# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "bifrost" in publications use:' type: software license: GPL-2.0-or-later title: 'bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits' version: 0.1.4 identifiers: - type: doi value: 10.32614/CRAN.package.bifrost abstract: 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) and Berv et al. (2024) . Methods build on multivariate GLS approaches described in Clavel et al. (2019) and implemented in the mvgls() function from the 'mvMORPH' package. Documentation and vignettes are available at , including worked examples for the jaw-shape dataset. authors: - family-names: Berv given-names: Jacob S. email: jacob.berv@gmail.com orcid: https://orcid.org/0000-0002-5962-0621 - family-names: Fox given-names: Nathan orcid: https://orcid.org/0000-0002-2816-9751 - family-names: Thorstensen given-names: Matt J. orcid: https://orcid.org/0000-0002-7870-3369 - family-names: Lloyd-Laney given-names: Henry orcid: https://orcid.org/0000-0003-4650-8937 - family-names: Troyer given-names: Emily M. orcid: https://orcid.org/0000-0001-7478-2306 - family-names: Rivero-Vega given-names: Rafael A. orcid: https://orcid.org/0000-0001-5937-6377 - family-names: Smith given-names: Stephen A. orcid: https://orcid.org/0000-0003-2035-9531 - family-names: Friedman given-names: Matt orcid: https://orcid.org/0000-0002-0114-7384 - family-names: Fouhey given-names: David F. orcid: https://orcid.org/0000-0001-5028-5161 - family-names: Weeks given-names: Brian C. orcid: https://orcid.org/0000-0003-2967-2970 preferred-citation: type: article title: Rates of passerine body plan evolution in time and space authors: - family-names: Berv given-names: Jacob S. email: jacob.berv@gmail.com orcid: https://orcid.org/0000-0002-5962-0621 - family-names: Probst given-names: Charlotte M. - family-names: Claramunt given-names: Santiago - family-names: Shipley given-names: J. Ryan - family-names: Friedman given-names: Matt orcid: https://orcid.org/0000-0002-0114-7384 - family-names: Smith given-names: Stephen A. orcid: https://orcid.org/0000-0003-2035-9531 - family-names: Fouhey given-names: David F. orcid: https://orcid.org/0000-0001-5028-5161 - family-names: Weeks given-names: Brian C. orcid: https://orcid.org/0000-0003-2967-2970 year: '2026' journal: Nature Ecology & Evolution notes: In press. repository: https://jakeberv.r-universe.dev repository-code: https://github.com/jakeberv/bifrost commit: 2c3477350657d8a3a4ab50d2bd9ceace4a82ebe2 url: https://jakeberv.com/bifrost/ date-released: '2026-06-04' contact: - family-names: Berv given-names: Jacob S. email: jacob.berv@gmail.com orcid: https://orcid.org/0000-0002-5962-0621 references: - type: article title: 'bifrost: an R package for scalable inference of phylogenetic shifts in multivariate evolutionary dynamics' authors: - family-names: Berv given-names: Jacob S. - family-names: Fox given-names: Nathan - family-names: Thorstensen given-names: Matt J. - family-names: Lloyd-Laney given-names: Henry - family-names: Troyer given-names: Emily M. - family-names: Rivero-Vega given-names: Rafael A. - family-names: Smith given-names: Stephen A. - family-names: Friedman given-names: Matt - family-names: Fouhey given-names: David F. - family-names: Weeks given-names: Brian C. year: '2026' journal: bioRxiv doi: 10.64898/2026.04.12.718036 notes: Preprint version 1. - type: manual title: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits authors: - family-names: Berv given-names: Jacob S. - family-names: Fox given-names: Nathan - family-names: Thorstensen given-names: Matt J. - family-names: Lloyd-Laney given-names: Henry - family-names: Troyer given-names: Emily M. - family-names: Rivero-Vega given-names: Rafael A. - family-names: Smith given-names: Stephen A. - family-names: Friedman given-names: Matt - family-names: Fouhey given-names: David F. - family-names: Weeks given-names: Brian C. year: '2026' notes: R package version 0.1.4 url: https://CRAN.R-project.org/package=bifrost - type: article title: 'mvmorph: an R package for fitting multivariate evolutionary models to morphometric data' authors: - family-names: Clavel given-names: Julien - family-names: Escarguel given-names: Gilles - family-names: Merceron given-names: Gildas year: '2015' journal: Methods in Ecology and Evolution volume: '6' issue: '11' doi: 10.1111/2041-210X.12420 start: 1311-1319 - type: article title: A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution authors: - family-names: Clavel given-names: Julien - family-names: Aristide given-names: Leandro - family-names: Morlon given-names: Hélène year: '2019' journal: Systematic Biology volume: '68' issue: '1' doi: 10.1093/sysbio/syy045 start: 93-116