diversitree (0.9-7)

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.

Maintainer: Rich 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, Rcpp, subplex, geiger, numDeriv, minqa, expm, lubridate, caper
Reverse suggests: hisse, secsse

Released almost 6 years ago.