sim.rates

multiOU

is a stochastic map format phylogenetic tree in modified <code>"phylo"</code> format (e.g., see <code><a rd-options="" href="/link/make.simmap?package=phytools&version=0.7-70" data-mini-rdoc="phytools::make.simmap">make.simmap</a></code>).

tree

a named vector containing the rates for each state; names should be states in <code>mtree</code>.

sig2

optional value for the root state.

nsim

logical value indicating whether to return states at internal nodes.

internal

logical value indicating whether or not to visual the rate heterogeneity (default value is <code>FALSE</code>.

plot

single value or vector of values of the OU \(\alpha\) parameter.

alpha

single value or vector of values of the OU \(\theta\) parameter.

theta

optional value of the root state. Defaults to zero.

The function <code>sim.rates</code> conducts BM simulation on a tree with multiple rates.	
The function <code>multiOU</code> conducts multi-regime OU simulations on the tree under a range of conditions.

Simulation

phylogenetics

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)

sim.rates function

is a stochastic map format phylogenetic tree in modified <code>"phylo"</code> format (e.g., see <code><a rd-options='' href='make.simmap'>make.simmap</a></code>).

sim.rates: Brownian or OU simulation with multiple evolutionary regimes

Description

Usage

Arguments

Value

Details

References

See Also