make.mkn.deriv

A phylogenetic tree, in <code>ape</code> <dquote>phylo</dquote> format.

tree

A vector of character states, each of which must be
 integers from 1 to <code>k</code>.

states

Not currently working Currently a restricted-feature-set version of
 <code><a href="/link/make.mkn?package=diversitree&version=0.9-3" rd-options="" data-mini-rdoc="diversitree::make.mkn">make.mkn</a></code>, but including gradient (first derivative)
 information along with the likelihood. Currently lacks several
 features of the full <code>mkn</code> model: no support for missing trait
 data, no support for different root treatments, no optimised 2-state
 method. In the future, this will roll back into <code><a href="/link/make.mkn?package=diversitree&version=0.9-3" rd-options="" data-mini-rdoc="diversitree::make.mkn">make.mkn</a></code>, so do
 not use or depend on this!

models

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. 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.

make.mkn.deriv: Mk2 and Mk-n Models of character evolution [temporary extension with derivatives]

Description

Arguments

See Also