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\name{plotdistreg}
\alias{plotdistreg}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Plots for within-groups and between-groups distance regression}
\description{
Visualisation of various regressions on distance (or dissimilarity)
data where objects are from two groups.
}
\usage{
plotdistreg(dmx,dmy,grouping,groups=levels(as.factor(grouping))[1:2],
cols=c(1,2,3,4),
pchs=rep(1,3),
ltys=c(1,2,1,2),
individual=TRUE,jointwithin=TRUE,jointall=TRUE,
oneplusjoint=TRUE,jittering=TRUE,bcenterline=TRUE,
xlim=NULL,ylim=NULL,xlab="geographical distance",
ylab="genetic distance",...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{dmx}{dissimilarity matrix or object of class
\code{dist}. Explanatory dissimilarities (often these will be proper
distances, but more general dissimilarities that do not
necessarily fulfill the triangle inequality can be used, same for \code{dmy}).}
\item{dmy}{dissimilarity matrix or object of class
\code{dist}. Response dissimilarities.}
\item{grouping}{something that can be coerced into a factor,
defining the grouping of
objects represented by the dissimilarities \code{dmx} and \code{dmy}
(i.e., if \code{grouping} has length n, \code{dmx} and \code{dmy}
must be dissimilarities between \code{n} objects).}
\item{groups}{Vector of two levels. The two groups defining the
regressions to be compared in the test. These can be
factor levels, integer numbers, or strings, depending on the entries
of \code{grouping}.}
\item{cols}{vector of four colors (or color numbers) to be used for
plotting distances
and regression lines within the first group, within the second group,
distances between groups, and a line marking the center of the
between-groups explanatory distances, see \code{col}-argument of
\code{\link{par}}.}
\item{pchs}{vector of three plot symbols (or numbers) to be used for
plotting distances within the first group, within the second group,
and distances between groups, see \code{pch}-argument of
\code{\link{par}}.}
\item{ltys}{vector of line type numbers to be used for single group
within-group regression, both groups combined within-group
regression, regression with all distances, and regression combining
within-groups distances of one group with between-groups distances,
see \code{lty}-argument of
\code{\link{par}}.}
\item{individual}{if \code{TRUE}, within-groups distances regression
lines are shown for both groups.}
\item{jointwithin}{if \code{TRUE}, the within-groups distances regression
line for both groups combined is shown.}
\item{jointall}{if \code{TRUE}, the regression
line based on all distances is shown.}
\item{oneplusjoint}{if \code{TRUE}, the regression lines combining
within-groups distances of one group with between-groups distances
are shown (the colors of these are the colors of the individual
groups, the first two components of the \code{cols}-argument).}
\item{jittering}{if \code{TRUE}, points are jittered to avoid
overplotting.}
\item{bcenterline}{if \code{TRUE}, a line is plotted to mark the
center of the between-groups distances on the explanatory variable.}
\item{xlim}{to be passed on to \code{\link{plot}}; the default is
determined from the involved distances.}
\item{ylim}{to be passed on to \code{\link{plot}}; the default is
determined from the involved distances.}
\item{xlab}{to be passed on to \code{\link{plot}}.}
\item{ylab}{to be passed on to \code{\link{plot}}.}
\item{...}{optional arguments to be passed on to \code{\link{plot}}.}
}
\references{
Hausdorf, B. and Hennig, C. (2019) Species delimitation and
geography. Submitted.
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\seealso{
\code{\link{regeqdist}}, \code{\link{regdistbetween}},
\code{\link{regdistbetweenone}}, \code{\link{regdistdiffone}}
}
\examples{
options(digits=4)
data(veronica)
ver.geo <- coord2dist(coordmatrix=veronica.coord[173:207,],file.format="decimal2")
vei <- prabinit(prabmatrix=veronica[173:207,],distance="jaccard")
species <-c(rep(1,13),rep(2,22))
loggeo <- log(ver.geo+quantile(as.vector(as.dist(ver.geo)),0.25))
plotdistreg(dmx=loggeo,dmy=vei$distmat,grouping=species,
jointwithin=FALSE,jointall=FALSE,groups=c(1,2))
legend(5,0.75,c("within species 1",
"within species 2","species 1 and between","species 2 and between"),lty=c(1,1,2,2),col=c(1,2,1,2))
plotdistreg(dmx=loggeo,dmy=vei$distmat,grouping=species,
jointwithin=TRUE,jointall=TRUE,oneplusjoint=FALSE,groups=c(1,2))
legend(5,0.75,c("within species 1",
"within species 2","all distances","all within species"),lty=c(1,1,1,2),col=c(1,2,3,3))
}
\keyword{htest}% __ONLY ONE__ keyword per line
\keyword{regression}% __ONLY ONE__ keyword per line
\keyword{spatial}% __ONLY ONE__ keyword per line
|
