mirror of https://github.com/msberends/AMR.git
397 lines
24 KiB
R
397 lines
24 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data 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) 2018-2022 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 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-hook.R")
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library(dplyr, warn.conflicts = FALSE)
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devtools::load_all(quiet = TRUE)
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set_AMR_locale("en")
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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(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 <- 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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LANGUAGES_SUPPORTED_NAMES <- c(list(en = list(exonym = "English", endonym = "English")),
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lapply(TRANSLATIONS[, which(nchar(colnames(TRANSLATIONS)) == 2)],
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function(x) list(exonym = x[1], endonym = x[2])))
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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$genus == "Staphylococcus"), , drop = FALSE]
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if (type == "CoNS") {
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MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae",
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"auricularis", "borealis", "caeli", "capitis", "caprae",
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"carnosus", "casei", "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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| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
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"mo", drop = TRUE]
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} else if (type == "CoPS") {
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MO_staph[which(MO_staph$species %in% c("coagulase-positive", "coagulans",
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"agnetis", "argenteus",
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"cornubiensis",
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"delphini", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schweitzeri", "simiae",
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"roterodami")
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| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
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"mo", drop = TRUE]
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}
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}
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create_MO_fullname_lower <- function() {
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MO_lookup <- AMR::microorganisms
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies)))
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ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
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MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
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MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
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MO_lookup$fullname_lower
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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 <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
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MO_FULLNAME_LOWER <- create_MO_fullname_lower()
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MO_PREVALENT_GENERA <- c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
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"Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
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"Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
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"Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
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"Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
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"Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
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"Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
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"Dermatobia", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
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"Empedobacter", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
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"Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
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"Heterophyes", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Lelliottia",
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"Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
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"Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
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"Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
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"Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
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"Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
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"Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
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"Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
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"Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",
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"Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
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"Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
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"Trichuris", "Tritirachium", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
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"Weeksella", "Wuchereria")
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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 %>% filter(group %like% "aminoglycoside") %>% pull(ab)
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AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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AB_ANTIFUNGALS <- AB_lookup %>% filter(group %like% "antifungal") %>% pull(ab)
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AB_ANTIMYCOBACTERIALS <- AB_lookup %>% filter(group %like% "antimycobacterial") %>% pull(ab)
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AB_CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
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AB_CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
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AB_CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
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AB_CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
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AB_CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
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AB_CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab)
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AB_CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab)
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AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
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AB_FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab)
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AB_GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% 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 %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab)
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AB_MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab)
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AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
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AB_PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
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AB_POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
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AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab)
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AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
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AB_TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab)
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AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
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AB_TRIMETHOPRIMS <- antibiotics %>% filter(group %like% "trimethoprim") %>% 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_lookup <- function() {
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AB_lookup <- AMR::antibiotics
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AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
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AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
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AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
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AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
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AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
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c("ab", "atc", "cid", "name",
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colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
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drop = FALSE]),
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stringsAsFactors = FALSE)),
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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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AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
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}
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AB_LOOKUP <- create_AB_lookup()
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# Export to package as internal data ----
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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_FULLNAME_LOWER,
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MO_PREVALENT_GENERA,
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AB_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_OXAZOLIDINONES,
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AB_PENICILLINS,
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AB_POLYMYXINS,
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AB_QUINOLONES,
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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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# 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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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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}, error = function(e) TRUE)
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}
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# give official names to ABs and MOs
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rsi <- rsi_translation %>%
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mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
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mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
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if (changed_md5(rsi)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}"))
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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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try(arrow::write_feather(rsi, "data-raw/rsi_translation.feather"), silent = TRUE)
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try(arrow::write_parquet(rsi, "data-raw/rsi_translation.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('/data-raw/')}"))
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write_md5(microorganisms)
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try(saveRDS(microorganisms, "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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max_50_snomed <- sapply(microorganisms$snomed, function(x) paste(x[seq_len(min(50, length(x), na.rm = TRUE))], collapse = " "))
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mo <- microorganisms
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mo$snomed <- max_50_snomed
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mo <- dplyr::mutate_if(mo, ~!is.numeric(.), as.character)
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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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try(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms.old)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.old')} to {usethis::ui_value('/data-raw/')}"))
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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)
|
|
try(arrow::write_feather(microorganisms.old, "data-raw/microorganisms.old.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms.old, "data-raw/microorganisms.old.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(write.table(antibiotics, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE)
|
|
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
|
|
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
|
|
try(openxlsx::write.xlsx(ab, "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(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE)
|
|
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
|
|
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
|
|
try(openxlsx::write.xlsx(av, "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$mo, language = NULL),
|
|
antibiotic = ab_name(intrinsic_resistant$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_sas(intrinsicR, "data-raw/intrinsic_resistant.sas"), 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_sas(dosage, "data-raw/dosage.sas"), 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)
|
|
}
|
|
|
|
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)
|
|
devtools::document()
|