AMR/tests/testthat/test-mdro.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. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mdro.R")
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test_that("mdro works", {
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skip_on_cran()
library(dplyr)
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
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outcome <- suppressWarnings(mdro(example_isolates))
outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c("ordered", "factor"))
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outcome <- mdro(example_isolates, "nl", info = TRUE)
# check class
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expect_equal(outcome %>% class(), c("ordered", "factor"))
# example_isolates should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))
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# test Dutch P. aeruginosa MDRO
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expect_equal(
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cfta = "S",
cipr = "S",
mero = "S",
imip = "S",
gent = "S",
tobr = "S",
pita = "S"),
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guideline = "BRMO",
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col_mo = "mo",
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info = FALSE)),
"Negative")
expect_equal(
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as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cefta = "R",
cipr = "R",
mero = "R",
imip = "R",
gent = "R",
tobr = "R",
pita = "R"),
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guideline = "BRMO",
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col_mo = "mo",
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info = FALSE)),
"Positive")
# German 3MRGN and 4MRGN
expect_equal(as.character(mrgn(
data.frame(mo = c("E. coli", "E. coli", "K. pneumoniae", "E. coli",
"A. baumannii", "A. baumannii", "A. baumannii",
"P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
PIP = c("S", "R", "R", "S",
"S", "R", "R",
"S", "R", "R"),
CTX = c("S", "R", "R", "S",
"R", "R", "R",
"R", "R", "R"),
IPM = c("S", "R", "S", "R",
"R", "R", "S",
"S", "R", "R"),
CIP = c("S", "R", "R", "S",
"R", "R", "R",
"R", "S", "R"),
stringsAsFactors = FALSE))),
c("Negative", "4MRGN", "3MRGN", "4MRGN", "4MRGN", "4MRGN", "3MRGN", "Negative", "3MRGN", "4MRGN"))
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# MDR TB
expect_equal(
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# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
example_isolates %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(example_isolates$RIF))
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sample_rsi <- function() {
sample(c("S", "I", "R"),
size = 5000,
prob = c(0.5, 0.1, 0.4),
replace = TRUE)
}
expect_gt(
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#suppressWarnings(
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data.frame(rifampicin = sample_rsi(),
inh = sample_rsi(),
gatifloxacin = sample_rsi(),
eth = sample_rsi(),
pza = sample_rsi(),
MFX = sample_rsi(),
KAN = sample_rsi()) %>%
mdr_tb() %>%
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n_distinct()
#)
,
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2)
# check the guideline by Magiorakos et al. (2012), the default guideline
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stau <- tribble(
~mo, ~GEN, ~RIF, ~CPT, ~OXA, ~CIP, ~MFX, ~SXT, ~FUS, ~VAN, ~TEC, ~TLV, ~TGC, ~CLI, ~DAP, ~ERY, ~LNZ, ~CHL, ~FOS, ~QDA, ~TCY, ~DOX, ~MNO,
"S. aureus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"S. aureus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"S. aureus", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R",
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"S. aureus", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"
)
expect_equal(as.integer(mdro(stau)), c(1:4))
expect_s3_class(mdro(stau, verbose = TRUE), "data.frame")
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ente <- tribble(
~mo, ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO,
"Enterococcus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"Enterococcus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"Enterococcus", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R",
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"Enterococcus", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"
)
expect_equal(as.integer(mdro(ente)), c(1:4))
expect_s3_class(mdro(ente, verbose = TRUE), "data.frame")
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entero <- tribble(
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~CPT, ~TCC, ~TZP, ~ETP, ~IPM, ~MEM, ~DOR, ~CZO, ~CXM, ~CTX, ~CAZ, ~FEP, ~FOX, ~CTT, ~CIP, ~SXT, ~TGC, ~ATM, ~AMP, ~AMC, ~SAM, ~CHL, ~FOS, ~COL, ~TCY, ~DOX, ~MNO,
"E. coli", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"E. coli", "R", "R", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"E. coli", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R",
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"E. coli", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"
)
expect_equal(as.integer(mdro(entero)), c(1:4))
expect_s3_class(mdro(entero, verbose = TRUE), "data.frame")
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pseud <- tribble(
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB,
"P. aeruginosa", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"P. aeruginosa", "R", "S", "S", "S", "R", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S",
"P. aeruginosa", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R",
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"P. aeruginosa", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"
)
expect_equal(as.integer(mdro(pseud)), c(1:4))
expect_s3_class(mdro(pseud, verbose = TRUE), "data.frame")
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acin <- tribble(
~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO,
"A. baumannii", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"A. baumannii", "R", "R", "R", "R", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S",
"A. baumannii", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R",
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"A. baumannii", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R"
)
expect_equal(as.integer(mdro(acin)), c(1:4))
expect_s3_class(mdro(acin, verbose = TRUE), "data.frame")
})