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(v1.8.1) prerelease 1.8.1

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dr. M.S. (Matthijs) Berends
2022-03-14 16:36:10 +01:00
parent 08d387b5ce
commit 1b0983e382
98 changed files with 2958 additions and 1291 deletions
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data-raw/_internals.R
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@ -122,9 +122,21 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
"mo", drop = TRUE]
}
}
create_MO_fullname_lower <- function() {
MO_lookup <- AMR::microorganisms
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower
}
MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
MO_FULLNAME_LOWER <- create_MO_fullname_lower()
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@ -160,6 +172,24 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
# this will be used for documentation:
DEFINED_AB_GROUPS <- ls(envir = globalenv())
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
create_AB_lookup <- function() {
AB_lookup <- AMR::antibiotics
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
c("ab", "atc", "cid", "name",
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
drop = FALSE]),
stringsAsFactors = FALSE)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}))
AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
}
AB_LOOKUP <- create_AB_lookup()
# Export to package as internal data ----
usethis::use_data(EUCAST_RULES_DF,
@ -169,6 +199,8 @@ usethis::use_data(EUCAST_RULES_DF,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_FULLNAME_LOWER,
AB_LOOKUP,
AB_AMINOGLYCOSIDES,
AB_AMINOPENICILLINS,
AB_ANTIFUNGALS,