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(v2.1.1.9123) add EFF code to antibiotics data set

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dr. M.S. (Matthijs) Berends
2025-01-15 16:14:09 +01:00
parent 2e31ec19c3
commit 08ddbaa930
32 changed files with 522 additions and 461 deletions
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46
data-raw/_pre_commit_checks.R
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@ -101,7 +101,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
# this function returns class <mo>
MO_staph <- AMR::microorganisms
MO_staph <- microorganisms
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {
MO_staph[
@ -152,12 +152,12 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
}
pre_commit_lst$MO_CONS <- create_species_cons_cops("CoNS")
pre_commit_lst$MO_COPS <- create_species_cons_cops("CoPS")
pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Streptococcus" &
tolower(AMR::microorganisms$species) %in% c(
pre_commit_lst$MO_STREP_ABCG <- microorganisms$mo[which(microorganisms$genus == "Streptococcus" &
tolower(microorganisms$species) %in% c(
"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
"group a", "group b", "group c", "group g"
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_LANCEFIELD <- microorganisms$mo[which(microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
# World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
"Acinetobacter",
@ -419,6 +419,9 @@ pre_commit_lst$AB_OXAZOLIDINONES <- antibiotics %>%
pre_commit_lst$AB_PENICILLINS <- antibiotics %>%
filter(group %like% "penicillin") %>%
pull(ab)
pre_commit_lst$AB_PHENICOLS <- antibiotics %>%
filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
pull(ab)
pre_commit_lst$AB_POLYMYXINS <- antibiotics %>%
filter(group %like% "polymyxin") %>%
pull(ab)
@ -445,34 +448,9 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antibiotics %>%
pull(ab)
# this will be used for documentation:
pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
create_AB_AV_lookup <- function(df) {
new_df <- df
new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
if ("abbreviations" %in% colnames(df)) {
new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
}
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
new_df$generalised_all <- unname(lapply(
as.list(as.data.frame(
t(new_df[,
c(
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
colnames(new_df)[colnames(new_df) %like% "generalised"]
),
drop = FALSE
]),
stringsAsFactors = FALSE
)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}
))
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
}
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antibiotics)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
# Export to package as internal data ----
# usethis::use_data() must receive unquoted object names, which is not flexible at all.
@ -521,8 +499,8 @@ changed_md5 <- function(object) {
# give official names to ABs and MOs
clin_break <- clinical_breakpoints %>%
mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
mutate(mo_name = microorganisms$fullname[match(mo, microorganisms$mo)], .after = mo) %>%
mutate(ab_name = antibiotics$name[match(ab, antibiotics$ab)], .after = ab)
if (changed_md5(clin_break)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
write_md5(clin_break)