mirror of https://github.com/msberends/AMR.git
68 lines
3.2 KiB
R
Executable File
68 lines
3.2 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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context("join_microorganisms.R")
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test_that("joins work", {
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skip_on_cran()
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unjoined <- example_isolates
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inner <- example_isolates %>% inner_join_microorganisms()
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left <- example_isolates %>% left_join_microorganisms()
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semi <- example_isolates %>% semi_join_microorganisms()
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anti <- example_isolates %>% anti_join_microorganisms()
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suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
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suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
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expect_true(ncol(unjoined) < ncol(inner))
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expect_true(nrow(unjoined) == nrow(inner))
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expect_true(ncol(unjoined) < ncol(left))
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expect_true(nrow(unjoined) == nrow(left))
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expect_true(ncol(semi) == ncol(semi))
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expect_true(nrow(semi) == nrow(semi))
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expect_true(nrow(anti) == 0)
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expect_true(nrow(unjoined) < nrow(right))
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expect_true(nrow(unjoined) < nrow(full))
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expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
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expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
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expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
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expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
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expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
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expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
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expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
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library(dplyr, warn.conflicts = FALSE)
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x <- tibble(bact = as.mo("E.coli"))
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expect_warning(left_join_microorganisms(x %>% group_by(bact), "bact"))
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})
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