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101 lines
4.8 KiB
R
Executable File
101 lines
4.8 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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test_that("test-misc.R", {
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skip_on_cran()
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expect_equal(AMR:::percentage(0.25), "25%")
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expect_equal(AMR:::percentage(0.5), "50%")
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expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%")
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expect_equal(AMR:::percentage(0.1234), "12.3%")
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# round up 0.5
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expect_equal(AMR:::percentage(0.0054), "0.5%")
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expect_equal(AMR:::percentage(0.0055), "0.6%")
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# test functions on all R versions - R < 3.3 did not contain these
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expect_equal(strrep("A", 5), "AAAAA")
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expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
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expect_equal(trimws(" test "), "test")
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expect_equal(trimws(" test ", "l"), "test ")
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expect_equal(trimws(" test ", "r"), " test")
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expect_equal(AMR:::trimws2(" test "), "test")
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expect_equal(AMR:::trimws2(" test ", "l"), "test ")
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expect_equal(AMR:::trimws2(" test ", "r"), " test")
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expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
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# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
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}
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# test get_current_data() ----
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is_right <- FALSE
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check_df <- function(check_element, return_val = 0) {
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is_right <<- FALSE
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for (env in sys.frames()) {
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if (!is.null(env[[check_element]]) && is.data.frame(env[[check_element]])) {
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is_right <<- all(colnames(example_isolates) %in% colnames(env[[check_element]]))
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}
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}
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return_val
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}
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df <- example_isolates[, check_df("x")]
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expect_true(is_right, info = "the environmental data cannot be found for base/x (1)")
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if (getRversion() < "4.0.0") {
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df <- example_isolates[c(1:3), check_df("xx")]
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expect_true(is_right, info = "the environmental data cannot be found for base/xx")
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} else {
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df <- example_isolates[c(1:3), check_df("x")]
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expect_true(is_right, info = "the environmental data cannot be found for base/x (2)")
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}
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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df <- example_isolates %>% select(mo, check_df("data123"))
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expect_false(is_right, info = "just a check if non-sense is not being gathered by get_current_data()")
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df <- example_isolates %>% select(mo, check_df(".data"))
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expect_true(is_right, info = "the environmental data cannot be found for dplyr/select()")
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df <- example_isolates %>% select_at(check_df(".tbl"))
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expect_true(is_right, info = "the environmental data cannot be found for dplyr/select_at()")
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}
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if (AMR:::pkg_is_available("tidymodels", also_load = TRUE)) {
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resistance_recipe <- recipe(mo ~ ., data = example_isolates) %>%
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step_corr(check_df("training")) %>%
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prep()
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expect_true(is_right, info = "the environmental data cannot be found for tidymodels/prep()")
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}
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})
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