mirror of https://github.com/msberends/AMR.git
117 lines
7.0 KiB
R
Executable File
117 lines
7.0 KiB
R
Executable File
% 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 unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{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}}.}
|
|
|
|
\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}}.}
|
|
|
|
\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}}.}
|
|
|
|
\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}}). 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{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{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}} 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}}). Without key antibiotic comparison it would not.
|
|
|
|
At default, the antibiotics that are used for \strong{Gram-positive bacteria} are: \cr
|
|
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.
|
|
|
|
At default, the antibiotics that are used for \strong{Gram-negative bacteria} are: \cr
|
|
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.
|
|
|
|
|
|
The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a 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: \cr
|
|
|
|
\strong{1. Using} \code{type = "keyantibiotics"} \strong{and parameter} \code{ignore_I} \cr
|
|
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}} function. \cr
|
|
|
|
\strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr
|
|
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{
|
|
# `septic_patients` is a dataset available in the AMR package. It is true, genuine data.
|
|
# See ?septic_patients.
|
|
|
|
library(dplyr)
|
|
# set key antibiotics to a new variable
|
|
my_patients <- septic_patients \%>\%
|
|
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}}
|
|
}
|