PostProcessChain {Geneland} | R Documentation |
Computes posterior probabilities of population membership for each pixel of the spatial domain.
PostProcessChain(repdat, repmcmc,nxdom, nydom,burnin)
repdat |
Path to input files directory |
repmcmc |
Path to output files directory |
nxdom |
Number of pixel for discretization of the spatial domain in the horizontal direction |
nydom |
Number of pixel for discretization of the spatial domain in the vertical direction |
burnin |
Number of iterations of the chain to throwaway |
repdat
directory should contain at least three files
named exactly :
coordinates.txt
, genotypes.txt
and
allele.numbers.txt
and containing respectively the spatial
coordinates, the genotypes and the number of alleles per locus.
See format of files simulated by simFmodel
for an
example.
Posterior probability of population membership for each pixel are
written in an ascii file called proba.pop.membership.txt
(one column per population,
nclassmax
values are computed for each pixel,
pixels are stored row-wise starting from bottom left).
Another file called proba.pop.membership.perm.txt
tries
to get rid of label switching
issues by labelling the population according to a fixed constraint.
(This has has proved to be usefull with a small number of loci, (e.g. nloc=3), for well
differentiated populations.)
Gilles Guillot
A spatial statistical model for landscape genetics, Guillot, Estoup, Mortier, Cosson, Genetics, 2005
Guillot, G., Geneland : A program for landscape genetics. Molecular Ecology Notes, submited.