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

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")

2.0.7 by Luke Harmon, 5 months ago


https://github.com/mwpennell/geiger-v2


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


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 RPANDA, RRphylo, Rarefy, Rphylopars, dispRity, evobiR, hillR, hilldiv, nichevol, ouxy, pmc, ratematrix, secsse, sensiPhy, treedata.table, treeplyr.

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

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


See at CRAN