PostProcessChain {Geneland}R Documentation

Computation for maps of posterior probability of population membership

Description

Computes posterior probabilities of population membership for each pixel of the spatial domain.

Usage

PostProcessChain(repdat, repmcmc,nxdom, nydom,burnin)

Arguments

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

Details

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.

Value

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.)

Author(s)

Gilles Guillot

References

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.

See Also

PlotTessellation


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