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completely updated antibiotics

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-30 14:31:45 +01:00
parent 3d9faf89cf
commit d40e0ef20b
60 changed files with 102028 additions and 95116 deletions
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20
R/mo.R
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@ -236,7 +236,7 @@ as.mo <- function(x,
# set up progress bar
progress <- progress_ticker(n = length(x_unique), n_min = 10, print = info)
on.exit(close(progress))
msg <- character(0)
# run it
@ -289,7 +289,7 @@ as.mo <- function(x,
} else {
mo_to_search <- AMR_env$MO_lookup$fullname[filtr]
}
AMR_env$mo_to_search <- mo_to_search
# determine the matching score on the original search value
m <- mo_matching_score(x = x_search_cleaned, n = mo_to_search)
@ -363,14 +363,14 @@ as.mo <- function(x,
"Microorganism translation was uncertain for ", examples,
". Run `mo_uncertainties()` to review ", plural[2], "."
))
for (m in msg) {
message_(m)
message_(m)
}
}
}
} # end of loop over all yet unknowns
# Keep or replace synonyms ----
gbif_matches <- AMR::microorganisms$gbif_renamed_to[match(out, AMR::microorganisms$mo)]
gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA
@ -565,7 +565,8 @@ pillar_shaft.mo <- function(x, ...) {
}
warning_(
col, " contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.", call = FALSE
"Please update your MO codes with `as.mo()`.",
call = FALSE
)
}
@ -652,7 +653,8 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
if (!all(x %in% c(AMR::microorganisms$mo, NA))) {
warning_(
"Some MO codes are from a previous AMR package version. ",
"Please update the MO codes with `as.mo()`.", call = FALSE
"Please update the MO codes with `as.mo()`.",
call = FALSE
)
}
print.default(x, quote = FALSE)
@ -918,12 +920,12 @@ convert_colloquial_input <- function(x) {
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese)
out[x %like_case% "([ck]oagulas[ea].negatie?[vf]|^[ck]o?ns[^a-z]*$)"] <- "B_STPHY_CONS"
out[x %like_case% "([ck]oagulas[ea].positie?[vf]|^[ck]o?ps[^a-z]*$)"] <- "B_STPHY_COPS"
# Gram stains
out[x %like_case% "gram[ -]?neg.*"] <- "B_GRAMN"
out[x %like_case% "gram[ -]?pos.*"] <- "B_GRAMP"
out[is.na(out) & x %like_case% "anaerob[a-z]+ (micro)?.*organism"] <- "B_ANAER"
# yeasts and fungi
out[x %like_case% "^yeast?"] <- "F_YEAST"
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"