AMR/tests/testthat/test-mo_property.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# 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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# 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("mo_property.R")
test_that("mo_property works", {
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expect_equal(mo_kingdom("E. coli"), "Bacteria")
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expect_equal(mo_subkingdom("E. coli"), "Negibacteria")
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expect_equal(mo_phylum("E. coli"), "Proteobacteria")
expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
expect_equal(mo_order("E. coli"), "Enterobacteriales")
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_)
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
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(mo_TSN("E. coli"), 285)
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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", "subkingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
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expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919")
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expect_equal(mo_authors("E. coli"), "Castellani and Chalmers")
expect_equal(mo_year("E. coli"), 1919)
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expect_equal(mo_shortname("MRSA"), "S. aureus")
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. aga"), "S. agalactiae")
expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
# test integrity
MOs <- AMR::microorganisms
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
# check languages
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expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("E. coli", language = "nl"), "Gram-negatief")
expect_output(print(mo_gramstain("E. coli", language = "en")))
expect_output(print(mo_gramstain("E. coli", language = "de")))
expect_output(print(mo_gramstain("E. coli", language = "nl")))
expect_output(print(mo_gramstain("E. coli", language = "es")))
expect_output(print(mo_gramstain("E. coli", language = "pt")))
expect_output(print(mo_gramstain("E. coli", language = "it")))
expect_output(print(mo_gramstain("E. coli", language = "fr")))
expect_error(mo_gramstain("E. coli", language = "UNKNOWN"))
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# manual property function
expect_error(mo_property("E. coli", property = c("tsn", "fullname")))
expect_error(mo_property("E. coli", property = "UNKNOWN"))
expect_identical(mo_property("E. coli", property = "fullname"),
mo_fullname("E. coli"))
expect_identical(mo_property("E. coli", property = "genus"),
mo_genus("E. coli"))
expect_identical(mo_property("E. coli", property = "species"),
mo_species("E. coli"))
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# check vector with random values
library(dplyr)
df_sample <- AMR::microorganisms %>% sample_n(100)
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expect_identical(df_sample %>% pull(mo) %>% mo_fullname(language = "en"),
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df_sample %>% pull(fullname))
})