BPEC: Bayesian Phylogeographic and Ecological Clustering
Version 1.0

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.

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AuthorIoanna Manolopoulou, Axel Hille
Date of publication2016-04-06 09:49:06
MaintainerIoanna Manolopoulou <ioanna.manolopoulou@gmail.com>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BPEC")

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.

Functions

BPEC-package Man page
BPEC.ContourPlot Man page Source code
BPEC.CovariatesPlot Man page Source code
BPEC.GeoTree Man page Source code
BPEC.MCMC Man page Source code
BPEC.Phylo2GE Source code
BPEC.TreeEdges Source code
BPEC.TreePlot Man page Source code
BPEC.circles Source code
CladeBrownFrogsCoordsLocs Man page
CladeBrownFrogsRawSeqs Man page
MacrocnemisCoordsLocs Man page
MacrocnemisRawSeqs Man page
TransalpinaCoordsLocs Man page
TransalpinaRawSeqs Man page
explode Source code
mynei Source code
network.to.newick Source code
network.to.tree Source code
obtain.newick Source code
postorder.traversal Source code

Files

src
src/Rinterface.h
src/matrices.h
src/randomnumbers.c
src/treelikelifunctions.h
src/randomnumbers.h
src/hashingfunctions.c
src/loopfunctions.c
src/hashingfunctions.h
src/BPEC.c
src/loopfunctions.h
src/matrices.c
src/treelikelifunctions.c
src/cexcept.h
NAMESPACE
data
data/TransalpinaRawSeqs.RData
data/TransalpinaCoordsLocs.RData
data/MacrocnemisCoordsLocs.RData
data/MacrocnemisRawSeqs.RData
data/CladeBrownFrogsCoordsLocs.RData
data/CladeBrownFrogsRawSeqs.RData
R
R/BPEC.TreePlot.R
R/BPEC.ContourPlot.R
R/BPEC.TreeEdges.R
R/BPEC.Phylo2GE.R
R/BPEC.CovariatesPlot.R
R/BPEC.MCMC.R
R/BPEC-internal.R
R/BPEC.functions.R
MD5
DESCRIPTION
man
man/TransalpinaRawSeqs.Rd
man/MacrocnemisRawSeqs.Rd
man/BPEC.TreePlot.Rd
man/BPEC.MCMC.Rd
man/BPEC-package.Rd
man/BPEC.GeoTree.Rd
man/TransalpinaCoordsLocs.Rd
man/BPEC.ContourPlot.Rd
man/BPEC.CovariatesPlot.Rd
man/CladeBrownFrogsRawSeqs.Rd
man/MacrocnemisCoordsLocs.Rd
man/CladeBrownFrogsCoordsLocs.Rd
BPEC documentation built on May 19, 2017, 9:58 p.m.