simFmodel              package:Geneland              R Documentation

_S_i_m_u_l_a_t_i_o_n _o_f _m_u_l_t_i-_l_o_c_u_s _g_e_n_e_t_i_c _d_a_t_a _f_r_o_m _t_h_e _s_p_a_t_i_a_l _F-_m_o_d_e_l

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

     Simulates multi-locus genotypes and spatial coordinates for 
     individuals belonging to some spatially organised populations.

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

     simFmodel(nindiv, coordinates = NULL, coord.lim, number.nuclei,
     coord.nuclei = NULL, color.nuclei = NULL,
     nloc, nall, npop, drift, seed=NULL, plots = TRUE, ploth = TRUE)

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

  nindiv: Integer:  Number of individuals

coordinates: Matrix (2 rows, 'nindiv' columns) of spatial coordinates
          of individuals

coord.lim: Vector of limits of spatial domain to be considered (x min,
          x max, y min, y max) 

number.nuclei: Integer: number of nuclei in the Voronoi tessellation

coord.nuclei: Coordinates of nuclei of Voronoi tessellation

color.nuclei: Population labels of the nuclei (vector of integers of
          size 'number.nuclei')

    nloc: number of loci

    nall: Vector of integers (of size 'nloc') giving number of alleles
          at each locus

    npop: Number of populations 

   drift: Vector (of size 'npop') of drift factors between 0 and 1

    seed: Seed to initialize the random number generator

   plots: Logical: if TRUE, spatial coordinates are ploted

   ploth: Logical: if TRUE, barplots for allele frequencies are ploted

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

     'number.nuclei' uniform i.i.d points are randomly spread on the
     rectangular domain. These points generates the so called Voronoi
     tessellation of the domain in 'number.nuclei' polygonal
     sub-domains. Each polygon is given a color uniformly on {1,
     'npop'}. The union of polygons of the color k gives the domain of
     population k. Then 'nindiv' uniform i.i.d  points are randomly
     spread on the domain and stand for the locations of individuals.
     Allele frequencies in the ancestral population are sampled from
     independent Dirichlet D(1,...,1). Allele frequencies in the
     present time population are drawn from Dirichlet distrubution
     whose parameters depend on drift factors 'drift' and allele
     frequencies in the ancestral population. Individual genotypes in
     each population are drawn from the allele frequencies of the
     corresponding population assuming Hardy-Weinberg equilibrium and
     linkage equilibrium.

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

     A list of variables involved in the simulation. The elements of
     this list are:  coordinates, genotypes, allele.numbers,
     coord.nuclei, color.nuclei,  frequencies,  ancestral.frequencies,
     drifts, index.nearest.nucleus

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

     Gilles Guillot

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

     Falush D., M. Stephens, J.K. Pritchard,  Inference of population
     structure using multilocus genotype data: Linked loci and
     correlated allele frequencies, Genetics, pp 1567-1587, vol 164,
     2003

     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:

     Function 'mcmcFmodel' for inference

