AMR/tests/testthat/test-data.R

52 lines
2.6 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# 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(antibiotics), length(unique(antibiotics$atc)))
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
# there should be no diacritics (i.e. non ASCII) characters in the datasets
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
for (i in 1:length(datasets)) {
dataset <- get(datasets[i], envir = asNamespace("AMR"))
expect_identical(dataset_UTF8_to_ASCII(dataset), dataset)
}
})
test_that("creation of data sets is valid", {
df <- make()
expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))
expect_lt(nrow(df[which(df$prevalence == 2), ]), nrow(df[which(df$prevalence == 3), ]))
DT <- make_DT()
expect_lt(nrow(DT[prevalence == 1]), nrow(DT[prevalence == 2]))
expect_lt(nrow(DT[prevalence == 2]), nrow(DT[prevalence == 3]))
old <- make_trans_tbl()
expect_gt(length(old), 0)
})
test_that("CoL version info works", {
expect_identical(class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list"))
})