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(v0.7.0.9005) ab algorithm update
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@ -24,12 +24,17 @@ context("data.R")
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test_that("data sets are valid", {
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# IDs should always be unique
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expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
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expect_identical(class(antibiotics$ab), "ab")
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expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
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expect_identical(class(microorganisms$mo), "mo")
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# check cross table reference
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expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
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# there should be no diacritics (i.e. non ASCII) characters in the datasets
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# antibiotic names must always be coercible to their original AB code
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expect_identical(antibiotics$ab, as.ab(antibiotics$name))
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# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
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datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
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for (i in 1:length(datasets)) {
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dataset <- get(datasets[i], envir = asNamespace("AMR"))
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@ -33,10 +33,13 @@ test_that("mo_property works", {
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expect_equal(mo_fullname("E. coli"), "Escherichia coli")
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expect_equal(mo_name("E. coli"), "Escherichia coli")
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expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
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expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
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expect_equal(mo_gramstain("E. coli", language = "en"), "Gram-negative")
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expect_equal(class(mo_taxonomy("E. coli")), "list")
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expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies"))
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expect_equal(names(mo_info("E. coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies",
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"url", "ref"))
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expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
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expect_equal(mo_authors("E. coli"), "Castellani et al.")
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