mirror of https://github.com/msberends/AMR.git
95 lines
4.6 KiB
R
95 lines
4.6 KiB
R
# ==================================================================== #
|
|
# 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("mo_property.R")
|
|
|
|
test_that("mo_property works", {
|
|
expect_equal(mo_kingdom("E. coli"), "Bacteria")
|
|
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"), "")
|
|
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
|
|
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
|
|
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
|
|
expect_equal(class(mo_taxonomy("E. coli")), "list")
|
|
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
|
|
"family", "genus", "species", "subspecies"))
|
|
|
|
expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
|
|
expect_equal(mo_authors("E. coli"), "Castellani et al.")
|
|
expect_equal(mo_year("E. coli"), 1919)
|
|
|
|
expect_equal(mo_shortname("MRSA"), "S. aureus")
|
|
expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
|
|
expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
|
|
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
|
|
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
|
|
|
|
# test integrity
|
|
MOs <- AMR::microorganisms
|
|
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
|
|
|
|
# check languages
|
|
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"))
|
|
|
|
# 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"))
|
|
|
|
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
|
|
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
|
|
|
|
|
|
# outcome of mo_fullname must always return the fullname from the data set
|
|
library(dplyr)
|
|
a <- microorganisms %>%
|
|
transmute(mo,
|
|
# fullname from the original data:
|
|
f1 = fullname,
|
|
# newly created fullname based on MO code:
|
|
f2 = mo_fullname(mo, language = "en")) %>%
|
|
filter(f1 != f2)
|
|
|
|
expect_equal(nrow(a), 0)
|
|
|
|
})
|