AMR/inst/tinytest/test-bug_drug_combinations.R

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# 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 #
# #
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# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
# 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. #
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# #
# 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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# ==================================================================== #
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b <- suppressWarnings(bug_drug_combinations(example_isolates))
expect_inherits(b, "bug_drug_combinations")
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expect_stdout(suppressMessages(print(b)))
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expect_true(is.data.frame(format(b)))
expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_true(example_isolates %>%
group_by(ward) %>%
bug_drug_combinations(FUN = mo_gramstain) %>%
is.data.frame())
}