AMR/man/key_antimicrobials.Rd

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R

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