sim.ratebystate

tree

variance of the Brownian process of evolution for x, \(\sigma_x^2\).

sig2x

variance of the Brownian process of evolution for y when <code>x-min(x)==1</code> (for <code>logarithm=FALSE</code>) or <code>x==0</code> (for <code>logarithm=TRUE</code>).

sig2y

intercept and slope of the relationship between the value of x and the Brownian rate in y.

beta

optional arguments which include <code>method</code> (<code>"by.node"</code> or <code>"by.branch"</code> indicating whether to assume the rate varies as a function of the node state or the mean branch state); <code>plot</code>, a logical value indicating whether or not to plot a phenogram with the branches used for simulation of <code>y</code> after rescaling by the state of <code>x</code>; and <code>logarithm</code>, a logical value indicating whether or not simulate changes in the variance of Brownian evolution for <code>y</code> as an additive <code>logarithm=FALSE</code> or multiplicative function of <code>x</code>. The default is <code>logarithm=FALSE</code>.

This function attempts to simulate two characters under a model in which the rate of evolution for the second (y) depends on the states for the first (x). See <code><a rd-options="" href="/link/ratebystate?package=phytools&version=0.7-70" data-mini-rdoc="phytools::ratebystate">ratebystate</a></code> for more details.

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.ratebystate function

This function attempts to simulate two characters under a model in which the rate of evolution for the second (y) depends on the states for the first (x). See <code><a rd-options='' href='ratebystate'>ratebystate</a></code> for more details.

sim.ratebystate: Conduct simulation of state dependent rate variation

Description

Usage

Arguments

Value

References

See Also