phyr: Model Based Phylogenetic Analysis (original) (raw)

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:

1.1.3

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