AMR/tests/testthat/test-join_microorganisms.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
context("join_microorganisms.R")
test_that("joins work", {
unjoined <- septic_patients
inner <- septic_patients %>% inner_join_microorganisms()
left <- septic_patients %>% left_join_microorganisms()
semi <- septic_patients %>% semi_join_microorganisms()
anti <- septic_patients %>% anti_join_microorganisms()
suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
expect_true(ncol(unjoined) < ncol(inner))
expect_true(nrow(unjoined) == nrow(inner))
expect_true(ncol(unjoined) < ncol(left))
expect_true(nrow(unjoined) == nrow(left))
expect_true(ncol(semi) == ncol(semi))
expect_true(nrow(semi) == nrow(semi))
expect_true(nrow(anti) == 0)
expect_true(nrow(unjoined) < nrow(right))
expect_true(nrow(unjoined) < nrow(full))
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COL")), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COL", by = c("mo" = "mo"))), 1)
expect_warning(inner_join_microorganisms("Escherichia", by = c("mo" = "genus")))
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COL")), 1)
expect_warning(left_join_microorganisms("Escherichia", by = c("mo" = "genus")))
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COL")), 1)
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COL")), 0)
expect_warning(right_join_microorganisms("B_ESCHR_COL"))
expect_warning(full_join_microorganisms("B_ESCHR_COL"))
})