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AMR/inst/tinytest/test-mdro.R

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# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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/ #
# ==================================================================== #
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, info = TRUE))))
expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.1", info = TRUE))))
expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.2", info = TRUE))))
expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.3", info = TRUE))))
expect_stdout(outcome <- suppressMessages(suppressWarnings(eucast_exceptional_phenotypes(example_isolates, info = TRUE))))
# check class
expect_identical(class(outcome), c("ordered", "factor"))
expect_stdout(outcome <- mdro(example_isolates, "nl", info = TRUE))
# check class
expect_identical(class(outcome), c("ordered", "factor"))
# example_isolates should have these finding using Dutch guidelines
expect_equal(
as.double(table(outcome)),
c(1954, 24, 6)
) # 1954 neg, 24 unconfirmed, 6 pos, rest is NA
expect_equal(
brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE)
)
# test Dutch P. aeruginosa MDRO
expect_equal(
as.character(mdro(data.frame(
mo = as.mo("P. aeruginosa"),
cfta = "S",
cipr = "S",
mero = "S",
imip = "S",
gent = "S",
tobr = "S",
pita = "S"
),
guideline = "BRMO",
col_mo = "mo",
info = FALSE
)),
"Negative"
)
expect_equal(
as.character(mdro(data.frame(
mo = as.mo("P. aeruginosa"),
cefta = "R",
cipr = "R",
mero = "R",
imip = "R",
gent = "R",
tobr = "R",
pita = "R"
),
guideline = "BRMO",
col_mo = "mo",
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")
)
# MDR TB
expect_equal(
# 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
as.double(table(mdr_tb(example_isolates[, "RIF", drop = FALSE])))[2],
count_R(example_isolates$RIF)
)
x <- data.frame(
rifampicin = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
inh = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
gatifloxacin = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
eth = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
pza = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
MFX = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5)),
KAN = random_sir(5000, prob_sir = c(0.4, 0.1, 0.5))
)
expect_true(length(unique(mdr_tb(x))) > 2)
# check the guideline by Magiorakos et al. (2012), the default guideline
stau <- data.frame(
mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"),
GEN = c("R", "R", "S", "R"),
RIF = c("S", "R", "S", "R"),
CPT = c("S", "R", "R", "R"),
OXA = c("S", "R", "R", "R"),
CIP = c("S", "S", "R", "R"),
MFX = c("S", "S", "R", "R"),
SXT = c("S", "S", "R", "R"),
FUS = c("S", "S", "R", "R"),
VAN = c("S", "S", "R", "R"),
TEC = c("S", "S", "R", "R"),
TLV = c("S", "S", "R", "R"),
TGC = c("S", "S", "R", "R"),
CLI = c("S", "S", "R", "R"),
DAP = c("S", "S", "R", "R"),
ERY = c("S", "S", "R", "R"),
LNZ = c("S", "S", "R", "R"),
CHL = c("S", "S", "R", "R"),
FOS = c("S", "S", "R", "R"),
QDA = c("S", "S", "R", "R"),
TCY = c("S", "S", "R", "R"),
DOX = c("S", "S", "R", "R"),
MNO = c("S", "S", "R", "R"),
stringsAsFactors = FALSE
)
expect_equal(as.integer(mdro(stau)), c(1:4))
expect_inherits(mdro(stau, verbose = TRUE), "data.frame")
ente <- data.frame(
mo = c("Enterococcus", "Enterococcus", "Enterococcus", "Enterococcus"),
GEH = c("R", "R", "S", "R"),
STH = c("S", "R", "S", "R"),
IPM = c("S", "R", "R", "R"),
MEM = c("S", "R", "R", "R"),
DOR = c("S", "S", "R", "R"),
CIP = c("S", "S", "R", "R"),
LVX = c("S", "S", "R", "R"),
MFX = c("S", "S", "R", "R"),
VAN = c("S", "S", "R", "R"),
TEC = c("S", "S", "R", "R"),
TGC = c("S", "S", "R", "R"),
DAP = c("S", "S", "R", "R"),
LNZ = c("S", "S", "R", "R"),
AMP = c("S", "S", "R", "R"),
QDA = c("S", "S", "R", "R"),
DOX = c("S", "S", "R", "R"),
MNO = c("S", "S", "R", "R"),
stringsAsFactors = FALSE
)
expect_equal(as.integer(mdro(ente)), c(1:4))
expect_inherits(mdro(ente, verbose = TRUE), "data.frame")
entero <- data.frame(
mo = c("E. coli", "E. coli", "E. coli", "E. coli"),
GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
CPT = c("S", "R", "R", "R"), TCC = c("S", "R", "R", "R"),
TZP = c("S", "S", "R", "R"), ETP = c("S", "S", "R", "R"),
IPM = c("S", "S", "R", "R"), MEM = c("S", "S", "R", "R"),
DOR = c("S", "S", "R", "R"), CZO = c("S", "S", "R", "R"),
CXM = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
CAZ = c("S", "S", "R", "R"), FEP = c("S", "S", "R", "R"),
FOX = c("S", "S", "R", "R"), CTT = c("S", "S", "R", "R"),
CIP = c("S", "S", "R", "R"), SXT = c("S", "S", "R", "R"),
TGC = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
AMP = c("S", "S", "R", "R"), AMC = c("S", "S", "R", "R"),
SAM = c("S", "S", "R", "R"), CHL = c("S", "S", "R", "R"),
FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
TCY = c("S", "S", "R", "R"), DOX = c("S", "S", "R", "R"),
MNO = c("S", "S", "R", "R"),
stringsAsFactors = FALSE
)
expect_equal(as.integer(mdro(entero)), c(1:4))
expect_inherits(mdro(entero, verbose = TRUE), "data.frame")
pseud <- data.frame(
mo = c("P. aeruginosa", "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
GEN = c("R", "R", "S", "R"), TOB = c("S", "S", "S", "R"),
AMK = c("S", "S", "R", "R"), NET = c("S", "S", "R", "R"),
IPM = c("S", "R", "R", "R"), MEM = c("S", "S", "R", "R"),
DOR = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
FEP = c("S", "R", "R", "R"), CIP = c("S", "S", "R", "R"),
LVX = c("S", "S", "R", "R"), TCC = c("S", "S", "R", "R"),
TZP = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
PLB = c("S", "S", "R", "R"),
stringsAsFactors = FALSE
)
expect_equal(as.integer(mdro(pseud)), c(1:4))
expect_inherits(mdro(pseud, verbose = TRUE), "data.frame")
acin <- data.frame(
mo = c("A. baumannii", "A. baumannii", "A. baumannii", "A. baumannii"),
GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
IPM = c("S", "S", "R", "R"), MEM = c("S", "R", "R", "R"),
DOR = c("S", "S", "R", "R"), CIP = c("S", "S", "R", "R"),
LVX = c("S", "S", "R", "R"), TZP = c("S", "S", "R", "R"),
TCC = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
CRO = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
FEP = c("S", "R", "R", "R"), SXT = c("S", "S", "R", "R"),
SAM = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
PLB = c("S", "S", "R", "R"), TCY = c("S", "S", "R", "R"),
DOX = c("S", "S", "R", "R"), MNO = c("S", "S", "R", "R"),
stringsAsFactors = FALSE
)
expect_equal(as.integer(mdro(acin)), c(1:4))
expect_inherits(mdro(acin, verbose = TRUE), "data.frame")
# custom rules
custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
"ERY == 'R' & age > 60" ~ "Elderly Type B",
as_factor = TRUE
)
expect_stdout(print(custom))
expect_stdout(print(c(custom, custom)))
expect_stdout(print(as.list(custom, custom)))
expect_stdout(x <- mdro(example_isolates, guideline = custom, info = TRUE))
expect_equal(as.double(table(x)), c(1070, 198, 732))
expect_stdout(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
expect_error(custom_mdro_guideline())
expect_error(custom_mdro_guideline("test"))
expect_error(custom_mdro_guideline("test" ~ c(1:3)))
expect_error(custom_mdro_guideline("test" ~ A))
# expect_warning(mdro(example_isolates,
# # since `test` gives an error, it will be ignored with a warning
# guideline = custom_mdro_guideline(test ~ "A"),
# info = FALSE
# ))
# print groups
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_stdout(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0))
expect_stdout(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE))
}
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