phylodyn: an R package for phylodynamic simulation and inference

We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo‐based methods and an i...

Full description

Saved in:
Bibliographic Details
Published inMolecular ecology resources Vol. 17; no. 1; pp. 96 - 100
Main Authors Karcher, Michael D., Palacios, Julia A., Lan, Shiwei, Minin, Vladimir N.
Format Journal Article
LanguageEnglish
Published England Wiley Subscription Services, Inc 01.01.2017
Subjects
Bayesian analysis
Biostatistics - methods
Computational Biology - methods
Computer Simulation
evolutionary theory
Genetics, Population - methods
Inla
Markov analysis
Mcmc
Monte Carlo simulation
Population Dynamics
population genetics – theoretical
Software
Inla
Mcmc
population genetics - theoretical
evolutionary theory
population dynamics
Online AccessGet full text

Cover

More Information
Summary:We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo‐based methods and an integrated nested Laplace approximation‐based approach for phylodynamic inference that have been developed in recent years. Genealogical data describe the timed ancestral relationships of individuals sampled from a population of interest. Here, individuals are assumed to be sampled at the same point in time (isochronous sampling) or at different points in time (heterochronous sampling); in addition, sampling events can be modelled with preferential sampling, which means that the intensity of sampling events is allowed to depend on the effective population size trajectory. We assume the coalescent and the sequentially Markov coalescent processes as generative models of genealogies. We include several coalescent simulation functions that are useful for testing our phylodynamics methods via simulation studies. We compare the performance and outputs of various methods implemented in phylodyn and outline their strengths and weaknesses. r package phylodyn is available at https://github.com/mdkarcher/phylodyn.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The first two authors contributed equally to this paper.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.12630