context("eucast.R") test_that("EUCAST rules work", { a <- EUCAST_rules(septic_patients) a <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae "PSEAER", # Pseudomonas aeruginosa "ENTAER"), # Enterobacter aerogenes amox = "-", # Amoxicillin stringsAsFactors = FALSE) b <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae "PSEAER", # Pseudomonas aeruginosa "ENTAER"), # Enterobacter aerogenes amox = "R", # Amoxicillin stringsAsFactors = FALSE) expect_equal(EUCAST_rules(a, info = FALSE), b) expect_equal(suppressWarnings(interpretive_reading(a, info = TRUE)), b) a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus "STCGRA"), # Streptococcus pyognenes (Lancefield Group A) coli = "-", # Colistin stringsAsFactors = FALSE) b <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus "STCGRA"), # Streptococcus pyognenes (Lancefield Group A) coli = "R", # Colistin stringsAsFactors = FALSE) expect_equal(EUCAST_rules(a, info = FALSE), b) }) test_that("MO properties work", { expect_equal(mo_property("ESCCOL"), "Escherichia coli") expect_equal(mo_property("STAAUR"), "Staphylococcus aureus") })