Package: bifrost
Title: Branch-Level Inference Framework for Recognizing Optimal Shifts
        in Traits
Version: 0.2.2
Authors@R: c(
    person(given = c("Jacob", "S."), family = "Berv", email = "jacob.berv@gmail.com", role = c("aut", "cre", "cph", "fnd"), comment = c(ORCID = "0000-0002-5962-0621")),
    person(given = "Nathan", family = "Fox", role = "aut", comment = c(ORCID = "0000-0002-2816-9751")),
    person(given = c("Matt", "J."), family = "Thorstensen", role = "aut", comment = c(ORCID = "0000-0002-7870-3369")),
    person(given = "Henry", family = "Lloyd-Laney", role = "aut", comment = c(ORCID = "0000-0003-4650-8937")),
    person(given = c("Emily", "M."), family = "Troyer", role = "aut", comment = c(ORCID = "0000-0001-7478-2306")),
    person(given = c("Rafael", "A."), family = "Rivero-Vega", role = "aut", comment = c(ORCID = "0000-0001-5937-6377")),
    person(given = c("Stephen", "A."), family = "Smith", role = c("aut", "fnd"), comment = c(ORCID = "0000-0003-2035-9531")),
    person(given = "Matt", family = "Friedman", role = c("aut", "fnd"), comment = c(ORCID = "0000-0002-0114-7384")),
    person(given = c("David", "F."), family = "Fouhey", role = c("aut", "fnd"), comment = c(ORCID = "0000-0001-5028-5161")),
    person(given = c("Brian", "C."), family = "Weeks", role = c("aut", "fnd"), comment = c(ORCID = "0000-0003-2967-2970")))
Description: Methods for detecting, visualizing, and evaluating
        cladogenic shifts in multivariate trait data on phylogenies.
        Implements penalized-likelihood multivariate generalized least
        squares models and a greedy step-wise shift search for
        high-dimensional trait datasets and large trees via
        searchOptimalConfiguration(). Provides tools for inspecting
        search trajectories, summarizing branch and lineage rates,
        analyzing shift timing and magnitudes, estimating post-hoc
        regime covariance and integration, and running simulation-based
        calibration and tuning. The search follows 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 generalized least squares approaches described in
        Clavel et al. (2019) <doi:10.1093/sysbio/syy045> and
        implemented in the mvgls() function from the 'mvMORPH' package.
        Documentation and worked examples are available at
        <https://jakeberv.com/bifrost/>.
License: GPL (>= 2)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
URL: https://jakeberv.com/bifrost/, https://github.com/jakeberv/bifrost
BugReports: https://github.com/jakeberv/bifrost/issues
Depends: R (>= 4.2)
Imports: ape, cli (>= 3.6.0), corpcor, digest, future (>= 1.49.0),
        future.apply, progressr, RhpcBLASctl, phytools (>= 2.0-3),
        plotrix, RRphylo, grDevices, graphics, grid, jsonlite, stats,
        mvMORPH, viridis, txtplot
Suggests: ComplexHeatmap, RColorBrewer, circlize, evd, phylolm,
        rmarkdown, testthat (>= 3.0.0), univariateML, withr, spelling
Config/Needs/website: classInt, geomorph, ggplot2, htmltools, knitr,
        patchwork, pkgload, plotly, png, scatterplot3d, yaml
Config/testthat/edition: 3
Config/testthat/parallel: false
Language: en-US
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://jakeberv.r-universe.dev
Date/Publication: 2026-10-28 22:40:55 UTC
RemoteUrl: https://github.com/jakeberv/bifrost
RemoteRef: HEAD
RemoteSha: e28481cb3613312282305b731f0fc172bfc2bbd3
NeedsCompilation: no
Packaged: 2026-10-28 23:56:19 UTC; root
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>