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bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits
Methods for detecting and visualizing cladogenic shifts in multivariate trait data on phylogenies. Implements penalized-likelihood multivariate generalized least squares models, enabling analyses of high-dimensional trait datasets and large trees via searchOptimalConfiguration(). Includes a greedy step-wise shift-search algorithm following approaches developed in Smith et al. (2023) <doi:10.1111/nph.19099> and Berv et al. (2024) <doi:10.1126/sciadv.adp0114>. Methods build on multivariate GLS approaches described in Clavel et al. (2019) <doi:10.1093/sysbio/syy045> and implemented in the mvgls() function from the 'mvMORPH' package. Documentation and vignettes are available at <https://jakeberv.com/bifrost/>, including worked examples for the jaw-shape dataset.
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| Author | Jacob S. Berv [aut, cre, cph, fnd] (ORCID: <https://orcid.org/0000-0002-5962-0621>), Nathan Fox [aut] (ORCID: <https://orcid.org/0000-0002-2816-9751>), Matt J. Thorstensen [aut] (ORCID: <https://orcid.org/0000-0002-7870-3369>), Henry Lloyd-Laney [aut] (ORCID: <https://orcid.org/0000-0003-4650-8937>), Emily M. Troyer [aut] (ORCID: <https://orcid.org/0000-0001-7478-2306>), Rafael A. Rivero-Vega [aut] (ORCID: <https://orcid.org/0000-0001-5937-6377>), Stephen A. Smith [aut, fnd] (ORCID: <https://orcid.org/0000-0003-2035-9531>), Matt Friedman [aut, fnd] (ORCID: <https://orcid.org/0000-0002-0114-7384>), David F. Fouhey [aut, fnd] (ORCID: <https://orcid.org/0000-0001-5028-5161>), Brian C. Weeks [aut, fnd] (ORCID: <https://orcid.org/0000-0003-2967-2970>) |
| Maintainer | Jacob S. Berv <jacob.berv@gmail.com> |
| License | GPL (>= 2) |
| Version | 0.1.4 |
| URL | https://jakeberv.com/bifrost/ https://github.com/jakeberv/bifrost |
| Package repository | View on CRAN |
| Installation |
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