mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 18:06:11 +01:00
119 lines
4.8 KiB
R
Executable File
119 lines
4.8 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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.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"))))
|
|
|
|
# check verbose output
|
|
expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE)))
|
|
|
|
})
|