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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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88
tests/testthat/test-av.R
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@ -27,54 +27,56 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(
as.character(as.av(c(
"J05AB01",
"J 05 AB 01",
"Aciclovir",
"aciclo",
" aciclo 123",
"ACICL",
"ACI",
"Virorax",
"Zovirax"
))),
rep("ACI", 9)
)
test_that("av works", {
expect_equal(
as.character(as.av(c(
"J05AB01",
"J 05 AB 01",
"Aciclovir",
"aciclo",
" aciclo 123",
"ACICL",
"ACI",
"Virorax",
"Zovirax"
))),
rep("ACI", 9)
)
expect_identical(class(as.av("acic")), c("av", "character"))
expect_identical(class(antivirals$av), c("av", "character"))
expect_true(is.av(as.av("acic")))
expect_stdout(print(as.av("acic")))
expect_stdout(print(data.frame(a = as.av("acic"))))
expect_identical(class(as.av("acic")), c("av", "character"))
expect_identical(class(antivirals$av), c("av", "character"))
expect_true(is.av(as.av("acic")))
expect_output(print(as.av("acic")))
expect_output(print(data.frame(a = as.av("acic"))))
# expect_warning(as.av("J00AA00")) # ATC not yet available in data set
# expect_warning(as.av("UNKNOWN"))
# expect_warning(as.av("J00AA00")) # ATC not yet available in data set
# expect_warning(as.av("UNKNOWN"))
expect_stdout(print(as.av("acic")))
expect_output(print(as.av("acic")))
expect_equal(
as.character(as.av("zovirax")),
"ACI"
)
expect_equal(
as.character(as.av("zovirax")),
"ACI"
)
expect_equal(
as.character(as.av(c("Abacaivr", "Celvudine"))),
c("ABA", "CLE")
)
expect_equal(
as.character(as.av(c("Abacaivr", "Celvudine"))),
c("ABA", "CLE")
)
# expect_warning(as.av("Abacavir Clevudine"))
# expect_warning(as.av("Abacavir Clevudine"))
# based on Levenshtein distance
expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
# based on Levenshtein distance
expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
# assigning and subsetting
x <- antivirals$av
expect_inherits(x[1], "av")
expect_inherits(x[[1]], "av")
expect_inherits(c(x[1], x[9]), "av")
expect_inherits(unique(x[1], x[9]), "av")
expect_inherits(rep(x[1], 2), "av")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))
# assigning and subsetting
x <- antivirals$av
expect_inherits(x[1], "av")
expect_inherits(x[[1]], "av")
expect_inherits(c(x[1], x[9]), "av")
expect_inherits(unique(x[1], x[9]), "av")
expect_inherits(rep(x[1], 2), "av")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))
})