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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/ #
# ==================================================================== #
expect_identical(as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter asburiae"))
suppressMessages(
add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO",
genus = "Enterobacter",
species = "asburiae/cloacae")
)
)
expect_identical(as.character(as.mo("ENT_ASB_CLO")), "ENT_ASB_CLO")
expect_identical(mo_name("ENT_ASB_CLO"), "Enterobacter asburiae/cloacae")
expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
# ==================================================================== #
# 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/ #
# ==================================================================== #
#
#
# # 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")) {
# expect_inherits(autoplot(ab1), "gg")
# expect_inherits(autoplot(ab2), "gg")
# expect_inherits(autoplot(ab3), "gg")
# expect_inherits(autoplot(ab4), "gg")
# expect_inherits(autoplot(ab5), "gg")
# expect_inherits(autoplot(ab6), "gg")
# expect_inherits(autoplot(ab7), "gg")
# expect_inherits(autoplot(ab8), "gg")
# }
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