_day_var is not a character vector"
   )
   expect_warning(
-    calculate_study_day(ae, "AESTDTC", "AENDY", "dm", "RFSTDTC"),
+    calculate_study_day(ae, dm, "AESTDTC", "RFSTDTC", "AENDY"),
     "Target date and the returned study day doesn't match."
   )
 
@@ -45,7 +45,7 @@ test_that("`calculate_study_day()` works as expected for invalid input", {
     stringsAsFactors = FALSE
   )
   expect_warning(
-    calculate_study_day(ae, "AESTDTC", "AESTDY", "dm1", "RFSTDTC"),
+    calculate_study_day(ae, dm1, "AESTDTC", "RFSTDTC", "AESTDY"),
     "Reference date is not unique for each patient!"
   )
 
@@ -55,13 +55,13 @@ test_that("`calculate_study_day()` works as expected for invalid input", {
     stringsAsFactors = FALSE
   )
   expect_warning(
-    calculate_study_day(ae, "AESTDTC", "AESTDY", "dm2", "RFSTDTC"),
+    calculate_study_day(ae, dm2, "AESTDTC", "RFSTDTC", "AESTDY"),
     "Encountered errors when converting refdt to dates."
   )
 })
 
 test_that("`calculate_study_day()` works as expected for valid input", {
-  res <- calculate_study_day(ae, "AESTDTC", "AESTDY", "dm", "RFSTDTC")
+  res <- calculate_study_day(ae, dm, "AESTDTC", "RFSTDTC", "AESTDY")
   expected <- c(-31L, 1L, NA)
   expect_equal(res$AESTDY, expected, tolerance = "1.5e-08")
 })