BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering
Dublin Core
Title
BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering
Subject
statistical phylogeography, biogeography, population genetics, Bayesian computation, R.
Description
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
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
Creator
Ioanna Manolopoulou
Source
https://www.jstatsoft.org/article/view/v092i05
Publisher
University College London
Date
February 2020
Contributor
Fajar Bagus W
Format
PDF
Language
Inggris
Type
Text
Files
Collection
Citation
Ioanna Manolopoulou, “BPEC: An R Package for Bayesian Phylogeographic and Ecological Clustering,” Repository Horizon University Indonesia, accessed April 4, 2025, https://repository.horizon.ac.id/items/show/8109.