  BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering
which allows geographical, environmental and phenotypic measurements to be
combined with DNA sequences in order to reveal clustered structure resulting
from migration events. DNA sequences are modelled using a collapsed version of
a simplified coalescent model projected onto haplotype trees, which
subsequently give rise to constrained clusterings as migrations occur. Within
each cluster, a multivariate Gaussian distribution of the covariates
(geographical, environmental, phenotypic) is used. Inference follows tailored
Reversible Jump Markov chain Monte Carlo sampling so that the number of
clusters (i.e., migrations) does not need to be pre-specified. A number of
output plots and visualizations are provided which reflect the posterior
distribution of the parameters of interest. BPEC also includes functions that
create output files which can be loaded into Google Earth. The package commands
are illustrated through an example dataset of the polytypic Near Eastern brown
frog Rana macrocnemis analysed using BPEC.
