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(v0.8.0.9031) as.mo() improvements

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dr. M.S. (Matthijs) Berends
2019-11-15 15:25:03 +01:00
parent 248b45da71
commit 09e2730b53
28 changed files with 751 additions and 598 deletions
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57
R/eucast_rules.R
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@ -24,8 +24,11 @@ EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' EUCAST rules
#'
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
#'
#' @description
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
#'
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
#' @param x data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
@ -36,6 +39,19 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
#' \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
#'
#' Before further processing, some non-EUCAST rules are applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are applied to all isolates, are:
#' \itemize{
#' \item{Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;}
#' \item{Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;}
#' \item{Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;}
#' \item{Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;}
#' \item{Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;}
#' \item{Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;}
#' \item{Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;}
#' \item{Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.}
#' }
#' To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
#'
#' The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
#'
#' @section Antibiotics:
@ -516,29 +532,7 @@ eucast_rules <- function(x,
as.data.frame(stringsAsFactors = FALSE)
)
if (info == TRUE) {
cat(paste0(
"\nRules by the ", bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", blue("http://eucast.org/"), "\n"))
}
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
if (!ab_missing(AMP) & !ab_missing(AMX)) {
if (verbose == TRUE) {
cat("\n VERBOSE: transforming",
length(which(x[, AMX] == "S" & !x[, AMP] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'S' based on amoxicillin. ")
cat("\n VERBOSE: transforming",
length(which(x[, AMX] == "I" & !x[, AMP] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'I' based on amoxicillin. ")
cat("\n VERBOSE: transforming",
length(which(x[, AMX] == "R" & !x[, AMP] %in% c("S", "I", "R"))),
"empty ampicillin fields to 'R' based on amoxicillin. \n")
}
x[which(x[, AMX] == "S" & !x[, AMP] %in% c("S", "I", "R")), AMP] <- "S"
x[which(x[, AMX] == "I" & !x[, AMP] %in% c("S", "I", "R")), AMP] <- "I"
x[which(x[, AMX] == "R" & !x[, AMP] %in% c("S", "I", "R")), AMP] <- "R"
} else if (ab_missing(AMP) & !ab_missing(AMX)) {
if (ab_missing(AMP) & !ab_missing(AMX)) {
# ampicillin column is missing, but amoxicillin is available
message(blue(paste0("NOTE: Using column `", bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
AMP <- AMX
@ -611,6 +605,7 @@ eucast_rules <- function(x,
}
}
eucast_notification_shown <- FALSE
eucast_rules_df <- eucast_rules_file # internal data file
no_added <- 0
no_changed <- 0
@ -648,6 +643,13 @@ eucast_rules <- function(x,
next
}
if (info == TRUE & !rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
cat(paste0(
"\n----\nRules by the ", bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", blue("http://eucast.org/"), "\n"))
eucast_notification_shown <- TRUE
}
if (info == TRUE) {
# Print rule (group) ------------------------------------------------------
@ -660,7 +662,7 @@ eucast_rules <- function(x,
rule_group_current %like% "expert" ~
paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"),
TRUE ~
"\nOther rules\n"
"\nOther rules by this AMR package\n"
)
))
}
@ -707,6 +709,7 @@ eucast_rules <- function(x,
}
if (like_is_one_of == "is") {
# so 'Enterococcus' will turn into '^Enterococcus$'
mo_value <- paste0("^", eucast_rules_df[i, 3], "$")
} else if (like_is_one_of == "one_of") {
# so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$'
@ -717,7 +720,7 @@ eucast_rules <- function(x,
} else if (like_is_one_of == "like") {
mo_value <- eucast_rules_df[i, 3]
} else {
stop("invalid like_is_one_of", call. = FALSE)
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
}
source_antibiotics <- eucast_rules_df[i, 4]