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\name{phipt}
\alias{phipt}
\alias{cfchord}
\alias{shared.problist}
\alias{diploidcomlist}
%- Also NEED an `\alias' for EACH other topic documented here.
\title{Distances between communities, auxiliary functions}
\description{
Auxiliary functions for \code{\link{communitydist}}. \code{phipt}
computes phiPT/phiST (Peakall and Smouse, 2012, Meirmans,
2006) between two communities. \code{cfchord} computes the
chord-distance (Cavalli-Sforza and Edwards, 1967) between two lists or
locus-wise relative allele frequencies. \code{shared.problist}
computes a straightforward generalisation of the shared allele
distance (Bowcock et al., 1994) between
individuals for communities, namely the `overlap', i.e., sum of the
minima of the
allele relative frequencies. \code{diploidcomlist} constructs the
input lists for \code{cfchord} and \code{shared.problist} from an
\code{alleleobject}. It provides relative frequencies for all
alles of all loci in all communities.
}
\usage{
phipt(alleleobj,comvector,i,j)
cfchord(p1,p2)
shared.problist(p1,p2)
diploidcomlist(alleleobj,comvector,diploid=TRUE)
}
%- maybe also `usage' for other objects documented here.
\arguments{
\item{alleleobj}{if \code{diploid=TRUE}, an object of class
\code{alleleobject} as produced by
function \code{\link[prabclus]{alleleinit}}. This has the required
information on the individuals that are grouped into communities. In
case \code{diploid=FALSE}, a list that needs to have components
\code{n.variables} (number of loci), \code{alevels} (vector of
allele names, see \code{\link{alleleinit}}) and
\code{charmatrix} (matrix of characters with one row for every
individual and one column for every locus giving the alleles; see
examples below for how this can be constructed for a
\code{prabobject} with presence-absence data).}
\item{comvector}{vector of integers indicating to which
community an individual belongs.}
\item{i}{integer. Number of community.}
\item{j}{integer. Number of community. The phiPT-distance is computed
between the communities numbered \code{i} and \code{j}}
\item{p1}{list. Every list entry refers to a locus and is a vector of
relative frequencies of the alleles present in that locus in a
community.}
\item{p2}{list. Every list entry refers to a locus and is a vector of
relative frequencies of the alleles present in that locus in a
community. The chord or shared allele distance is computed between
the communities encoded by \code{p1} and \code{p2}.}
\item{diploid}{logical, indicating whether loci are diploid, see
\code{alleleobj}.}
}
\value{
\code{cfchord} gives out the value of the chord
distance. \code{shared.problist} gives out the distance
value. \code{diploidcomlist} gives out a two-dimensional list. The
list has one entry for each community, which is itself a list. This
community list has one entry for each locus, which is a vector that
gives the relative frequencies of the different alleles in
\code{phipt} gives out a list with components \code{phipt, vap, n0,
sst, ssg, msa, msw}. These refer to the notation on p.2.12 and 2.15 of
Peakall and Smouse (2012).
\item{phipt}{value of phiPT.}
\item{vap}{variance among (between) populations (communities).}
\item{n0}{standardisation factor N0, see p.2.12 of Peakall and Smouse (2012).}
\item{sst}{total distances sum of squares.}
\item{ssg}{vector with two non-\code{NA} entriesm, within community
sums of squares for communities \code{i} and \code{j}.}
\item{msa}{mean square between communities.}
\item{msw}{mean square within communities.}
}
\references{
Bowcock, A. M., Ruiz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J. R.,
Cavalli-Sforza, L. L. (1994) High resolution of human evolutionary
trees with polymorphic microsatellites. \emph{Nature} 368, 455-457.
Cavalli-Sforza, L. L. and Edwards, A. W. F. (1967) Phylogenetic
Analysis - Models and Estimation Procedures. \emph{The American Journal of
Human Genetics} 19, 233-257.
Meirmans, P. G. (2006) Using the AMOVA framework to estimate a
standardized genetic differentiation measure. \emph{Evolution} 60, 2399-2402.
Peakall, R. and Smouse P.E. (2012) GenAlEx Tutorial 2.
\url{https://biology-assets.anu.edu.au/GenAlEx/Tutorials.html}
}
\author{Christian Hennig
\email{christian.hennig@unibo.it}
\url{https://www.unibo.it/sitoweb/christian.hennig/en}}
\seealso{
\code{\link{communitydist}}
}
\examples{
options(digits=4)
data(tetragonula)
tnb <-
coord2dist(coordmatrix=tetragonula.coord[83:120,],cut=50,file.format="decimal2",neighbors=TRUE)
ta <- alleleconvert(strmatrix=tetragonula[83:120,])
tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist)
tetracoms <-
c(rep(1:3,each=3),4,5,rep(6:11,each=2),12,rep(13:19,each=2))
phipt(tai,tetracoms,4,6)
tdip <- diploidcomlist(tai,tetracoms,diploid=TRUE)
cfchord(tdip[[4]],tdip[[6]])
shared.problist(tdip[[4]],tdip[[6]])
}
\keyword{spatial}% __ONLY ONE__ keyword per line
\keyword{multivariate}% __ONLY ONE__ keyword per line
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