PostProcessMultChain {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

PostProcessMultChain(coordinates,genotypes,
path.all,nrun,nxdom, nydom,burnin)

Arguments

coordinates Spatial coordinates of individuals. A matrix with 2 columns and one line per individual.
genotypes Genotypes of individuals. A matrix with one line per individual and 2 columns per locus
path.all Path to output files directory
nrun Number of runs
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 throw away. WARNING : this argument should be given the number of stored iterations (and not the number of computed iterations which differ if burnin !=1). If you have nit=100000 and thinning=100, then only 1000 iterations are stored. Then burnin=10 will throw away 10 stored iterations, namely 100*10 computed iterations.

Value

Posterior probability of population membership for each pixel: They are written in an ascii file called ‘proba.pop.membership.txt’ (one column per population, npopmax values are computed for each pixel. Images in each column of ‘proba.pop.membership.txt’ are stored column-wise starting from the bottom left pixel. First line of ‘proba.pop.membership.txt’ = bottom left pixel , second line of ‘proba.pop.membership.txt’ = upward neighboor of the previous pixel, etc...)
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 proved to be usefull with a small number of loci, (e.g. nloc=3), for well differentiated populations.)
Posterior probability of population membership for each individual: They are written in a file named ‘proba.pop.membership.indiv.txt’.
Label of modal population for pixels and individuals: They are written in files named ‘modal.pop.txt’ and ‘modal.pop.indiv.txt’ respectively. See the example section of function MCMC to see how they can be added in a plot.

Author(s)

Gilles Guillot

References

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.

See Also

PlotTessellation


[Package Geneland version 3.1.4 Index]