diversitree: diversitree: comparative phylogenetic tests of diversification
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. 69: 619), and GeoSSE
(Geographic State Speciation and Extinction; Goldberg et al.
2011: Syst. Biol.). Other included methods include Markov
models of discrete and continuous trait evolution and constant
rate speciation and extinction.