{ "_id": "6aec69c22e87f76f20ad3abb", "Package": "bifrost", "Title": "Branch-Level Inference Framework for Recognizing Optimal Shifts\nin Traits", "Version": "0.2.3", "Authors@R": "c(\nperson(given = c(\"Jacob\", \"S.\"), family = \"Berv\", email = \"jacob.berv@gmail.com\", role = c(\"aut\", \"cre\", \"cph\", \"fnd\"), comment = c(ORCID = \"0000-0002-5962-0621\")),\nperson(given = \"Nathan\", family = \"Fox\", role = \"aut\", comment = c(ORCID = \"0000-0002-2816-9751\")),\nperson(given = c(\"Matt\", \"J.\"), family = \"Thorstensen\", role = \"aut\", comment = c(ORCID = \"0000-0002-7870-3369\")),\nperson(given = \"Henry\", family = \"Lloyd-Laney\", role = \"aut\", comment = c(ORCID = \"0000-0003-4650-8937\")),\nperson(given = c(\"Emily\", \"M.\"), family = \"Troyer\", role = \"aut\", comment = c(ORCID = \"0000-0001-7478-2306\")),\nperson(given = c(\"Rafael\", \"A.\"), family = \"Rivero-Vega\", role = \"aut\", comment = c(ORCID = \"0000-0001-5937-6377\")),\nperson(given = c(\"Stephen\", \"A.\"), family = \"Smith\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0003-2035-9531\")),\nperson(given = \"Matt\", family = \"Friedman\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0002-0114-7384\")),\nperson(given = c(\"David\", \"F.\"), family = \"Fouhey\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0001-5028-5161\")),\nperson(given = c(\"Brian\", \"C.\"), family = \"Weeks\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0003-2967-2970\")))", "Description": "Methods for detecting, visualizing, and evaluating\ncladogenic shifts in multivariate trait data on phylogenies.\nImplements penalized-likelihood multivariate generalized least\nsquares models and a greedy step-wise shift search for\nhigh-dimensional trait datasets and large trees via\nsearchOptimalConfiguration(). Provides tools for inspecting\nsearch trajectories, summarizing branch and lineage rates,\nanalyzing shift timing and magnitudes, estimating post-hoc\nregime covariance and integration, and running simulation-based\ncalibration and tuning. The search follows approaches developed\nin Smith et al. (2023) and Berv et al.\n(2024) . Methods build on\nmultivariate generalized least squares approaches described in\nClavel et al. (2019) and\nimplemented in the mvgls() function from the 'mvMORPH' package.\nDocumentation and worked examples are available at\n.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "URL": "https://jakeberv.com/bifrost/, https://github.com/jakeberv/bifrost", "BugReports": "https://github.com/jakeberv/bifrost/issues", "Config/Needs/website": "classInt, geomorph, ggplot2, htmltools, knitr,\npatchwork, pkgload, plotly, png, scatterplot3d, yaml", "Config/testthat/edition": "3", "Config/testthat/parallel": "false", "Config/build/copy-method": "copy", "Language": "en-US", "Config/roxygen2/version": "8.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-05 11:25:42 UTC", "User": "root" }, "Author": "Jacob S. Berv [aut, cre, cph, fnd] (ORCID:\n), Nathan Fox [aut]\n(ORCID: ), Matt J.\nThorstensen [aut] (ORCID:\n), Henry Lloyd-Laney\n[aut] (ORCID: ), Emily\nM. Troyer [aut] (ORCID:\n), Rafael A. Rivero-Vega\n[aut] (ORCID: ), Stephen\nA. Smith [aut, fnd] (ORCID:\n), Matt Friedman [aut,\nfnd] (ORCID: ), David F.\nFouhey [aut, fnd] (ORCID:\n), Brian C. Weeks [aut,\nfnd] (ORCID: )", "Maintainer": "Jacob S. Berv ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-11-05 07:02:11 UTC", "RemoteUrl": "https://github.com/cran/bifrost", "RemoteRef": "HEAD", "RemoteSha": "6748090c3cc7157a99d76b1d3fe355b22c75831d", "_user": "cran", "_type": "src", "_file": "bifrost_0.2.3.tar.gz", "_fileid": "https://r2.ropensci.org/dc44a270d909a23a6b869954a9d434c8353bcd6982bd87fca47a7aceaefca884", "_filesize": 1955566, "_sha256": "dc44a270d909a23a6b869954a9d434c8353bcd6982bd87fca47a7aceaefca884", "_expires": "2027-02-13T11:34:23.000Z", "_created": "2026-11-05T11:25:42.000Z", "_published": "2026-11-05T11:34:26.042Z", "_upstream": "https://github.com/cran/bifrost", "_status": "success", "_maintainer": { "name": "Jacob S. 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