# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # 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. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # library(AMR) library(dplyr) int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE) for (i in seq_len(nrow(antibiotics))) { int_resis$new <- as.rsi("S") colnames(int_resis)[ncol(int_resis)] <- antibiotics$name[i] } int_resis <- eucast_rules(int_resis, eucast_rules_df = subset(AMR:::EUCAST_RULES_DF, is.na(have_these_values) & reference.version == 3.3), info = FALSE) int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>% tidyr::pivot_longer(-microorganism) %>% filter(value == "R") %>% select(microorganism, antibiotic = name) # remove lab drugs untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "name", drop = TRUE] int_resis2 <- int_resis2 %>% filter(!antibiotic %in% untreatable) %>% arrange(microorganism, antibiotic) int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL) intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE) usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz") rm(intrinsic_resistant) # AFTER THIS: # DO NOT FORGET TO UPDATE THE VERSION NUMBER IN mo_is_intrinsic_resistant()