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phytools (version 0.2-40)

Phylogenetic Tools for comparative biology (and other things)

Description

phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.

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Version

Install

install.packages('phytools')

Monthly Downloads

11,829

Version

0.2-40

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

April 8th, 2013

Functions in phytools (0.2-40)

anc.Bayes

Bayesian ancestral character estimation

allFurcTrees

Generate all bi- and multifurcating unrooted trees

fancyTree

Plots special types of phylogenetic trees

branching.diffusion

Animation of branching random diffusion

vcvPhylo

Calculates cophenetic (i.e., phylogenetic VCV) matrix

applyBranchLengths

Applies the branch lengths of a reference tree to a target

pgls.Ives

Phylogenetic regression with intraspecific sampling error

repPhylo

Replicate a tree into a list of trees

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

roundBranches

Rounds the branch lengths of a tree

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

sim.history

Simulate stochastic character history under some model

add.color.bar

Add color bar to a plot

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

ave.rates

Average the posterior rates

anc.trend

Ancestral character estimation with a trend

lambda.transform

Lambda transformation of matrix

mrp.supertree

Matrix representation parsimony supertree estimation

findMRCA

Get the MRCA of a set of taxa

getStates

Get the states at nodes or tips from a mapped tree

phylANOVA

Phylogenetic ANOVA and post-hoc tests

plotTree

Plots rooted phylogenetic tree

sampleFrom

Sample from a set of distributions

phyl.pca

Phylogenetic principal components analysis

brownieREML

REML version of brownie.lite

brownie.lite

Likelihood test for rate variation

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

countSimmap

Counts the number of character changes on a SIMMAP style tree or set of trees

gammatest

Gamma test of Pybus & Harvey (2000)

fastBM

Fast Brownian simulation

minSplit

Finding the minimum (median) split in the posterior sample

ls.tree

Least squares branch lengths for a given tree

map.overlap

Proportional overlap between two mapped character histories on a tree

fastAnc

Fast estimation of ML ancestral states

phytools-package

phytools: Phylogenetic Tools for comparative biology (and other things)

sim.ratebystate

Conduct simulation of state dependent rate variation

threshState

Computes value for a threshold character from a liability and thresholds

contMap

Map continuous trait evolution on the tree

bind.tip

Attaches a new tip to a tree

getExtant

Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips

phyl.resid

Phylogenetic size-correction via GLS regression

describe.simmap

Summarizes a stochastic mapped tree or set of trees

phyloDesign

Compute design matrix for least squares analyses

splitTree

Split tree at a point

untangle

Attempts to untangle crossing branches for plotting

expm

Matrix exponential

likMlambda

Likelihood for joint lambda

phyl.cca

Phylogenetic canonical correlation analysis

drop.clade

Drop clade from a tree

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

phylomorphospace

Creates phylomorphospace plot

phylomorphospace3d

Creates phylomorphospace plot

plotSimmap

Plot stochastic character mapped tree

reorderSimmap

Reorder edges of a simmap tree

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

phylosig

Compute phylogenetic signal with two methods

estDiversity

Estimate diversity at each node of the tree

export.as.xml

Export trees & data in XML format

splitplotTree

Plots a phylogeny in two columns

threshDIC

Deviance Information Criterion from the threshold model

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

getSisters

Get the sister node, label, or set of nodes for a node or tip

treeSlice

Slices the tree at a particular point and returns all subtrees

orderMappedEdge

Order the columns of mapped.edge to match across trees

phenogram

Plot phenogram (traitgram)

phyl.pairedttest

Phylogenetic paired t-test

exhaustiveMP

Exhaustive and branch & bound MP optimization

ratebystate

Method for investigating the rate of one trait as a function of the state of another

write.simmap

Write a stochastic character mapped tree to file

read.simmap

Read SIMMAP style trees from file

sim.rates

Brownian simulation with multiple evolutionary rates

add.everywhere

Add tip to all edges in a tree

anc.ML

Ancestral character estimation using likelihood

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

paste.tree

Paste two trees together

paintSubTree

Paint sub-trees with a discrete character

optim.phylo.ls

Phylogeny inference using the least squares method

fastMRCA

Get the MRCA of a pair of tip taxa

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

rstate

Pick a random state according to a vector of probabilities

writeNexus

Write a tree to file in Nexus format

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

drop.tip.simmap

Drop tip from SIMMAP format tree

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

nodeHeights

Compute the heights above the root of each node

rescaleSimmap

Rescale SIMMAP style tree

reroot

Re-root a tree along an edge

plotThresh

Tree plotting with posterior probabilities of ancestral states from the threshold model

pbtree

Simulate pure-birth stochastic tree or trees

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

make.era.map

Create "era" map on a phylogenetic tree

threshBayes

Threshold model using Bayesian MCMC

xkcdTree

Plot xkcd style tree

add.random

Add tips at random to the tree

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

densityMap

Plot posterior density of stochastic mapping on a tree

getDescendants

Get descendant node numbers

multi.mantel

Multiple matrix regression (partial Mantel test)

ltt

Creates lineage-through-time plot (including extinct lineages)

matchNodes

Matches nodes between two trees

read.newick

Read Newick style tree

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

writeAncestors

Write a tree to file with ancestral states and (optionally) CIs at nodes

starTree

Create star phylogeny