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\name{randpop.nb}
\alias{randpop.nb}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Simulation of presence-absence matrices (non-clustered)}
\description{
Generates a simulated matrix where the rows are interpreted as regions
and the columns as species, 1 means that a species is present in the
region and 0 means that the species is absent. Species are generated
i.i.d.. Spatial autocorrelation of a species' presences is governed by
the parameter \code{p.nb} and a list of neighbors for each region.
}
\usage{
randpop.nb(neighbors, p.nb = 0.5, n.species, n.regions =
length(neighbors), vector.species = rep(1, n.species),
species.fixed = FALSE, pdf.regions = rep(1/n.regions, n.regions),
count = TRUE, pdfnb = FALSE)
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{neighbors}{A list with a component for every region. The
components are vectors of integers indicating
neighboring regions. A region without neighbors (e.g., an island)
should be assigned a list \code{numeric(0)}.}
\item{p.nb}{numerical between 0 and 1. The probability that a new
region is drawn from the non-neighborhood of the previous regions
belonging to a species under generation. Note that for a given
presence-absence matrix, this parameter can be estimated by
\code{autoconst} (called \code{pd} there).}
\item{n.species}{integer. Number of species.}
\item{n.regions}{integer. Number of regions.}
\item{vector.species}{vector of integers. If
\code{species.fixed=TRUE}, \code{vector.species} must have length
\code{n.species} and gives the sizes (i.e., numbers of regions) of
the species to generate. Else, the sizes are generated randomly from
the empirical distribution of \code{vector.species}.}
\item{species.fixed}{logical. See \code{vector.species}.}
\item{pdf.regions}{numerical vector of length \code{n.species}. The
entries must sum up to 1 and give probabilities for the regions to
be drawn during the generation of a species. These probabilities are
used conditional on the new region being a neighbor or a
non-neighbor of the previous regions of the species, see
\code{p.nb}.}
\item{count}{logical. If \code{TRUE}, the number of the currently
generated species is printed.}
\item{pdfnb}{logical. If \code{TRUE}, the probabilities of the regions
are modified according to the number of neighboring regions by
dividing them relative to the others by min(1,number of neighbors).}
}
\details{
The principle is that a single species with given size is generated
one-by-one region. The first region is drawn according to
\code{pdf.regions}. For all following regions, a neighbor or
non-neighbor of the previous configuration is added (if possible),
as explained in \code{pdf.regions}, \code{p.nb}.
}
\value{
A 0-1-matrix, rows are regions, columns are species.
}
\references{
Hennig, C. and Hausdorf, B. (2004) Distance-based parametric bootstrap
tests for clustering of species ranges. \emph{Computational Statistics
and
Data Analysis} 45, 875-896.
\url{http://stat.ethz.ch/Research-Reports/110.html}.
Hausdorf, B. and Hennig, C. (2003) Biotic Element Analysis in
Biogeography. \emph{Systematic Biology} 52, 717-723.
Hausdorf, B. and Hennig, C. (2003) Nestedness of nerth-west European
land snail ranges as a consequence of differential immigration from
Pleistocene glacial refuges. \emph{Oecologia} 135, 102-109.
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\seealso{
\code{\link{autoconst}} estimates \code{p.nb} from matrices of class
\code{prab}. These are generated by \code{\link{prabinit}}.
\code{\link{prabtest}} uses \code{randpop.nb} as a null model for
tests of clustering. An alternative model is given by
\code{\link{cluspop.nb}}.
}
\examples{
data(nb)
set.seed(2346)
randpop.nb(nb, p.nb=0.1, n.species=5, vector.species=c(1,10,20,30,34))
}
\keyword{spatial}% at least one, from doc/KEYWORDS
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