Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) .

This is the development version of the geiger package for manipulating phylogenetic comparative data and fitting macroevolutionary models. The package can be downloaded from CRAN

install.packages("geiger")

or installed directly from github with the devtools package

install.packages("devtools")
install_github("mwpennell/geiger-v2")

Major features

geiger is a (growing) collection of methods developed over the years by many researchers. Here is a a non-comprehensive list of methods:

• Fit continuous models of evolution (BM, OU, EB, Pagel models, etc.)
• Fit discrete models of evolution (Mk and variants)
• Identify shifts in the rate of continuous trait evolution
• Fit continuous trait models to unresolved data using ABC
• Use fossil information to improve macroevolutionary inference
• Identify shifts in the rate of diversification
• Posterior predictive model assessment
• Time-scaling large phylogenies with 'congruification'

Citing geiger

If you use geiger, please cite:

Pennell, M.W., J.M. Eastman, G.J. Slater, J.W. Brown, J.C. Uyeda, R.G. FitzJohn, M.E. Alfaro, and L.J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 15:2216-2218.

in addition to the original papers describing the methods.

Feedback

We are always looking to improve geiger. If you have comments/questions/ideas, we encourage you to get in contact by posting an issue or making a pull request.