From 233c0c029dcad47cbb07a7b770d920de1fc094cb Mon Sep 17 00:00:00 2001 From: yun Date: Mon, 6 Nov 2023 23:35:09 +0800 Subject: [PATCH] remove duplicated primaryids --- R/methods-utils.R | 2 +- tests/testthat/test_methods.R | 23 +++++++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) diff --git a/R/methods-utils.R b/R/methods-utils.R index 72e73cb..c17a7ce 100644 --- 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 index bf77c5b..95dd4b0 100644 --- 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", {