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move object assignment to AMR_env
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.8.2.9014
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Date: 2022-10-11
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Version: 1.8.2.9016
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Date: 2022-10-14
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9014
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# AMR 1.8.2.9016
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -626,7 +626,7 @@ create_eucast_ab_documentation <- function() {
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if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
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# antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `CARBAPENEMS`
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val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
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} else if (val %in% AB_lookup$ab) {
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} else if (val %in% AMR_env$AB_lookup$ab) {
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# separate drugs, such as `AMX`
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val <- as.ab(val)
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} else {
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50
R/ab.R
50
R/ab.R
@ -100,7 +100,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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if (is.ab(x)) {
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return(x)
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}
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if (all(x %in% c(AB_lookup$ab, NA))) {
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if (all(x %in% c(AMR_env$AB_lookup$ab, NA))) {
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# all valid AB codes, but not yet right class
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return(set_clean_class(x,
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new_class = c("ab", "character")
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@ -147,25 +147,25 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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# Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
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known_names <- x %in% AB_lookup$generalised_name
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x_new[known_names] <- AB_lookup$ab[match(x[known_names], AB_lookup$generalised_name)]
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known_codes_ab <- x %in% AB_lookup$ab
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known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AB_lookup$atc), USE.NAMES = FALSE)
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known_codes_cid <- x %in% AB_lookup$cid
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x_new[known_codes_ab] <- AB_lookup$ab[match(x[known_codes_ab], AB_lookup$ab)]
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x_new[known_codes_atc] <- AB_lookup$ab[vapply(
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known_names <- x %in% AMR_env$AB_lookup$generalised_name
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x_new[known_names] <- AMR_env$AB_lookup$ab[match(x[known_names], AMR_env$AB_lookup$generalised_name)]
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known_codes_ab <- x %in% AMR_env$AB_lookup$ab
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known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AMR_env$AB_lookup$atc), USE.NAMES = FALSE)
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known_codes_cid <- x %in% AMR_env$AB_lookup$cid
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x_new[known_codes_ab] <- AMR_env$AB_lookup$ab[match(x[known_codes_ab], AMR_env$AB_lookup$ab)]
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x_new[known_codes_atc] <- AMR_env$AB_lookup$ab[vapply(
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FUN.VALUE = integer(1),
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x[known_codes_atc],
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function(x_) {
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which(vapply(
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FUN.VALUE = logical(1),
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AB_lookup$atc,
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AMR_env$AB_lookup$atc,
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function(atc) x_ %in% atc
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))[1L]
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},
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USE.NAMES = FALSE
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)]
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x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
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x_new[known_codes_cid] <- AMR_env$AB_lookup$ab[match(x[known_codes_cid], AMR_env$AB_lookup$cid)]
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previously_coerced <- x %in% AMR_env$ab_previously_coerced$x
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x_new[previously_coerced & is.na(x_new)] <- AMR_env$ab_previously_coerced$ab[match(x[is.na(x_new) & x %in% AMR_env$ab_previously_coerced$x], AMR_env$ab_previously_coerced$x)]
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already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid | previously_coerced
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@ -217,10 +217,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# exact LOINC code
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loinc_found <- unlist(lapply(
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AB_lookup$generalised_loinc,
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AMR_env$AB_lookup$generalised_loinc,
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function(s) x[i] %in% s
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))
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found <- AB_lookup$ab[loinc_found == TRUE]
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found <- AMR_env$AB_lookup$ab[loinc_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -228,10 +228,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# exact synonym
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synonym_found <- unlist(lapply(
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AB_lookup$generalised_synonyms,
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AMR_env$AB_lookup$generalised_synonyms,
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function(s) x[i] %in% s
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))
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found <- AB_lookup$ab[synonym_found == TRUE]
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found <- AMR_env$AB_lookup$ab[synonym_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -239,11 +239,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# exact abbreviation
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abbr_found <- unlist(lapply(
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AB_lookup$generalised_abbreviations,
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AMR_env$AB_lookup$generalised_abbreviations,
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# require at least 2 characters for abbreviations
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function(s) x[i] %in% s && nchar(x[i]) >= 2
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))
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found <- AB_lookup$ab[abbr_found == TRUE]
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found <- AMR_env$AB_lookup$ab[abbr_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -251,9 +251,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# length of input is quite long, and Levenshtein distance is only max 2
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if (nchar(x[i]) >= 10) {
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levenshtein <- as.double(utils::adist(x[i], AB_lookup$generalised_name))
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levenshtein <- as.double(utils::adist(x[i], AMR_env$AB_lookup$generalised_name))
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if (any(levenshtein <= 2)) {
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found <- AB_lookup$ab[which(levenshtein <= 2)]
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found <- AMR_env$AB_lookup$ab[which(levenshtein <= 2)]
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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}
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@ -290,13 +290,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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# try if name starts with it
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found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
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found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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}
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# try if name ends with it
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found <- AB_lookup[which(AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
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found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
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if (nchar(x[i]) >= 4 && length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -304,10 +304,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# and try if any synonym starts with it
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synonym_found <- unlist(lapply(
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AB_lookup$generalised_synonyms,
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AMR_env$AB_lookup$generalised_synonyms,
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function(s) any(s %like% paste0("^", x_spelling))
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))
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found <- AB_lookup$ab[synonym_found == TRUE]
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found <- AMR_env$AB_lookup$ab[synonym_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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next
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@ -585,7 +585,7 @@ as.data.frame.ab <- function(x, ...) {
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"[<-.ab" <- function(i, j, ..., value) {
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y <- NextMethod()
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attributes(y) <- attributes(i)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab)
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}
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#' @method [[<- ab
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#' @export
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@ -593,7 +593,7 @@ as.data.frame.ab <- function(x, ...) {
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"[[<-.ab" <- function(i, j, ..., value) {
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y <- NextMethod()
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attributes(y) <- attributes(i)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab)
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}
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#' @method c ab
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#' @export
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@ -602,7 +602,7 @@ c.ab <- function(...) {
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x <- list(...)[[1L]]
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y <- NextMethod()
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attributes(y) <- attributes(x)
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return_after_integrity_check(y, "antimicrobial code", AB_lookup$ab)
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return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab)
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}
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#' @method unique ab
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@ -452,22 +452,22 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
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}
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ab_validate <- function(x, property, ...) {
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if (tryCatch(all(x[!is.na(x)] %in% AB_lookup$ab), error = function(e) FALSE)) {
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if (tryCatch(all(x[!is.na(x)] %in% AMR_env$AB_lookup$ab), error = function(e) FALSE)) {
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# special case for ab_* functions where class is already <ab>
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x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
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x <- AMR_env$AB_lookup[match(x, AMR_env$AB_lookup$ab), property, drop = TRUE]
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} else {
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# try to catch an error when inputting an invalid argument
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% AB_lookup[1, property, drop = TRUE],
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tryCatch(x[1L] %in% AMR_env$AB_lookup[1, property, drop = TRUE],
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error = function(e) stop(e$message, call. = FALSE)
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)
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if (!all(x %in% AB_lookup[, property, drop = TRUE])) {
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if (!all(x %in% AMR_env$AB_lookup[, property, drop = TRUE])) {
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x <- as.ab(x, ...)
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if (all(is.na(x)) && is.list(AB_lookup[, property, drop = TRUE])) {
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if (all(is.na(x)) && is.list(AMR_env$AB_lookup[, property, drop = TRUE])) {
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x <- rep(NA_character_, length(x))
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} else {
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x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
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x <- AMR_env$AB_lookup[match(x, AMR_env$AB_lookup$ab), property, drop = TRUE]
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}
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}
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}
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@ -216,7 +216,7 @@ ab_selector <- function(filter,
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sort = FALSE, fn = "ab_selector"
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)
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call <- substitute(filter)
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agents <- tryCatch(AB_lookup[which(eval(call, envir = AB_lookup)), "ab", drop = TRUE],
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agents <- tryCatch(AMR_env$AB_lookup[which(eval(call, envir = AMR_env$AB_lookup)), "ab", drop = TRUE],
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error = function(e) stop_(e$message, call = -5)
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)
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agents <- ab_in_data[ab_in_data %in% agents]
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@ -424,8 +424,8 @@ administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
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info = FALSE, only_rsi_columns = only_rsi_columns,
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sort = FALSE, fn = "administrable_per_os"
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)
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agents_all <- AB_lookup[which(!is.na(AB_lookup$oral_ddd)), "ab", drop = TRUE]
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agents <- AB_lookup[which(AB_lookup$ab %in% ab_in_data & !is.na(AB_lookup$oral_ddd)), "ab", drop = TRUE]
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agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$oral_ddd)), "ab", drop = TRUE]
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agents <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% ab_in_data & !is.na(AMR_env$AB_lookup$oral_ddd)), "ab", drop = TRUE]
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agents <- ab_in_data[ab_in_data %in% agents]
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message_agent_names(
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function_name = "administrable_per_os",
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@ -462,8 +462,8 @@ administrable_iv <- function(only_rsi_columns = FALSE, ...) {
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info = FALSE, only_rsi_columns = only_rsi_columns,
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sort = FALSE, fn = "administrable_iv"
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)
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agents_all <- AB_lookup[which(!is.na(AB_lookup$iv_ddd)), "ab", drop = TRUE]
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agents <- AB_lookup[which(AB_lookup$ab %in% ab_in_data & !is.na(AB_lookup$iv_ddd)), "ab", drop = TRUE]
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agents_all <- AMR_env$AB_lookup[which(!is.na(AMR_env$AB_lookup$iv_ddd)), "ab", drop = TRUE]
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agents <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% ab_in_data & !is.na(AMR_env$AB_lookup$iv_ddd)), "ab", drop = TRUE]
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agents <- ab_in_data[ab_in_data %in% agents]
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message_agent_names(
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function_name = "administrable_iv",
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@ -544,7 +544,7 @@ ab_select_exec <- function(function_name,
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# untreatable drugs
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if (only_treatable == TRUE) {
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untreatable <- AB_lookup[which(AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
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untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
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if (any(untreatable %in% names(ab_in_data))) {
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if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
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warning_(
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@ -571,16 +571,16 @@ ab_select_exec <- function(function_name,
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if (is.null(ab_class_args) || isTRUE(function_name %in% c("antifungals", "antimycobacterials"))) {
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ab_group <- NULL
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if (isTRUE(function_name == "antifungals")) {
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abx <- AB_lookup$ab[which(AB_lookup$group == "Antifungals")]
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abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antifungals")]
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} else if (isTRUE(function_name == "antimycobacterials")) {
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abx <- AB_lookup$ab[which(AB_lookup$group == "Antimycobacterials")]
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abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
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} else {
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# their upper case equivalent are vectors with class <ab>, created in data-raw/_pre_commit_hook.R
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# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
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abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
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# manually added codes from add_custom_antimicrobials() must also be supported
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if (length(AMR_env$custom_ab_codes) > 0) {
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custom_ab <- AB_lookup[which(AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
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custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
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check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
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if (function_name == "betalactams") {
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find_group <- "beta-lactams"
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@ -602,7 +602,7 @@ ab_select_exec <- function(function_name,
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} else {
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# this for the 'manual' ab_class() function
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abx <- subset(
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AB_lookup,
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AMR_env$AB_lookup,
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group %like% ab_class_args |
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atc_group1 %like% ab_class_args |
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atc_group2 %like% ab_class_args
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@ -792,7 +792,7 @@ is_all <- function(el1) {
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find_ab_group <- function(ab_class_args) {
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ab_class_args <- gsub("[^a-zA-Z0-9]", ".*", ab_class_args)
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AB_lookup %pm>%
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AMR_env$AB_lookup %pm>%
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subset(group %like% ab_class_args |
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atc_group1 %like% ab_class_args |
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atc_group2 %like% ab_class_args) %pm>%
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@ -807,16 +807,16 @@ find_ab_names <- function(ab_group, n = 3) {
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ab_group <- gsub("[^a-zA-Z|0-9]", ".*", ab_group)
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# try popular first, they have DDDs
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drugs <- AB_lookup[which((!is.na(AB_lookup$iv_ddd) | !is.na(AB_lookup$oral_ddd)) &
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AB_lookup$name %unlike% " " &
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AB_lookup$group %like% ab_group &
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AB_lookup$ab %unlike% "[0-9]$"), ]$name
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drugs <- AMR_env$AB_lookup[which((!is.na(AMR_env$AB_lookup$iv_ddd) | !is.na(AMR_env$AB_lookup$oral_ddd)) &
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AMR_env$AB_lookup$name %unlike% " " &
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AMR_env$AB_lookup$group %like% ab_group &
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AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
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if (length(drugs) < n) {
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# now try it all
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drugs <- AB_lookup[which((AB_lookup$group %like% ab_group |
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AB_lookup$atc_group1 %like% ab_group |
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AB_lookup$atc_group2 %like% ab_group) &
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AB_lookup$ab %unlike% "[0-9]$"), ]$name
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drugs <- AMR_env$AB_lookup[which((AMR_env$AB_lookup$group %like% ab_group |
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AMR_env$AB_lookup$atc_group1 %like% ab_group |
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AMR_env$AB_lookup$atc_group2 %like% ab_group) &
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AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
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}
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if (length(drugs) == 0) {
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return("??")
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@ -86,18 +86,18 @@
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#'
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#' # even antibiotic selectors work
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#' x <- data.frame(random_column = "test",
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#' coflu = as.rsi("S"),
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#' ampicillin = as.rsi("R"))
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#' coflu = as.rsi("S"),
|
||||
#' ampicillin = as.rsi("R"))
|
||||
#' x
|
||||
#' x[, betalactams()]
|
||||
add_custom_antimicrobials <- function(x) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
stop_ifnot(all(c("ab", "name") %in% colnames(x)),
|
||||
"`x` must contain columns \"ab\" and \"name\".")
|
||||
stop_if(any(x$ab %in% AB_lookup$ab),
|
||||
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
|
||||
stop_if(any(x$ab %in% AMR_env$AB_lookup$ab),
|
||||
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
|
||||
|
||||
x <- x[, colnames(AB_lookup)[colnames(AB_lookup) %in% colnames(x)], drop = FALSE]
|
||||
x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]
|
||||
x$generalised_name <- generalise_antibiotic_name(x$name)
|
||||
x$generalised_all <- as.list(x$generalised_name)
|
||||
if ("atc" %in% colnames(x)) {
|
||||
@ -108,27 +108,16 @@ add_custom_antimicrobials <- function(x) {
|
||||
}
|
||||
AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
|
||||
|
||||
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(bind_rows)) {
|
||||
new_df <- bind_rows(AB_lookup, x)
|
||||
} else {
|
||||
new_df <- tryCatch(rbind(AB_lookup, x, stringsAsFactors = FALSE),
|
||||
error = function(x) stop("Error while adding antimicrobials. Try installing the 'dplyr' package for extended support.", call. = FALSE))
|
||||
}
|
||||
new_df <- unique(new_df)
|
||||
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = TRUE)
|
||||
AMR_env$AB_lookup <- unique(bind_rows(AMR_env$AB_lookup, x))
|
||||
|
||||
assignInNamespace(x = "AB_lookup",
|
||||
value = new_df,
|
||||
ns = asNamespace("AMR"))
|
||||
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
|
||||
}
|
||||
|
||||
#' @rdname add_custom_antimicrobials
|
||||
#' @export
|
||||
clear_custom_antimicrobials <- function() {
|
||||
assignInNamespace(x = "AB_lookup",
|
||||
value = create_AB_lookup(),
|
||||
ns = asNamespace("AMR"))
|
||||
AMR_env$AB_lookup <- create_AB_lookup()
|
||||
AMR_env$custom_ab_codes <- character(0)
|
||||
message_("Custom antimicrobials cleared.")
|
||||
}
|
||||
|
||||
@ -435,11 +435,11 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
|
||||
all_staph <- MO_lookup[which(MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
|
||||
all_staph <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
|
||||
all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
|
||||
}
|
||||
if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
|
||||
all_strep <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), , drop = FALSE]
|
||||
all_strep <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Streptococcus"), , drop = FALSE]
|
||||
all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
|
||||
}
|
||||
|
||||
|
||||
@ -173,7 +173,7 @@ get_column_abx <- function(x,
|
||||
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
|
||||
# or already have the <rsi> class (as.rsi)
|
||||
# and that they have no more than 50% invalid values
|
||||
vectr_antibiotics <- unlist(AB_lookup$generalised_all)
|
||||
vectr_antibiotics <- unlist(AMR_env$AB_lookup$generalised_all)
|
||||
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
|
||||
x_columns <- vapply(
|
||||
FUN.VALUE = character(1),
|
||||
@ -335,7 +335,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
|
||||
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
|
||||
# antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `AB_CARBAPENEMS`
|
||||
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
|
||||
} else if (val %in% AB_lookup$ab) {
|
||||
} else if (val %in% AMR_env$AB_lookup$ab) {
|
||||
# separate drugs, such as `AMX`
|
||||
val <- as.ab(val)
|
||||
} else {
|
||||
|
||||
@ -71,7 +71,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
|
||||
search_strings <- gsub("[^a-zA-Z-]", "", s_split)
|
||||
|
||||
ind_species <- search_strings != "" &
|
||||
search_strings %in% MO_lookup[which(MO_lookup$rank %in% c(
|
||||
search_strings %in% AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
|
||||
"family",
|
||||
"genus",
|
||||
"species",
|
||||
@ -85,7 +85,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
|
||||
|
||||
ind_fullname <- search_strings != "" &
|
||||
search_strings %in% c(
|
||||
MO_lookup[which(MO_lookup$rank %in% c(
|
||||
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
|
||||
"family",
|
||||
"genus",
|
||||
"species",
|
||||
@ -96,7 +96,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
|
||||
"fullname",
|
||||
drop = TRUE
|
||||
],
|
||||
MO_lookup[which(MO_lookup$rank %in% c(
|
||||
AMR_env$MO_lookup[which(AMR_env$MO_lookup$rank %in% c(
|
||||
"family",
|
||||
"genus",
|
||||
"species",
|
||||
|
||||
@ -145,7 +145,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
|
||||
}
|
||||
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
|
||||
}
|
||||
if (!all(x[, by, drop = TRUE] %in% MO_lookup$mo, na.rm = TRUE)) {
|
||||
if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
|
||||
x$join.mo <- as.mo(x[, by, drop = TRUE])
|
||||
by <- c("join.mo" = "mo")
|
||||
} else {
|
||||
|
||||
2
R/mdro.R
2
R/mdro.R
@ -326,7 +326,7 @@ mdro <- function(x = NULL,
|
||||
"No column found as input for `col_mo`, ",
|
||||
font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), "."))
|
||||
)
|
||||
x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: MO_lookup[which(MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
|
||||
x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: AMR_env$MO_lookup[which(AMR_env$MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
|
||||
col_mo <- "mo"
|
||||
}
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
|
||||
32
R/mo.R
32
R/mo.R
@ -163,7 +163,7 @@ as.mo <- function(x,
|
||||
language <- validate_language(language)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (tryCatch(all(x %in% c(MO_lookup$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$fullname_lower %like_case% name]
|
||||
if (length(results) > 1) {
|
||||
all_direct_matches <<- FALSE
|
||||
}
|
||||
|
||||
@ -109,9 +109,9 @@ mo_matching_score <- function(x, n) {
|
||||
l_n.lev[lev == l_n] <- lev[lev == l_n]
|
||||
|
||||
# human pathogenic prevalence (1 to 3), see ?as.mo
|
||||
p_n <- MO_lookup[match(n, MO_lookup$fullname), "prevalence", drop = TRUE]
|
||||
p_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "prevalence", drop = TRUE]
|
||||
# kingdom index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
|
||||
k_n <- MO_lookup[match(n, MO_lookup$fullname), "kingdom_index", drop = TRUE]
|
||||
k_n <- AMR_env$MO_lookup[match(n, AMR_env$MO_lookup$fullname), "kingdom_index", drop = TRUE]
|
||||
|
||||
# matching score:
|
||||
(l_n - 0.5 * l_n.lev) / (l_n * p_n * k_n)
|
||||
|
||||
4
R/zzz.R
4
R/zzz.R
@ -147,8 +147,8 @@ if (utf8_supported && !is_latex) {
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
||||
assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
|
||||
assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
|
||||
AMR_env$AB_lookup <- create_AB_lookup()
|
||||
AMR_env$MO_lookup <- create_MO_lookup()
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
|
||||
}
|
||||
|
||||
@ -145,22 +145,22 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
}
|
||||
}
|
||||
create_MO_fullname_lower <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
AMR_env$MO_lookup <- AMR::microorganisms
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
MO_lookup$fullname_lower <- tolower(trimws(paste(
|
||||
MO_lookup$genus,
|
||||
MO_lookup$species,
|
||||
MO_lookup$subspecies
|
||||
AMR_env$MO_lookup$fullname_lower <- tolower(trimws(paste(
|
||||
AMR_env$MO_lookup$genus,
|
||||
AMR_env$MO_lookup$species,
|
||||
AMR_env$MO_lookup$subspecies
|
||||
)))
|
||||
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
|
||||
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
|
||||
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
|
||||
MO_lookup$fullname_lower
|
||||
ind <- AMR_env$MO_lookup$genus == "" | grepl("^[(]unknown ", AMR_env$MO_lookup$fullname, perl = TRUE)
|
||||
AMR_env$MO_lookup[ind, "fullname_lower"] <- tolower(AMR_env$MO_lookup[ind, "fullname", drop = TRUE])
|
||||
AMR_env$MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", AMR_env$MO_lookup$fullname_lower, perl = TRUE))
|
||||
AMR_env$MO_lookup$fullname_lower
|
||||
}
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
MO_STREP_ABCG <- MO_lookup$mo[which(MO_lookup$genus == "Streptococcus" &
|
||||
MO_lookup$species %in% c(
|
||||
MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
|
||||
AMR_env$MO_lookup$species %in% c(
|
||||
"pyogenes", "agalactiae", "dysgalactiae", "equi", "anginosus", "sanguinis", "salivarius",
|
||||
"group A", "group B", "group C", "group D", "group F", "group G", "group H", "group K", "group L"
|
||||
))]
|
||||
@ -198,10 +198,10 @@ AB_AMINOGLYCOSIDES <- antibiotics %>%
|
||||
filter(group %like% "aminoglycoside") %>%
|
||||
pull(ab)
|
||||
AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
|
||||
AB_ANTIFUNGALS <- AB_lookup %>%
|
||||
AB_ANTIFUNGALS <- AMR_env$AB_lookup %>%
|
||||
filter(group %like% "antifungal") %>%
|
||||
pull(ab)
|
||||
AB_ANTIMYCOBACTERIALS <- AB_lookup %>%
|
||||
AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>%
|
||||
filter(group %like% "antimycobacterial") %>%
|
||||
pull(ab)
|
||||
AB_CARBAPENEMS <- antibiotics %>%
|
||||
@ -268,16 +268,16 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
|
||||
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
||||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
|
||||
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_all <- unname(lapply(
|
||||
as.list(as.data.frame(t(AB_lookup[,
|
||||
AMR_env$AB_lookup <- AMR::antibiotics
|
||||
AMR_env$AB_lookup$generalised_name <- generalise_antibiotic_name(AMR_env$AB_lookup$name)
|
||||
AMR_env$AB_lookup$generalised_synonyms <- lapply(AMR_env$AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AMR_env$AB_lookup$generalised_abbreviations <- lapply(AMR_env$AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AMR_env$AB_lookup$generalised_loinc <- lapply(AMR_env$AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AMR_env$AB_lookup$generalised_all <- unname(lapply(
|
||||
as.list(as.data.frame(t(AMR_env$AB_lookup[,
|
||||
c(
|
||||
"ab", "atc", "cid", "name",
|
||||
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]
|
||||
colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "generalised"]
|
||||
),
|
||||
drop = FALSE
|
||||
]),
|
||||
@ -288,7 +288,7 @@ create_AB_lookup <- function() {
|
||||
x[x != ""]
|
||||
}
|
||||
))
|
||||
AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
|
||||
AMR_env$AB_lookup[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %like% "^generalised"]]
|
||||
}
|
||||
AB_LOOKUP <- create_AB_lookup()
|
||||
|
||||
|
||||
@ -64,7 +64,7 @@ if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
|
||||
}
|
||||
}
|
||||
|
||||
df <- AMR:::MO_lookup
|
||||
df <- AMR:::AMR_env$MO_lookup
|
||||
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
|
||||
expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
|
||||
expect_true(all(c(
|
||||
|
||||
@ -69,8 +69,8 @@ ab_name("J01CR50")
|
||||
|
||||
# even antibiotic selectors work
|
||||
x <- data.frame(random_column = "test",
|
||||
coflu = as.rsi("S"),
|
||||
ampicillin = as.rsi("R"))
|
||||
coflu = as.rsi("S"),
|
||||
ampicillin = as.rsi("R"))
|
||||
x
|
||||
x[, betalactams()]
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user