anc.Bayes

tree

a vector of tip values for species; <code>names(x)</code> should be the species names.

a integer indicating the number of generations for the MCMC.

ngen

a list of control parameters containing the following elements: <code>sig2</code>: starting value for $\sigma^2$ (BM rate); <code>a</code>: starting for the state at the root node; <code>y</code>: starting values for the states at all internal nodes excluding the root (should be labeled with node numbers); <code>pr.mean</code>: means for the prior distributions in the following order - <code>sig2</code>, <code>a</code>, <code>y</code>, note that the prior probability distribution is exponential for <code>sig2</code> and normal for <code>a</code> and <code>y</code>; <code>pr.var</code>: variances on the prior distributions, same order as <code>pr.mean</code> (but the variance is not used for <code>sig2</code>); <code>prop</code>: variances on the normal proposal distributions in the same order as <code>pr.mean</code>; <code>sample</code>: sample frequency from the MCMC.

control


	This function uses Bayesian MCMC to sample from the posterior distribution for the states at internal nodes in the tree.


phylogenetics

comparative method

Bayesian

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.

anc.Bayes: Bayesian ancestral character estimation

Description

Usage

Arguments

Value

References

See Also

Examples