P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 17:02:03 +02:00
Code Releases Activity

(v2.1.1.9272) (v2.1.1.9271) add sensititre AB and animal codes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-05-04 16:38:09 +02:00
parent dc5559a2c4
commit a778eb9bcf
20 changed files with 841 additions and 309 deletions
Download Patch File Download Diff File Expand all files Collapse all files

18
R/ab.R
View File

@ -279,7 +279,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
# length of input is quite long, and Levenshtein distance is only max 2
if (nchar(x[i]) >= 10) {
levenshtein <- as.double(utils::adist(x[i], AMR_env$AB_lookup$generalised_name))
levenshtein <- as.double(utils::adist(x[i], AMR_env$AB_lookup$generalised_name,
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 3),
counts = FALSE
))
if (any(levenshtein <= 2)) {
found <- AMR_env$AB_lookup$ab[which(levenshtein <= 2)]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
@ -350,7 +355,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
ab_df$lev_name <- as.double(utils::adist(x[i], ab_df$generalised_name,
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
costs = c(insertions = 1, deletions = 1, substitutions = 3),
counts = FALSE
))
ab_df$lev_syn <- vapply(
@ -362,7 +367,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
min(as.double(utils::adist(x[i], y[nchar(y) >= 5],
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
costs = c(insertions = 1, deletions = 1, substitutions = 3),
counts = FALSE
)), na.rm = TRUE)
)
@ -374,7 +379,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
ab_df$lev_trans <- as.double(utils::adist(x[i], ab_df$trans,
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
costs = c(insertions = 1, deletions = 1, substitutions = 3),
counts = FALSE
))
} else {
@ -637,12 +642,17 @@ generalise_antibiotic_name <- function(x) {
# spaces around non-characters must be removed: amox + clav -> amox clav
x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
# rewrite ph to f, and th to t
x <- gsub("PH", "F", x, perl = TRUE)
x <- gsub("TH", "T", x, perl = TRUE)
# remove hyphen after a starting "co"
x <- gsub("^CO-", "CO", x, perl = TRUE)
# replace operators with a space
x <- gsub("(/| AND | WITH | W/|[+]|[-])+", " ", x, perl = TRUE)
# replace more than 1 space
x <- trimws(gsub(" +", " ", x, perl = TRUE))
# remove last couple of words if they are 1-3 characters
x <- gsub("( .{1,3})+$", "", x)
# move HIGH to end
x <- trimws(gsub("(.*) HIGH(.*)", "\\1\\2 HIGH", x, perl = TRUE))
x