{"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/estimating-effective-population-size-changes","title":"Estimating effective population size changes from preferentially sampled genetic sequences","arxiv_id":"1903.11797","date":"2019-03-28","proceeding":null,"authors":[],"abstract":"Coalescent theory combined with statistical modeling allows us to estimate\neffective population size fluctuations from molecular sequences of individuals\nsampled from a population of interest. When sequences are sampled serially\nthrough time and the distribution of the sampling times depends on the\neffective population size, explicit statistical modeling of sampling times\nimproves population size estimation. Previous work assumed that the genealogy\nrelating sampled sequences is known and modeled sampling times as an\ninhomogeneous Poisson process with log-intensity equal to a linear function of\nthe log-transformed effective population size. We improve this approach in two\nways. First, we extend the method to allow for joint Bayesian estimation of the\ngenealogy, effective population size trajectory, and other model parameters.\nNext, we improve the sampling time model by incorporating additional sources of\ninformation in the form of time-varying covariates. We validate our new\nmodeling framework using a simulation study and apply our new methodology to\nanalyses of population dynamics of seasonal influenza and to the recent Ebola\nvirus outbreak in West Africa.","url_abs":"http://arxiv.org/abs/1903.11797v1","url_pdf":"http://arxiv.org/pdf/1903.11797v1.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":"estimating-effective-population-size-changes","repo_url":"https://github.com/mdkarcher/BEAST-XML","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null},{"paper_slug":"estimating-effective-population-size-changes","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}