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
| Package: |
| Geneland |
| Type: |
| Package |
| License: |
| GPL |