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add oxygen tolerance

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-05-11 21:56:27 +02:00
parent bf08d136a0
commit 91fa73dedf
28 changed files with 52310 additions and 52203 deletions
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0
inst/tinytest/test-add_custom_antimicrobials.R → inst/tinytest/test-custom_antimicrobials.R
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3
inst/tinytest/test-add_custom_microorganisms.R → inst/tinytest/test-custom_microorganisms.R
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@ -41,3 +41,6 @@ suppressMessages(
expect_identical(as.character(as.mo("ENT_ASB_CLO")), "ENT_ASB_CLO")
expect_identical(mo_name("ENT_ASB_CLO"), "Enterobacter asburiae/cloacae")
expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
expect_identical(paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
as.character(as.mo("Klebsiella pneumoniae")))

7
inst/tinytest/test-mo_property.R
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@ -98,11 +98,14 @@ expect_equal(names(mo_info("Escherichia coli")), c(
"mo",
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"status", "synonyms", "gramstain", "url", "ref",
"snomed"
"status", "synonyms", "gramstain", "oxygen_tolerance",
"url", "ref", "snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
c("aerobe", "anaerobe"))
expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
c("1561", "422", "1", "16"))