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move object assignment to AMR_env

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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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32
R/mo.R
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@ -163,7 +163,7 @@ as.mo <- function(x,
language <- validate_language(language)
meet_criteria(info, allow_class = "logical", has_length = 1)
if (tryCatch(all(x %in% c(MO_lookup$mo, NA)) &&
if (tryCatch(all(x %in% c(AMR_env$MO_lookup$mo, NA)) &&
isFALSE(Becker) &&
isFALSE(Lancefield), error = function(e) FALSE)) {
# don't look into valid MO codes, just return them
@ -194,9 +194,9 @@ as.mo <- function(x,
out[x %in% reference_df[[1]]] <- reference_df[[2]][match(x[x %in% reference_df[[1]]], reference_df[[1]])]
}
# From MO code ----
out[is.na(out) & x %in% MO_lookup$mo] <- x[is.na(out) & x %in% MO_lookup$mo]
out[is.na(out) & x %in% AMR_env$MO_lookup$mo] <- x[is.na(out) & x %in% AMR_env$MO_lookup$mo]
# From full name ----
out[is.na(out) & x_lower %in% MO_lookup$fullname_lower] <- MO_lookup$mo[match(x_lower[is.na(out) & x_lower %in% MO_lookup$fullname_lower], MO_lookup$fullname_lower)]
out[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower] <- AMR_env$MO_lookup$mo[match(x_lower[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower], AMR_env$MO_lookup$fullname_lower)]
# one exception: "Fungi" matches the kingdom, but instead it should return the 'unknown' code for fungi
out[out == "F_[KNG]_FUNGI"] <- "F_FUNGUS"
# From known codes ----
@ -204,7 +204,7 @@ as.mo <- function(x,
# From SNOMED ----
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) {
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(microorganisms$snomed)] <- microorganisms$mo[rep(seq_along(microorganisms$snomed), vapply(FUN.VALUE = double(1), microorganisms$snomed, length))[match(x[is.na(out) & x %in% unlist(microorganisms$snomed)], unlist(microorganisms$snomed))]]
out[is.na(out) & x %in% unlist(AMR::microorganisms$snomed)] <- AMR::microorganisms$mo[rep(seq_along(AMR::microorganisms$snomed), vapply(FUN.VALUE = double(1), AMR::microorganisms$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR::microorganisms$snomed)], unlist(AMR::microorganisms$snomed))]]
}
# From other familiar output ----
# such as Salmonella groups, colloquial names, etc.
@ -261,16 +261,16 @@ as.mo <- function(x,
# do a pre-match on first character (and if it contains a space, first chars of first two terms)
if (length(x_parts) %in% c(2, 3)) {
# for genus + species + subspecies
filtr <- which(MO_lookup$full_first == substr(x_parts[1], 1, 1) & MO_lookup$species_first == substr(x_parts[2], 1, 1))
filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) & AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1))
} else if (length(x_parts) > 3) {
first_chars <- paste0("(^| )", "[", paste(substr(x_parts, 1, 1), collapse = ""), "]")
filtr <- which(MO_lookup$full_first %like_case% first_chars)
filtr <- which(AMR_env$MO_lookup$full_first %like_case% first_chars)
} else if (nchar(x_out) == 4) {
# no space and 4 characters - probably a code such as STAU or ESCO!
if (isTRUE(info)) {
message_("Input \"", x_search, "\" is assumed to be a microorganism code - trying to match on ", vector_and(c(substr(x_out, 1, 2), substr(x_out, 3, 4)), sort = FALSE))
}
filtr <- which(MO_lookup$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 2), ".* ", substr(x_out, 3, 4)))
filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 2), ".* ", substr(x_out, 3, 4)))
} else if (nchar(x_out) <= 6) {
# no space and 5-6 characters - probably a code such as STAAUR or ESCCOL!
first_part <- paste0(substr(x_out, 1, 2), "[a-z]*", substr(x_out, 3, 3))
@ -278,14 +278,14 @@ as.mo <- function(x,
if (isTRUE(info)) {
message_("Input \"", x_search, "\" is assumed to be a microorganism code - trying to match on ", vector_and(c(gsub("[a-z]*", "(...)", first_part, fixed = TRUE), second_part), sort = FALSE))
}
filtr <- which(MO_lookup$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part))
filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part))
} else {
filtr <- which(MO_lookup$full_first == substr(x_out, 1, 1))
filtr <- which(AMR_env$MO_lookup$full_first == substr(x_out, 1, 1))
}
if (length(filtr) == 0) {
mo_to_search <- MO_lookup$fullname
mo_to_search <- AMR_env$MO_lookup$fullname
} else {
mo_to_search <- MO_lookup$fullname[filtr]
mo_to_search <- AMR_env$MO_lookup$fullname[filtr]
}
AMR_env$mo_to_search <- mo_to_search
# determine the matching score on the original search value
@ -293,9 +293,9 @@ as.mo <- function(x,
if (is.null(minimum_matching_score)) {
minimum_matching_score_current <- min(0.6, min(10, nchar(x_search_cleaned)) * 0.08)
# correct back for prevalence
minimum_matching_score_current <- minimum_matching_score_current / MO_lookup$prevalence[match(mo_to_search, MO_lookup$fullname)]
minimum_matching_score_current <- minimum_matching_score_current / AMR_env$MO_lookup$prevalence[match(mo_to_search, AMR_env$MO_lookup$fullname)]
# correct back for kingdom
minimum_matching_score_current <- minimum_matching_score_current / MO_lookup$kingdom_index[match(mo_to_search, MO_lookup$fullname)]
minimum_matching_score_current <- minimum_matching_score_current / AMR_env$MO_lookup$kingdom_index[match(mo_to_search, AMR_env$MO_lookup$fullname)]
} else {
minimum_matching_score_current <- minimum_matching_score
}
@ -306,7 +306,7 @@ as.mo <- function(x,
warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"), minimum_matching_score), ". Try setting this value lower or even to 0.")
result_mo <- NA_character_
} else {
result_mo <- MO_lookup$mo[match(top_hits[1], MO_lookup$fullname)]
result_mo <- AMR_env$MO_lookup$mo[match(top_hits[1], AMR_env$MO_lookup$fullname)]
AMR_env$mo_uncertainties <- rbind(AMR_env$mo_uncertainties,
data.frame(
original_input = x_search,
@ -997,8 +997,8 @@ replace_old_mo_codes <- function(x, property) {
name <- tolower(paste0(name, ".*", collapse = ""))
name <- gsub(" .*", " ", name, fixed = TRUE)
name <- paste0("^", name)
results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom &
MO_lookup$fullname_lower %like_case% name]
results <- AMR_env$MO_lookup$mo[AMR_env$MO_lookup$kingdom %like_case% kingdom &
AMR_env$MO_lookup$fullname_lower %like_case% name]
if (length(results) > 1) {
all_direct_matches <<- FALSE
}