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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
committed by GitHub
parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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51
R/ab.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -91,8 +95,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
meet_criteria(info, allow_class = "logical", has_length = 1)
check_dataset_integrity()
if (is.ab(x)) {
return(x)
}
@ -109,7 +111,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_bak <- x
x <- toupper(x)
x_nonNA <- x[!is.na(x)]
# remove diacritics
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
@ -128,7 +129,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_unknown_ATCs <- character(0)
note_if_more_than_one_found <- function(found, index, from_text) {
if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
if (initial_search == TRUE && isTRUE(length(from_text) > 1)) {
abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|avibactam)") {
abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam")]
@ -165,7 +166,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid
if (initial_search == TRUE & sum(already_known) < length(x)) {
if (initial_search == TRUE && sum(already_known) < length(x)) {
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress))
}
@ -175,10 +176,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
progress$tick()
}
if (is.na(x[i]) | is.null(x[i])) {
if (is.na(x[i]) || is.null(x[i])) {
next
}
if (identical(x[i], "") |
if (identical(x[i], "") ||
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it:
identical(tolower(x[i]), "bacteria")) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
@ -211,7 +212,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_loinc,
function(s) x[i] %in% s
))
found <- antibiotics$ab[loinc_found == TRUE]
found <- AMR::antibiotics$ab[loinc_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -222,7 +223,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) x[i] %in% s
))
found <- antibiotics$ab[synonym_found == TRUE]
found <- AMR::antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -232,9 +233,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
abbr_found <- unlist(lapply(
AB_lookup$generalised_abbreviations,
# require at least 2 characters for abbreviations
function(s) x[i] %in% s & nchar(x[i]) >= 2
function(s) x[i] %in% s && nchar(x[i]) >= 2
))
found <- antibiotics$ab[abbr_found == TRUE]
found <- AMR::antibiotics$ab[abbr_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -281,14 +282,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# try if name starts with it
found <- antibiotics[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try if name ends with it
found <- antibiotics[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 & length(found) > 0) {
found <- AMR::antibiotics[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -298,7 +299,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AB_lookup$generalised_synonyms,
function(s) any(s %like% paste0("^", x_spelling))
))
found <- antibiotics$ab[synonym_found == TRUE]
found <- AMR::antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
@ -312,16 +313,16 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# try by removing all spaces
if (x[i] %like% " ") {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), initial_search = FALSE))
if (length(found) > 0 & !is.na(found)) {
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
}
# try by removing all spaces and numbers
if (x[i] %like% " " | x[i] %like% "[0-9]") {
if (x[i] %like% " " || x[i] %like% "[0-9]") {
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), initial_search = FALSE))
if (length(found) > 0 & !is.na(found)) {
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -477,7 +478,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}
if (initial_search == TRUE & sum(already_known) < length(x)) {
if (initial_search == TRUE && sum(already_known) < length(x)) {
close(progress)
}
@ -566,7 +567,7 @@ as.data.frame.ab <- function(x, ...) {
"[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
}
#' @method [[<- ab
#' @export
@ -574,7 +575,7 @@ as.data.frame.ab <- function(x, ...) {
"[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
}
#' @method c ab
#' @export
@ -583,7 +584,7 @@ c.ab <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
attributes(y) <- attributes(x)
return_after_integrity_check(y, "antimicrobial code", antibiotics$ab)
return_after_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
}
#' @method unique ab