simFmodel: Simulation of multi-locus genetic data from the spatial...
In Geneland: Detection of Structure from Multilocus Genetic Data

Description Usage Arguments Details Value Author(s)

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

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

`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 is treated as a recessive allele and all heterozigous are converted into homozigous for the dominant allele. The presence of the "dominant" allele is coded as 1, the absence of the "dominant" allele is coded as 0.
`plots`	Logical: if TRUE, spatial coordinates are ploted
`ploth`	Logical: if TRUE, barplots for allele frequencies are ploted

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.

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

Gilles Guillot

Geneland documentation built on April 14, 2017, 2:31 p.m.