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synced 2025-07-10 14:21:48 +02:00
(v2.1.1.9081) HUGE microorganisms update for fungi!
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@ -158,10 +158,11 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
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"group a", "group b", "group c", "group g"
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))]
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pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
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pre_commit_lst$MO_PREVALENT_GENERA <- c(
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pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Absidia",
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"Acanthamoeba",
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"Acremonium",
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"Actinomucor",
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"Aedes",
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"Alternaria",
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"Amoeba",
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@ -175,20 +176,31 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Aureobasidium",
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"Basidiobolus",
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"Beauveria",
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"Bipolaris",
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"Blastobotrys",
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"Blastocystis",
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"Blastomyces",
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"Candida",
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"Capillaria",
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"Chaetomium",
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"Chilomastix",
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"Chrysonilia",
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"Chrysosporium",
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"Cladophialophora",
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"Cladosporium",
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"Clavispora",
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"Coccidioides",
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"Cokeromyces",
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"Conidiobolus",
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"Coniochaeta",
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"Contracaecum",
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"Cordylobia",
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"Cryptococcus",
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"Cryptosporidium",
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"Cunninghamella",
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"Curvularia",
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"Cyberlindnera",
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"Debaryozyma",
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"Demodex",
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"Dermatobia",
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"Dientamoeba",
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@ -197,6 +209,8 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Echinostoma",
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"Entamoeba",
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"Enterobius",
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"Epidermophyton",
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"Exidia",
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"Exophiala",
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"Exserohilum",
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"Fasciola",
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@ -204,6 +218,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Fusarium",
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"Geotrichum",
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"Giardia",
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"Graphium",
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"Haloarcula",
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"Halobacterium",
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"Halococcus",
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@ -212,16 +227,19 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Heterophyes",
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"Histomonas",
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"Histoplasma",
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"Hortaea",
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"Hymenolepis",
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"Hypomyces",
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"Hysterothylacium",
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"Kloeckera",
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"Kluyveromyces",
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"Kodamaea",
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"Lacazia",
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"Leishmania",
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"Lichtheimia",
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"Lodderomyces",
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"Lomentospora",
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"Madurella",
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"Malassezia",
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"Malbranchea",
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"Metagonimus",
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@ -232,6 +250,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Mortierella",
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"Mucor",
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"Mycocentrospora",
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"Nannizzia",
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"Necator",
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"Nectria",
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"Ochroconis",
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@ -239,8 +258,12 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Oidiodendron",
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"Opisthorchis",
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"Paecilomyces",
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"Paracoccidioides",
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"Pediculus",
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"Penicillium",
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"Phaeoacremonium",
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"Phaeomoniella",
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"Phialophora",
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"Phlebotomus",
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"Phoma",
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"Pichia",
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@ -252,24 +275,34 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Pseudoscopulariopsis",
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"Pseudoterranova",
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"Pulex",
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"Purpureocillium",
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"Quambalaria",
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"Rhinocladiella",
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"Rhizomucor",
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"Rhizopus",
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"Rhodotorula",
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"Saccharomyces",
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"Saksenaea",
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"Saprochaete",
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"Sarcoptes",
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"Scedosporium",
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"Schistosoma",
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"Schizosaccharomyces",
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"Scolecobasidium",
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"Scopulariopsis",
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"Scytalidium",
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"Spirometra",
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"Sporobolomyces",
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"Sporopachydermia",
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"Sporothrix",
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"Sporotrichum",
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"Stachybotrys",
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"Strongyloides",
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"Syncephalastrum",
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"Syngamus",
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"Taenia",
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"Talaromyces",
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"Teleomorph",
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"Toxocara",
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"Trichinella",
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"Trichobilharzia",
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@ -283,8 +316,15 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
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"Trombicula",
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"Trypanosoma",
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"Tunga",
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"Ulocladium",
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"Ustilago",
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"Verticillium",
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"Wuchereria"
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"Wallemia",
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"Wangiella",
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"Wickerhamomyces",
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"Wuchereria",
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"Yarrowia",
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"Zygosaccharomyces"
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)
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# antibiotic groups
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@ -450,7 +490,6 @@ if (changed_md5(clin_break)) {
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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(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
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@ -466,7 +505,6 @@ if (changed_md5(microorganisms)) {
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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_xpt(mo, "data-raw/microorganisms.xpt"), 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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mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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@ -481,7 +519,6 @@ if (changed_md5(microorganisms.codes)) {
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write_md5(microorganisms.codes)
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try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
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try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
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@ -494,7 +531,6 @@ if (changed_md5(microorganisms.groups)) {
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write_md5(microorganisms.groups)
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try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
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try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
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@ -507,7 +543,6 @@ if (changed_md5(ab)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
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write_md5(ab)
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try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_xpt(ab, "data-raw/antibiotics.xpt"), silent = TRUE)
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try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
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try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
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ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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@ -522,7 +557,6 @@ if (changed_md5(av)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
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write_md5(av)
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try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_xpt(av, "data-raw/antivirals.xpt"), silent = TRUE)
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try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
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try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
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av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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@ -543,7 +577,6 @@ if (changed_md5(intrinsicR)) {
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write_md5(intrinsicR)
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try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), silent = TRUE)
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try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
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try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
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@ -556,7 +589,6 @@ if (changed_md5(dosage)) {
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write_md5(dosage)
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try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_xpt(dosage, "data-raw/dosage.xpt"), silent = TRUE)
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try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
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try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
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