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AMR/R/custom_eucast_rules.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Create Custom EUCAST Rules
#'
#' @inheritSection lifecycle Experimental Lifecycle
#' @param ... rules in formula notation, see *Examples*
#' @details
#' This documentation page will be updated shortly. **This function is experimental.**
#'
#' @section How it works:
#' ..
#'
#' It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): `r vector_and(tolower(DEFINED_AB_GROUPS), quote = "``")`.
#' @export
#' @examples
#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
#' eucast_rules(example_isolates,
#' rules = "custom",
#' custom_rules = x,
#' info = FALSE)
#'
#' # combine rule sets
#' x2 <- c(x,
#' custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
#' x2
custom_eucast_rules <- function(...) {
dots <- tryCatch(list(...),
error = function(e) "error")
stop_if(identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`")
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(inherits(dots[[i]], "formula"),
"rule ", i, " must be a valid formula input (e.g., using '~'), see `?custom_eucast_rules`")
# Query
qry <- dots[[i]][[2]]
if (inherits(qry, "call")) {
qry <- as.expression(qry)
}
qry <- as.character(qry)
# these will prevent vectorisation, so replace them:
qry <- gsub("&&", "&", qry, fixed = TRUE)
qry <- gsub("||", "|", qry, fixed = TRUE)
# format nicely, setting spaces around operators
qry <- gsub(" *([&|+-/*^><==]+) *", " \\1 ", qry)
qry <- gsub(" ?, ?", ", ", qry)
qry <- gsub("'", "\"", qry, fixed = TRUE)
out[[i]]$query <- as.expression(qry)
# Resulting rule
result <- dots[[i]][[3]]
stop_ifnot(deparse(result) %like% "==",
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`")
result_group <- as.character(result)[[2]]
if (paste0(toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
result_group <- paste0(result_group, "s")
}
if (toupper(result_group) %in% DEFINED_AB_GROUPS) {
result_group <- eval(parse(text = toupper(result_group)), envir = asNamespace("AMR"))
} else {
result_group <- tryCatch(
suppressWarnings(as.ab(result_group,
fast_mode = TRUE,
info = FALSE,
flag_multiple_results = FALSE)),
error = function(e) NA_character_)
}
stop_if(any(is.na(result_group)),
"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"",
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ",
vector_or(tolower(DEFINED_AB_GROUPS), quotes = FALSE), ".")
result_value <- as.character(result)[[3]]
result_value[result_value == "NA"] <- NA
stop_ifnot(result_value %in% c("R", "S", "I", NA),
"the resulting value of rule ", i, " must be either \"R\", \"S\", \"I\" or NA")
result_value <- as.rsi(result_value)
out[[i]]$result_group <- result_group
out[[i]]$result_value <- result_value
}
names(out) <- paste0("rule", seq_len(n_dots))
set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
}
#' @method c custom_eucast_rules
#' @noRd
#' @export
c.custom_eucast_rules <- function(x, ...) {
if (length(list(...)) == 0) {
return(x)
}
out <- unclass(x)
for (e in list(...)) {
out <- c(out, unclass(e))
}
names(out) <- paste0("rule", seq_len(length(out)))
set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
}
#' @method as.list custom_eucast_rules
#' @noRd
#' @export
as.list.custom_eucast_rules <- function(x, ...) {
c(x, ...)
}
#' @method print custom_eucast_rules
#' @export
#' @noRd
print.custom_eucast_rules <- function(x, ...) {
cat("A set of custom EUCAST rules:\n")
for (i in seq_len(length(x))) {
rule <- x[[i]]
rule$query <- format_custom_query_rule(rule$query)
if (rule$result_value == "R") {
val <- font_rsi_R_bg(font_black(" R "))
} else if (rule$result_value == "S") {
val <- font_rsi_S_bg(font_black(" S "))
} else {
val <- font_rsi_I_bg(font_black(" I "))
}
agents <- paste0(font_blue(ab_name(rule$result_group, language = NULL, tolower = TRUE),
collapse = NULL),
" (", rule$result_group, ")")
agents <- sort(agents)
rule_if <- word_wrap(paste0(i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then "),
"set to {result}:"),
extra_indent = 5)
rule_if <- gsub("{result}", val, rule_if, fixed = TRUE)
rule_then <- paste0(" ", word_wrap(paste0(agents, collapse = ", "), extra_indent = 5))
cat("\n ", rule_if, "\n", rule_then, "\n", sep = "")
}
}
run_custom_eucast_rules <- function(df, rule, info) {
n_dots <- length(rule)
stop_if(n_dots == 0, "no custom rules set", call = -2)
out <- character(length = NROW(df))
reasons <- character(length = NROW(df))
for (i in seq_len(n_dots)) {
qry <- tryCatch(eval(parse(text = rule[[i]]$query), envir = df, enclos = parent.frame()),
error = function(e) {
pkg_env$err_msg <- e$message
return("error")
})
if (identical(qry, "error")) {
warning_("in custom_eucast_rules(): rule ", i,
" (`", as.character(rule[[i]]$query), "`) was ignored because of this error message: ",
pkg_env$err_msg,
call = FALSE,
add_fn = font_red)
next
}
stop_ifnot(is.logical(qry), "in custom_eucast_rules(): rule ", i, " (`", rule[[i]]$query,
"`) must return `TRUE` or `FALSE`, not ",
format_class(class(qry), plural = FALSE), call = FALSE)
new_eucasts <- which(qry == TRUE & out == "")
if (info == TRUE) {
cat(word_wrap("- Custom EUCAST rule ", i, ": `", as.character(rule[[i]]$query),
"` (", length(new_eucasts), " rows matched)"), "\n", sep = "")
}
val <- rule[[i]]$value
out[new_eucasts] <- val
reasons[new_eucasts] <- paste0("matched rule ", gsub("rule", "", names(rule)[i]), ": ", as.character(rule[[i]]$query))
}
out[out == ""] <- "Negative"
reasons[out == "Negative"] <- "no rules matched"
if (isTRUE(attributes(rule)$as_factor)) {
out <- factor(out, levels = attributes(rule)$values, ordered = TRUE)
}
columns_nonsusceptible <- as.data.frame(t(df[, is.rsi(df)] == "R"))
columns_nonsusceptible <- vapply(FUN.VALUE = character(1),
columns_nonsusceptible,
function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " "))
columns_nonsusceptible[is.na(out)] <- NA_character_
data.frame(row_number = seq_len(NROW(df)),
EUCAST = out,
reason = reasons,
columns_nonsusceptible = columns_nonsusceptible,
stringsAsFactors = FALSE)
}
format_custom_query_rule <- function(query, colours = has_colour()) {
query <- gsub(" & ", font_black(font_bold(" and ")), query, fixed = TRUE)
query <- gsub(" | ", font_black(" or "), query, fixed = TRUE)
query <- gsub(" + ", font_black(" plus "), query, fixed = TRUE)
query <- gsub(" - ", font_black(" minus "), query, fixed = TRUE)
query <- gsub(" / ", font_black(" divided by "), query, fixed = TRUE)
query <- gsub(" * ", font_black(" times "), query, fixed = TRUE)
query <- gsub(" == ", font_black(" is "), query, fixed = TRUE)
query <- gsub(" > ", font_black(" is higher than "), query, fixed = TRUE)
query <- gsub(" < ", font_black(" is lower than "), query, fixed = TRUE)
query <- gsub(" >= ", font_black(" is higher than or equal to "), query, fixed = TRUE)
query <- gsub(" <= ", font_black(" is lower than or equal to "), query, fixed = TRUE)
query <- gsub(" ^ ", font_black(" to the power of "), query, fixed = TRUE)
query <- gsub(" %in% ", font_black(" is one of "), query, fixed = TRUE)
query <- gsub(" %like% ", font_black(" resembles "), query, fixed = TRUE)
if (colours == TRUE) {
query <- gsub('"R"', font_rsi_R_bg(font_black(" R ")), query, fixed = TRUE)
query <- gsub('"S"', font_rsi_S_bg(font_black(" S ")), query, fixed = TRUE)
query <- gsub('"I"', font_rsi_I_bg(font_black(" I ")), query, fixed = TRUE)
}
# replace the black colour 'stops' with blue colour 'starts'
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
# start with blue
query <- paste0("\033[34m", query)
if (colours == FALSE) {
query <- font_stripstyle(query)
}
query
}
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