mirror of https://github.com/msberends/AMR.git
90 lines
3.7 KiB
R
Executable File
90 lines
3.7 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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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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# #
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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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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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context("aa_helper_functions.R")
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test_that("percentages works", {
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skip_on_cran()
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expect_equal(percentage(0.25), "25%")
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expect_equal(percentage(0.5), "50%")
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expect_equal(percentage(0.500, digits = 1), "50.0%")
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expect_equal(percentage(0.1234), "12.3%")
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# round up 0.5
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expect_equal(percentage(0.0054), "0.5%")
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expect_equal(percentage(0.0055), "0.6%")
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})
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test_that("functions missing in older R versions work", {
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skip_on_cran()
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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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})
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test_that("looking up ab columns works", {
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skip_on_cran()
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expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
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expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
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expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
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expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
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expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
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expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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})
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test_that("imports work", {
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skip_on_cran()
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import_functions <- c(
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"anti_join" = "dplyr",
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"cur_column" = "dplyr",
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"freq.default" = "cleaner",
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"full_join" = "dplyr",
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"has_internet" = "curl",
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"html_attr" = "rvest",
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"html_children" = "rvest",
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"html_node" = "rvest",
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"html_nodes" = "rvest",
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"html_table" = "rvest",
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"html_text" = "rvest",
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"inline_hist" = "skimr",
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"inner_join" = "dplyr",
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"insertText" = "rstudioapi",
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"left_join" = "dplyr",
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"new_pillar_shaft_simple" = "pillar",
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"peek_mask" = "dplyr",
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"peek_vars" = "tidyselect",
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"read_excel" = "readxl",
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"read_html" = "xml2",
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"right_join" = "dplyr",
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"semi_join" = "dplyr",
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"sfl" = "skimr",
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"showQuestion" = "rstudioapi")
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for (i in seq_len(length(import_functions))) {
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fn <- names(import_functions)[i]
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pkg <- unname(import_functions[i])
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expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
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failure_message = paste0("Function ", pkg, "::", fn, "() does not exist"))
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}
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})
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