Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Ioanna Manolopoulou, Axel Hille, Brent Emerson
Title: BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering
Abstract: BPEC is an R package for Bayesian phylogeographic and ecological clustering which allows geographical, environmental and phenotypic measurements to be combined with deoxyribonucleic acid (DNA) sequences in order to reveal geographic structuring of DNA sequence clusters consistent with 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 analyzed using BPEC.

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Paper: BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering     Download PDF (Downloads: 287)
Supplements:
BPEC_1.3.1.tar.gz: R source package Download (Downloads: 21; 4MB)
v92i05.R: R replication code Download (Downloads: 25; 4KB)
coordsLocsFile.txt: Replication data Download (Downloads: 25; 2KB)
haplotypes.nex: Replication data Download (Downloads: 30; 20KB)

DOI: 10.18637/jss.v092.i05

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.