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AMR/inst/tinytest/test-rsi.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 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/ #
# ==================================================================== #
# we must only have EUCAST and CLSI, because otherwise the rules in as.rsi() will fail
expect_identical(
unique(gsub("[^A-Z]", "", AMR::rsi_translation$guideline)),
c("EUCAST", "CLSI")
)
expect_true(as.rsi("S") < as.rsi("I"))
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S")))
x <- example_isolates$AMX
expect_inherits(x[1], "rsi")
expect_inherits(x[[1]], "rsi")
expect_inherits(c(x[1], x[9]), "rsi")
expect_inherits(unique(x[1], x[9]), "rsi")
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_silent(plot(as.rsi(c("S", "I", "R"))))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.rsi(c("S", "I", "R"))), "gg")
}
expect_stdout(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
expect_equal(
summary(as.rsi(c("S", "R"))),
structure(c(
"Class" = "rsi",
"%R" = "50.0% (n=1)",
"%SI" = "50.0% (n=1)",
"- %S" = "50.0% (n=1)",
"- %I" = " 0.0% (n=0)"
), class = c("summaryDefault", "table"))
)
expect_identical(
as.logical(lapply(example_isolates, is.rsi.eligible)),
as.logical(lapply(example_isolates, is.rsi))
)
expect_error(as.rsi.mic(as.mic(16)))
expect_error(as.rsi.disk(as.disk(16)))
expect_error(get_guideline("this one does not exist"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
# 40 rsi columns
expect_equal(
example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
lapply(is.rsi.eligible) %>%
as.logical() %>%
sum(),
40
)
expect_equal(sum(is.rsi(example_isolates)), 40)
expect_stdout(print(tibble(ab = as.rsi("S"))))
}
if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
expect_inherits(
skim(example_isolates),
"data.frame"
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_inherits(
example_isolates %>%
mutate(
m = as.mic(2),
d = as.disk(20)
) %>%
skim(),
"data.frame"
)
}
}
expect_equal(as.rsi(c("", "-", NA, "NULL")), c(NA_rsi_, NA_rsi_, NA_rsi_, NA_rsi_))
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(
as.character(
as.rsi(
x = as.mic(c(0.125, 0.5, 1, 2, 4)),
mo = "B_STRPT_PNMN",
ab = "AMP",
guideline = "EUCAST 2020"
)
),
c("S", "S", "I", "I", "R")
)
# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
expect_equal(
as.character(
as.rsi(
x = as.mic(c(1, 2, 4, 8, 16)),
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "CLSI 2019"
)
),
c("S", "S", "I", "R", "R")
)
# cutoffs at MIC = 8
expect_equal(
as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("S")
)
expect_equal(
as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R")
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
as.rsi() %>%
pull(amox_mic) %>%
is.rsi()))
}
expect_equal(
as.character(
as.rsi(
x = as.disk(22),
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI"
)
),
"S"
)
expect_equal(
as.character(
as.rsi(
x = as.disk(18),
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI"
)
),
"I"
)
expect_equal(
as.character(
as.rsi(
x = as.disk(10),
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI"
)
),
"R"
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%
as.rsi(guideline = "CLSI") %>%
pull(amox_disk) %>%
is.rsi())
}
# frequency tables
if (AMR:::pkg_is_available("cleaner")) {
expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
}
df <- data.frame(
microorganism = "Escherichia coli",
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
ERY = "R", # note about assigning <rsi> class
CLR = "V"
) # note about cleaning
expect_inherits(
suppressWarnings(as.rsi(df)),
"data.frame"
)
expect_inherits(
suppressWarnings(as.rsi(data.frame(
mo = "Escherichia coli",
amoxi = c("R", "S", "I", "invalid")
))$amoxi),
"rsi"
)
expect_warning(as.rsi(data.frame(
mo = "E. coli",
NIT = c("<= 2", 32)
)))
expect_message(as.rsi(data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
uti = TRUE
)))
expect_message(as.rsi(data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")
)))
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