\HeaderA{PostProcessChain}{Computation for  maps of posterior probability of population membership}{PostProcessChain}
\begin{Description}\relax
Computes posterior probabilities of population membership for each pixel
of the spatial domain.
\end{Description}
\begin{Usage}
\begin{verbatim}
PostProcessChain(coordinates,genotypes,
path.mcmc,nxdom, nydom,burnin)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{coordinates}] Spatial coordinates of individuals. A matrix with 2
columns and one line per individual.
\item[\code{genotypes}] Genotypes of individuals. A matrix with one line per
individual and 2 columns per locus
\item[\code{path.mcmc}] Path to output files directory 
\item[\code{nxdom}] Number of pixel for discretization of the spatial domain
in the horizontal direction
\item[\code{nydom}] Number of pixel for discretization of the spatial domain
in the vertical direction
\item[\code{burnin}] Number of iterations of the chain to throw away.
WARNING : this argument should be given the number of stored
iterations (and not the number of computed iterations which differ
if \code{burnin} !=1). If you have
\code{nit}=100000 and \code{thinning}=100, then only 1000 iterations
are stored. Then \code{burnin}=10 will throw away 10 stored
iterations, namely 100*10 computed iterations.
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{Posterior probability of population membership for each pixel:}] They  are
written in an ascii file called \file{proba.pop.membership.txt}
(one column per population,
\code{npopmax} values are computed for each pixel.
Images in each column of \file{proba.pop.membership.txt} are stored
column-wise starting from the bottom left pixel.
First line of \file{proba.pop.membership.txt}  = bottom left pixel ,
second line of \file{proba.pop.membership.txt} = upward neighboor of
the previous pixel, etc...)

Another file called \file{proba.pop.membership.perm.txt} tries
to get rid of label switching
issues by labelling the population according to a fixed constraint.
(This has proved to be usefull with a small number of loci, (e.g. nloc=3), for well
differentiated populations.)
\item[\code{Posterior probability of population membership for each
individual:}] They are written in a file named
\file{proba.pop.membership.indiv.txt}.

\item[\code{Label of modal population for individuals:}] They are written in a file named \file{modal.pop.indiv.txt}. 
See the example section  of function \code{\LinkA{mcmcFmodel}{mcmcFmodel}} to see
how they can be added in a plot.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Gilles Guillot
\end{Author}
\begin{References}\relax
G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical
model for landscape genetics. Genetics, 170, 1261-1280, 2005.

G. Guillot, Mortier, F., Estoup, A. Geneland : A program for landscape
genetics. Molecular Ecology Notes, 5, 712-715, 2005.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{PlotTessellation}{PlotTessellation}}
\end{SeeAlso}

