phyl.vcv

lambda

matrix containing the height above the root of each pair of species in the tree. Typically this will have been produced by calling <code><a rd-options="" href="/link/vcv.phylo?package=phytools&version=0.5-38" data-mini-rdoc="phytools::vcv.phylo">vcv.phylo</a></code>.


	Primarily an internal function for <code><a rd-options="" href="/link/phyl.pca?package=phytools&version=0.5-38" data-mini-rdoc="phytools::phyl.pca">phyl.pca</a></code>; this can be used to compute the phylogenetic trait variance-covariance matrix given a phylogenetic VCV, lambda, and a data matrix. Should not be confused with <code><a rd-options="" href="/link/vcv.phylo?package=phytools&version=0.5-38" data-mini-rdoc="phytools::vcv.phylo">vcv.phylo</a></code> in the "ape" package (although one of the objects returned is the output of <code>vcv.phylo</code>).


utilities

Statistics

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; 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.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

phyl.vcv function

matrix containing the height above the root of each pair of species in the tree. Typically this will have been produced by calling <code><a rd-options='' href='vcv.phylo'>vcv.phylo</a></code>.


	Primarily an internal function for <code><a rd-options='' href='phyl.pca'>phyl.pca</a></code>; this can be used to compute the phylogenetic trait variance-covariance matrix given a phylogenetic VCV, lambda, and a data matrix. Should not be confused with <code><a rd-options='' href='vcv.phylo'>vcv.phylo</a></code> in the "ape" package (although one of the objects returned is the output of <code>vcv.phylo</code>).


phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset

Description

Usage

Arguments

Value

Details

References