PostProcessChain: Computation for maps of posterior probability of population...

Description Usage Arguments Value Author(s) References See Also


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


path.mcmc,nxdom, nydom,burnin)



Spatial coordinates of individuals. A matrix with 2 columns and one line per individual.


Path to output files directory


Number of pixel for discretization of the spatial domain in the horizontal direction


Number of pixel for discretization of the spatial domain in the vertical direction


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 thinning !=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.


Posterior probability of population membership for each pixel:

They are written in an ascii file called ‘proba.pop.membership.txt’. Two first columns are coordinates of pixels then one column per population (thus npopmax values are computed for each pixel). Images in each column of ‘proba.pop.membership.txt’ are stored 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...

Posterior probability of population membership for each individual:

They are written in a file named ‘proba.pop.membership.indiv.txt’. One line per individuals and 2+npopmax columns per individual. Two first columns are spatial coordinates.

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.


Gilles Guillot


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


Geneland documentation built on April 14, 2017, 2:31 p.m.