{"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/a-diffusion-based-approach-for-simulating","title":"A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics","arxiv_id":"2402.00246","date":"2024-02-01","proceeding":null,"authors":["Albert C. Soewongsono","Michael J. Landis"],"abstract":"We establish a general framework using a diffusion approximation to simulate forward-in-time state counts or frequencies for cladogenetic state-dependent speciation-extinction (ClaSSE) models. We apply the framework to various two- and three-region geographic-state speciation-extinction (GeoSSE) models. We show that the species range state dynamics simulated under tree-based and diffusion-based processes are comparable. We derive a method to infer rate parameters that are compatible with given observed stationary state frequencies and obtain an analytical result to compute stationary state frequencies for a given set of rate parameters. We also describe a procedure to find the time to reach the stationary frequencies of a ClaSSE model using our diffusion-based approach, which we demonstrate using a worked example for a two-region GeoSSE model. Finally, we discuss how the diffusion framework can be applied to formalize relationships between evolutionary patterns and processes under state-dependent diversification scenarios.","url_abs":"https://arxiv.org/abs/2402.00246v2","url_pdf":"https://arxiv.org/pdf/2402.00246v2.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":"a-diffusion-based-approach-for-simulating","repo_url":"https://github.com/alberts2/diffusion_geosse","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[{"method_slug":"diffusion","method_name":"Diffusion"},{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}