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(v1.5.0.9041) SNOMED update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-03-11 21:42:30 +01:00
parent 8d6ceb6a15
commit 4e0a9533ad
65 changed files with 86943 additions and 67626 deletions
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4
tests/testthat/test-eucast_rules.R
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@ -56,7 +56,7 @@ test_that("EUCAST rules work", {
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter cloacae"),
amox = "-", # Amoxicillin
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
@ -124,7 +124,7 @@ test_that("EUCAST rules work", {
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = "R",
ampc_cephalosporin_resistance = TRUE,
info = FALSE)$cefotax,
as.rsi(c("S", "R")))
expect_identical(

5
tests/testthat/test-mo_property.R
View File

@ -50,7 +50,8 @@ test_that("mo_property works", {
expect_equal(class(mo_synonyms(c("Candida albicans", "Escherichia coli"))), "list")
expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref"))
"synonyms", "gramstain", "url", "ref",
"snomed"))
expect_equal(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list")
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
@ -102,7 +103,7 @@ test_that("mo_property works", {
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
expect_equal(mo_snomed("Escherichia coli"), 112283007)
expect_true(112283007 %in% mo_snomed("Escherichia coli"))
# old codes must throw a warning in mo_* family
expect_message(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))