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(v2.1.1.9236) documentation

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dr. M.S. (Matthijs) Berends
2025-04-12 11:46:42 +02:00
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tests/testthat.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(testthat)

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tests/testthat/helper-functions.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# add functions from the tinytest package (which we use for older R versions)

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tests/testthat/test-_deprecated.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-_deprecated.R", {

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tests/testthat/test-_misc.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-misc.R", {

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tests/testthat/test-ab.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab.R", {

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tests/testthat/test-ab_from_text.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab_from_text.R", {

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tests/testthat/test-ab_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab_property.R", {

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tests/testthat/test-age.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-age.R", {

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tests/testthat/test-amr_selectors.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-amr selectors.R", {

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tests/testthat/test-antibiogram.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-antibiogram.R", {

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tests/testthat/test-atc_online.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-atc_online.R", {

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tests/testthat/test-av.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-av.R", {

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tests/testthat/test-av_from_text.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-av_from_text.R", {

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tests/testthat/test-av_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab_property.R", {

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tests/testthat/test-availability.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-availibility.R", {

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tests/testthat/test-bug_drug_combinations.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-bug/drug.R", {

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tests/testthat/test-count.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-count.R", {

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tests/testthat/test-custom_antimicrobials.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-custom ab.R", {

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tests/testthat/test-custom_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #

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tests/testthat/test-data.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-data.R", {

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tests/testthat/test-disk.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-disk.R", {

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tests/testthat/test-eucast_rules.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-eucast_rules.R", {

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tests/testthat/test-first_isolate.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-first_isolate.R", {

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tests/testthat/test-g.test.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-g.test.R", {

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tests/testthat/test-get_episode.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-get_episode.R", {

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tests/testthat/test-ggplot_sir.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ggplot_sir.R", {

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tests/testthat/test-guess_ab_col.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-guess_ab_col.R", {

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tests/testthat/test-italicise_taxonomy.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-italicise_taxonomy.R", {

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tests/testthat/test-join_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-join_microorganisms.R", {

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tests/testthat/test-key_antimicrobials.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-key_antimicrobials.R", {

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tests/testthat/test-kurtosis.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-kurtosis.R", {

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tests/testthat/test-like.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-like.R", {

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tests/testthat/test-mdro.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mdro.R", {

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tests/testthat/test-mean_amr_distance.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mean_amr_distance.R", {

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tests/testthat/test-mic.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mic.R", {

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tests/testthat/test-mo.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mo.R", {

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tests/testthat/test-mo_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-mo_property.R", {

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tests/testthat/test-pca.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-pca.R", {

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tests/testthat/test-plotting.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-plotting.R", {

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tests/testthat/test-proportion.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-proportion.R", {

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tests/testthat/test-random.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-random.R", {

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tests/testthat/test-resistance_predict.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-resistance_predict.R", {

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tests/testthat/test-sir.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-sir.R", {

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tests/testthat/test-skewness.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-skewness.R", {

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tests/testthat/test-top_n_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-top_n_microorganisms.R", {

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tests/testthat/test-translate.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-translate.R", {

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tests/testthat/test-vctrs.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-vctrs.R", {

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tests/testthat/test-zzz.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-zzz.R", {

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tests/tinytest.R.old
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# we use {tinytest} for older R versions to allow unit testing in R >= 3.0.0.