PostProcessChain {Geneland} | R Documentation |
Computes posterior probabilities of population membership for each pixel of the spatial domain.
PostProcessChain(coordinates,genotypes, path.mcmc,nxdom, nydom,burnin)
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. |
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.