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\name{prabinit}
\alias{prabinit}
\alias{print.prab}
\alias{prab}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Presence-absence/abundance matrix initialization}
\description{
\code{prabinit} converts a matrix into an object
of class \code{prab} (presence-absence). The matrix may be read from a
file or an R-object. It may be a 0-1 matrix or a matrix with
non-negative entries (usually abundances).
\code{print.prab} is a print method for such
objects.
Documentation here is in terms of biotic elements analysis (species
are to be clustered). For species delimitation with dominant markers,
see Hausdorf and Hennig (2010), individuals take the role of species
and loci take the role of regions.
}
\usage{
prabinit(file = NULL, prabmatrix = NULL, rows.are.species = TRUE,
neighborhood = "none", nbbetweenregions=TRUE, geodist=NULL, gtf=0.1,
distance = "kulczynski", toprab = FALSE, toprabp
= 0.05, outc = 5.2)
\method{print}{prab}(x, ...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{file}{string. non-negative matrix ASCII file (such as example dataset
\code{kykladspecreg.dat}) from which the
matrix is read by \code{read.table}. The usual interpretation is
that it is a species-by-regions matrix of species presences/absences
(0-1 matrix) or abundances.}
\item{prabmatrix}{matrix with non-negative entries. Either \code{file}
or \code{prabmatrix} should be \code{NA}.}
\item{rows.are.species}{logical. If \code{TRUE}, rows are interpreted
as species and columns are interpreted as regions. In this case,
rows and columns are interchanged by \code{prabinit}.}
\item{neighborhood}{A string or 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 vector \code{numeric(0)}. If \code{neighborhood}
is a filename, it is attempted to read such a list from a file,
where every row should correspond to one region (such as example
dataset \code{nb.dat}). If
\code{neighborhood="none"}, all neighborhoods are set to
\code{numeric(0)}. The neighborhood can be tested by
\code{\link{nbtest}} for consistency.}
\item{nbbetweenregions}{logical. If \code{TRUE}, the neighborhood is
defined between regions as explained above. Otherwise it is defined
between species (or individuals, if this is used for species
delimitation).}
\item{geodist}{matrix of non-negative reals. Geographical distances
between regions. Only used if \code{distance="geco"}.}
\item{gtf}{tuning constant for geco-distance if \code{distance="geco"},
see \code{geco}.}
\item{distance}{\code{"kulczynski"}, \code{"jaccard"}, \code{"geco"},
\code{"qkulczynski"}, \code{"logkulczynski"} (this calls function
\code{qkulczynski} with \code{log.distance=TRUE}), \code{"dice"}, or
\code{"none"}. The distance measure
between species to compute by \code{prabinit}.}
\item{toprab}{logical. If \code{TRUE}, a presence-absence matrix is
computed from the non-negative input matrix. "Absence", i.e., the
entry 0, is chosen if the original entry is 0, or the original entry
is smaller than or equal to \code{toprabp} times the
sum of entries in the
corresponding region, and log(original entry) is considered to be a
lower outlier compared with the other entries of the corresponding
species (see \code{outc}). "Presence", i.e., the entry 1, thus
means that the original
entry is non-negligible w.r.t. the species or w.r.t. the region.}
\item{toprabp}{numerical between 0 and 1, see \code{toprab}.}
\item{outc}{numerical. Tuning constant for the outlier identification
associated with \code{toprab=TRUE}. An entry smaller than or equal to
\code{outc*mad} times the median is considered as a lower outlier.}
\item{x}{object of class \code{prab}.}
\item{...}{necessary for print method.}
}
\details{
Species that are absent in all regions are omitted.}
\value{
\code{prabinit} produces
an object of class \code{prab}, which is a list with components
\item{distmat}{distance matrix between species.}
\item{prab}{abundance or presence/absence matrix (if presence/absence,
the entries are logical). Rows are regions, columns are
species.}
\item{nb}{neighborhood list, see above.}
\item{regperspec}{vector of the number of regions occupied by a
species.}
\item{specperreg}{vector of the number of species present in a region.}
\item{n.species}{number of species (in the \code{prab}-object, see
\code{nonzero}).}
\item{n.regions}{number of regions.}
\item{distance}{string denoting the chosen distance measure.}
\item{geodist}{non-negative matrix. see above.}
\item{gtf}{numeric. see above.}
\item{spatial}{\code{TRUE}, if there is a specified neighborhood
structure.}
\item{nonempty.species}{logical vector. The length is the number of species
in the original file/matrix. If \code{FALSE}, the corresponding species
had only zero entries and was therefore absent. Note that these species
are not included in any other component of a \code{prab} object, i.e.,
\code{n.species} is the number of \code{TRUE}-entries in
\code{nonzero}.}
\item{nbbetweenregions}{see above.}
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\references{
Hausdorf, B. and Hennig, C. (2010) Species Delimitation Using Dominant
and Codominant Multilocus Markers. \emph{Systematic Biology}, 59, 491-503.
}
\seealso{\code{\link{read.table}}, \code{\link{jaccard}},
\code{\link{kulczynski}}, \code{\link{geco}},
\code{\link{qkulczynski}}, \code{\link{nbtest}},
\code{\link{alleleinit}}
}
\examples{
# If you want to use your own ASCII data files, use
# x <- prabinit(file="path/prabmatrixfile",
# neighborhood="path/neighborhoodfile")
data(kykladspecreg)
data(nb)
prabinit(prabmatrix=kykladspecreg, neighborhood=nb)
}
\keyword{spatial}% at least one, from doc/KEYWORDS
\keyword{cluster}% __ONLY ONE__ keyword per line
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