Package: phyr
Type: Package
Title: Model Based Phylogenetic Analysis
Version: 1.2.1
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,
        reformulas, nloptr, gridExtra, mvtnorm, latticeExtra, tidyr
Roxygen: list(markdown = TRUE)
LinkingTo: Rcpp, RcppArmadillo, nloptr
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
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev libjpeg-dev libpng-dev
Repository: https://daijiang.r-universe.dev
Date/Publication: 2026-05-18 20:05:08 UTC
RemoteUrl: https://github.com/daijiang/phyr
RemoteRef: HEAD
RemoteSha: b34dc3a3674c852f535a33b384dedcc0cff4447e
NeedsCompilation: yes
Packaged: 2026-06-17 07:03:24 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>