Analysis of Evolutionary Diversification

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

Build Status

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


or installed directly from github with the devtools package


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:

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.


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.


Reference manual

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2.0.7 by Luke Harmon, 2 years ago

Browse source code at

Authors: Luke Harmon , Matthew Pennell , Chad Brock , Joseph Brown , Wendell Challenger , Jon Eastman , Rich FitzJohn , Rich Glor , Gene Hunt , Liam Revell , Graham Slater , Josef Uyeda , and Jason Weir

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

GPL (>= 2) license

Imports MASS, mvtnorm, subplex, deSolve, digest, Rcpp, coda, ncbit, colorspace, methods, phytools

Depends on ape

Linking to Rcpp

Imported by FishPhyloMaker, RRphylo, Rarefy, Rphylopars, datelife, dispRity, evobiR, hillR, hilldiv, hisse, nichevol, nodeSub, ouxy, pcmabc, pmc, ratematrix, secsse, sensiPhy, treedata.table, treeplyr.

Depended on by OUwie, TreeSim, convevol, iteRates, surface, windex.

Suggested by BBMV, RNeXML, diversitree, fishtree, mvSLOUCH, ouch, phytools.

See at CRAN