Model Based Phylogenetic Analysis R package phyr version 1.1.3 CRAN Task View: MixedModels (https://CRAN.R-project.org/view=MixedModels) 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>). Software Depends: R (>= 3.1) Imports: stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4, nloptr, gridExtra, mvtnorm, latticeExtra, tidyr LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, pez, knitr, rmarkdown, covr, picante, rbenchmark, INLA, MCMCglmm, logistf, phylolm, ggplot2, ggridges, DHARMa, rr2, future.apply Daijiang Li <daijianglee@gmail.com> Comprehensive R Archive Network (CRAN) 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>) GPL-3 2025-11-11 application/tgz https://CRAN.R-project.org/package=phyr doi:10.32614/CRAN.package.phyr