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. #
# Visit our website for more info: https://msberends.gitab.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
library(dplyr)
# check only character variables:
test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
# and compare them with their transformed version:
expect_identical(test_microorganisms,
test_microorganisms %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_microorganisms.old,
test_microorganisms.old %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_antibiotics,
test_antibiotics %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_septic_patients,
test_septic_patients %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
})
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test_that("creation of data sets is valid", {
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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), ]))
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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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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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})