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 = NULL, coord.lim, number.nuclei,
    coord.nuclei = NULL, color.nuclei = NULL,nall, npop, freq.model="Dirichlet",drift=NULL, seed=NULL, 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:"Falush" or "Dirichlet"
`drift` | Vector (of size `npop`) of drift factors between 0 and 1 (only for the Falush model)
`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

### 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

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

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.

### See Also

Function `mcmcFmodel` for inference

[Package Geneland version 1.0.5 Index]