Package: bifrost
Title: Branch-Level Inference Framework for Recognizing Optimal Shifts
        in Traits
Version: 0.1.4
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 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.
License: GPL (>= 2)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://jakeberv.com/bifrost/, https://github.com/jakeberv/bifrost
BugReports: https://github.com/jakeberv/bifrost/issues
Depends: R (>= 4.1)
Imports: ape, future, future.apply, progressr, phytools, grDevices,
        stats, mvMORPH, viridis, txtplot
Suggests: RColorBrewer, boot, classInt, evd, fitdistrplus, geomorph,
        knitr, palaeoverse, parallel, patchwork, pbmcapply, phylolm,
        plotly, png, readxl, rmarkdown, scales, scatterplot3d, testthat
        (>= 3.0.0), univariateML, spelling, htmltools
Config/testthat/edition: 3
Config/testthat/parallel: false
Language: en-US
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://jakeberv.r-universe.dev
Date/Publication: 2026-07-02 18:51:09 UTC
RemoteUrl: https://github.com/jakeberv/bifrost
RemoteRef: HEAD
RemoteSha: e9130e7b99fbf3732beb20512afdd7ba7b7baaf2
NeedsCompilation: no
Packaged: 2026-07-02 20:44:32 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>