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reftbl in plots, speedup for as.sir() and mo_validate

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dr. M.S. (Matthijs) Berends
2023-07-10 16:43:46 +02:00
parent 70c601ca11
commit a4e2e25e3f
14 changed files with 128 additions and 65 deletions
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48
R/mo_property.R
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@ -913,26 +913,36 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
Lancefield <- FALSE
}
has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all")
# get microorganisms data set, but remove synonyms if keep_synonyms is FALSE
mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) {
# do nothing, just don't run the other if-else's
} else if (all(x %in% c(unlist(mo_data_check[[property]]), NA)) && !has_Becker_or_Lancefield) {
# no need to do anything, just return it
return(x)
if (isFALSE(has_Becker_or_Lancefield) && isTRUE(keep_synonyms) && all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
# fastest way to get properties
if (property == "snomed") {
x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)]))
} else {
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
}
} else {
# we need to get MO codes now
x <- replace_old_mo_codes(x, property = property)
x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
}
# get property reeaaally fast using match()
if (property == "snomed") {
x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)]))
} else {
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
# get microorganisms data set, but remove synonyms if keep_synonyms is FALSE
mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) {
# do nothing, just don't run the other if-else's
} else if (all(x %in% c(unlist(mo_data_check[[property]]), NA)) && !has_Becker_or_Lancefield) {
# no need to do anything, just return it
return(x)
} else {
# we need to get MO codes now
x <- replace_old_mo_codes(x, property = property)
x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
}
# get property reeaaally fast using match()
if (property == "snomed") {
x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)]))
} else {
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
}
}
if (property == "mo") {