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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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53
tests/testthat/test-custom_microorganisms.R
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@ -27,33 +27,36 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_identical(
as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter asburiae")
)
suppressMessages(
add_custom_microorganisms(
data.frame(
mo = "ENT_ASB_CLO",
genus = "Enterobacter",
species = "asburiae/cloacae"
test_that("custom mo works", {
expect_identical(
as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter asburiae")
)
suppressMessages(
add_custom_microorganisms(
data.frame(
mo = "ENT_ASB_CLO",
genus = "Enterobacter",
species = "asburiae/cloacae"
)
)
)
)
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(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")
if (getRversion() >= "3.3.0") {
# until R 3.2, abbreviate() used a completely different algorithm, making these tests unreproducible
expect_identical(
paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
as.character(as.mo("Klebsiella pneumoniae"))
)
expect_identical(
paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
as.character(as.mo("Aerococcus urinae"))
)
}
if (getRversion() >= "3.3.0") {
# until R 3.2, abbreviate() used a completely different algorithm, making these tests unreproducible
expect_identical(
paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
as.character(as.mo("Klebsiella pneumoniae"))
)
expect_identical(
paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
as.character(as.mo("Aerococcus urinae"))
)
}
})