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.
Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen Magnuson-Ford [aut], Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <email@example.com>
Diversitree contains methods described in the following papers (all of which aside from Maddison et al. 2007 were originally published as a diversitree implementation).
FitzJohn R.G., Maddison W.P., and Otto S.P. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. systematic biology 58:595-611. Systematic Biology 58:595-611.
FitzJohn R.G. 2010. Quantitative traits and diversification. Systematic Biology 59:619-633.
Goldberg E.E., Lancaster L.T., Ree R.H. 2011. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology 60: 451-465.
Maddison W.P., Midford P.E., and Otto S.P. 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56: 701-710.
Magnuson-Ford K. and Otto S.P. 2012. Linking the investigations of character evolution and species diversification. The American Naturalist 180: 225-245.
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