mirror of
https://github.com/msberends/AMR.git
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128 lines
6.2 KiB
R
128 lines
6.2 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_true(AMR:::check_dataset_integrity()) # in misc.R
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# IDs should always be unique
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expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
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expect_identical(class(microorganisms$mo), c("mo", "character"))
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expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
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expect_true(all(is.na(antibiotics$atc[duplicated(antibiotics$atc)])))
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expect_identical(class(antibiotics$ab), c("ab", "character"))
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# check cross table reference
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expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
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expect_true(all(example_isolates$mo %in% microorganisms$mo))
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expect_true(all(rsi_translation$mo %in% microorganisms$mo))
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expect_true(all(rsi_translation$ab %in% antibiotics$ab))
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expect_true(all(intrinsic_resistant$mo %in% microorganisms$mo))
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expect_true(all(intrinsic_resistant$ab %in% antibiotics$ab))
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expect_false(any(is.na(microorganisms.codes$code)))
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expect_false(any(is.na(microorganisms.codes$mo)))
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expect_true(all(dosage$ab %in% antibiotics$ab))
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expect_true(all(dosage$name %in% antibiotics$name))
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# check valid disks/MICs
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expect_false(any(is.na(as.mic(rsi_translation[which(rsi_translation$method == "MIC"), "breakpoint_S"]))))
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expect_false(any(is.na(as.mic(rsi_translation[which(rsi_translation$method == "MIC"), "breakpoint_R"]))))
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expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "DISK"), "breakpoint_S"]))))
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expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "DISK"), "breakpoint_R"]))))
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# antibiotic names must always be coercible to their original AB code
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expect_identical(as.ab(antibiotics$name), antibiotics$ab)
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# check if all languages are included in package environmental variable
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expect_identical(sort(c("en", colnames(AMR:::TRANSLATIONS)[nchar(colnames(AMR:::TRANSLATIONS)) == 2])),
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unname(AMR:::LANGUAGES_SUPPORTED))
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# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
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datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
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for (i in seq_len(length(datasets))) {
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dataset <- get(datasets[i], envir = asNamespace("AMR"))
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expect_identical(class(dataset), "data.frame")
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expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
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}
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df <- AMR:::MO_lookup
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expect_true(nrow(df[which(df$prevalence == 1), ]) < nrow(df[which(df$prevalence == 2), ]))
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expect_true(nrow(df[which(df$prevalence == 2), ]) < nrow(df[which(df$prevalence == 3), ]))
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expect_true(all(c("mo", "fullname",
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"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
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"rank", "ref", "species_id", "source", "prevalence", "snomed",
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"kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
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expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
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"fullname_lower", "g_species") %in% colnames(AMR:::MO.old_lookup)))
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expect_inherits(AMR:::MO_CONS, "mo")
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expect_identical(class(catalogue_of_life_version()),
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c("catalogue_of_life_version", "list"))
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expect_stdout(print(catalogue_of_life_version()))
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uncategorised <- subset(microorganisms,
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genus == "Staphylococcus" &
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!species %in% c("", "aureus") &
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!mo %in% c(AMR:::MO_CONS, AMR:::MO_COPS))
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expect_true(NROW(uncategorised) == 0,
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info = ifelse(NROW(uncategorised) == 0,
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"All staphylococcal species categorised as CoNS/CoPS.",
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paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
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uncategorised$species, " (", uncategorised$mo, ")")))
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# THIS WILL CHECK NON-ASCII STRINGS IN ALL FILES:
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# check_non_ascii <- function() {
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# purrr::map_df(
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# .id = "file",
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# # list common text files
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# .x = fs::dir_ls(
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# recurse = TRUE,
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# type = "file",
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# # ignore images, compressed
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# regexp = "\\.(png|ico|rda|ai|tar.gz|zip|xlsx|csv|pdf|psd)$",
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# invert = TRUE
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# ),
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# .f = function(path) {
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# x <- readLines(path, warn = FALSE)
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# # from tools::showNonASCII()
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# asc <- iconv(x, "latin1", "ASCII")
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# ind <- is.na(asc) | asc != x
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# # make data frame
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# if (any(ind)) {
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# tibble::tibble(
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# row = which(ind),
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# line = iconv(x[ind], "latin1", "ASCII", sub = "byte")
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# )
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# } else {
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# tibble::tibble()
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# }
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# }
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# )
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# }
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# x <- check_non_ascii() %>%
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# filter(file %unlike% "^(data-raw|docs|git_)")
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