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mean AMR distance

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dr. M.S. (Matthijs) Berends
2022-10-21 16:02:14 +02:00
parent 178ab5e5ff
commit faca6d608a
5 changed files with 14 additions and 14 deletions
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10
man/mean_amr_distance.Rd
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@ -7,7 +7,7 @@
\alias{mean_amr_distance.disk}
\alias{mean_amr_distance.rsi}
\alias{mean_amr_distance.data.frame}
\alias{mean_distance_from_row}
\alias{amr_distance_from_row}
\title{Mean AMR Distance}
\usage{
mean_amr_distance(x, ...)
@ -22,7 +22,7 @@ mean_amr_distance(x, ...)
\method{mean_amr_distance}{data.frame}(x, ..., combine_SI = TRUE)
mean_distance_from_row(mean_distance, row)
amr_distance_from_row(amr_distance, row)
}
\arguments{
\item{x}{a vector of class \link[=as.rsi]{rsi}, \link[=as.rsi]{rsi} or \link[=as.rsi]{rsi}, or a \link{data.frame} containing columns of any of these classes}
@ -31,7 +31,7 @@ mean_distance_from_row(mean_distance, row)
\item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to \code{TRUE}}
\item{mean_distance}{the outcome of \code{\link[=mean_amr_distance]{mean_amr_distance()}}}
\item{amr_distance}{the outcome of \code{\link[=mean_amr_distance]{mean_amr_distance()}}}
\item{row}{an index, such as a row number}
}
@ -47,7 +47,7 @@ R/SI values (see \code{\link[=as.rsi]{as.rsi()}}) are transformed using \code{"S
For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using \code{\link[=rowMeans]{rowMeans()}}), see \emph{Examples}.
Use \code{\link[=mean_distance_from_row]{mean_distance_from_row()}} to subtract distances from the distance of one row, see \emph{Examples}.
Use \code{\link[=amr_distance_from_row]{amr_distance_from_row()}} to subtract distances from the distance of one row, see \emph{Examples}.
}
\section{Interpretation}{
@ -75,7 +75,7 @@ if (require("dplyr")) {
y \%>\%
mutate(
amr_distance = mean_amr_distance(., where(is.mic)),
check_id_C = mean_distance_from_row(amr_distance, id == "C")
check_id_C = amr_distance_from_row(amr_distance, id == "C")
) \%>\%
arrange(check_id_C)
}