Package: fibre
Title: Fast Evolutionary Trait Modelling on Phylogenies using Branch
        Regression Models
Version: 0.0.0.9000
Authors@R: 
    person(given = "Russell",
           family = "Dinnage",
           role = c("aut", "cre"),
           email = "r.dinnage@gmail.com",
           comment = c(ORCID = "0000-0003-0846-2819"))
Description: Implements Phylogenetic Branch Regression models which
        allow for flexible and versatile models of evolution along a
        phylogeny. The model can be used to detect shifts in rates of
        evolution along branches. The model uses a continuous and
        linear model structure and so can be easily combined with other
        non-phylogenetic statistical structures, as long as they are
        implemented using the R package INLA. One major uses of this
        are to condition on phylogeny in a standard regression between
        two traits, thus 'accounting' for phylogenetic structure in the
        response variable, similar to how pgls is used but allowing for
        a more flexible phylogenetic model. This also allows the
        phylogenetic model to be combined with the spatial models that
        INLA excels at (and with comparable flexibility to those
        spatial models).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: knitr, rmarkdown, bench, RPANDA, testthat (>= 3.0.0), INLA,
        tidytree, recipes, learnr, roxygen2, rgl, patchwork,
        rmarchingcubes, Rvcg, orientlib, Morpho, einsum, imager, movMF,
        furrr, ggridges, ggforce
VignetteBuilder: knitr
Imports: ape, dplyr, igraph, magrittr, fastmatch, MCMCglmm, phytools,
        phangorn, ivs, phyf (>= 0.0.0.9000), hardhat, rlang (>=
        0.4.11), stats, vctrs, zeallot, torch, glue, Matrix, generics,
        ggplot2, glmnet, purrr, skimr, cli, tidyr, methods, utils
Config/testthat/edition: 3
Depends: R (>= 2.10)
Remotes: rdinnager/phyf
URL: https://rdinnager.github.io/fibre/
Additional_repositories: https://inla.r-inla-download.org/R/stable
Config/pak/sysreqs: libabsl-dev libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libgdal-dev gdal-bin libgeos-dev libglpk-dev
        make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libproj-dev libsqlite3-dev libudunits2-dev
Repository: https://rdinnager.r-universe.dev
Date/Publication: 2024-12-10 13:23:58 UTC
RemoteUrl: https://github.com/rdinnager/fibre
RemoteRef: HEAD
RemoteSha: 069e04c036172e1a6a0c39472bd499a33d231a4f
NeedsCompilation: no
Packaged: 2026-06-09 05:53:04 UTC; root
Author: Russell Dinnage [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0846-2819>)
Maintainer: Russell Dinnage <r.dinnage@gmail.com>