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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) and its unresolved tree extensions, 'MuSSE' (Multiple State Speciation and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.

diversitree.pdf