phylodyn: an R package for phylodynamic simulation

10 We introduce phylodyn, an R package for phylodynamic analysis based on gene 11 genealogies. The package main functionality is Bayesian nonparametric estimation of 12 effective population size fluctuations over time. Our implementation includes sev13 eral Markov chain Monte Carlo-based methods and an integrated nested Laplace 14 approximation-based approach for phylodynamic inference that have been developed 15 in recent years. Genealogical data describe the timed ancestral relationships of indi16 viduals sampled from a population of interest. Here, individuals are assumed to be 17 sampled at the same point in time (isochronous sampling) or at different points in 18 time (heterochronous sampling); in addition, sampling events can be modeled with 19 preferential sampling, which means that the intensity of sampling events is allowed 20 to depend on the effective population size trajectory. We assume the coalescent and 21 the sequentially Markov coalescent processes as generative models of genealogies. We 22 ∗The first two authors contributed equally to this paper. 1 include several coalescent simulation functions that are useful for testing our phylody23 namics methods via simulation studies. We compare the performance and outputs of 24 various methods implemented in phylodyn and outline their strengths and weaknesses. 25 R package phylodyn is available at https://github.com/mdkarcher/phylodyn. 26