AMR/tests/testthat/test-eucast.R

context("eucast.R")

test_that("EUCAST rules work", {
  expect_identical(colnames(septic_patients),
                   colnames(suppressWarnings(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_warning(EUCAST_rules(a, info = FALSE))
  expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
  expect_identical(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(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
})