phyr: Model Based Phylogenetic Analysis

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 (<>).

Version: 1.0.2
Depends: R (≥ 3.1)
Imports: stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4, nloptr, gridExtra, mvtnorm, latticeExtra
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, pez, tidyr, knitr, rmarkdown, covr, picante, rbenchmark, INLA, MCMCglmm, logistf, phylolm
Published: 2019-11-13
Author: Anthony Ives [aut], Russell Dinnage ORCID iD [aut], Lucas A. Nell ORCID iD [aut], Matthew Helmus [aut], Daijiang Li ORCID iD [aut, cre]
Maintainer: Daijiang Li <daijianglee at>
License: GPL-3
NeedsCompilation: yes
Materials: README
CRAN checks: phyr results


Reference manual: phyr.pdf
Vignettes: Performance benchmark
Usage of pglmm()
Plot random terms of communityPGLMM
Package source: phyr_1.0.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: phyr_1.0.2.tgz, r-oldrel: phyr_1.0.2.tgz
Old sources: phyr archive


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