2016/10/18 by Michael D. Karcher, Karcher, Michael D., Julia A. Palacios +5 · 2 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Bayesian Methods and Mixture Models #Computation (stat.CO) #FOS: Biological sciences #FOS: Computer and information sciences #Genetic Mapping and Diversity in Plants and Animals #Genetic diversity and population structure #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.1610.05817
openalex publication_date 2016/10/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.