mirror of
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58 lines
3.2 KiB
R
58 lines
3.2 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# 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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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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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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