meddra function augment argument primary_soc to help save the ful…

…l meddra data

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: faers
 Title: R interface for FDA Adverse Event Reporting System
-Version: 1.1.4
+Version: 1.1.5
 Authors@R: 
  c(
  person("Yun", "Peng", , "yunyunp96@163.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2801-3332")),

NEWS.md

@@ -1,3 +1,9 @@
 # faers 0.99.0
 
 * Initial Bioconductor submission.
+
+# faers 1.1.4
+
+* fix error when download failed
+
+* meddra augment additional argument `primary_soc` to help save the full meddra data

R/meddra.R

@@ -28,10 +28,12 @@ NULL
 #' @param path A string, define the path of MedDRA directory.
 #' @param add_smq A bool, indicates whether Standardised MedDRA Queries (SMQ)
 #' should be added. If `TRUE`, "smq_content.asc", and "smq_list.asc" must exist.
+#' @param primary_soc A bool, indicates whether keep primary soc only.
 #' @export
 #' @rdname MedDRA-class
-meddra <- function(path, add_smq = FALSE) {
- hierarchy <- meddra_load_hierarchy(path, primary_soc = FALSE)
+meddra <- function(path, add_smq = FALSE, primary_soc = FALSE) {
+ assert_bool(primary_soc)
+ hierarchy <- meddra_load_hierarchy(path, primary_soc = primary_soc)
  version <- meddra_load_version(path)
  if (add_smq) {
  smq_data <- meddra_load_smq(path)

R/period.R

@@ -18,7 +18,7 @@ faers_before_period <- function(years, quarters, y, q, inclusive = TRUE) {
  if (!rlang::is_string(q, string = faers_file_quarters)) {
  cli::cli_abort("{.arg q} must be a string in {.val {faers_file_quarters}}")
  }
- assert_bool(inclusive, 1L)
+ assert_bool(inclusive)
  do.call(
  is_before_period,
  c(periods, list(y = y, q = q, inclusive = inclusive))

R/standardize.R

@@ -28,7 +28,7 @@ methods::setMethod("faers_standardize", "FAERSascii", function(object, meddra_pa
  # standardize PT terms
  # for indi
  assert_string(meddra_path)
- meddra_data <- meddra(meddra_path, add_smq = add_smq)
+ meddra_data <- meddra(meddra_path, add_smq = add_smq, primary_soc = TRUE)
  # https://stackoverflow.com/questions/70181149/is-a-saved-and-loaded-data-table-with-qs-a-correct-data-table
  # fix error: when load a saved FAERS object, don't change by reference
  cli::cli_alert("standardize {.field Preferred Term} in indi")

tests/testthat/test_meddra.R

@@ -8,19 +8,26 @@ testthat::test_that("meddra works well", {
  testthat::expect_true(rlang::is_string(meddra_load_version(path), "26.1"))
  testthat::expect_s3_class(data <- meddra_load_hierarchy(path), "data.table")
  testthat::expect_true(all(data$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(data$llt_code) == 0L)
  testthat::expect_s3_class(data <- meddra_load_smq(path), "data.table")
 
  # meddra() works well
- testthat::expect_s4_class(data <- meddra(path), "MedDRA")
+ testthat::expect_s4_class(
+ data <- meddra(path, primary_soc = TRUE), "MedDRA"
+ )
  testthat::expect_true(rlang::is_string(meddra_version(data), "26.1"))
  testthat::expect_s3_class(hierarchy <- meddra_hierarchy(data), "data.table")
  testthat::expect_null(hierarchy$smq_code)
+ testthat::expect_true(all(hierarchy$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(hierarchy$llt_code) == 0L)
  testthat::expect_null(meddra_smq(data))
 
  # meddra() with add_smq = TRUE, works well
- testthat::expect_s4_class(data <- meddra(path, TRUE), "MedDRA")
+ testthat::expect_s4_class(data <- meddra(path, TRUE, TRUE), "MedDRA")
  testthat::expect_true(rlang::is_string(meddra_version(data), "26.1"))
  testthat::expect_s3_class(hierarchy <- meddra_hierarchy(data), "data.table")
  testthat::expect_true(any(!is.na(hierarchy$smq_code)))
+ testthat::expect_true(all(hierarchy$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(hierarchy$llt_code) == 0L)
  testthat::expect_s3_class(meddra_smq(data), "data.table")
 })