mirror of https://github.com/msberends/AMR.git
57 lines
2.7 KiB
R
57 lines
2.7 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$ab)))
|
|
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
|
|
|
|
# check cross table reference
|
|
expect_true(all(microorganisms.codes$mo %in% microorganisms$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"))
|
|
|
|
expect_output(print(catalogue_of_life_version()))
|
|
})
|