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Fix for antibiogram() in R <=3.4

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-13 10:21:43 +01:00
parent 45a9697c84
commit b6d2b1398d
5 changed files with 40 additions and 37 deletions
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9
inst/tinytest/test-mo.R
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@ -124,8 +124,8 @@ expect_identical(as.character(as.mo(" ")), NA_character_)
expect_warning(as.mo("ab"))
expect_identical(
suppressWarnings(as.character(as.mo(c("Qq species", "", "MRSA", "K. pneu rhino", "esco")))),
c("UNKNOWN", NA_character_, "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
)
# check for Becker classification
@ -317,10 +317,7 @@ expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))
# ignoring patterns
expect_identical(
as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
c("B_ESCHR_COLI", NA)
)
expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))
# frequency tables
if (AMR:::pkg_is_available("cleaner")) {