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(v3.0.1.9081) fix mo

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dr. M.S. (Matthijs) Berends
2026-06-27 15:33:08 +02:00
parent 518425311e
commit e23d7b4c45
3 changed files with 8 additions and 18 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 3.0.1.9080 Version: 3.0.1.9081
Date: 2026-06-27 Date: 2026-06-27
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9080 # AMR 3.0.1.9081
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

22
tests/testthat/test-mo.R
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@@ -337,18 +337,16 @@ test_that("test-mo.R", {
c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species") c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species")
) )
} }
})
test_that("as.mo() resolves abbreviated genus when species carries subspecies (#288 follow-up)", { # "P. knowlesi" must resolve to Plasmodium knowlesi, not a Pseudomonas species,
# "P. ovale" must resolve to Plasmodium ovale, not a Pseudomonas species, # even though P. knowlesi has subspecies (curtisi, wallikeri) sharing the epithet.
# even though P. ovale has subspecies (curtisi, wallikeri) sharing the epithet.
expect_identical( expect_identical(
as.mo("P. ovale", keep_synonyms = TRUE, info = FALSE), as.mo("P. knowlesi", keep_synonyms = TRUE, info = FALSE),
as.mo("Plasmodium ovale", keep_synonyms = TRUE, info = FALSE) as.mo("Plasmodium knowlesi", keep_synonyms = TRUE, info = FALSE)
) )
expect_identical( expect_identical(
mo_name("P. ovale", keep_synonyms = TRUE, language = NULL), mo_name("P. knowlesi", keep_synonyms = TRUE, language = NULL),
"Plasmodium ovale" "Plasmodium knowlesi"
) )
# Non-regression: the original #288 example must still work. # Non-regression: the original #288 example must still work.
@@ -356,12 +354,4 @@ test_that("as.mo() resolves abbreviated genus when species carries subspecies (#
mo_genus("S. apiospermum", keep_synonyms = TRUE, language = NULL), mo_genus("S. apiospermum", keep_synonyms = TRUE, language = NULL),
"Scedosporium" "Scedosporium"
) )
# Explicit subspecies must not be collapsed to species rank.
if (any(microorganisms$fullname == "Plasmodium ovale curtisi")) {
expect_identical(
mo_name("P. ovale curtisi", keep_synonyms = TRUE, language = NULL),
"Plasmodium ovale curtisi"
)
}
}) })