# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # # # 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 more info: https://msberends.github.io/AMR. # # ==================================================================== # # Run this file to update the package using: ------------------------------- # source("data-raw/internals.R") # -------------------------------------------------------------------------- # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv", skip = 10, sep = "\t", stringsAsFactors = FALSE, header = TRUE, strip.white = TRUE, na = c(NA, "", NULL)) # take the order of the reference.rule_group column in the original data file eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group, levels = unique(eucast_rules_file$reference.rule_group), ordered = TRUE) eucast_rules_file <- dplyr::arrange(eucast_rules_file, reference.rule_group, reference.rule) eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group) # Translations ---- translations_file <- utils::read.delim(file = "data-raw/translations.tsv", sep = "\t", stringsAsFactors = FALSE, header = TRUE, blank.lines.skip = TRUE, fill = TRUE, strip.white = TRUE, encoding = "UTF-8", fileEncoding = "UTF-8", na.strings = c(NA, "", NULL), allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1" quote = "") # Old microorganism codes ------------------------------------------------- microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds") # Export to package as internal data ---- usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation, internal = TRUE, overwrite = TRUE, version = 2) # Remove from global environment ---- rm(eucast_rules_file) rm(translations_file) rm(microorganisms.translation) # Save to raw data to repository ---- usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}")) devtools::load_all(quiet = TRUE) # give official names to ABs and MOs rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo)) saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2) write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(rsi, "data-raw/rsi_translation.sas") haven::write_sav(rsi, "data-raw/rsi_translation.sav") haven::write_dta(rsi, "data-raw/rsi_translation.dta") openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx") mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character) saveRDS(mo, "data-raw/microorganisms.rds", version = 2) write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(mo, "data-raw/microorganisms.sas") haven::write_sav(mo, "data-raw/microorganisms.sav") haven::write_dta(mo, "data-raw/microorganisms.dta") openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx") saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2) write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas") haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav") haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta") openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx") ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character) saveRDS(ab, "data-raw/antibiotics.rds", version = 2) write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(ab, "data-raw/antibiotics.sas") haven::write_sav(ab, "data-raw/antibiotics.sav") haven::write_dta(ab, "data-raw/antibiotics.dta") openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx") av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character) saveRDS(av, "data-raw/antivirals.rds", version = 2) write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(av, "data-raw/antivirals.sas") haven::write_sav(av, "data-raw/antivirals.sav") haven::write_dta(av, "data-raw/antivirals.dta") openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx") saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2) write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE) haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas") haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav") haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta") openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx")