Bayesian Phylogeographic and Ecological Clustering


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Documentation for package ‘BPEC’ version 1.3.1

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bpec Bayesian Phylogeographic and Ecological Clustering (BPEC)
bpec.contourPlot Plot contours of inferred clusters on geographical map
bpec.covariatesPlot Plot posterior marginal distribution of each covariate for the inferred clusters
bpec.geoTree Phylogeographic GoogleEarth plot
bpec.loadCoords Load location data
bpec.loadSeq Load sequence data
bpec.mcmc Markov chain Monte Carlo sampler for BPEC
bpec.treePlot Treeplot indicating cluster membership
CladeBrownFrogsCoordsLocs Coordinates and haplotypes for the Brown Frog dataset
CladeBrownFrogsRawSeqs Sequences for the Brown Frog dataset
input Load location data
input.bpec Load location data
MacrocnemisCoordsLocs Coordinates and haplotypes for the R.macrocnemis Brown Frog dataset
MacrocnemisCoordsLocsMini Coordinates and haplotypes for the R.macrocnemis Brown Frog dataset
MacrocnemisRawSeqs Sequences for the R.macrocnemis Brown Frog dataset
mean.bpec Bayesian Phylogeographic and Ecological Clustering (BPEC)
output.clust Load location data
output.clust.bpec Load location data
output.mcmc Load location data
output.mcmc.bpec Load location data
output.tree Load location data
output.tree.bpec Load location data
plot.bpec Bayesian Phylogeographic and Ecological Clustering (BPEC)
preproc Load location data
preproc.bpec Load location data
print.bpec Bayesian Phylogeographic and Ecological Clustering (BPEC)
summary.bpec Bayesian Phylogeographic and Ecological Clustering (BPEC)
TransalpinaCoordsLocs Coordinates and haplotypes for the burnet moth dataset.
TransalpinaRawSeqs Sequences for the burnet moth dataset.