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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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26
tests/testthat/test-custom_microorganisms.R
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@@ -27,14 +27,18 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_identical(as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter asburiae"))
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")
data.frame(
mo = "ENT_ASB_CLO",
genus = "Enterobacter",
species = "asburiae/cloacae"
)
)
)
@@ -44,8 +48,12 @@ 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")))
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"))
)
}