AMR/tests/testthat/test-data.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("data.R")
test_that("data sets are valid", {
# IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
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expect_identical(class(microorganisms$mo), "mo")
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expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
expect_identical(class(antibiotics$ab), "ab")
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# check cross table reference
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
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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_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
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# antibiotic names must always be coercible to their original AB code
expect_identical(antibiotics$ab, as.ab(antibiotics$name))
# 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"))
expect_identical(dataset_UTF8_to_ASCII(dataset), dataset, label = datasets[i])
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}
})
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test_that("creation of data sets is valid", {
DT <- make_DT()
expect_lt(nrow(DT[prevalence == 1]), nrow(DT[prevalence == 2]))
expect_lt(nrow(DT[prevalence == 2]), nrow(DT[prevalence == 3]))
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expect_true(all(c("mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "col_id", "species_id", "source", "ref", "prevalence",
"kingdom_index", "fullname_lower", "g_species") %in% colnames(DT)))
oldDT <- make_oldDT()
expect_true(all(c("col_id", "col_id_new", "fullname", "ref", "prevalence",
"fullname_lower", "g_species") %in% colnames(oldDT)))
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old <- make_trans_tbl()
expect_gt(length(old), 0)
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})
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test_that("CoL version info works", {
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expect_identical(class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list"))
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expect_output(print(catalogue_of_life_version()))
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})