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 (<https://www.r-inla.org>).

Version: 1.1.0
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
Published: 2020-12-18
DOI: 10.32614/CRAN.package.phyr
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 gmail.com>
BugReports: https://github.com/daijiang/phyr/issues
License: GPL-3
URL: https://daijiang.github.io/phyr/, https://github.com/daijiang/phyr/
NeedsCompilation: yes
Additional_repositories: https://inla.r-inla-download.org/R/stable/
Materials: README NEWS
In views: MixedModels
CRAN checks: phyr results

Documentation:

Reference manual: phyr.pdf
Vignettes: Performance benchmark
Usage of pglmm()
Plot random terms of communityPGLMM

Downloads:

Package source: phyr_1.1.0.tar.gz
Windows binaries: r-devel: phyr_1.1.0.zip, r-release: phyr_1.1.0.zip, r-oldrel: phyr_1.1.0.zip
macOS binaries: r-release (arm64): phyr_1.1.0.tgz, r-oldrel (arm64): phyr_1.1.0.tgz, r-release (x86_64): phyr_1.1.0.tgz, r-oldrel (x86_64): phyr_1.1.0.tgz
Old sources: phyr archive

Reverse dependencies:

Reverse imports: rr2
Reverse suggests: phylosem
Reverse enhances: DHARMa

Linking:

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