mirror of https://github.com/msberends/AMR.git
47 lines
2.1 KiB
R
47 lines
2.1 KiB
R
context("mo_property.R")
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test_that("mo_property works", {
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expect_equal(mo_subkingdom("E. coli"), "Negibacteria")
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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(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"), "CoPS")
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expect_equal(mo_shortname("S. aga"), "S. agalactiae")
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expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
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# test integrity
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library(dplyr)
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rnd <- sample(1:nrow(AMR::microorganisms), 500, replace = FALSE) # random 500 rows
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MOs <- AMR::microorganisms %>% filter(!is.na(mo),
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species != "species",
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dplyr::row_number() %in% rnd)
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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_type("E. coli", language = "nl"), "Bacteri\u00ebn")
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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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})
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