diversitree: diversitree: comparative phylogenetic analyses of diversification

Contains a number of comparative phylogenetic methods, mostly focusing on analysing diversification and character evolution. Contains implementations of BiSSE (Binary State Speciation and Extinction; Maddison et al. 2007: Syst. Biol. 56: 701) and its unresolved tree extensions (FitzJohn et al. 2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation and Extinction), QuaSSE (Quantitative State Speciation and Extinction; FitzJohn 2010: Syst. Biol. 59: 619), GeoSSE (Geographic State Speciation and Extinction; Goldberg et al. 2011: Syst. Biol. 60: 451), and BiSSE-ness (Magnuson-Ford and Otto 2012: Am. Nat.) Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.

Version: 0.9-7
Depends: R (≥ 2.10), deSolve (≥ 1.7), ape, subplex, methods, Rcpp (≥ 0.10.0)
LinkingTo: Rcpp
Suggests: numDeriv, minqa, lubridate, expm, caper, geiger
Published: 2014-02-20
Author: Richard G. FitzJohn, with GeoSSE and ClaSSE by Emma E. Goldberg, and BiSSE-ness by Karen Magnuson-Ford.
Maintainer: Richard G. FitzJohn <rich.fitzjohn at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://www.zoology.ubc.ca/prog/diversitree
NeedsCompilation: yes
SystemRequirements: fftw3 (>= 3.1.2), gsl (>= 1.15)
Citation: diversitree citation info
Materials: README ChangeLog
In views: Phylogenetics
CRAN checks: diversitree results

Downloads:

Reference manual: diversitree.pdf
Package source: diversitree_0.9-7.tar.gz
MacOS X binary: diversitree_0.9-7.tgz
Windows binary: diversitree_0.9-7.zip
Old sources: diversitree archive