AMR/man/key_antibiotics.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/key_antibiotics.R
\name{key_antibiotics}
\alias{key_antibiotics}
\alias{key_antibiotics_equal}
\title{Key antibiotics for first \emph{weighted} isolates}
\usage{
key_antibiotics(
  x,
  col_mo = NULL,
  universal_1 = guess_ab_col(x, "amoxicillin"),
  universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
  universal_3 = guess_ab_col(x, "cefuroxime"),
  universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
  universal_5 = guess_ab_col(x, "ciprofloxacin"),
  universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
  GramPos_1 = guess_ab_col(x, "vancomycin"),
  GramPos_2 = guess_ab_col(x, "teicoplanin"),
  GramPos_3 = guess_ab_col(x, "tetracycline"),
  GramPos_4 = guess_ab_col(x, "erythromycin"),
  GramPos_5 = guess_ab_col(x, "oxacillin"),
  GramPos_6 = guess_ab_col(x, "rifampin"),
  GramNeg_1 = guess_ab_col(x, "gentamicin"),
  GramNeg_2 = guess_ab_col(x, "tobramycin"),
  GramNeg_3 = guess_ab_col(x, "colistin"),
  GramNeg_4 = guess_ab_col(x, "cefotaxime"),
  GramNeg_5 = guess_ab_col(x, "ceftazidime"),
  GramNeg_6 = guess_ab_col(x, "meropenem"),
  warnings = TRUE,
  ...
)

key_antibiotics_equal(
  y,
  z,
  type = c("keyantibiotics", "points"),
  ignore_I = TRUE,
  points_threshold = 2,
  info = FALSE
)
}
\arguments{
\item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}}

\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_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}

\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}

\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}

\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored}

\item{...}{other parameters passed on to function}

\item{y, z}{characters to compare}

\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}

\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}

\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}

\item{info}{print progress}
}
\description{
These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
}
\details{
The function \code{\link[=key_antibiotics]{key_antibiotics()}} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link[=first_isolate]{first_isolate()}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link[=first_isolate]{first_isolate()}}). Without key antibiotic comparison it would not.

At default, the antibiotics that are used for \strong{Gram-positive bacteria} are:
\itemize{
\item Amoxicillin
\item Amoxicillin/clavulanic acid
\item Cefuroxime
\item Piperacillin/tazobactam
\item Ciprofloxacin
\item Trimethoprim/sulfamethoxazole
\item Vancomycin
\item Teicoplanin
\item Tetracycline
\item Erythromycin
\item Oxacillin
\item Rifampin
}

At default the antibiotics that are used for \strong{Gram-negative bacteria} are:
\itemize{
\item Amoxicillin
\item Amoxicillin/clavulanic acid
\item Cefuroxime
\item Piperacillin/tazobactam
\item Ciprofloxacin
\item Trimethoprim/sulfamethoxazole
\item Gentamicin
\item Tobramycin
\item Colistin
\item Cefotaxime
\item Ceftazidime
\item Meropenem
}

The function \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}} checks the characters returned by \code{\link[=key_antibiotics]{key_antibiotics()}} for equality, and returns a \code{\link{logical}} vector.
}
\section{Key antibiotics}{

There are two ways to determine whether isolates can be included as first \emph{weighted} isolates which will give generally the same results:
\enumerate{
\item Using \code{type = "keyantibiotics"} and parameter \code{ignore_I}

Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
\item Using \code{type = "points"} and parameter \code{points_threshold}

A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
}
}

\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\examples{
# `example_isolates` is a dataset available in the AMR package.
# See ?example_isolates.

library(dplyr)
# set key antibiotics to a new variable
my_patients <- example_isolates \%>\%
  mutate(keyab = key_antibiotics(.)) \%>\%
  mutate(
    # now calculate first isolates
    first_regular = first_isolate(., col_keyantibiotics = FALSE),
    # and first WEIGHTED isolates
    first_weighted = first_isolate(., col_keyantibiotics = "keyab")
  )

# Check the difference, in this data set it results in 7\% more isolates:
sum(my_patients$first_regular, na.rm = TRUE)
sum(my_patients$first_weighted, na.rm = TRUE)


# output of the `key_antibiotics` function could be like this:
strainA <- "SSSRR.S.R..S"
strainB <- "SSSIRSSSRSSS"

key_antibiotics_equal(strainA, strainB)
# TRUE, because I is ignored (as well as missing values)

key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
# FALSE, because I is not ignored and so the 4th value differs
}
\seealso{
\code{\link[=first_isolate]{first_isolate()}}
}