Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees.


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

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:

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.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("geiger")

2.0.6.1 by ORPHANED, 6 days ago


http://www.webpages.uidaho.edu/~lukeh/software.html


Browse source code at https://github.com/cran/geiger


Authors: Luke Harmon <[email protected]> , Jason Weir , Chad Brock , Rich Glor , Wendell Challenger , Gene Hunt , Rich FitzJohn , Matt Pennell , Graham Slater , Joseph Brown , Josef Uyeda , and Jon Eastman <[email protected]>


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 BMhyb, BMhyd, PhyInformR, RPANDA, RRphylo, Rphylopars, dispRity, entropart, evobiR, geomorph, lefse, metricTester, pcmabc, phylocurve, pmc, ratematrix, sensiPhy, treeplyr.

Depended on by DAMOCLES, TreeSim, bayou, convevol, iteRates, surface, windex.

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


See at CRAN