{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/phylodyn-an-r-package-for-phylodynamic","title":"phylodyn: an R package for phylodynamic simulation and inference","arxiv_id":"1610.05817","date":"2016-10-18","proceeding":null,"authors":[],"abstract":"We introduce phylodyn, an R package for phylodynamic analysis based on gene\ngenealogies. The package main functionality is Bayesian nonparametric\nestimation of effective population size fluctuations over time. Our\nimplementation includes several Markov chain Monte Carlo-based methods and an\nintegrated nested Laplace approximation-based approach for phylodynamic\ninference that have been developed in recent years. Genealogical data describe\nthe timed ancestral relationships of individuals sampled from a population of\ninterest. Here, individuals are assumed to be sampled at the same point in time\n(isochronous sampling) or at different points in time (heterochronous\nsampling); in addition, sampling events can be modeled with preferential\nsampling, which means that the intensity of sampling events is allowed to\ndepend on the effective population size trajectory. We assume the coalescent\nand the sequentially Markov coalescent processes as generative models of\ngenealogies. We include several coalescent simulation functions that are useful\nfor testing our phylodynamics methods via simulation studies. We compare the\nperformance and outputs of various methods implemented in phylodyn and outline\ntheir strengths and weaknesses. R package phylodyn is available at\nhttps://github.com/mdkarcher/phylodyn.","url_abs":"http://arxiv.org/abs/1610.05817v1","url_pdf":"http://arxiv.org/pdf/1610.05817v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"phylodyn-an-r-package-for-phylodynamic","repo_url":"https://github.com/mdkarcher/phylodyn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}