diversitree-package:
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}diversitreeComparative 'Phylogenetic' Analyses of Diversification
Description
\Sexpr[results=rd,stage=build]{tools:::Rd_package_description("#1")}diversitreeContains 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.References
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.