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remove MO_lookup from sysdata.rda

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-21 19:55:19 +01:00
parent 79c8415d3e
commit 8a92c5a869
16 changed files with 89 additions and 236 deletions
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17
data-raw/_pre_commit_hook.R
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@@ -144,21 +144,6 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
]
}
}
create_MO_fullname_lower <- function() {
AMR_env$MO_lookup <- AMR::microorganisms
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
AMR_env$MO_lookup$fullname_lower <- tolower(trimws(paste(
AMR_env$MO_lookup$genus,
AMR_env$MO_lookup$species,
AMR_env$MO_lookup$subspecies
)))
ind <- AMR_env$MO_lookup$genus == "" | grepl("^[(]unknown ", AMR_env$MO_lookup$fullname, perl = TRUE)
AMR_env$MO_lookup[ind, "fullname_lower"] <- tolower(AMR_env$MO_lookup[ind, "fullname", drop = TRUE])
AMR_env$MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", AMR_env$MO_lookup$fullname_lower, perl = TRUE))
# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
AMR_env$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$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
AMR_env$MO_lookup$fullname_lower
}
MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
@@ -166,7 +151,6 @@ MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptoc
"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
"group A", "group B", "group C", "group G"
))]
MO_FULLNAME_LOWER <- create_MO_fullname_lower()
MO_PREVALENT_GENERA <- c(
"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
@@ -298,7 +282,6 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_FULLNAME_LOWER,
MO_PREVALENT_GENERA,
AB_LOOKUP,
AV_LOOKUP,