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https://github.com/msberends/AMR.git
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67 lines
3.2 KiB
R
67 lines
3.2 KiB
R
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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library(AMR)
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library(dplyr)
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int_resis <- data.frame(mo = microorganisms$mo, stringsAsFactors = FALSE)
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for (i in seq_len(nrow(antibiotics))) {
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int_resis$new <- as.sir("S")
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colnames(int_resis)[ncol(int_resis)] <- antibiotics$ab[i]
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}
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int_resis <- eucast_rules(int_resis,
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eucast_rules_df = subset(
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AMR:::EUCAST_RULES_DF,
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is.na(have_these_values) & reference.version == 3.3
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),
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info = FALSE
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)
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int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.sir(x) | x == "R")), drop = FALSE] %>%
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tidyr::pivot_longer(-mo) %>%
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filter(value == "R") %>%
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select(mo, ab = name)
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# remove lab drugs
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untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
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# takes ages with filter()..., weird
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int_resis3 <- int_resis2[which(!int_resis2$ab %in% untreatable), ]
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class(int_resis3$ab) <- c("ab", "character")
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int_resis3
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all(int_resis3$mo %in% microorganisms$mo)
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all(int_resis3$ab %in% antibiotics$ab)
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intrinsic_resistant <- df_remove_nonASCII(int_resis3)
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usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
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rm(intrinsic_resistant)
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# AFTER THIS:
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# DO NOT FORGET TO UPDATE THE VERSION NUMBER IN mo_is_intrinsic_resistant() AND R/data.R
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