multirateBM

an object of class <code>"phylo"</code>.

tree

method of optimization. Currently only <code>method="ML"</code>.

method

optimization routine to be used by <code><a rd-options="" href="/link/optim?package=phytools&version=0.7-80" data-mini-rdoc="phytools::optim">optim</a></code>. If more than one is specified and <code>n.iter&gt;1</code> then they will be alternated.

optim

to be passed to <code>optim</code>. If set to <code>maxit=NULL</code>, the default value of <code>maxit</code> will be used, depending on the optimization method.

maxit

number of times to reiterate failed optimization.

n.iter

lambda penalty term. High values of <code>lambda</code> correspond to high penalty for rate heterogeneity among edges. Low values of <code>lambda</code> correspond to low penalty.

lambda

This function fits a flexible Brownian multi-rate model using penalized likelihood.

phylogenetics

maximum likelihood

comparative method

continuous character

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

multirateBM function

optimization routine to be used by <code><a rd-options='' href='optim'>optim</a></code>. If more than one is specified and <code>n.iter&gt;1</code> then they will be alternated.

multirateBM: Function to fit a multi-rate Brownian evolution model

Description

Usage

Arguments

Value

References

See Also