AMR/tests/testthat/test-eucast_rules.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# 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. #
# #
# This R package was created for academic research and 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.gitab.io/AMR. #
# ==================================================================== #
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context("eucast_rules.R")
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test_that("EUCAST rules work", {
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expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
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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(mo = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
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amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
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b <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
amox = "R", # Amoxicillin
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stringsAsFactors = FALSE)
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expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
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expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
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a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "R", # Colistin
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stringsAsFactors = FALSE)
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expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
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# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr)
expect_equal(suppressWarnings(
septic_patients %>%
mutate(tica = as.rsi("R"),
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pipe = as.rsi("S")) %>%
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eucast_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
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pull(pipe) %>%
unique() %>%
as.character()),
"R")
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# azit and clar must be equal to eryt
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a <- suppressWarnings(
septic_patients %>%
transmute(mo,
eryt,
azit = as.rsi("R"),
clar = as.rsi("R")) %>%
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eucast_rules(col_mo = "mo") %>%
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pull(clar))
b <- suppressWarnings(
septic_patients %>%
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select(mo, eryt) %>%
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eucast_rules(col_mo = "mo") %>%
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pull(eryt))
expect_identical(a[!is.na(b)],
b[!is.na(b)])
# amox is inferred by benzylpenicillin in Kingella kingae
expect_equal(
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suppressWarnings(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
peni = "S",
amox = "-",
stringsAsFactors = FALSE)
, info = FALSE))$amox
),
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"S")
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# also test norf
expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(norf = "S", nali = "S"))))
# check verbose output
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expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
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})