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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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 the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# thoroughly check input table
expect_equal(colnames(AMR:::EUCAST_RULES_DF),
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",
"reference.version",
"note"))
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
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", stringsAsFactors = TRUE)))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
expect_stdout(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter cloacae"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter cloacae"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_stdout(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
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
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
pull(PIP) %>%
unique() %>%
as.character()),
"R")
}
# azithromycin and clarythromycin must be equal to Erythromycin
a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
ERY = example_isolates$ERY,
AZM = as.rsi("R"),
CLR = factor("R"),
stringsAsFactors = FALSE),
version_expertrules = 3.1,
only_rsi_columns = FALSE)$CLR))
b <- example_isolates$ERY
expect_identical(a[!is.na(b)],
b[!is.na(b)])
# amox is inferred by benzylpenicillin in Kingella kingae
expect_equal(
suppressWarnings(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
PEN = "S",
AMX = "-",
stringsAsFactors = FALSE)
, info = FALSE))$AMX
),
"S")
# also test norf
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}
# check verbose output
expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
# AmpC de-repressed cephalo mutants
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = TRUE,
info = FALSE)$cefotax,
as.rsi(c("S", "R")))
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = NA,
info = FALSE)$cefotax,
as.rsi(c("S", NA)))
expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))),
ampc_cephalosporin_resistance = NULL,
info = FALSE)$cefotax,
as.rsi(c("S", "S")))
# EUCAST dosage -----------------------------------------------------------
expect_equal(nrow(eucast_dosage(c("tobra", "genta", "cipro"))), 3)
expect_inherits(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I",
AMX == "S" ~ AMC == "S")
expect_stdout(print(x))
expect_stdout(print(c(x, x)))
expect_stdout(print(as.list(x, x)))
# this custom rules makes 8 changes
expect_equal(nrow(eucast_rules(example_isolates,
rules = "custom",
custom_rules = x,
info = FALSE,
verbose = TRUE)),
8, tolerance = 0.5)