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95 lines
4.6 KiB
R
95 lines
4.6 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("mo_property.R")
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test_that("mo_property works", {
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expect_equal(mo_kingdom("E. coli"), "Bacteria")
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expect_equal(mo_phylum("E. coli"), "Proteobacteria")
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expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
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expect_equal(mo_order("E. coli"), "Enterobacteriales")
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expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
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expect_equal(mo_genus("E. coli"), "Escherichia")
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expect_equal(mo_species("E. coli"), "coli")
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expect_equal(mo_subspecies("E. coli"), "")
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expect_equal(mo_fullname("E. coli"), "Escherichia coli")
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expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
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expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
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expect_equal(class(mo_taxonomy("E. coli")), "list")
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expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies"))
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expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
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expect_equal(mo_authors("E. coli"), "Castellani et al.")
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expect_equal(mo_year("E. coli"), 1919)
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expect_equal(mo_shortname("MRSA"), "S. aureus")
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expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
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expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
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expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
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expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
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# test integrity
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MOs <- AMR::microorganisms
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expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
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# check languages
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expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
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expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")
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expect_output(print(mo_gramstain("E. coli", language = "en")))
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expect_output(print(mo_gramstain("E. coli", language = "de")))
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expect_output(print(mo_gramstain("E. coli", language = "nl")))
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expect_output(print(mo_gramstain("E. coli", language = "es")))
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expect_output(print(mo_gramstain("E. coli", language = "pt")))
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expect_output(print(mo_gramstain("E. coli", language = "it")))
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expect_output(print(mo_gramstain("E. coli", language = "fr")))
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expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
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# manual property function
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expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
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expect_error(mo_property("E. coli", property = "UNKNOWN"))
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expect_identical(mo_property("E. coli", property = "fullname"),
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mo_fullname("E. coli"))
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expect_identical(mo_property("E. coli", property = "genus"),
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mo_genus("E. coli"))
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expect_identical(mo_property("E. coli", property = "species"),
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mo_species("E. coli"))
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expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
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expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
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# outcome of mo_fullname must always return the fullname from the data set
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library(dplyr)
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a <- microorganisms %>%
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transmute(mo,
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# fullname from the original data:
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f1 = fullname,
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# newly created fullname based on MO code:
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f2 = mo_fullname(mo, language = "en")) %>%
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filter(f1 != f2)
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expect_equal(nrow(a), 0)
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})
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