phylodyn: an R package for phylodynamic simulation and inference

TL;DR

phylodyn is an R package that provides Bayesian nonparametric methods for inferring effective population size changes over time from genealogical data, supporting various sampling schemes and simulation functions.

Contribution

The paper introduces phylodyn, a comprehensive R package implementing recent Bayesian and Laplace approximation methods for phylodynamic inference from gene genealogies.

Findings

Includes multiple MCMC and Laplace approximation methods.

Supports isochronous and heterochronous sampling.

Provides simulation tools for testing phylodynamic methods.

Abstract

We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package 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 modeled 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.