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(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
This commit is contained in:
@ -6,9 +6,9 @@
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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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# 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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@ -36,12 +36,14 @@ 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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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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EUCAST_RULES_DF <- utils::read.delim(
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pre_commit_lst$EUCAST_RULES_DF <- utils::read.delim(
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file = "data-raw/eucast_rules.tsv",
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skip = 9,
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sep = "\t",
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@ -67,7 +69,7 @@ EUCAST_RULES_DF <- utils::read.delim(
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mutate(reference.rule_group = as.character(reference.rule_group)) %>%
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select(-sorting_rule)
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TRANSLATIONS <- utils::read.delim(
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pre_commit_lst$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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@ -82,15 +84,15 @@ TRANSLATIONS <- utils::read.delim(
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quote = ""
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)
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LANGUAGES_SUPPORTED_NAMES <- c(
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pre_commit_lst$LANGUAGES_SUPPORTED_NAMES <- c(
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list(en = list(exonym = "English", endonym = "English")),
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lapply(
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TRANSLATIONS[, which(nchar(colnames(TRANSLATIONS)) == 2), drop = FALSE],
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TRANSLATIONS[, which(nchar(colnames(pre_commit_lst$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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LANGUAGES_SUPPORTED <- names(LANGUAGES_SUPPORTED_NAMES)
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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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@ -147,115 +149,223 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
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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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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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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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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_PREVALENT_GENERA <- c(
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"Absidia",
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"Acanthamoeba",
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"Acremonium",
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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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"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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"Chrysonilia",
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"Chrysosporium",
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"Cladophialophora",
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"Cladosporium",
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"Conidiobolus",
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"Contracaecum",
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"Cordylobia",
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"Cryptococcus",
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"Curvularia",
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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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"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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"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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"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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"Leishmania",
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"Lichtheimia",
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"Lodderomyces",
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"Lomentospora",
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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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"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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"Pediculus",
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"Penicillium",
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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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"Rhizomucor",
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"Rhizopus",
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"Rhodotorula",
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"Saccharomyces",
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"Saprochaete",
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"Sarcoptes",
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"Scedosporium",
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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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"Sporotrichum",
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"Stachybotrys",
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"Strongyloides",
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"Syngamus",
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"Taenia",
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"Talaromyces",
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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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"Verticillium",
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"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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pre_commit_lst$AB_AMINOGLYCOSIDES <- antibiotics %>%
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filter(group %like% "aminoglycoside") %>%
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pull(ab)
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AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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AB_ANTIFUNGALS <- antibiotics %>%
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pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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pre_commit_lst$AB_ANTIFUNGALS <- antibiotics %>%
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filter(group %like% "antifungal") %>%
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pull(ab)
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AB_ANTIMYCOBACTERIALS <- antibiotics %>%
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pre_commit_lst$AB_ANTIMYCOBACTERIALS <- antibiotics %>%
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filter(group %like% "antimycobacterial") %>%
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pull(ab)
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AB_CARBAPENEMS <- antibiotics %>%
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pre_commit_lst$AB_CARBAPENEMS <- antibiotics %>%
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filter(group %like% "carbapenem") %>%
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pull(ab)
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AB_CEPHALOSPORINS <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS <- antibiotics %>%
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filter(group %like% "cephalosporin") %>%
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pull(ab)
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AB_CEPHALOSPORINS_1ST <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_1ST <- antibiotics %>%
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filter(group %like% "cephalosporin.*1") %>%
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pull(ab)
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AB_CEPHALOSPORINS_2ND <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_2ND <- antibiotics %>%
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filter(group %like% "cephalosporin.*2") %>%
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pull(ab)
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AB_CEPHALOSPORINS_3RD <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_3RD <- antibiotics %>%
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filter(group %like% "cephalosporin.*3") %>%
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pull(ab)
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AB_CEPHALOSPORINS_4TH <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_4TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*4") %>%
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pull(ab)
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AB_CEPHALOSPORINS_5TH <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antibiotics %>%
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filter(group %like% "cephalosporin.*5") %>%
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pull(ab)
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AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
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AB_FLUOROQUINOLONES <- antibiotics %>%
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pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
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pre_commit_lst$AB_FLUOROQUINOLONES <- antibiotics %>%
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filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
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pull(ab)
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AB_GLYCOPEPTIDES <- antibiotics %>%
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pre_commit_lst$AB_GLYCOPEPTIDES <- antibiotics %>%
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filter(group %like% "glycopeptide") %>%
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pull(ab)
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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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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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AB_MACROLIDES <- antibiotics %>%
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pre_commit_lst$AB_MACROLIDES <- antibiotics %>%
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filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
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pull(ab)
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AB_NITROFURANS <- antibiotics %>%
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pre_commit_lst$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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AB_OXAZOLIDINONES <- antibiotics %>%
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pre_commit_lst$AB_OXAZOLIDINONES <- antibiotics %>%
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filter(group %like% "oxazolidinone") %>%
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pull(ab)
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AB_PENICILLINS <- antibiotics %>%
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pre_commit_lst$AB_PENICILLINS <- antibiotics %>%
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filter(group %like% "penicillin") %>%
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pull(ab)
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AB_POLYMYXINS <- antibiotics %>%
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pre_commit_lst$AB_POLYMYXINS <- antibiotics %>%
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filter(group %like% "polymyxin") %>%
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pull(ab)
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AB_QUINOLONES <- antibiotics %>%
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pre_commit_lst$AB_QUINOLONES <- antibiotics %>%
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filter(group %like% "quinolone") %>%
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pull(ab)
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AB_RIFAMYCINS <- antibiotics %>%
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pre_commit_lst$AB_RIFAMYCINS <- antibiotics %>%
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filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
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pull(ab)
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AB_STREPTOGRAMINS <- antibiotics %>%
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pre_commit_lst$AB_STREPTOGRAMINS <- antibiotics %>%
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filter(atc_group2 %like% "streptogramin") %>%
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pull(ab)
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AB_TETRACYCLINES <- antibiotics %>%
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pre_commit_lst$AB_TETRACYCLINES <- antibiotics %>%
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filter(group %like% "tetracycline") %>%
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||||
pull(ab)
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AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
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AB_TRIMETHOPRIMS <- antibiotics %>%
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pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
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||||
pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
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filter(group %like% "trimethoprim") %>%
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||||
pull(ab)
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AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
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||||
AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
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||||
pre_commit_lst$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:
|
||||
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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||||
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$name)
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||||
@ -282,62 +392,26 @@ create_AB_AV_lookup <- function(df) {
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||||
))
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||||
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
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||||
}
|
||||
AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
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||||
AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
|
||||
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
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||||
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::ui_info(paste0("Updating internal package data"))
|
||||
suppressMessages(usethis::use_data(EUCAST_RULES_DF,
|
||||
TRANSLATIONS,
|
||||
LANGUAGES_SUPPORTED_NAMES,
|
||||
LANGUAGES_SUPPORTED,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
MO_STREP_ABCG,
|
||||
MO_LANCEFIELD,
|
||||
MO_PREVALENT_GENERA,
|
||||
AB_LOOKUP,
|
||||
AV_LOOKUP,
|
||||
AB_AMINOGLYCOSIDES,
|
||||
AB_AMINOPENICILLINS,
|
||||
AB_ANTIFUNGALS,
|
||||
AB_ANTIMYCOBACTERIALS,
|
||||
AB_CARBAPENEMS,
|
||||
AB_CEPHALOSPORINS,
|
||||
AB_CEPHALOSPORINS_1ST,
|
||||
AB_CEPHALOSPORINS_2ND,
|
||||
AB_CEPHALOSPORINS_3RD,
|
||||
AB_CEPHALOSPORINS_4TH,
|
||||
AB_CEPHALOSPORINS_5TH,
|
||||
AB_CEPHALOSPORINS_EXCEPT_CAZ,
|
||||
AB_FLUOROQUINOLONES,
|
||||
AB_LIPOGLYCOPEPTIDES,
|
||||
AB_GLYCOPEPTIDES,
|
||||
AB_GLYCOPEPTIDES_EXCEPT_LIPO,
|
||||
AB_LINCOSAMIDES,
|
||||
AB_MACROLIDES,
|
||||
AB_NITROFURANS,
|
||||
AB_OXAZOLIDINONES,
|
||||
AB_PENICILLINS,
|
||||
AB_POLYMYXINS,
|
||||
AB_QUINOLONES,
|
||||
AB_RIFAMYCINS,
|
||||
AB_STREPTOGRAMINS,
|
||||
AB_TETRACYCLINES,
|
||||
AB_TETRACYCLINES_EXCEPT_TGC,
|
||||
AB_TRIMETHOPRIMS,
|
||||
AB_UREIDOPENICILLINS,
|
||||
AB_BETALACTAMS,
|
||||
DEFINED_AB_GROUPS,
|
||||
internal = TRUE,
|
||||
overwrite = TRUE,
|
||||
version = 2,
|
||||
compress = "xz"
|
||||
))
|
||||
# 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", "openxlsx", "arrow")) {
|
||||
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.")
|
||||
}
|
||||
@ -378,7 +452,7 @@ if (changed_md5(clin_break)) {
|
||||
try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), 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(openxlsx::write.xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), 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)
|
||||
}
|
||||
@ -396,7 +470,7 @@ if (changed_md5(microorganisms)) {
|
||||
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(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)
|
||||
}
|
||||
@ -409,7 +483,7 @@ if (changed_md5(microorganisms.codes)) {
|
||||
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(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)
|
||||
}
|
||||
@ -422,7 +496,7 @@ if (changed_md5(microorganisms.groups)) {
|
||||
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(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)
|
||||
}
|
||||
@ -437,7 +511,7 @@ if (changed_md5(ab)) {
|
||||
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(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)
|
||||
}
|
||||
@ -452,7 +526,7 @@ if (changed_md5(av)) {
|
||||
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(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)
|
||||
}
|
||||
@ -471,7 +545,7 @@ if (changed_md5(intrinsicR)) {
|
||||
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(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)
|
||||
}
|
||||
@ -484,18 +558,13 @@ if (changed_md5(dosage)) {
|
||||
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(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())
|
||||
|
||||
# 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"))
|
||||
|
||||
@ -509,19 +578,6 @@ 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())
|
||||
|
||||
Reference in New Issue
Block a user