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dr. M.S. (Matthijs) Berends
2022-12-30 13:02:37 +01:00
parent e4ea96cbf9
commit 77d9cf1936
5 changed files with 12 additions and 21 deletions
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2
man/g.test.Rd
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@ -21,7 +21,7 @@ g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)
\item{y}{a numeric vector; ignored if \code{x} is a matrix. If
\code{x} is a factor, \code{y} should be a factor of the same length.}
\item{p}{a vector of probabilities of the same length as \code{x}.
\item{p}{a vector of probabilities of the same length of \code{x}.
An error is given if any entry of \code{p} is negative.}
\item{rescale.p}{a logical scalar; if TRUE then \code{p} is rescaled

15
man/mean_amr_distance.Rd
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@ -2,22 +2,13 @@
% Please edit documentation in R/mean_amr_distance.R
\name{mean_amr_distance}
\alias{mean_amr_distance}
\alias{mean_amr_distance.default}
\alias{mean_amr_distance.mic}
\alias{mean_amr_distance.disk}
\alias{mean_amr_distance.rsi}
\alias{mean_amr_distance.data.frame}
\alias{amr_distance_from_row}
\title{Mean AMR Distance}
\title{Calculate the Mean AMR Distance}
\usage{
mean_amr_distance(x, ...)
\method{mean_amr_distance}{default}(x, ...)
\method{mean_amr_distance}{mic}(x, ...)
\method{mean_amr_distance}{disk}(x, ...)
\method{mean_amr_distance}{rsi}(x, ..., combine_SI = TRUE)
\method{mean_amr_distance}{data.frame}(x, ..., combine_SI = TRUE)
@ -27,7 +18,7 @@ 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}
\item{...}{variables to select (supports tidy selection such as \code{column1:column4} and \code{\link[tidyselect:language]{where(is.mic)}}), and can thus also be \link[=ab_selector]{antibiotic selectors}}
\item{...}{variables to select (supports \link[tidyselect:language]{tidyselect language} such as \code{column1:column4} and \code{where(is.mic)}, and can thus also be \link[=ab_selector]{antibiotic selectors}}
\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}}
@ -36,7 +27,7 @@ amr_distance_from_row(amr_distance, row)
\item{row}{an index, such as a row number}
}
\description{
This function calculates a normalised mean for antimicrobial resistance between multiple observations.
Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.
}
\details{
The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand. For common numeric data this distance is equal to \href{https://en.wikipedia.org/wiki/Standard_score}{Z scores} (the number of standard deviations from the mean).