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652 lines
25 KiB
R
652 lines
25 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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/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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# Run this file to update the package using:
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# source("data-raw/_pre_commit_checks.R")
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library(dplyr, warn.conflicts = FALSE)
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try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like
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devtools::load_all(quiet = TRUE)
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suppressMessages(set_AMR_locale("English"))
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pre_commit_lst <- list()
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# Save internal data to R/sysdata.rda -------------------------------------
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usethis::ui_info(paste0("Updating internal package data"))
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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pre_commit_lst$EUCAST_RULES_DF <- utils::read.delim(
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file = "data-raw/eucast_rules.tsv",
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skip = 9,
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)
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) %>%
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# take the order of the reference.rule_group column in the original data file
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mutate(
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reference.rule_group = factor(reference.rule_group,
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levels = unique(reference.rule_group),
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ordered = TRUE
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),
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sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)
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) %>%
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arrange(
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reference.rule_group,
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reference.version,
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sorting_rule,
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reference.rule
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) %>%
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mutate(reference.rule_group = as.character(reference.rule_group)) %>%
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select(-sorting_rule)
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pre_commit_lst$TRANSLATIONS <- utils::read.delim(
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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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)
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pre_commit_lst$LANGUAGES_SUPPORTED_NAMES <- c(
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list(en = list(exonym = "English", endonym = "English")),
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lapply(
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TRANSLATIONS[, which(nchar(colnames(pre_commit_lst$TRANSLATIONS)) == 2), drop = FALSE],
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function(x) list(exonym = x[1], endonym = x[2])
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)
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)
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pre_commit_lst$LANGUAGES_SUPPORTED <- names(pre_commit_lst$LANGUAGES_SUPPORTED_NAMES)
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# vectors of CoNS and CoPS, improves speed in as.mo()
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create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
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# Determination of which staphylococcal species are CoNS/CoPS according to:
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2020, PMID 32056452
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# this function returns class <mo>
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MO_staph <- AMR::microorganisms
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MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
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if (type == "CoNS") {
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MO_staph[
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which(MO_staph$species %in% c(
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"coagulase-negative", "argensis", "arlettae",
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"auricularis", "borealis", "caeli", "capitis", "caprae",
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"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
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"croceilyticus",
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"debuckii", "devriesei", "edaphicus", "epidermidis",
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"equorum", "felis", "fleurettii", "gallinarum",
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"haemolyticus", "hominis", "jettensis", "kloosii",
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"lentus", "lugdunensis", "massiliensis", "microti",
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"muscae", "nepalensis", "pasteuri", "petrasii",
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"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
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"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
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"sciuri", "simulans", "stepanovicii", "succinus",
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"ureilyticus",
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"vitulinus", "vitulus", "warneri", "xylosus",
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"caledonicus", "canis",
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"durrellii", "lloydii",
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"ratti", "taiwanensis", "veratri", "urealyticus",
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"americanisciuri", "marylandisciuri", "shinii", "brunensis"
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) |
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# old, now renamed to S. schleiferi (but still as synonym in our data of course):
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(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
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"mo",
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drop = TRUE
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]
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} else if (type == "CoPS") {
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MO_staph[
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which(MO_staph$species %in% c(
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"coagulase-positive", "coagulans",
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"agnetis", "argenteus",
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"cornubiensis",
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"delphini", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schweitzeri", "simiae",
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"roterodami",
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"singaporensis"
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) |
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# old, now renamed to S. coagulans (but still as synonym in our data of course):
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(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
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"mo",
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drop = TRUE
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]
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}
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}
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pre_commit_lst$MO_CONS <- create_species_cons_cops("CoNS")
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pre_commit_lst$MO_COPS <- create_species_cons_cops("CoPS")
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pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Streptococcus" &
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tolower(AMR::microorganisms$species) %in% c(
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"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
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"group a", "group b", "group c", "group g"
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))]
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pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
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pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
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# World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
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"Acinetobacter",
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"Aspergillus",
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"Blastomyces",
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"Campylobacter",
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"Candida",
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"Citrobacter",
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"Clostridioides",
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"Coccidioides",
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"Cryptococcus",
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"Edwardsiella",
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"Enterobacter",
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"Enterococcus",
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"Escherichia",
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"Fusarium",
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"Haemophilus",
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"Helicobacter",
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"Histoplasma",
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"Klebsiella",
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"Morganella",
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"Mycobacterium",
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"Neisseria",
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"Paracoccidioides",
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"Pneumocystis",
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"Proteus",
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"Providencia",
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"Pseudomonas",
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"Salmonella",
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"Serratia",
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"Shigella",
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"Staphylococcus",
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"Streptococcus",
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"Yersinia"
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)
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pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Absidia",
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"Acanthamoeba",
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"Acremonium",
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"Actinomucor",
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"Aedes",
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"Alternaria",
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"Amoeba",
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"Ancylostoma",
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"Angiostrongylus",
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"Anisakis",
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"Anopheles",
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"Apophysomyces",
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"Arthroderma",
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"Aspergillus",
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"Aureobasidium",
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"Basidiobolus",
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"Beauveria",
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"Bipolaris",
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"Blastobotrys",
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"Blastocystis",
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"Blastomyces",
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"Candida",
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"Capillaria",
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"Chaetomium",
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"Chilomastix",
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"Chrysonilia",
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"Chrysosporium",
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"Cladophialophora",
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"Cladosporium",
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"Clavispora",
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"Coccidioides",
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"Cokeromyces",
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"Conidiobolus",
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"Coniochaeta",
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"Contracaecum",
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"Cordylobia",
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"Cryptococcus",
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"Cryptosporidium",
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"Cunninghamella",
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"Curvularia",
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"Cyberlindnera",
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"Debaryozyma",
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"Demodex",
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"Dermatobia",
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"Dientamoeba",
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"Diphyllobothrium",
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"Dirofilaria",
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"Echinostoma",
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"Entamoeba",
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"Enterobius",
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"Epidermophyton",
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"Exidia",
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"Exophiala",
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"Exserohilum",
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"Fasciola",
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"Fonsecaea",
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"Fusarium",
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"Geotrichum",
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"Giardia",
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"Graphium",
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"Haloarcula",
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"Halobacterium",
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"Halococcus",
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"Hansenula",
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"Hendersonula",
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"Heterophyes",
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"Histomonas",
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"Histoplasma",
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"Hortaea",
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"Hymenolepis",
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"Hypomyces",
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"Hysterothylacium",
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"Kloeckera",
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"Kluyveromyces",
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"Kodamaea",
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"Lacazia",
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"Leishmania",
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"Lichtheimia",
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"Lodderomyces",
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"Lomentospora",
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"Madurella",
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"Malassezia",
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"Malbranchea",
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"Metagonimus",
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"Meyerozyma",
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"Microsporidium",
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"Microsporum",
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"Millerozyma",
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"Mortierella",
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"Mucor",
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"Mycocentrospora",
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"Nannizzia",
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"Necator",
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"Nectria",
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"Ochroconis",
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"Oesophagostomum",
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"Oidiodendron",
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"Opisthorchis",
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"Paecilomyces",
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"Paracoccidioides",
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"Pediculus",
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"Penicillium",
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"Phaeoacremonium",
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"Phaeomoniella",
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"Phialophora",
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"Phlebotomus",
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"Phoma",
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"Pichia",
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"Piedraia",
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"Pithomyces",
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"Pityrosporum",
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"Pneumocystis",
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"Pseudallescheria",
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"Pseudoscopulariopsis",
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"Pseudoterranova",
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"Pulex",
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"Purpureocillium",
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"Quambalaria",
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"Rhinocladiella",
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"Rhizomucor",
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"Rhizopus",
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"Rhodotorula",
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"Saccharomyces",
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"Saksenaea",
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"Saprochaete",
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"Sarcoptes",
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"Scedosporium",
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"Schistosoma",
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"Schizosaccharomyces",
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"Scolecobasidium",
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"Scopulariopsis",
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"Scytalidium",
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"Spirometra",
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"Sporobolomyces",
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"Sporopachydermia",
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"Sporothrix",
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"Sporotrichum",
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"Stachybotrys",
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"Strongyloides",
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"Syncephalastrum",
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"Syngamus",
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"Taenia",
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"Talaromyces",
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"Teleomorph",
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"Toxocara",
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"Trichinella",
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"Trichobilharzia",
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"Trichoderma",
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"Trichomonas",
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"Trichophyton",
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"Trichosporon",
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"Trichostrongylus",
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"Trichuris",
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"Tritirachium",
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"Trombicula",
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"Trypanosoma",
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"Tunga",
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"Ulocladium",
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"Ustilago",
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"Verticillium",
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"Wallemia",
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"Wangiella",
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"Wickerhamomyces",
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"Wuchereria",
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"Yarrowia",
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"Zygosaccharomyces"
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)
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# antibiotic groups
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# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
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pre_commit_lst$AB_AMINOGLYCOSIDES <- antibiotics %>%
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filter(group %like% "aminoglycoside") %>%
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pull(ab)
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pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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pre_commit_lst$AB_ANTIFUNGALS <- antibiotics %>%
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filter(group %like% "antifungal") %>%
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pull(ab)
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pre_commit_lst$AB_ANTIMYCOBACTERIALS <- antibiotics %>%
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filter(group %like% "antimycobacterial") %>%
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pull(ab)
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pre_commit_lst$AB_CARBAPENEMS <- antibiotics %>%
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filter(group %like% "carbapenem") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS <- antibiotics %>%
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filter(group %like% "cephalosporin") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_1ST <- antibiotics %>%
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filter(group %like% "cephalosporin.*1") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_2ND <- antibiotics %>%
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filter(group %like% "cephalosporin.*2") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_3RD <- antibiotics %>%
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filter(group %like% "cephalosporin.*3") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_4TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*4") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*5") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
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pre_commit_lst$AB_FLUOROQUINOLONES <- antibiotics %>%
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filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
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pull(ab)
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pre_commit_lst$AB_GLYCOPEPTIDES <- antibiotics %>%
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filter(group %like% "glycopeptide") %>%
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pull(ab)
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pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
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pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
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pre_commit_lst$AB_LINCOSAMIDES <- antibiotics %>%
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filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
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pull(ab)
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pre_commit_lst$AB_MACROLIDES <- antibiotics %>%
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filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
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pull(ab)
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pre_commit_lst$AB_NITROFURANS <- antibiotics %>%
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filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
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pull(ab)
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pre_commit_lst$AB_OXAZOLIDINONES <- antibiotics %>%
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filter(group %like% "oxazolidinone") %>%
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pull(ab)
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pre_commit_lst$AB_PENICILLINS <- antibiotics %>%
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filter(group %like% "penicillin") %>%
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pull(ab)
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pre_commit_lst$AB_POLYMYXINS <- antibiotics %>%
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filter(group %like% "polymyxin") %>%
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pull(ab)
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pre_commit_lst$AB_QUINOLONES <- antibiotics %>%
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filter(group %like% "quinolone") %>%
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pull(ab)
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pre_commit_lst$AB_RIFAMYCINS <- antibiotics %>%
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filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
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pull(ab)
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pre_commit_lst$AB_STREPTOGRAMINS <- antibiotics %>%
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filter(atc_group2 %like% "streptogramin") %>%
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pull(ab)
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pre_commit_lst$AB_TETRACYCLINES <- antibiotics %>%
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filter(group %like% "tetracycline") %>%
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pull(ab)
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pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
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pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
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filter(group %like% "trimethoprim") %>%
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pull(ab)
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pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
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pre_commit_lst$AB_BETALACTAMS <- c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS)
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# this will be used for documentation:
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pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
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create_AB_AV_lookup <- function(df) {
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new_df <- df
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new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
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new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
|
|
if ("abbreviations" %in% colnames(df)) {
|
|
new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
|
|
}
|
|
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
|
|
new_df$generalised_all <- unname(lapply(
|
|
as.list(as.data.frame(
|
|
t(new_df[,
|
|
c(
|
|
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
|
|
colnames(new_df)[colnames(new_df) %like% "generalised"]
|
|
),
|
|
drop = FALSE
|
|
]),
|
|
stringsAsFactors = FALSE
|
|
)),
|
|
function(x) {
|
|
x <- generalise_antibiotic_name(unname(unlist(x)))
|
|
x[x != ""]
|
|
}
|
|
))
|
|
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
|
|
}
|
|
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
|
|
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
|
|
|
|
# Export to package as internal data ----
|
|
# usethis::use_data() must receive unquoted object names, which is not flexible at all.
|
|
# we'll use good old base::save() instead
|
|
save(list = names(pre_commit_lst),
|
|
file = "R/sysdata.rda",
|
|
envir = as.environment(pre_commit_lst),
|
|
compress = "xz",
|
|
version = 2,
|
|
ascii = FALSE)
|
|
usethis::ui_done("Saved to {usethis::ui_value('R/sysdata.rda')}")
|
|
|
|
|
|
|
|
|
|
# Export data sets to the repository in different formats -----------------
|
|
|
|
for (pkg in c("haven", "openxlsx2", "arrow")) {
|
|
if (!pkg %in% rownames(utils::installed.packages())) {
|
|
message("NOTE: package '", pkg, "' not installed! Ignoring export where this package is required.")
|
|
}
|
|
}
|
|
if ("digest" %in% rownames(utils::installed.packages())) {
|
|
md5 <- function(object) digest::digest(object, "md5")
|
|
} else {
|
|
# will write all files anyway, since MD5 hash cannot be determined
|
|
md5 <- function(object) "unknown-md5-hash"
|
|
}
|
|
|
|
write_md5 <- function(object) {
|
|
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
|
|
writeLines(md5(object), conn)
|
|
close(conn)
|
|
}
|
|
changed_md5 <- function(object) {
|
|
tryCatch(
|
|
{
|
|
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
|
|
compared <- md5(object) != readLines(con = conn)
|
|
close(conn)
|
|
compared
|
|
},
|
|
error = function(e) TRUE
|
|
)
|
|
}
|
|
|
|
# give official names to ABs and MOs
|
|
clin_break <- clinical_breakpoints %>%
|
|
mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
|
|
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
|
|
if (changed_md5(clin_break)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(clin_break)
|
|
try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
|
|
try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(clin_break, "data-raw/clinical_breakpoints.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(clin_break, "data-raw/clinical_breakpoints.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(microorganisms)
|
|
try(saveRDS(microorganisms, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
max_50_snomed <- sapply(microorganisms$snomed, function(x) paste(x[seq_len(min(50, length(x), na.rm = TRUE))], collapse = " "))
|
|
mo <- microorganisms
|
|
mo$snomed <- max_50_snomed
|
|
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
|
|
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
|
|
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
|
|
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(mo_all_snomed, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(mo_all_snomed, "data-raw/microorganisms.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms.codes)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(microorganisms.codes)
|
|
try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
|
|
try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms.codes, "data-raw/microorganisms.codes.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms.codes, "data-raw/microorganisms.codes.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms.groups)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(microorganisms.groups)
|
|
try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
|
|
try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms.groups, "data-raw/microorganisms.groups.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms.groups, "data-raw/microorganisms.groups.parquet"), silent = TRUE)
|
|
}
|
|
|
|
ab <- dplyr::mutate_if(antibiotics, ~ !is.numeric(.), as.character)
|
|
if (changed_md5(ab)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(ab)
|
|
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
|
|
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
|
|
ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(ab_lists, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(ab_lists, "data-raw/antibiotics.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(antibiotics, "data-raw/antibiotics.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(antibiotics, "data-raw/antibiotics.parquet"), silent = TRUE)
|
|
}
|
|
|
|
av <- dplyr::mutate_if(antivirals, ~ !is.numeric(.), as.character)
|
|
if (changed_md5(av)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(av)
|
|
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
|
|
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
|
|
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(av_lists, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(av_lists, "data-raw/antivirals.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(antivirals, "data-raw/antivirals.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(antivirals, "data-raw/antivirals.parquet"), silent = TRUE)
|
|
}
|
|
|
|
# give official names to ABs and MOs
|
|
intrinsicR <- data.frame(
|
|
microorganism = mo_name(intrinsic_resistant$mo, language = NULL, keep_synonyms = TRUE, info = FALSE),
|
|
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
if (changed_md5(intrinsicR)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(intrinsicR)
|
|
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
|
|
try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(intrinsicR, "data-raw/intrinsic_resistant.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(intrinsicR, "data-raw/intrinsic_resistant.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(dosage)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/')}"))
|
|
write_md5(dosage)
|
|
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
|
|
try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(dosage, "data-raw/dosage.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(dosage, "data-raw/dosage.parquet"), silent = TRUE)
|
|
}
|
|
|
|
suppressMessages(reset_AMR_locale())
|
|
|
|
devtools::load_all(quiet = TRUE)
|
|
suppressMessages(set_AMR_locale("English"))
|
|
|
|
# Update URLs -------------------------------------------------------------
|
|
usethis::ui_info("Checking URLs for redirects")
|
|
invisible(capture.output(urlchecker::url_update()))
|
|
|
|
|
|
# Document pkg ------------------------------------------------------------
|
|
usethis::ui_info("Documenting package")
|
|
suppressMessages(devtools::document(quiet = TRUE))
|
|
|
|
|
|
# Finished ----------------------------------------------------------------
|
|
usethis::ui_done("All done")
|
|
suppressMessages(reset_AMR_locale())
|