Geneland-package {Geneland} | R Documentation |
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.
The overall population is viewed as a co-existence of HWLE sub-populations . The sub-populations are supposed to be spatially organised through the so-called colored Poisson-Voronoi tessellation. The particular case of a non-spatial model is also handled. Allele frequencies are assumed to be drawn from the correlated frequency model described in (Falush et al. Genetics 2003) but the particular case of uncorrelated allele frequencies, described by Pritchard et al. (Genetics 2000), is also handled.
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
Arnaud Estoup, Gilles Guillot, Filipe Santos
http://folk.uio.no/gillesg/Geneland/Geneland.html