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,
     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

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.

_V_a_l_u_e:

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:: Th
          ey 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.

_A_u_t_h_o_r(_s):

     Gilles Guillot

_R_e_f_e_r_e_n_c_e_s:

     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.

_S_e_e _A_l_s_o:

     'PlotTessellation'

