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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install.packages("geiger") by Luke Harmon, a month ago

Browse source code at

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

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

GPL (>= 2) license

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

Depends on ape

Linking to Rcpp

Imported by PhyInformR, RPANDA, RRphylo, Rphylopars, dispRity, evobiR, hilldiv, metricTester, ouxy, phylocurve, pmc, ratematrix, secsse, sensiPhy, treeplyr.

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

Suggested by BBMV, RNeXML, diversitree, fishtree, ouch, pcmabc, phytools, tracerer.

See at CRAN