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(coordinates,genotypes,
    path.mcmc,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.mcmc` | 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 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 individuals:` | They are written in a file named ‘`modal.pop.indiv.txt`’. See the example section of function `mcmcFmodel` 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 1.0.5 Index]