BPEC: Bayesian Phylogeographic and Ecological Clustering

Share:

Model-based clustering for phylogeographic data comprising mtDNA sequences and geographical locations along with optional environmental characteristics, aiming to identify migration events that led to homogeneous population clusters.

Author
Ioanna Manolopoulou, Axel Hille
Date of publication
2016-04-06 09:49:06
Maintainer
Ioanna Manolopoulou <ioanna.manolopoulou@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

Man pages

BPEC.ContourPlot
Plot contours of inferred clusters on geographical map
BPEC.CovariatesPlot
Plot posterior marginal distribution of each covariate for...
BPEC.GeoTree
Phylogeographic GoogleEarth plot
BPEC.MCMC
Markov chain Monte Carlo sampler for BPEC
BPEC-package
Bayesian Phylogeographic and Ecological Clustering (BPEC)
BPEC.TreePlot
Treeplot indicating cluster membership
CladeBrownFrogsCoordsLocs
Coordinates and haplotypes for the Brown Frog dataset
CladeBrownFrogsRawSeqs
Sequences for the Brown Frog dataset
MacrocnemisCoordsLocs
Coordinates and haplotypes for the R.macrocnemis Brown Frog...
MacrocnemisRawSeqs
Sequences for the R.macrocnemis Brown Frog dataset
TransalpinaCoordsLocs
Coordinates and haplotypes for the burnet moth dataset.
TransalpinaRawSeqs
Sequences for the burnet moth dataset.

Files in this package

BPEC
BPEC/src
BPEC/src/Rinterface.h
BPEC/src/matrices.h
BPEC/src/randomnumbers.c
BPEC/src/treelikelifunctions.h
BPEC/src/randomnumbers.h
BPEC/src/hashingfunctions.c
BPEC/src/loopfunctions.c
BPEC/src/hashingfunctions.h
BPEC/src/BPEC.c
BPEC/src/loopfunctions.h
BPEC/src/matrices.c
BPEC/src/treelikelifunctions.c
BPEC/src/cexcept.h
BPEC/NAMESPACE
BPEC/data
BPEC/data/TransalpinaRawSeqs.RData
BPEC/data/TransalpinaCoordsLocs.RData
BPEC/data/MacrocnemisCoordsLocs.RData
BPEC/data/MacrocnemisRawSeqs.RData
BPEC/data/CladeBrownFrogsCoordsLocs.RData
BPEC/data/CladeBrownFrogsRawSeqs.RData
BPEC/R
BPEC/R/BPEC.TreePlot.R
BPEC/R/BPEC.ContourPlot.R
BPEC/R/BPEC.TreeEdges.R
BPEC/R/BPEC.Phylo2GE.R
BPEC/R/BPEC.CovariatesPlot.R
BPEC/R/BPEC.MCMC.R
BPEC/R/BPEC-internal.R
BPEC/R/BPEC.functions.R
BPEC/MD5
BPEC/DESCRIPTION
BPEC/man
BPEC/man/TransalpinaRawSeqs.Rd
BPEC/man/MacrocnemisRawSeqs.Rd
BPEC/man/BPEC.TreePlot.Rd
BPEC/man/BPEC.MCMC.Rd
BPEC/man/BPEC-package.Rd
BPEC/man/BPEC.GeoTree.Rd
BPEC/man/TransalpinaCoordsLocs.Rd
BPEC/man/BPEC.ContourPlot.Rd
BPEC/man/BPEC.CovariatesPlot.Rd
BPEC/man/CladeBrownFrogsRawSeqs.Rd
BPEC/man/MacrocnemisCoordsLocs.Rd
BPEC/man/CladeBrownFrogsCoordsLocs.Rd