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\name{communities}
\alias{communities}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Construct communities from individuals}
\description{
Construct communities from individuals using geographical distance and
hierarchical clustering. Communities are clusters of geographically
close individuals, formed by \code{\link{hclust}} with specified
distance cutoff.
}
\usage{
communities(geodist,grouping=NULL,
cutoff=1e-5,method="single")
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{geodist}{\code{dist}-object or matrix of geographical distances
between individuals.}
\item{grouping}{something that can be coerced into a factor. Different
groups indicated by \code{grouping} cannot be together in the same
community. (If \code{NULL}, there is no constraint.)}
\item{cutoff}{numeric; clustering distance cutoff value, passed on as
parameter \code{h} to \code{cutree}. Note that if this is smaller
than the smallest nonzero geographical distance, communities will be
all sets of individuals that have zero geographical distance to each
other.}
\item{method}{\code{method}-parameter for \code{\link{hclust}}.}
}
\value{
Vector of community memberships for the individuals (integer numbers
from 1 to the number of communities without interruption.
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\seealso{
\code{\link{communitydist}}
}
\examples{
data(veronica)
ver.geo <- coord2dist(coordmatrix=veronica.coord[1:90,],file.format="decimal2")
species <-c(rep(1,64),rep(2,17),rep(3,9))
communities(ver.geo,species)
}
\keyword{spatial}% __ONLY ONE__ keyword per line
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