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528 lines
24 KiB
R
528 lines
24 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, 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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# 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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old_globalenv <- ls(envir = globalenv())
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# Save internal data to R/sysdata.rda -------------------------------------
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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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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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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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(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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LANGUAGES_SUPPORTED <- names(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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) |
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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$subspecies == "coagulans")),
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"mo",
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drop = TRUE
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]
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}
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}
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MO_CONS <- create_species_cons_cops("CoNS")
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MO_COPS <- create_species_cons_cops("CoPS")
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MO_STREP_ABCG <- AMR::microorganisms$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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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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MO_PREVALENT_GENERA <- c(
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"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
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"Anisakis", "Anopheles", "Apophysomyces", "Arthroderma", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
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"Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Chrysosporium", "Cladophialophora",
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"Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex",
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"Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Echinostoma", "Entamoeba", "Enterobius",
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"Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Geotrichum", "Giardia", "Haloarcula", "Halobacterium",
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"Halococcus", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces",
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"Hysterothylacium", "Kloeckera", "Kodamaea", "Leishmania", "Lichtheimia", "Lodderomyces",
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"Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
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"Microsporum", "Millerozyma", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
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"Oidiodendron", "Opisthorchis", "Paecilomyces", "Pediculus", "Penicillium", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
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"Pityrosporum", "Pneumocystis", "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus",
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"Rhodotorula", "Saccharomyces", "Saprochaete", "Sarcoptes", "Scedosporium", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
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"Sporobolomyces", "Sporotrichum", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Trichinella",
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"Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris",
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"Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Verticillium", "Wuchereria"
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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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globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
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AB_AMINOGLYCOSIDES <- antibiotics %>%
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filter(group %like% "aminoglycoside") %>%
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pull(ab)
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AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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AB_ANTIFUNGALS <- antibiotics %>%
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filter(group %like% "antifungal") %>%
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pull(ab)
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AB_ANTIMYCOBACTERIALS <- antibiotics %>%
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filter(group %like% "antimycobacterial") %>%
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pull(ab)
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AB_CARBAPENEMS <- antibiotics %>%
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filter(group %like% "carbapenem") %>%
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pull(ab)
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AB_CEPHALOSPORINS <- antibiotics %>%
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filter(group %like% "cephalosporin") %>%
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pull(ab)
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AB_CEPHALOSPORINS_1ST <- antibiotics %>%
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filter(group %like% "cephalosporin.*1") %>%
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pull(ab)
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AB_CEPHALOSPORINS_2ND <- antibiotics %>%
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filter(group %like% "cephalosporin.*2") %>%
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pull(ab)
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AB_CEPHALOSPORINS_3RD <- antibiotics %>%
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filter(group %like% "cephalosporin.*3") %>%
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pull(ab)
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AB_CEPHALOSPORINS_4TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*4") %>%
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pull(ab)
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AB_CEPHALOSPORINS_5TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*5") %>%
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pull(ab)
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AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
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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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AB_GLYCOPEPTIDES <- antibiotics %>%
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filter(group %like% "glycopeptide") %>%
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pull(ab)
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AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
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AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES]
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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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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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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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AB_OXAZOLIDINONES <- antibiotics %>%
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filter(group %like% "oxazolidinone") %>%
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pull(ab)
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AB_PENICILLINS <- antibiotics %>%
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filter(group %like% "penicillin") %>%
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pull(ab)
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AB_POLYMYXINS <- antibiotics %>%
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filter(group %like% "polymyxin") %>%
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pull(ab)
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AB_QUINOLONES <- antibiotics %>%
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filter(group %like% "quinolone") %>%
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pull(ab)
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AB_RIFAMYCINS <- antibiotics %>%
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filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
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pull(ab)
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AB_STREPTOGRAMINS <- antibiotics %>%
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filter(atc_group2 %like% "streptogramin") %>%
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pull(ab)
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AB_TETRACYCLINES <- antibiotics %>%
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filter(group %like% "tetracycline") %>%
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pull(ab)
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AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
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AB_TRIMETHOPRIMS <- antibiotics %>%
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filter(group %like% "trimethoprim") %>%
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pull(ab)
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AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
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AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
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# this will be used for documentation:
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DEFINED_AB_GROUPS <- ls(envir = globalenv())
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DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
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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$synonyms, generalise_antibiotic_name)
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if ("abbreviations" %in% colnames(df)) {
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new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
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}
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new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
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new_df$generalised_all <- unname(lapply(
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as.list(as.data.frame(
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t(new_df[,
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c(
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colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
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colnames(new_df)[colnames(new_df) %like% "generalised"]
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),
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drop = FALSE
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]),
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stringsAsFactors = FALSE
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)),
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function(x) {
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x <- generalise_antibiotic_name(unname(unlist(x)))
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x[x != ""]
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}
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))
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new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
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}
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AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
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AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
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# Export to package as internal data ----
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usethis::ui_info(paste0("Updating internal package data"))
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suppressMessages(usethis::use_data(EUCAST_RULES_DF,
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TRANSLATIONS,
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LANGUAGES_SUPPORTED_NAMES,
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LANGUAGES_SUPPORTED,
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MO_CONS,
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MO_COPS,
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MO_STREP_ABCG,
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MO_LANCEFIELD,
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MO_PREVALENT_GENERA,
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AB_LOOKUP,
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AV_LOOKUP,
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AB_AMINOGLYCOSIDES,
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AB_AMINOPENICILLINS,
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AB_ANTIFUNGALS,
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AB_ANTIMYCOBACTERIALS,
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AB_CARBAPENEMS,
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AB_CEPHALOSPORINS,
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AB_CEPHALOSPORINS_1ST,
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AB_CEPHALOSPORINS_2ND,
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AB_CEPHALOSPORINS_3RD,
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AB_CEPHALOSPORINS_4TH,
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AB_CEPHALOSPORINS_5TH,
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AB_CEPHALOSPORINS_EXCEPT_CAZ,
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AB_FLUOROQUINOLONES,
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AB_LIPOGLYCOPEPTIDES,
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AB_GLYCOPEPTIDES,
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AB_GLYCOPEPTIDES_EXCEPT_LIPO,
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AB_LINCOSAMIDES,
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AB_MACROLIDES,
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AB_NITROFURANS,
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AB_OXAZOLIDINONES,
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AB_PENICILLINS,
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AB_POLYMYXINS,
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AB_QUINOLONES,
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AB_RIFAMYCINS,
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AB_STREPTOGRAMINS,
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AB_TETRACYCLINES,
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AB_TETRACYCLINES_EXCEPT_TGC,
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AB_TRIMETHOPRIMS,
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AB_UREIDOPENICILLINS,
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AB_BETALACTAMS,
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DEFINED_AB_GROUPS,
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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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))
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# Export data sets to the repository in different formats -----------------
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for (pkg in c("haven", "openxlsx", "arrow")) {
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if (!pkg %in% rownames(utils::installed.packages())) {
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message("NOTE: package '", pkg, "' not installed! Ignoring export where this package is required.")
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}
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}
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if ("digest" %in% rownames(utils::installed.packages())) {
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md5 <- function(object) digest::digest(object, "md5")
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} else {
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# will write all files anyway, since MD5 hash cannot be determined
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md5 <- function(object) "unknown-md5-hash"
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}
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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(md5(object), 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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{
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conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
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compared <- md5(object) != readLines(con = conn)
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close(conn)
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compared
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},
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error = function(e) TRUE
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)
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}
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# give official names to ABs and MOs
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clin_break <- clinical_breakpoints %>%
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mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
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mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
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if (changed_md5(clin_break)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
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write_md5(clin_break)
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try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
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try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
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try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
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try(openxlsx::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_xpt(mo, "data-raw/microorganisms.xpt"), silent = TRUE)
|
|
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(openxlsx::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_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), 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(openxlsx::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_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), 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(openxlsx::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_xpt(ab, "data-raw/antibiotics.xpt"), 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(openxlsx::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_xpt(av, "data-raw/antivirals.xpt"), 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(openxlsx::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_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), 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(openxlsx::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_xpt(dosage, "data-raw/dosage.xpt"), 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(openxlsx::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())
|
|
|
|
# remove leftovers from global env
|
|
current_globalenv <- ls(envir = globalenv())
|
|
rm(list = current_globalenv[!current_globalenv %in% old_globalenv])
|
|
rm(current_globalenv)
|
|
|
|
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))
|
|
|
|
|
|
# Style pkg ---------------------------------------------------------------
|
|
if (!"styler" %in% rownames(utils::installed.packages())) {
|
|
message("Package 'styler' not installed!")
|
|
} else if (interactive()) {
|
|
# only when sourcing this file ourselves
|
|
# usethis::ui_info("Styling package")
|
|
# styler::style_pkg(
|
|
# style = styler::tidyverse_style,
|
|
# filetype = c("R", "Rmd")
|
|
# )
|
|
}
|
|
|
|
|
|
# Finished ----------------------------------------------------------------
|
|
usethis::ui_done("All done")
|
|
suppressMessages(reset_AMR_locale())
|