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phytools (version 0.2-50)

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

12,126

Version

0.2-50

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

April 20th, 2013

Functions in phytools (0.2-50)

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

brownie.lite

Likelihood test for rate variation

add.random

Add tips at random to the tree

minSplit

Finding the minimum (median) split in the posterior sample

branching.diffusion

Animation of branching random diffusion

phyl.pairedttest

Phylogenetic paired t-test

allFurcTrees

Generate all bi- and multifurcating unrooted trees

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

ave.rates

Average the posterior rates

drop.clade

Drop clade from a tree

add.everywhere

Add tip to all edges in a tree

brownieREML

REML version of brownie.lite

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

bind.tip

Attaches a new tip to a tree

drop.tip.simmap

Drop tip from SIMMAP format tree

lambda.transform

Lambda transformation of matrix

anc.trend

Ancestral character estimation with a trend

getDescendants

Get descendant node numbers

map.overlap

Proportional overlap between two mapped character histories on a tree

optim.phylo.ls

Phylogeny inference using the least squares method

phyloDesign

Compute design matrix for least squares analyses

multi.mantel

Multiple matrix regression (partial Mantel test)

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

phyl.pca

Phylogenetic principal components analysis

exhaustiveMP

Exhaustive and branch & bound MP optimization

phylosig

Compute phylogenetic signal with two methods

estDiversity

Estimate diversity at each node of the tree

phyl.resid

Phylogenetic size-correction via GLS regression

plotTree

Plots rooted phylogenetic tree

sim.rates

Brownian simulation with multiple evolutionary rates

densityMap

Plot posterior density of stochastic mapping on a tree

fastBM

Fast Brownian simulation

to.matrix

Convert a character vector to a binary matrix

mrp.supertree

Matrix representation parsimony supertree estimation

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

rescaleSimmap

Rescale SIMMAP style tree

threshState

Computes value for a threshold character from a liability and thresholds

phenogram

Plot phenogram (traitgram)

treeSlice

Slices the tree at a particular point and returns all subtrees

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

fastAnc

Fast estimation of ML ancestral states

getStates

Get the states at nodes or tips from a mapped tree

ltt95

Creates a (1-alpha)-percent CI for a set of LTTs

make.era.map

Create "era" map on a phylogenetic tree

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

read.newick

Read Newick style tree

plotSimmap

Plot stochastic character mapped tree

sim.ratebystate

Conduct simulation of state dependent rate variation

splitplotTree

Plots a phylogeny in two columns

add.color.bar

Add color bar to a plot

getSisters

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

pgls.Ives

Phylogenetic regression with intraspecific sampling error

read.simmap

Read SIMMAP style trees from file

ltt

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

splitTree

Split tree at a point

write.simmap

Write a stochastic character mapped tree to file

untangle

Attempts to untangle crossing branches for plotting

applyBranchLengths

Applies the branch lengths of a reference tree to a target

contMap

Map continuous trait evolution on the tree

orderMappedEdge

Order the columns of mapped.edge to match across trees

writeAncestors

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

writeNexus

Write a tree to file in Nexus format

countSimmap

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

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

describe.simmap

Summarizes a stochastic mapped tree or set of trees

fancyTree

Plots special types of phylogenetic trees

phyl.cca

Phylogenetic canonical correlation analysis

phytools-package

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

rstate

Pick a random state according to a vector of probabilities

paste.tree

Paste two trees together

likMlambda

Likelihood for joint lambda

export.as.xml

Export trees & data in XML format

expm

Matrix exponential

paintSubTree

Paint sub-trees with a discrete character

sampleFrom

Sample from a set of distributions

xkcdTree

Plot xkcd style tree

anc.Bayes

Bayesian ancestral character estimation

fastMRCA

Get the MRCA of a pair of tip taxa

getExtant

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

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

nodeHeights

Compute the heights above the root of each node

pbtree

Simulate pure-birth or birth-death stochastic tree or trees

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

phylANOVA

Phylogenetic ANOVA and post-hoc tests

reroot

Re-root a tree along an edge

reorderSimmap

Reorder edges of a simmap tree

ratebystate

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

roundBranches

Rounds the branch lengths of a tree

sim.history

Simulate stochastic character history under some model

repPhylo

Replicate a tree into a list of trees

findMRCA

Get the MRCA of a set of taxa

ls.tree

Least squares branch lengths for a given tree

gammatest

Gamma test of Pybus & Harvey (2000)

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

matchNodes

Matches nodes between two trees

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

plotThresh

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

vcvPhylo

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

threshBayes

Threshold model using Bayesian MCMC

threshDIC

Deviance Information Criterion from the threshold model

strahlerNumber

Computes Strahler number for trees and nodes

anc.ML

Ancestral character estimation using likelihood

phylomorphospace

Creates phylomorphospace plot

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

starTree

Create star phylogeny