simFmodel: 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 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

Value

this list are: coordinates, genotypes, allele.numbers, number.nuclei, coord.nuclei, color.nuclei, frequencies, ancestral.frequencies, drifts, index.nearest.nucleus

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.