PostProcessChain: PostProcessChain

In gilles-guillot/Geneland: Clustering of living organisms from geo-referenced genetic and/or morphometrics data

Description

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

Usage

PostProcessChain(coordinates,
                   path.mcmc,nxdom, nydom,burnin)
  @param coordinates Spatial coordinates of individuals. A matrix with 2
    columns and one line per individual.
  
  @param path.mcmc  Path to output files directory 
  
  @param nxdom Number of pixel for discretization of the spatial domain
    in the horizontal direction
  
  @param nydom Number of pixel for discretization of the spatial domain
    in the vertical direction
  
  @param 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 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.

Details

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.

gilles-guillot/Geneland documentation built on Feb. 24, 2020, 11:44 a.m.