densityTree

an object of class <code>"multiPhylo"</code> or <code>"multiSimmap"</code>.

trees

a color or a named vector of colors in which names correspond to mapped states in an object of class <code>"multiSimmap"</code>.

colors

transparency level for plotted trees. By default will be one divided by the number of trees.

alpha

plotting method to be used internally. Can be <code>"plotTree"</code> or <code>"plotSimmap"</code>.

method

logical value indicating whether or not to plot trees with a fixed depth or to permit plotted trees to have different depths.

fix.depth

logical value indicating whether to use the edge lengths of the input tree. Defaults to <code>use.edge.length=TRUE</code> unless any input tree edge lengths are <code>NULL</code>.

use.edge.length

logical value indicating whether or not to use the tip order from a consensus tree. (Defaults to <code>compute.consensus=FALSE</code>.

compute.consensus

arguments to be passed to <code>plotTree</code> or <code>plotSimmap</code>.

Functions plots a posterior sample of trees, including with mapped discrete characters.

phylogenetics

plotting

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; and fitting a model in which a discrete 
	character evolves under the threshold model. 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; a wide range
	of visualizations of trees; and a variety of other manipulations
	and analyses that phylogenetic biologists may find useful for
	their research.

densityTree: Plots a posterior sample of trees

Description

Usage

Arguments

Value

References