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 |
| Author: | Anthony Ives [aut],
Russell Dinnage 
[aut],
Lucas A. Nell
[aut],
Matthew Helmus [aut],
Daijiang Li [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 |
| 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 enhances: | DHARMa |
Linking:
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