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: 2025-11-10 22:46:40 UTC; dli
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: CRAN
Date/Publication: 2025-11-11 08:30:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-04-19 03:33:32 UTC; windows
Archs: x64
