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


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Reference manual

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install.packages("phyr")

1.0.2 by Daijiang Li, 4 days ago


https://github.com/daijiang/phyr/


Report a bug at https://github.com/daijiang/phyr/issues


Browse source code at https://github.com/cran/phyr


Authors: Anthony Ives [aut] , Russell Dinnage [aut] , Lucas A. Nell [aut] , Matthew Helmus [aut] , Daijiang Li [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4, nloptr, gridExtra, mvtnorm, latticeExtra

Suggests testthat, pez, tidyr, knitr, rmarkdown, covr, picante, rbenchmark, INLA, MCMCglmm, logistf, phylolm

Linking to Rcpp, RcppArmadillo


See at CRAN