AMR/tests/testthat/test-eucast.R

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R
Executable File

context("eucast.R")
test_that("EUCAST rules work", {
expect_error(EUCAST_rules(septic_patients, col_mo = "Non-existing"))
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(EUCAST_rules(septic_patients))))
a <- data.frame(mo =
c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo =
c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
a <- data.frame(mo =
c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "-", # Colistin
stringsAsFactors = FALSE)
b <- data.frame(mo =
c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
# pita must be R in Enterobacteriaceae when tica is R
library(dplyr)
expect_equal(suppressWarnings(
septic_patients %>%
mutate(tica = as.rsi("R"),
pita = as.rsi("S")) %>%
EUCAST_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(pita) %>%
unique() %>%
as.character()),
"R")
# azit and clar must be equal to eryt
expect_equal(suppressWarnings(
septic_patients %>%
mutate(azit = as.rsi("R"),
clar = as.rsi("R")) %>%
EUCAST_rules(col_mo = "mo") %>%
pull(clar)),
suppressWarnings(
septic_patients %>%
EUCAST_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
pull(eryt)))
})