Package: phyr
Type: Package
Title: Model Based Phylogenetic Analysis
Version: 1.1.3
Authors@R: c(
    person("Anthony", "Ives", , "arives@wisc.edu", role = c("aut")),
    person("Russell", "Dinnage", , "r.dinnage@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-0846-2819")),
    person(c("Lucas", "A."), "Nell", , "lucas@lucasnell.com", role = c("aut"), comment = c(ORCID = "0000-0003-3209-0517")),
    person("Matthew", "Helmus", , "mrhelmus@temple.edu", role = c("aut")),
    person("Daijiang", "Li", , "daijianglee@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0925-3421")))
Description: A collection of functions to do model-based phylogenetic
        analysis. It includes functions to calculate community
        phylogenetic diversity, to estimate correlations among
        functional traits while accounting for phylogenetic
        relationships, and to fit phylogenetic generalized linear mixed
        models. The Bayesian phylogenetic generalized linear mixed
        models are fitted with the 'INLA' package
        (<https://www.r-inla.org>).
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1)
Imports: stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4,
        nloptr, gridExtra, mvtnorm, latticeExtra, tidyr
RoxygenNote: 7.3.3
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, pez, knitr, rmarkdown, covr, picante, rbenchmark,
        INLA, MCMCglmm, logistf, phylolm, ggplot2, ggridges, DHARMa,
        rr2, future.apply
VignetteBuilder: knitr
URL: https://daijiang.github.io/phyr/,
        https://github.com/daijiang/phyr/
BugReports: https://github.com/daijiang/phyr/issues
Additional_repositories: https://inla.r-inla-download.org/R/stable/
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2026-10-28 10:18:10 UTC; root
Author: Anthony Ives [aut], Russell Dinnage [aut] (ORCID:
        <https://orcid.org/0000-0003-0846-2819>), Lucas A. Nell [aut]
        (ORCID: <https://orcid.org/0000-0003-3209-0517>), Matthew
        Helmus [aut], Daijiang Li [aut, cre] (ORCID:
        <https://orcid.org/0000-0002-0925-3421>)
Maintainer: Daijiang Li <daijianglee@gmail.com>
Repository: https://cran.r-universe.dev
Date/Publication: 2025-11-11 08:30:02 UTC
RemoteUrl: https://github.com/cran/phyr
RemoteRef: HEAD
RemoteSha: 5ffe68357908d7cc3f508b867467049cef640d8e