remove duplicated primaryids

Yunuuuu · Nov 6, 2023 · 233c0c0 · 233c0c0
1 parent 7920385
commit 233c0c0
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Showing 2 changed files with 24 additions and 1 deletion.
diff --git a/R/methods-utils.R b/R/methods-utils.R
@@ -155,7 +155,7 @@ methods::setMethod("faers_keep", "FAERSascii", function(object, primaryid = NULL
  }
  # as all data has a column primaryid, we just rename the variable to use it
  # in the data.table `i`
- .__primaryid__. <- as.character(primaryid)
+ .__primaryid__. <- unique(as.character(primaryid))
  if (isTRUE(invert)) {
  object@data <- lapply(object@data, function(x) {
  x[!.__primaryid__., on = "primaryid"]

diff --git a/tests/testthat/test_methods.R b/tests/testthat/test_methods.R
@@ -120,6 +120,7 @@ testthat::test_that("faers_keep works well", {
  testthat::expect_in(data2_invert$rpsr$primaryid, ids2_invert)
  testthat::expect_in(data2_invert$outc$primaryid, ids2_invert)
 
+ # for non-exist primarids
  ids3 <- "none_exist_ids"
  data3 <- faers_keep(data, ids3)
  testthat::expect_equal(nrow(data3$drug), 0L)
@@ -130,6 +131,28 @@ testthat::test_that("faers_keep works well", {
  testthat::expect_equal(nrow(data3$outc), 0L)
  data4 <- faers_keep(data, ids3, invert = TRUE)
  testthat::expect_identical(data4, data)
+
+ # for duplicated primarids
+ ids4 <- rep(ids2, 2L)
+ ids4_invert <- setdiff(faers_primaryid(data), ids4)
+ data4 <- faers_keep(data, ids4)
+ data4_invert <- faers_keep(data, ids4, invert = TRUE)
+ testthat::expect_true(anyDuplicated(data4$demo) == 0L)
+ testthat::expect_setequal(data4$demo$primaryid, ids4)
+ testthat::expect_in(data4$drug$primaryid, ids4)
+ testthat::expect_in(data4$indi$primaryid, ids4)
+ testthat::expect_in(data4$reac$primaryid, ids4)
+ testthat::expect_in(data4$ther$primaryid, ids4)
+ testthat::expect_in(data4$rpsr$primaryid, ids4)
+ testthat::expect_in(data4$outc$primaryid, ids4)
+
+ testthat::expect_setequal(data4_invert$demo$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$drug$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$indi$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$reac$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$ther$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$rpsr$primaryid, ids4_invert)
+ testthat::expect_in(data4_invert$outc$primaryid, ids4_invert)
 })
 
 testthat::test_that("faers_filter works well", {