AMR/inst/tinytest/test-antibiogram.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/ #
# ==================================================================== #
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# Traditional antibiogram ----------------------------------------------
ab1 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
ab2 <- antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain")
ab3 <- antibiogram(example_isolates,
antibiotics = carbapenems(),
ab_transform = "name",
mo_transform = "name")
expect_inherits(ab1, "antibiogram")
expect_inherits(ab2, "antibiogram")
expect_inherits(ab3, "antibiogram")
expect_equal(colnames(ab1), c("Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
expect_equal(colnames(ab3), c("Pathogen (N min-max)", "Imipenem", "Meropenem"))
expect_equal(ab3$Meropenem, c(52, NA, 100, 100, NA))
# Combined antibiogram -------------------------------------------------
# combined antibiotics yield higher empiric coverage
ab4 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
ab5 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ",
add_total_n = FALSE)
expect_inherits(ab4, "antibiogram")
expect_inherits(ab5, "antibiogram")
expect_equal(colnames(ab4), c("Pathogen (N min-max)", "TZP", "TZP + GEN", "TZP + TOB"))
expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam & Tobramycin"))
# Syndromic antibiogram ------------------------------------------------
# the data set could contain a filter for e.g. respiratory specimens
ab6 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
# with a custom language, though this will be determined automatically
# (i.e., this table will be in Spanish on Spanish systems)
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
ab7 <- antibiogram(ex1,
antibiotics = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"UCI", "No UCI"),
language = "es")
expect_inherits(ab6, "antibiogram")
expect_inherits(ab7, "antibiogram")
expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
# the data set could contain a filter for e.g. respiratory specimens
ab8 <- antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
expect_inherits(ab8, "antibiogram")
expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen (N min-max)", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
# Generate plots with ggplot2 or base R --------------------------------
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(ab1))
expect_silent(plot(ab2))
expect_silent(plot(ab3))
expect_silent(plot(ab4))
expect_silent(plot(ab5))
expect_silent(plot(ab6))
expect_silent(plot(ab7))
expect_silent(plot(ab8))
if (AMR:::pkg_is_available("ggplot2")) {
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expect_inherits(ggplot2::autoplot(ab1), "gg")
expect_inherits(ggplot2::autoplot(ab2), "gg")
expect_inherits(ggplot2::autoplot(ab3), "gg")
expect_inherits(ggplot2::autoplot(ab4), "gg")
expect_inherits(ggplot2::autoplot(ab5), "gg")
expect_inherits(ggplot2::autoplot(ab6), "gg")
expect_inherits(ggplot2::autoplot(ab7), "gg")
expect_inherits(ggplot2::autoplot(ab8), "gg")
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}