phylodyn: an R package for phylodynamic simulation and inference

摘要: We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo-based methods and integrated nested Laplace approximation-based approach inference that have been developed in recent years. Genealogical data describe the timed ancestral relationships individuals sampled from a interest. Here, are assumed to be at same point time (isochronous sampling) or different points (heterochronous sampling); addition, sampling events can modeled with preferential sampling, which means intensity allowed depend trajectory. assume coalescent sequentially processes as generative models include simulation functions useful testing our phylodynamics via studies. compare performance outputs various implemented phylodyn outline their strengths weaknesses. available this https URL.