# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (2022). # # AMR: An R Package for Working with Antimicrobial Resistance Data. # # Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/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://amr-for-r.org # # ==================================================================== # test_that("test-misc.R", { skip_on_cran() expect_equal(AMR:::percentage(0.25), "25%") expect_equal(AMR:::percentage(0.5), "50%") expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%") expect_equal(AMR:::percentage(0.1234), "12.3%") # round up 0.5 expect_equal(AMR:::percentage(0.0054), "0.5%") expect_equal(AMR:::percentage(0.0055), "0.6%") # test functions on all R versions - R < 3.3 did not contain these expect_equal(strrep("A", 5), "AAAAA") expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB")) expect_equal(trimws(" test "), "test") expect_equal(trimws(" test ", "l"), "test ") expect_equal(trimws(" test ", "r"), " test") expect_equal(AMR:::trimws2(" test "), "test") expect_equal(AMR:::trimws2(" test ", "l"), "test ") expect_equal(AMR:::trimws2(" test ", "r"), " test") expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS")) # we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this: if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward))) } # test where() ---- # where() must be AMR's own function, decided at runtime: a copy of tidyselect::where() made at installation fails without tidyselect at runtime expect_identical(environment(AMR:::where), asNamespace("AMR")) expect_identical(colnames(example_isolates[, AMR:::where(is.sir), drop = FALSE]), colnames(example_isolates)[vapply(FUN.VALUE = logical(1), example_isolates, is.sir)]) expect_identical(colnames(example_isolates[, c(1:2, AMR:::where(is.mo)), drop = FALSE]), c("date", "patient", "mo")) expect_error(AMR:::where("is.sir")) # default argument where(is.sir) of antibiogram() works with and without tidyselect expect_inherits(antibiogram(example_isolates), "antibiogram") if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { expect_identical(colnames(example_isolates %>% select(AMR:::where(is.sir))), colnames(example_isolates[, AMR:::where(is.sir), drop = FALSE])) expect_identical(colnames(example_isolates %>% select(mo, AMR:::where(is.sir))), c("mo", colnames(example_isolates[, AMR:::where(is.sir), drop = FALSE]))) } # test get_current_data() ---- is_right <- FALSE check_df <- function(check_element, return_val = 0) { is_right <<- FALSE for (env in sys.frames()) { # in R < 4.2, reading a promise that is still being evaluated (such as `x` in tibble's `[`) gives an error val <- tryCatch(env[[check_element]], error = function(e) NULL) if (!is.null(val) && is.data.frame(val)) { is_right <<- all(colnames(example_isolates) %in% colnames(val)) } } return_val } df <- example_isolates[, check_df("x")] expect_true(is_right, info = "the environmental data cannot be found for base `x`") # should work on R >=3.6.3 or so df <- example_isolates[c(1:3), check_df("x")] if (!is_right) { # otherwise, this is needed for older versions df <- example_isolates[c(1:3), check_df("xx")] expect_true(is_right, info = "the environmental data cannot be found for base `x` or `xx`") } if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { df <- example_isolates %>% select(mo, check_df("data123")) expect_false(is_right, info = "just a check if non-sense is not being gathered by get_current_data()") df <- example_isolates %>% select(mo, check_df(".data")) expect_true(is_right, info = "the environmental data cannot be found for dplyr/select()") df <- example_isolates %>% select_at(check_df(".tbl")) expect_true(is_right, info = "the environmental data cannot be found for dplyr/select_at()") } if (AMR:::pkg_is_available("tidymodels", also_load = TRUE)) { resistance_recipe <- recipe(mo ~ ., data = example_isolates) %>% step_corr(check_df("training")) %>% prep() expect_true(is_right, info = "the environmental data cannot be found for tidymodels/prep()") } }) test_that("test-cli_to_plain", { # plain-text fallback for when cli or rlang is unavailable: must always terminate, also when # word wrapping breaks a line within markup, or for expressions that cannot be evaluated expect_identical(AMR:::cli_to_plain("a {.code\nx()} b"), "a `x()` b") expect_identical(AMR:::cli_to_plain("{.arg x} {not_an_object_in_AMR} {1 + 1}"), "`x` {not_an_object_in_AMR} 2") msg <- "Setting {.code parallel = TRUE} requires a non-sequential {.help [{.fun future::plan}](future::plan)} to be active." expect_identical( gsub("[[:space:]]+", " ", AMR:::cli_to_plain(AMR:::word_wrap(msg, width = 40))), "Setting `parallel = TRUE` requires a non-sequential `future::plan()` to be active." ) })