mirror of https://github.com/msberends/AMR.git
67 lines
3.4 KiB
R
67 lines
3.4 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.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))
|
|
|
|
})
|
|
|
|
|
|
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]))
|
|
old <- make_trans_tbl()
|
|
expect_gt(length(old), 0)
|
|
})
|