mirror of https://github.com/msberends/AMR.git
41 lines
1.7 KiB
R
Executable File
41 lines
1.7 KiB
R
Executable File
context("eucast.R")
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test_that("EUCAST rules work", {
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expect_identical(colnames(septic_patients),
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colnames(suppressWarnings(EUCAST_rules(septic_patients))))
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a <- data.frame(bactid =
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(bactid =
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as.bactid(
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER")), # Enterobacter aerogenes
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amox = "R", # Amoxicillin
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stringsAsFactors = FALSE)
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expect_identical(EUCAST_rules(a, info = FALSE), b)
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expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
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a <- data.frame(bactid =
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c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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coli = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(bactid =
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as.bactid(
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c("STAAUR", # Staphylococcus aureus
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"STCGRA")), # Streptococcus pyognenes (Lancefield Group A)
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coli = "R", # Colistin
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stringsAsFactors = FALSE)
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expect_equal(EUCAST_rules(a, info = FALSE), b)
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})
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test_that("MO properties work", {
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expect_equal(mo_property("ESCCOL"), "Escherichia coli")
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expect_equal(mo_property("STAAUR"), "Staphylococcus aureus")
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})
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