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fix for mo codes

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dr. M.S. (Matthijs) Berends
2023-06-22 15:24:18 +02:00
parent f065945d7b
commit 1d9ee39cc7
4 changed files with 11 additions and 6 deletions
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9
R/mo.R
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@ -302,17 +302,17 @@ as.mo <- function(x,
filtr <- which(AMR_env$MO_lookup$full_first %like_case% first_chars)
} else if (nchar(x_out) == 3) {
# no space and 3 characters - probably a code such as SAU or ECO
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", substr(x_out, 1, 1), AMR_env$dots, " ", substr(x_out, 2, 3), AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 1)), AMR_env$dots, " ", substr(x_out, 2, 3), AMR_env$dots, "\""))
filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", substr(x_out, 1, 1), ".* ", substr(x_out, 2, 3)))
} else if (nchar(x_out) == 4) {
# no space and 4 characters - probably a code such as STAU or ESCO
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", substr(x_out, 1, 2), AMR_env$dots, " ", substr(x_out, 3, 4), AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", totitle(substr(x_out, 1, 2)), AMR_env$dots, " ", substr(x_out, 3, 4), AMR_env$dots, "\""))
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))
second_part <- substr(x_out, 4, nchar(x_out))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$dots, first_part, fixed = TRUE), " ", second_part, AMR_env$dots, "\""))
msg <<- c(msg, paste0("Input \"", x_search, "\" was assumed to be a microorganism code - tried to match on \"", gsub("[a-z]*", AMR_env$dots, totitle(first_part), fixed = TRUE), " ", second_part, AMR_env$dots, "\""))
filtr <- which(AMR_env$MO_lookup$fullname_lower %like_case% paste0("(^| )", first_part, ".* ", second_part))
} else {
# for genus or species or subspecies
@ -336,9 +336,10 @@ as.mo <- function(x,
# correct back for kingdom
minimum_matching_score_current <- minimum_matching_score_current / AMR_env$MO_lookup$kingdom_index[match(mo_to_search, AMR_env$MO_lookup$fullname)]
minimum_matching_score_current <- pmax(minimum_matching_score_current, m)
if (length(m) > 1 && all(m <= 0.55, na.rm = TRUE)) {
if (length(x_parts) > 1 && all(m <= 0.55, na.rm = TRUE)) {
# if the highest score is 0.5, we have nothing serious - 0.5 is the lowest for pathogenic group 1
# make everything NA so the results will get removed below
# (we added length(x_parts) > 1 to exclude microbial codes from this rule, such as "STAU")
m[seq_len(length(m))] <- NA_real_
}
} else {