Geneland-package {Geneland}R Documentation

Simulation and inference for subdivided populations

Description

The main function MCMC takes multilocus genetic data and tries to detect population structure (i.e sub-populations), making use of both genetic (and optionally geographic) information.

Details

Package: Geneland
Type: Package
Version: 3.0.0
Date: 2008-11-15
License: GPL

The main purpose of the program is to perform Bayesian inference of all the parameters involved through Markov Chain Monte-Carlo simulation. This is achievied by the function MCMC. Function PostProcessChain read some output files of MCMC and computes some statistics suitable to print maps of inferred populations.

See Storage format section in MCMC help page.

The following functions are provided by the package:

simFmodel: simulation from the prior of the spatial F-model

simdata: Simulation of georeferenced genotypes under an IBD + barrier model

show.simdata: Graphical display of data simulated by simdata

MCMC: Full Bayesian Markov Chain Monte Carlo inference of parameters in the spatial F-model

PostProcessChain: Post-procesing of MCMC output for maps of posterior probability of populations subdomains

PlotTessellation: Graphical display of inferred sub-domains

The following functions are very basic and are only intended to be an aid for those not familiar with R. Most probably you may want to use directly the output files of MCMC and PostProcessChain to print your own figures.

PlotDrift: Graphical display of drift factors along MCMC run

PlotFreqA: Graphical display of allele frequencies in the ancestral population along MCMC run

PlotFreq: Graphical display of allele frequencies in the present time population along MCMC run

Plotnpop: Graphical display of number of populations along MCMC run

Plotntile: Graphical display of number of tiles along MCMC run

PosteriorMode: Computation and/or graphical display of mode in the posterior distribution of class membership at each pixel

Fstat: Computations of pairwise F statistics between known subpopulations of a dataset

Fstat.output: Computations of pairwise F statistics between inferred subpopulations

nullify: Alter genotpyes of a dataset by simulating null alleles.

FormatGenotypes: Internal function. Transform a file of genotypes into a format suitable for function MCMC

Author(s)

Arnaud Estoup, Gilles Guillot, Filipe Santos

www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/welcome.html

See also

www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/Geneland.html

References

[1] G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280, 2005.

[2] G. Guillot, Mortier, F., Estoup, A. Geneland : A program for landscape genetics. Molecular Ecology Notes, 5, 712-715, 2005.

[3] A. Coulon, Guillot G., Cosson J.-F., Angibault J.M.A., Aulagnier S. , Cargnelutti B., Galan M., Hewison A.J.M. Genetics structure is influenced by lansdcape features. Empirical evidence from a roe deer population. Molecular Ecology, 15 1669-1679, 2006.

[4] G. Guillot, F. Santos and A. Estoup. Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. To appear in Bioinformatics.


[Package Geneland version 3.1.2 Index]