{"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/fast-likelihood-evaluation-for-multivariate","title":"Fast likelihood evaluation for multivariate phylogenetic comparative methods: the PCMBase R package","arxiv_id":"1809.09014","date":"2018-09-24","proceeding":null,"authors":["Venelin Mitov","Krzysztof Bartoszek","Georgios Asimomitis","Tanja Stadler"],"abstract":"We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offers the user the functionality to very easily implement a wide range of models where the transition along a branch is multivariate normal. We demonstrate the package's possibilities on the now standard, multitrait Ornstein-Uhlenbeck process as well as the novel multivariate punctuated equilibrium model. The package can handle trees of various types (e.g. ultrametric, nonultrametric, polytomies, e.t.c.), as well as measurement error, missing measurements or non-existing traits for some of the species in the tree.","url_abs":"http://arxiv.org/abs/1809.09014v1","url_pdf":"http://arxiv.org/pdf/1809.09014v1.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":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"fast-likelihood-evaluation-for-multivariate","repo_url":"https://github.com/venelin/PCMBaseCpp","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"fast-likelihood-evaluation-for-multivariate","repo_url":"https://github.com/venelin/PCMFit","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}