simFmodel {Geneland}R Documentation

Simulation of multi-locus genetic data from the spatial F-model

Description

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

Usage

simFmodel(nindiv, coordinates, coord.lim, number.nuclei,
coord.nuclei, color.nuclei,nall, npop, freq.model="Uncorrelated",drift,dominance="Codominant", plots = FALSE, ploth = FALSE)

Arguments

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)
nall Vector of integers giving number of alleles at each locus
npop Number of populations
freq.model model for frequencies:"Correlated" or "Uncorrelated"
drift Vector (of size npop) of drift factors between 0 and 1 (only for the Correlated model)
dominance A character string "Codominant" or "Dominant". If "Dominant" is chosen, the first allele (labelled 1) is treated as a recessive allele and all heterozigous are converted into homozigous for the dominant allele (labelled 2).
plots Logical: if TRUE, spatial coordinates are ploted
ploth Logical: if TRUE, barplots for allele frequencies are ploted

Details

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.

Value

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

Author(s)

Gilles Guillot

References

Correlated 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

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.


[Package Geneland version 3.1.4 Index]