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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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19
R/zzz.R
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@ -20,6 +20,10 @@
# ==================================================================== #
.onLoad <- function(libname, pkgname) {
assign(x = "AB_lookup",
value = create_AB_lookup(),
envir = asNamespace("AMR"))
assign(x = "MO_lookup",
value = create_MO_lookup(),
envir = asNamespace("AMR"))
@ -60,14 +64,27 @@
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use options(AMR_silentstart = TRUE) ]")
}
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
}
create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms
MO_lookup$kingdom_index <- 99
MO_lookup$kingdom_index <- NA_real_
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
MO_lookup$prevalence_kingdom_index <- MO_lookup$prevalence * MO_lookup$kingdom_index
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,