mirror of https://github.com/msberends/AMR.git
164 lines
8.7 KiB
R
164 lines
8.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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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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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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 analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# Run this file to update the package using: -------------------------------
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# source("data-raw/internals.R")
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# --------------------------------------------------------------------------
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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library(dplyr, warn.conflicts = FALSE)
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eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
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skip = 10,
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)) %>%
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# take the order of the reference.rule_group column in the original data file
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mutate(reference.rule_group = factor(reference.rule_group,
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levels = unique(reference.rule_group),
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ordered = TRUE),
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sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>%
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arrange(reference.rule_group,
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reference.version,
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sorting_rule,
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reference.rule) %>%
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mutate(reference.rule_group = as.character(reference.rule_group)) %>%
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select(-sorting_rule)
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# Translations ----
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translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL),
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allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
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quote = "")
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# Old microorganism codes -------------------------------------------------
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microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
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# Export to package as internal data ----
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usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
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internal = TRUE,
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overwrite = TRUE,
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version = 2,
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compress = "xz")
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# Remove from global environment ----
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rm(eucast_rules_file)
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rm(translations_file)
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rm(microorganisms.translation)
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# Save to raw data to repository ----
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write_md5 <- function(object) {
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conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
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writeLines(digest::digest(object, "md5"), conn)
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close(conn)
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}
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changed_md5 <- function(object) {
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tryCatch({
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conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
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compared <- digest::digest(object, "md5") != readLines(con = conn)
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close(conn)
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compared
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}, error = function(e) TRUE)
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}
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usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
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devtools::load_all(quiet = TRUE)
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# give official names to ABs and MOs
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rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
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if (changed_md5(rsi)) {
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write_md5(rsi)
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try(saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(rsi, "data-raw/rsi_translation.sas"), silent = TRUE)
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try(haven::write_sav(rsi, "data-raw/rsi_translation.sav"), silent = TRUE)
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try(haven::write_dta(rsi, "data-raw/rsi_translation.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx"), silent = TRUE)
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}
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mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character)
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if (changed_md5(mo)) {
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write_md5(mo)
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try(saveRDS(mo, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(mo, "data-raw/microorganisms.sas"), silent = TRUE)
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try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
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try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
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}
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if (changed_md5(microorganisms.old)) {
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write_md5(microorganisms.old)
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try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE)
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try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE)
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}
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ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character)
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if (changed_md5(ab)) {
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write_md5(ab)
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try(saveRDS(ab, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE)
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try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
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try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx"), silent = TRUE)
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}
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av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character)
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if (changed_md5(av)) {
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write_md5(av)
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try(saveRDS(av, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE)
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try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
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try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
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}
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if (changed_md5(intrinsic_resistant)) {
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write_md5(intrinsic_resistant)
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try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
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try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
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try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
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try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
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}
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rm(write_md5)
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rm(changed_md5)
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