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remove MO_lookup from sysdata.rda
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@ -144,21 +144,6 @@ 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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create_MO_fullname_lower <- function() {
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AMR_env$MO_lookup <- AMR::microorganisms
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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AMR_env$MO_lookup$fullname_lower <- tolower(trimws(paste(
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AMR_env$MO_lookup$genus,
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AMR_env$MO_lookup$species,
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AMR_env$MO_lookup$subspecies
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)))
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ind <- AMR_env$MO_lookup$genus == "" | grepl("^[(]unknown ", AMR_env$MO_lookup$fullname, perl = TRUE)
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AMR_env$MO_lookup[ind, "fullname_lower"] <- tolower(AMR_env$MO_lookup[ind, "fullname", drop = TRUE])
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AMR_env$MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", AMR_env$MO_lookup$fullname_lower, perl = TRUE))
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# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
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AMR_env$MO_lookup$fullname_lower[which(AMR_env$MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", AMR_env$MO_lookup$fullname_lower[which(AMR_env$MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
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AMR_env$MO_lookup$fullname_lower
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}
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MO_CONS <- create_species_cons_cops("CoNS")
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MO_COPS <- create_species_cons_cops("CoPS")
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MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
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@ -166,7 +151,6 @@ MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptoc
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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_FULLNAME_LOWER <- create_MO_fullname_lower()
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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", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
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@ -298,7 +282,6 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
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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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AV_LOOKUP,
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