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146 lines
6.3 KiB
R
146 lines
6.3 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/key_antimicrobials.R
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\name{key_antimicrobials}
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\alias{key_antimicrobials}
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\alias{all_antimicrobials}
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\alias{antimicrobials_equal}
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\title{(Key) Antimicrobials for First Weighted Isolates}
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\usage{
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key_antimicrobials(
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x = NULL,
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col_mo = NULL,
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universal = c("ampicillin", "amoxicillin/clavulanic acid", "cefuroxime",
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"piperacillin/tazobactam", "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
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gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime", "ceftazidime",
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"meropenem"),
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gram_positive = c("vancomycin", "teicoplanin", "tetracycline", "erythromycin",
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"oxacillin", "rifampin"),
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antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole", "nystatin",
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"voriconazole"),
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only_rsi_columns = FALSE,
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...
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)
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all_antimicrobials(x = NULL, only_rsi_columns = FALSE, ...)
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antimicrobials_equal(
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y,
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z,
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type = c("points", "keyantimicrobials"),
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ignore_I = TRUE,
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points_threshold = 2,
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...
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)
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}
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\arguments{
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\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically}
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\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{universal}{names of \strong{broad-spectrum} antimicrobial drugs, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antimicrobial drugs}
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\item{gram_negative}{names of antibiotic drugs for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
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\item{gram_positive}{names of antibiotic drugs for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
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\item{antifungal}{names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs}
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\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
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\item{...}{ignored, only in place to allow future extensions}
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\item{y, z}{\link{character} vectors to compare}
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\item{type}{type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}}
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\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
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\item{points_threshold}{minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
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}
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\description{
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These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see \code{\link[=first_isolate]{first_isolate()}}). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
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}
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\details{
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The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
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The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial drug results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
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Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
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The default antimicrobial drugs used for \strong{all rows} (set in \code{universal}) are:
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\itemize{
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\item Ampicillin
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\item Amoxicillin/clavulanic acid
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\item Cefuroxime
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\item Ciprofloxacin
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\item Piperacillin/tazobactam
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\item Trimethoprim/sulfamethoxazole
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}
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The default antimicrobial drugs used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
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\itemize{
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\item Cefotaxime
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\item Ceftazidime
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\item Colistin
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\item Gentamicin
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\item Meropenem
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\item Tobramycin
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}
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The default antimicrobial drugs used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
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\itemize{
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\item Erythromycin
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\item Oxacillin
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\item Rifampin
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\item Teicoplanin
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\item Tetracycline
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\item Vancomycin
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}
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The default antimicrobial drugs used for \strong{fungi} (set in \code{antifungal}) are:
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\itemize{
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\item Anidulafungin
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\item Caspofungin
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\item Fluconazole
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\item Miconazole
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\item Nystatin
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\item Voriconazole
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}
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}
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\examples{
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# `example_isolates` is a data set available in the AMR package.
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# See ?example_isolates.
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# output of the `key_antimicrobials()` function could be like this:
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strainA <- "SSSRR.S.R..S"
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strainB <- "SSSIRSSSRSSS"
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# those strings can be compared with:
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antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
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# TRUE, because I is ignored (as well as missing values)
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antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
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# FALSE, because I is not ignored and so the 4th [character] differs
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\donttest{
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if (require("dplyr")) {
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# set key antibiotics to a new variable
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my_patients <- example_isolates \%>\%
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mutate(keyab = key_antimicrobials(antifungal = NULL)) \%>\% # no need to define `x`
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mutate(
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# now calculate first isolates
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first_regular = first_isolate(col_keyantimicrobials = FALSE),
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# and first WEIGHTED isolates
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first_weighted = first_isolate(col_keyantimicrobials = "keyab")
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)
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# Check the difference in this data set, 'weighted' results in more isolates:
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sum(my_patients$first_regular, na.rm = TRUE)
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sum(my_patients$first_weighted, na.rm = TRUE)
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}
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}
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}
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\seealso{
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\code{\link[=first_isolate]{first_isolate()}}
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}
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