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small improvement for is.rsi.eligible, more unit tests
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@ -4,7 +4,12 @@ context("mdro.R")
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test_that("MDRO works", {
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library(dplyr)
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outcome <- suppressWarnings(MDRO(septic_patients, "EUCAST", info = TRUE))
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expect_error(suppressWarnings(MDRO(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
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expect_error(suppressWarnings(MDRO(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
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expect_error(suppressWarnings(MDRO(septic_patients, country = c("de", "nl"), info = TRUE)))
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expect_error(suppressWarnings(MDRO(septic_patients, col_mo = "invalid", info = TRUE)))
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outcome <- suppressWarnings(MDRO(septic_patients))
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outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
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# check class
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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@ -22,6 +22,11 @@ test_that("as.mo works", {
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expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
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expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
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expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
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expect_equal(as.character(as.mo("Strepto")), "STC") # not Streptobacillus
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expect_equal(as.character(as.mo("Streptococcus")), "STC") # not Peptostreptoccus
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expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))
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expect_equal(as.character(as.mo("S. pyo")), "STCPYO") # not Actinomyces pyogenes
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@ -31,7 +36,7 @@ test_that("as.mo works", {
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expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
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# GLIMS
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expect_equal(as.character(as.mo("shiboy")), "SHIBOY")
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expect_equal(as.character(as.mo("bctfgr")), "BACFRA")
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expect_equal(as.character(as.mo("MRSE")), "STAEPI")
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expect_equal(as.character(as.mo("VRE")), "ENC")
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