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(v1.5.0.9041) SNOMED update
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@ -56,7 +56,7 @@ test_that("EUCAST rules work", {
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a <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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"Enterobacter cloacae"),
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amox = "-", # Amoxicillin
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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@ -124,7 +124,7 @@ test_that("EUCAST rules work", {
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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ampc_cephalosporin_resistance = "R",
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ampc_cephalosporin_resistance = TRUE,
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info = FALSE)$cefotax,
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as.rsi(c("S", "R")))
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expect_identical(
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@ -50,7 +50,8 @@ test_that("mo_property works", {
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expect_equal(class(mo_synonyms(c("Candida albicans", "Escherichia coli"))), "list")
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expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
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"family", "genus", "species", "subspecies",
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"synonyms", "gramstain", "url", "ref"))
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"synonyms", "gramstain", "url", "ref",
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"snomed"))
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expect_equal(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list")
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expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
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@ -102,7 +103,7 @@ test_that("mo_property works", {
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expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
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expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
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expect_equal(mo_snomed("Escherichia coli"), 112283007)
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expect_true(112283007 %in% mo_snomed("Escherichia coli"))
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# old codes must throw a warning in mo_* family
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expect_message(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
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