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\name{stressvals}
\alias{stressvals}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Stress values for different dimensions of Kruskal's MDS}
\description{
Computes Kruskal's nonmetric multidimensional scaling
\code{\link{isoMDS}} on \code{\link{alleleobject}} or
\code{\link{prab}}-objects for
different output dimensions in order to compare stress values.
}
\usage{
stressvals(x,mdsdim=1:12,trace=FALSE)
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{x}{object of class \code{\link{alleleobject}} or \code{link{prab}}.
generated by \code{\link{alleleinit}} or \code{\link{prabinit}}.}
\item{mdsdim}{integer vector of MDS numbers of dimensions to be
tried.}
\item{trace}{logical. \code{trace}-argument for \code{\link{isoMDS}}
(should trace information be printed during execution?).}
}
\details{
Note that zero distances between
non-identical objects are replaced by the smallest nonzero distance
divided by 10 to prevent \code{\link{isoMDS}} from producing an error.
}
\value{
A list with components
\item{MDSstress}{vector of stress values.}
\item{mdsout}{list of full outputs of \code{\link{isoMDS}}.}
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\examples{
options(digits=4)
data(tetragonula)
set.seed(112233)
taiselect <- sample(236,40)
# Use data subset to make execution faster.
tnb <-
coord2dist(coordmatrix=tetragonula.coord[taiselect,],
cut=50,file.format="decimal2",neighbors=TRUE)
ta <- alleleconvert(strmatrix=tetragonula[taiselect,])
tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist)
stressvals(tai,mdsdim=1:3)$MDSstress
}
\keyword{multivariate}% at least one, from doc/KEYWORDS
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