sim.history

a phylogenetic tree as an object of class <code>"phylo"</code>.

tree

a matrix containing the instantaneous transition rates between states. Note that normally this is the transpose of the matrix produced by <code>fitDiscrete</code> in the geiger package or <code><a rd-options="" href="/link/make.simmap?package=phytools&version=0.5-64" data-mini-rdoc="phytools::make.simmap">make.simmap</a></code> in phytools; that is to say the transition rate from <code>i -> j</code> should be given by <code>Q[j,i]</code>. However, if your matrix is properly conformed (i.e., rows or columns sum to 0), then <code>sim.history</code> will attempt to transpose your matrix correctly & will return an informative message (if <code>message=TRUE</code>, see below).

an optional value for the state at the root node; if <code>NULL</code>, a random state will be assigned. <code>anc</code> can be a vector of states, in which one of the states will be chosen randomly for each simulation. <code>anc</code> can be a vector of probabilities with names, in which case a state will be chosen in proportion to the given probabilities.

nsim

other optional arguments. Currently only <code>message</code>, a logical value indicating whether or not to turn on informational messages (defaults to <code>message=TRUE</code>).

This function simulates a stochastic character history for a discretely valued character trait on the tree. The resultant tree is stored as a modified <code>"phylo"</code> object in stochastic character map (e.g., <code><a rd-options="" href="/link/make.simmap?package=phytools&version=0.5-64" data-mini-rdoc="phytools::make.simmap">make.simmap</a></code>) format.

Simulation

phylogenetics

Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; fitting a model in which a discrete character
evolves under the threshold model; visualization of cospeciation; a
simple statistical test for cospeciation between two trees. In
addition to this phylogenetic comparative method functionality, the
package also contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; computing a
consensus tree under multiple methods, including via minimization
of the distance to other trees in the set; a wide range of
visualizations of trees; and a variety of other manipulations and
analyses that phylogenetic biologists may find useful for their
research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

sim.history function

a matrix containing the instantaneous transition rates between states. Note that normally this is the transpose of the matrix produced by <code>fitDiscrete</code> in the geiger package or <code><a rd-options='' href='make.simmap'>make.simmap</a></code> in phytools; that is to say the transition rate from <code>i -> j</code> should be given by <code>Q[j,i]</code>. However, if your matrix is properly conformed (i.e., rows or columns sum to 0), then <code>sim.history</code> will attempt to transpose your matrix correctly & will return an informative message (if <code>message=TRUE</code>, see below).

This function simulates a stochastic character history for a discretely valued character trait on the tree. The resultant tree is stored as a modified <code>"phylo"</code> object in stochastic character map (e.g., <code><a rd-options='' href='make.simmap'>make.simmap</a></code>) format.

sim.history: Simulate stochastic character history under some model

Description

Usage

Arguments

Value

References

See Also