AMR/tests/testthat/test-eucast_rules.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("eucast_rules.R")
test_that("EUCAST rules work", {
skip_on_cran()
# thoroughly check input table
expect_equal(colnames(eucast_rules_file),
c("if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group"))
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))
expect_error(eucast_rules(data.frame(a = "test")))
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S")))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates))))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
COL = "-", # Colistin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
COL = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr)
expect_equal(suppressWarnings(
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
unique() %>%
as.character()),
"R")
# Azithromicin and Clarythromycin must be equal to Erythromycin
a <- suppressWarnings(
example_isolates %>%
transmute(mo,
ERY,
AZM = as.rsi("R"),
CLR = as.rsi("R")) %>%
eucast_rules(col_mo = "mo") %>%
pull(CLR))
b <- suppressWarnings(
example_isolates %>%
select(mo, ERY) %>%
eucast_rules(col_mo = "mo") %>%
pull(ERY))
expect_identical(a[!is.na(b)],
b[!is.na(b)])
# amox is inferred by benzylpenicillin in Kingella kingae
expect_equal(
suppressWarnings(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
PEN = "S",
AMX = "-",
stringsAsFactors = FALSE)
, info = FALSE))$AMX
),
"S")
# also test norf
expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
# check verbose output
expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, info = TRUE)))
})