densityTree

make.transparent

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 which is passed to internally used function, <code>make.transparent</code>. (<code>0</code> is fully transparent, which <code>1</code> is fully opaque.) 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>.

in <code>make.transparent</code>, the color to render transparent.

color


	Functions plots a posterior sample of trees, including with mapped discrete characters.
	
	<code>make.transparent</code> is used internally and converts a color to transparent with a certain user-specified <code>alpha</code> level.


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; 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.

densityTree: Plots a posterior sample of trees

Description

Usage

Arguments

Value

References