mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 09:26:11 +01:00
85 lines
4.7 KiB
R
85 lines
4.7 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
expect_true(check_dataset_integrity()) # in misc.R
|
|
|
|
# IDs should always be unique
|
|
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
|
|
expect_identical(class(microorganisms$mo), c("mo", "character"))
|
|
expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
|
|
expect_identical(class(antibiotics$ab), c("ab", "character"))
|
|
|
|
# check cross table reference
|
|
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
|
|
expect_true(all(example_isolates$mo %in% microorganisms$mo))
|
|
expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
|
|
expect_true(all(rsi_translation$mo %in% microorganisms$mo))
|
|
expect_true(all(rsi_translation$ab %in% antibiotics$ab))
|
|
expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
|
|
expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
|
|
expect_false(any(is.na(microorganisms.codes$code)))
|
|
expect_false(any(is.na(microorganisms.codes$mo)))
|
|
expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
|
|
expect_true(all(dosage$ab %in% antibiotics$ab))
|
|
expect_true(all(dosage$name %in% antibiotics$name))
|
|
|
|
# antibiotic names must always be coercible to their original AB code
|
|
expect_identical(as.ab(antibiotics$name), antibiotics$ab)
|
|
|
|
# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
|
|
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
|
|
for (i in seq_len(length(datasets))) {
|
|
dataset <- get(datasets[i], envir = asNamespace("AMR"))
|
|
expect_identical(dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
|
|
}
|
|
|
|
df <- AMR:::MO_lookup
|
|
expect_true(nrow(df[which(df$prevalence == 1), ]) < nrow(df[which(df$prevalence == 2), ]))
|
|
expect_true(nrow(df[which(df$prevalence == 2), ]) < nrow(df[which(df$prevalence == 3), ]))
|
|
expect_true(all(c("mo", "fullname",
|
|
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
|
|
"rank", "ref", "species_id", "source", "prevalence", "snomed",
|
|
"kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
|
|
|
|
expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
|
|
"fullname_lower", "g_species") %in% colnames(AMR:::MO.old_lookup)))
|
|
|
|
expect_inherits(AMR:::MO_CONS, "mo")
|
|
|
|
expect_identical(class(catalogue_of_life_version()),
|
|
c("catalogue_of_life_version", "list"))
|
|
|
|
expect_stdout(print(catalogue_of_life_version()))
|
|
|
|
uncategorised <- subset(microorganisms,
|
|
genus == "Staphylococcus" &
|
|
!species %in% c("", "aureus") &
|
|
!mo %in% c(MO_CONS, MO_COPS))
|
|
expect_true(NROW(uncategorised) == 0,
|
|
info = ifelse(NROW(uncategorised) == 0,
|
|
"All staphylococcal species categorised as CoNS/CoPS.",
|
|
paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
|
|
uncategorised$species, " (", uncategorised$mo, ")")))
|