diversitree (0.9-3)

diversitree: comparative phylogenetic analyses of diversification.

http://www.zoology.ubc.ca/prog/diversitree
http://cran.r-project.org/web/packages/diversitree

Contains a number of comparative phylogenetic methods, mostly focussing 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.

Maintainer: Richard G. FitzJohn
Author(s): Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with GeoSSE and ClaSSE by Emma E. Goldberg <eeg@uic.edu>, and BiSSE-ness by Karen Magnuson-Ford.

License: GPL (>= 2)

Uses: ape, deSolve, subplex, numDeriv, tgp, multicore, minqa
Reverse suggests: hisse, secsse

Released over 7 years ago.