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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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132
tests/testthat/test-ab.R
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@ -27,80 +27,82 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
ab_reset_session()
test_that("ab works", {
ab_reset_session()
expect_equal(
as.character(as.ab(c(
"J01FA01",
"J 01 FA 01",
"Erythromycin",
"eryt",
"ERYT",
"ERY",
"erytromicine",
"Erythrocin",
"Romycin"
))),
rep("ERY", 9)
)
expect_equal(
as.character(as.ab(c(
"J01FA01",
"J 01 FA 01",
"Erythromycin",
"eryt",
"ERYT",
"ERY",
"erytromicine",
"Erythrocin",
"Romycin"
))),
rep("ERY", 9)
)
expect_identical(class(as.ab("amox")), c("ab", "character"))
expect_identical(class(antibiotics$ab), c("ab", "character"))
expect_true(is.ab(as.ab("amox")))
expect_stdout(print(as.ab("amox")))
expect_stdout(print(data.frame(a = as.ab("amox"))))
expect_identical(class(as.ab("amox")), c("ab", "character"))
expect_identical(class(AMR::antimicrobials$ab), c("ab", "character"))
expect_true(is.ab(as.ab("amox")))
expect_output(print(as.ab("amox")))
expect_output(print(data.frame(a = as.ab("amox"))))
expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
# expect_warning(as.ab("UNKNOWN"))
expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
# expect_warning(as.ab("UNKNOWN"))
expect_stdout(print(as.ab("amox")))
expect_output(print(as.ab("amox")))
expect_equal(
as.character(as.ab("Phloxapen")),
"FLC"
)
expect_equal(
as.character(as.ab("Phloxapen")),
"FLC"
)
expect_equal(
suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP")
)
expect_equal(
suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP")
)
expect_equal(
as.character(as.ab("Amoxy + clavulaanzuur")),
"AMC"
)
expect_equal(
as.character(as.ab("Amoxy + clavulaanzuur")),
"AMC"
)
expect_equal(
as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
c("MEM", "AMC")
)
expect_equal(
as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
c("MEM", "AMC")
)
# expect_warning(as.ab("cipro mero"))
# expect_warning(as.ab("cipro mero"))
# based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
# based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
expect_identical(
as.character(as.ab(c(
"gentamicine High Level",
"gentamicine High",
"gentamicine (High Level)",
"gentamicine (High)",
"gentamicine HL",
"gentamicine H-L",
"gentamicine (HL)",
"gentamicine (H-L)"
))),
rep("GEH", 8)
)
expect_identical(
as.character(as.ab(c(
"gentamicine High Level",
"gentamicine High",
"gentamicine (High Level)",
"gentamicine (High)",
"gentamicine HL",
"gentamicine H-L",
"gentamicine (HL)",
"gentamicine (H-L)"
))),
rep("GEH", 8)
)
# assigning and subsetting
x <- antibiotics$ab
expect_inherits(x[1], "ab")
expect_inherits(x[[1]], "ab")
expect_inherits(c(x[1], x[9]), "ab")
expect_inherits(unique(x[1], x[9]), "ab")
expect_inherits(rep(x[1], 2), "ab")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))
# assigning and subsetting
x <- AMR::antimicrobials$ab
expect_inherits(x[1], "ab")
expect_inherits(x[[1]], "ab")
expect_inherits(c(x[1], x[9]), "ab")
expect_inherits(unique(x[1], x[9]), "ab")
expect_inherits(rep(x[1], 2), "ab")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))
})