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move object assignment to AMR_env

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-14 13:02:50 +02:00
parent dfae4c7e7d
commit 76bcd3528c
18 changed files with 116 additions and 127 deletions
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44
data-raw/_pre_commit_hook.R
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@ -145,22 +145,22 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
}
}
create_MO_fullname_lower <- function() {
MO_lookup <- AMR::microorganisms
AMR_env$MO_lookup <- AMR::microorganisms
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(
MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies
AMR_env$MO_lookup$fullname_lower <- tolower(trimws(paste(
AMR_env$MO_lookup$genus,
AMR_env$MO_lookup$species,
AMR_env$MO_lookup$subspecies
)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower
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))
AMR_env$MO_lookup$fullname_lower
}
MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- MO_lookup$mo[which(MO_lookup$genus == "Streptococcus" &
MO_lookup$species %in% c(
MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
AMR_env$MO_lookup$species %in% c(
"pyogenes", "agalactiae", "dysgalactiae", "equi", "anginosus", "sanguinis", "salivarius",
"group A", "group B", "group C", "group D", "group F", "group G", "group H", "group K", "group L"
))]
@ -198,10 +198,10 @@ AB_AMINOGLYCOSIDES <- antibiotics %>%
filter(group %like% "aminoglycoside") %>%
pull(ab)
AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
AB_ANTIFUNGALS <- AB_lookup %>%
AB_ANTIFUNGALS <- AMR_env$AB_lookup %>%
filter(group %like% "antifungal") %>%
pull(ab)
AB_ANTIMYCOBACTERIALS <- AB_lookup %>%
AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>%
filter(group %like% "antimycobacterial") %>%
pull(ab)
AB_CARBAPENEMS <- antibiotics %>%
@ -268,16 +268,16 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
DEFINED_AB_GROUPS <- ls(envir = globalenv())
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
create_AB_lookup <- function() {
AB_lookup <- AMR::antibiotics
AB_lookup$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[,
AMR_env$AB_lookup <- AMR::antibiotics
AMR_env$AB_lookup$generalised_name <- generalise_antibiotic_name(AMR_env$AB_lookup$name)
AMR_env$AB_lookup$generalised_synonyms <- lapply(AMR_env$AB_lookup$synonyms, generalise_antibiotic_name)
AMR_env$AB_lookup$generalised_abbreviations <- lapply(AMR_env$AB_lookup$abbreviations, generalise_antibiotic_name)
AMR_env$AB_lookup$generalised_loinc <- lapply(AMR_env$AB_lookup$loinc, generalise_antibiotic_name)
AMR_env$AB_lookup$generalised_all <- unname(lapply(
as.list(as.data.frame(t(AMR_env$AB_lookup[,
c(
"ab", "atc", "cid", "name",
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]
colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "generalised"]
),
drop = FALSE
]),
@ -288,7 +288,7 @@ create_AB_lookup <- function() {
x[x != ""]
}
))
AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
AMR_env$AB_lookup[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "^generalised"]]
}
AB_LOOKUP <- create_AB_lookup()