  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.
