PostProcessChain          package:Geneland          R Documentation

_C_o_m_p_u_t_a_t_i_o_n _f_o_r  _m_a_p_s _o_f _p_o_s_t_e_r_i_o_r _p_r_o_b_a_b_i_l_i_t_y _o_f _p_o_p_u_l_a_t_i_o_n _m_e_m_b_e_r_s_h_i_p

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     PostProcessChain(coordinates,genotypes,allele.numbers,
     path.mcmc,nxdom, nydom,burnin)

_A_r_g_u_m_e_n_t_s:

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

allele.numbers: A vector of integer containing the number of possible
          allele for each 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 1000*10 computed
          iterations.

_D_e_t_a_i_l_s:

     'path.data' directory should contain at least three files named  
     exactly : 'coordinates.txt', 'genotypes.txt' and
     'allele.numbers.txt' and containing respectively the spatial
     coordinates, the genotypes and the number of alleles per locus.

     See format of files simulated by 'simFmodel' for an example.

_V_a_l_u_e:

     Posterior probability of population membership for each pixel are
     written in an ascii file called 'proba.pop.membership.txt' (one
     column per population, 'npopmax' values are computed for each
     pixel,  pixels are stored  row-wise starting from bottom left).

     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.)

_A_u_t_h_o_r(_s):

     Gilles Guillot

_R_e_f_e_r_e_n_c_e_s:

     A spatial statistical model for landscape genetics, Guillot,
     Estoup, Mortier, Cosson, Genetics, 2005

     Guillot, G., Geneland : A program for landscape genetics.
     Molecular Ecology  Notes, submited.

_S_e_e _A_l_s_o:

     'PlotTessellation'

