mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
250 lines
7.7 KiB
R
250 lines
7.7 KiB
R
# ==================================================================== #
|
|
# 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/ #
|
|
# ==================================================================== #
|
|
|
|
# we must only have EUCAST and CLSI, because otherwise the rules in as.sir() will fail
|
|
expect_identical(
|
|
unique(gsub("[^A-Z]", "", AMR::clinical_breakpoints$guideline)),
|
|
c("EUCAST", "CLSI")
|
|
)
|
|
|
|
expect_true(as.sir("S") < as.sir("I"))
|
|
expect_true(as.sir("I") < as.sir("R"))
|
|
expect_true(is.sir(as.sir("S")))
|
|
x <- example_isolates$AMX
|
|
expect_inherits(x[1], "sir")
|
|
expect_inherits(x[[1]], "sir")
|
|
expect_inherits(c(x[1], x[9]), "sir")
|
|
expect_inherits(unique(x[1], x[9]), "sir")
|
|
pdf(NULL) # prevent Rplots.pdf being created
|
|
expect_silent(barplot(as.sir(c("S", "I", "R"))))
|
|
expect_silent(plot(as.sir(c("S", "I", "R"))))
|
|
if (AMR:::pkg_is_available("ggplot2")) {
|
|
expect_inherits(autoplot(as.sir(c("S", "I", "R"))), "gg")
|
|
}
|
|
expect_stdout(print(as.sir(c("S", "I", "R"))))
|
|
expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
|
|
expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
|
|
expect_equal(suppressWarnings(as.logical(as.sir("INVALID VALUE"))), NA)
|
|
expect_equal(
|
|
summary(as.sir(c("S", "R"))),
|
|
structure(c(
|
|
"Class" = "sir",
|
|
"%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_sir_eligible)),
|
|
as.logical(lapply(example_isolates, is.sir))
|
|
)
|
|
expect_error(as.sir.mic(as.mic(16)))
|
|
expect_error(as.sir.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 sir columns
|
|
expect_equal(
|
|
example_isolates %>%
|
|
mutate_at(vars(PEN:RIF), as.character) %>%
|
|
lapply(is_sir_eligible) %>%
|
|
as.logical() %>%
|
|
sum(),
|
|
40
|
|
)
|
|
expect_equal(sum(is.sir(example_isolates)), 40)
|
|
|
|
expect_stdout(print(tibble(ab = as.sir("S"))))
|
|
|
|
expect_true(example_isolates %>%
|
|
select(AMC, MEM) %>%
|
|
mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>%
|
|
pull(MEM) %>%
|
|
is.sir())
|
|
}
|
|
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.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))
|
|
|
|
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
|
|
expect_equal(suppressMessages(
|
|
as.character(
|
|
as.sir(
|
|
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(suppressMessages(
|
|
as.character(
|
|
as.sir(
|
|
x = as.mic(c(1, 2, 4, 8, 16)),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "AMX",
|
|
guideline = "CLSI 2019"
|
|
)
|
|
)),
|
|
c("S", "S", "I", "R", "R")
|
|
)
|
|
|
|
expect_true(is.data.frame(sir_interpretation_history(clean = FALSE)))
|
|
expect_true(is.data.frame(sir_interpretation_history(clean = TRUE)))
|
|
expect_true(is.null(sir_interpretation_history()))
|
|
|
|
# cutoffs at MIC = 8
|
|
expect_equal(
|
|
suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
|
|
as.sir("S")
|
|
)
|
|
expect_equal(
|
|
suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
|
|
as.sir("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.sir() %>%
|
|
pull(amox_mic) %>%
|
|
is.sir()))
|
|
}
|
|
|
|
expect_equal(
|
|
as.character(
|
|
as.sir(
|
|
x = as.disk(22),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "ERY",
|
|
guideline = "CLSI"
|
|
)
|
|
),
|
|
"S"
|
|
)
|
|
expect_equal(
|
|
as.character(
|
|
as.sir(
|
|
x = as.disk(18),
|
|
mo = "B_STRPT_PNMN",
|
|
ab = "ERY",
|
|
guideline = "CLSI"
|
|
)
|
|
),
|
|
"I"
|
|
)
|
|
expect_equal(
|
|
as.character(
|
|
as.sir(
|
|
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.sir(guideline = "CLSI") %>%
|
|
pull(amox_disk) %>%
|
|
is.sir())
|
|
|
|
# used by group_by() on sir_calc_df(), check some internals to see if grouped calculation without tidyverse works
|
|
groups <- example_isolates %>%
|
|
group_by(mo) %>%
|
|
attributes() %>%
|
|
.$groups
|
|
expect_equal(nrow(groups),
|
|
90)
|
|
expect_equal(class(groups$.rows),
|
|
c("vctrs_list_of", "vctrs_vctr", "list"))
|
|
expect_equal(groups$.rows[[1]],
|
|
c(101, 524, 1368))
|
|
expect_equal(example_isolates[c(101, 524, 1368), "mo", drop = TRUE],
|
|
rep(groups$mo[1], 3))
|
|
}
|
|
# frequency tables
|
|
if (AMR:::pkg_is_available("cleaner")) {
|
|
expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
|
|
}
|
|
|
|
|
|
df <- data.frame(
|
|
microorganism = "Escherichia coli",
|
|
AMP = as.mic(8),
|
|
CIP = as.mic(0.256),
|
|
GEN = as.disk(18),
|
|
TOB = as.disk(16),
|
|
ERY = "R", # note about assigning <rsi> class
|
|
CLR = "V"
|
|
) # note about cleaning
|
|
expect_inherits(
|
|
suppressWarnings(as.sir(df)),
|
|
"data.frame"
|
|
)
|
|
expect_inherits(
|
|
suppressWarnings(as.sir(data.frame(
|
|
mo = "Escherichia coli",
|
|
amoxi = c("S", "I", "R", "invalid")
|
|
))$amoxi),
|
|
"sir"
|
|
)
|
|
# expect_warning(as.sir(data.frame(mo = "E. coli", NIT = c("<= 2", 32))))
|
|
expect_message(as.sir(data.frame(
|
|
mo = "E. coli",
|
|
NIT = c("<= 2", 32),
|
|
uti = TRUE
|
|
)))
|
|
expect_message(as.sir(data.frame(
|
|
mo = "E. coli",
|
|
NIT = c("<= 2", 32),
|
|
specimen = c("urine", "blood")
|
|
)))
|