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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-01-12 22:08:04 +01:00
parent 3b84b8be75
commit d014955ce0
93 changed files with 3631 additions and 374 deletions
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6
tests/testthat.R
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@ -23,10 +23,10 @@
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# the testthat package is in Suggests, but very old R versions will not be
# able to install it. Yet, we want checks in those R versions as well, so
# only run unit tests in later R versions:
if (require("testthat")) {
# the testthat package is in Suggests, but very old R versions will not be
# able to install it. Yet, we want checks in those R versions as well, so
# only run unit tests in later R versions:
library(testthat, warn.conflicts = FALSE)
library(AMR)
test_check("AMR")

5
tests/testthat/test-data.R
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@ -40,14 +40,17 @@ test_that("data sets are valid", {
expect_true(all(example_isolates$mo %in% microorganisms$mo))
expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
expect_true(all(rsi_translation$mo %in% microorganisms$mo))
expect_true(all(rsi_translation$ab %in% antibiotics$ab))
expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
expect_true(all(dosage$ab %in% antibiotics$ab))
expect_true(all(dosage$name %in% antibiotics$name))
# antibiotic names must always be coercible to their original AB code
expect_identical(antibiotics$ab, as.ab(antibiotics$name))
expect_identical(as.ab(antibiotics$name), antibiotics$ab)
# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]