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55 lines
2.9 KiB
R
55 lines
2.9 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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context("data.R")
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test_that("data sets are valid", {
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# IDs should always be unique
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expect_identical(nrow(antibiotics), length(unique(antibiotics$atc)))
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expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
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# there should be no diacritics (i.e. non ASCII) characters in the datasets
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library(dplyr)
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# check only character variables:
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test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
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test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
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test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
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test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
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# and compare them with their transformed version:
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expect_identical(test_microorganisms,
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test_microorganisms %>%
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lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
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as.data.frame(stringsAsFactors = FALSE))
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expect_identical(test_microorganisms.old,
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test_microorganisms.old %>%
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lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
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as.data.frame(stringsAsFactors = FALSE))
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expect_identical(test_antibiotics,
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test_antibiotics %>%
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lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
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as.data.frame(stringsAsFactors = FALSE))
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expect_identical(test_septic_patients,
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test_septic_patients %>%
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lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
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as.data.frame(stringsAsFactors = FALSE))
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})
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