Phylogenetic Tools for Comparative Biology (and Other Things)

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Documentation for package ‘phytools’ version 0.7-20

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

-- A --

add.arrow Add an arrow pointing to a tip or node on the tree
add.color.bar Add color bar to a plot
add.everywhere Add tip to all edges in a tree
add.random Add tips at random to the tree
add.simmap.legend Add legend to stochastically mapped tree
add.species.to.genus Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree
aic.w Computes AIC weights
allFurcTrees Generate all bi- and multifurcating unrooted trees
allRotations Rotates a node or set of nodes in a phylogenetic tree
anc.Bayes Bayesian ancestral character estimation
anc.ML Ancestral character estimation using likelihood
anc.trend Ancestral character estimation with a trend
ancThresh Ancestral character estimation under the threshold model using Bayesian MCMC
anoletree Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character
applyBranchLengths Applies the branch lengths of a reference tree to a target
arc.cladelabels Add labels to subtrees of a plotted phylogeny
as.multiPhylo Conversion to object of class '"multiPhylo"'
as.multiPhylo.multiSimmap Conversion to object of class '"multiPhylo"'
as.multiPhylo.phylo Conversion to object of class '"multiPhylo"'
ave.rates Average the posterior rates
averageTree Compute an average tree from a set of trees and related operations

-- B --

backbone.toPhylo Converts tree to backbone or vice versa
bd Convert object of class "birthdeath" to raw birth & death rates
bind.tip Attaches a new tip to a tree
bind.tree.simmap Attaches a new tip to a tree
biplot.phyl.pca Phylogenetic principal components analysis
bmPlot Simulates and visualizes discrete-time Brownian evolution on a phylogeny
branching.diffusion Animation of branching random diffusion
brownie.lite Likelihood test for rate variation in a continuous trait
brownieREML REML version of brownie.lite

-- C --

cladelabels Add labels to subtrees of a plotted phylogeny
coef.phyl.RMA Phylogenetic reduced major axis (RMA) regression
collapse.to.star Collapse a subtree to a star phylogeny
collapseTree Interactive tree visualizer
compare.chronograms Compares two chronograms with precisely matching nodes in a visual manner
compute.mr Matrix representation parsimony supertree estimation
consensus.edges Compute consensus edges for a tree under some criterion
contMap Map continuous trait evolution on the tree
cophylo Creates a co-phylogenetic plot
cospeciation Conducts a statistical test of cospeciation between two trees
countSimmap Counts the number of character changes on a object of class "simmap" or "multiSimmap"
ctt Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories

-- D --

density.mcmcMk Fits Mk model
density.multiSimmap Computes a posterior distribution for the number and types of changes on the tree
densityMap Plot posterior density of stochastic mapping on a tree
densityTree Plots a posterior sample of trees
describe.simmap Summarizes a stochastic mapped tree or set of trees
di2multi.contMap Collapse or resolve polytomies in a tree with a character painted on the edges
di2multi.densityMap Collapse or resolve polytomies in a tree with a character painted on the edges
di2multi.multiSimmap Collapse or resolve polytomies in a tree with a character painted on the edges
di2multi.simmap Collapse or resolve polytomies in a tree with a character painted on the edges
dot.legend Creates a phylogenetic dot plot
dotTree Creates a phylogenetic dot plot
drop.clade Drop a clade from a tree
drop.leaves Drop all the leaves (tips) from a tree
drop.tip.contMap Drop tip or tips from an object of class "contMap" or "densityMap"
drop.tip.densityMap Drop tip or tips from an object of class "contMap" or "densityMap"
drop.tip.simmap Drop tips or extract clade from tree with mapped discrete character
drop.tip.singleton Converts a tree without singletons to a tree with singleton nodes
Dtest Conducts correlational D-test from stochastic mapping

-- E --

edgelabels.cophylo Add labels to a plotted "cophylo" object
edgeProbs Compute the relative frequencies of state changes along edges
errorbar.contMap Map continuous trait evolution on the tree
estDiversity Estimate diversity at each node of the tree
evol.rate.mcmc Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
evol.vcv Likelihood test for variation in the evolutionary variance-covariance matrix
evolvcv.lite Likelihood test for a shift in the evolutionary correlation between traits
exhaustiveMP Exhaustive and branch & bound MP optimization
expand.clade Expands (or contracts) the tip-spacing of a given clade or clades
export.as.xml Export trees & data in XML format
extract.clade.simmap Drop tips or extract clade from tree with mapped discrete character
extract.strahlerNumber Computes Strahler number for trees and nodes

-- F --

fancyTree Plots special types of phylogenetic trees
fastAnc (Reasonably) fast estimation of ML ancestral states
fastBM (Reasonably) fast quantitative trait simulation on phylogenies
fastDist Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
fastHeight Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
fastMRCA Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
findMRCA Get the MRCA of a set of taxa
fit.bd Fits birth-death (speciation/extinction) model to reconstructed phylogeny
fit.yule Fits birth-death (speciation/extinction) model to reconstructed phylogeny
fitBayes Evolutionary model fitting with intraspecific variability using Bayesian MCMC
fitDiversityModel Fit diversity-dependent phenotypic evolution model
fitMk Fits Mk model
fitmultiMk Fits Mk model
fitPagel Function to test for correlated evolution of binary traits
fitpolyMk Fits Mk model
force.ultrametric Forces a phylogenetic tree to be ultrametric

-- G --

gammatest Gamma test of Pybus & Harvey (2000)
genSeq Simulate a DNA alignment on the tree under a model
genus.to.species.tree Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree
geo.legend Adds a geological (or other temporal) legend to a plotted tree
geo.palette Adds a geological (or other temporal) legend to a plotted tree
get.treepos Get position or node of a plotted tree interactively
getCladesofSize Get all subtrees larger than or equal to a specified size
getDescendants Get descendant node numbers
getExtant Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
getExtinct Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
getnode Get position or node of a plotted tree interactively
getParent Get descendant node numbers
getSisters Get the sister node number, label, or set of nodes for a node or tip
getStates Get the states at nodes or tips from a mapped tree
gtt Creates lineage-through-time plot (including extinct lineages)

-- L --

labelnodes Function to interactively label nodes of a plotted tree
ladderize.simmap Ladderize a tree with a mapped discrete character
lambda.transform Lambda transformation of matrix
lik.bd Fits birth-death (speciation/extinction) model to reconstructed phylogeny
likMlambda Likelihood for joint lambda
likSurface.rateshift Find the temporal position of one or more rate shifts
linklabels Function to add tip labels to a plotted tree with linking lines
locate.fossil Locate a fossil lineage in a tree using continuous characters
locate.yeti Locate a cryptic, recently extinct, or missing taxon on a tree
logLik.fitDiversityModel Fit diversity-dependent phenotypic evolution model
logLik.gfit Fits Mk model
ls.consensus Compute an average tree from a set of trees and related operations
ls.tree Least squares branch lengths for a given tree
ltt Creates lineage-through-time plot (including extinct lineages)
ltt95 Creates a (1-alpha)-percent CI for a set of LTTs

-- M --

make.era.map Create "era" map on a phylogenetic tree
make.simmap Simulate stochastic character maps on a phylogenetic tree or trees
make.transparent Plots a posterior sample of trees
Map.Overlap Proportional overlap between two mapped character histories on a tree
map.overlap Proportional overlap between two mapped character histories on a tree
map.to.singleton Converts a tree without singletons to a tree with singleton nodes
mapped.states Returns a vector, matrix, or list of the mapped states on a tree or set of trees
markChanges Add marked changes to a plotted tree with mapped discrete character
matchLabels Matches nodes between two trees
matchNodes Matches nodes between two trees
mccr Creates lineage-through-time plot (including extinct lineages)
mcmcMk Fits Mk model
mergeMappedStates Merge two or more mapped states into one state
midpoint.root Midpoint root a phylogeny
minRotate Rotates all nodes of the tree to minimize the difference in order with a vector
minSplit Finding the minimum (median) split in the posterior sample
minTreeDist Compute an average tree from a set of trees and related operations
modified.Grafen Computes modified Grafen edge lengths
mrp.supertree Matrix representation parsimony supertree estimation
multi.mantel Multiple matrix regression (partial Mantel test)
multi2di.contMap Collapse or resolve polytomies in a tree with a character painted on the edges
multi2di.densityMap Collapse or resolve polytomies in a tree with a character painted on the edges
multi2di.multiSimmap Collapse or resolve polytomies in a tree with a character painted on the edges
multi2di.simmap Collapse or resolve polytomies in a tree with a character painted on the edges
multiC Returns a list with phylogenetic VCV matrix for each mapped state
multiOU Brownian or OU simulation with multiple evolutionary regimes
multiRF Computes Robinson-Foulds distance between a set of trees

-- N --

node.paths Computes modified Grafen edge lengths
nodeheight Compute the heights above the root of each node
nodeHeights Compute the heights above the root of each node
nodelabels.cophylo Add labels to a plotted "cophylo" object

-- O --

optim.phylo.ls Phylogeny inference using the least squares method
orderMappedEdge Order the columns of mapped.edge to match across trees

-- P --

paintBranches Paint sub-trees with a discrete character
paintSubTree Paint sub-trees with a discrete character
paste.tree Paste two trees together
pbtree Simulate pure-birth or birth-death stochastic tree or trees
pgls.Ives Phylogenetic regression with intraspecific sampling error
pgls.SEy Phylogenetic regression with intraspecific sampling error
phenogram Plot phenogram (traitgram)
phenogram95 Plots special types of phylogenetic trees
phyl.cca Phylogenetic canonical correlation analysis
phyl.pairedttest Phylogenetic paired t-test
phyl.pca Phylogenetic principal components analysis
phyl.resid Phylogenetic size-correction via GLS regression
phyl.RMA Phylogenetic reduced major axis (RMA) regression
phyl.vcv Compute evolutionary VCV matrix for a tree & dataset
phylANOVA Phylogenetic ANOVA and post-hoc tests
phylo.heatmap Creates a phylogenetic heat map
phylo.impute Phylogenetic imputation for multivariate continuous character data
phylo.to.map Plot tree with tips linked to geographic coordinates
phylo.toBackbone Converts tree to backbone or vice versa
phyloDesign Compute design matrix for least squares analyses
phylomorphospace Creates phylomorphospace plot
phylomorphospace3d Creates tree-dimensional phylomorphospace plot
phyloScattergram Plots special types of phylogenetic trees
phylosig Compute phylogenetic signal with two methods
phytools phytools: Phylogenetic Tools for comparative biology (and other things)
plot.backbonePhylo Plots backbone tree with triangles as clades
plot.changesMap Computes a posterior distribution for the number and types of changes on the tree
plot.contMap Map continuous trait evolution on the tree
plot.cophylo Creates a co-phylogenetic plot
plot.cospeciation Conducts a statistical test of cospeciation between two trees
plot.density.mcmcMk Fits Mk model
plot.densityMap Plot posterior density of stochastic mapping on a tree
plot.describe.simmap Summarizes a stochastic mapped tree or set of trees
plot.expand.clade Expands (or contracts) the tip-spacing of a given clade or clades
plot.fitMk Fits Mk model
plot.fitPagel Function to test for correlated evolution of binary traits
plot.fitpolyMk Fits Mk model
plot.gfit Fits Mk model
plot.ltt95 Creates a (1-alpha)-percent CI for a set of LTTs
plot.mcmcMk Fits Mk model
plot.multiSimmap Plot stochastic character mapped tree
plot.phyl.RMA Phylogenetic reduced major axis (RMA) regression
plot.phylo.to.map Plot tree with tips linked to geographic coordinates
plot.phylosig Compute phylogenetic signal with two methods
plot.rateshift Find the temporal position of one or more rate shifts
plot.simBMphylo Creates a graphical illustration of Brownian motion evolution on a phylogeny
plot.simmap Plot stochastic character mapped tree
plot.summary.evol.rate.mcmc Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
plotBranchbyTrait Plot branch colors by a quantitative trait or value
plotSimmap Plot stochastic character mapped tree
plotThresh Tree plotting with posterior probabilities of ancestral states from the threshold model
plotTree Plots rooted phylogenetic tree
plotTree.barplot Plot a tree with bars at the tips
plotTree.boxplot Plot a tree with bars at the tips
plotTree.datamatrix Plot a tree with a discrete character data matrix at the tips
plotTree.errorbars Plot a tree with error bars around divergence dates
plotTree.singletons Converts a tree without singletons to a tree with singleton nodes
plotTree.splits Plots a phylogeny in two columns
plotTree.wBars Plot a tree with bars at the tips
posterior.evolrate Analysis of the posterior sample from evol.rate.mcmc
posthoc Generic post-hoc test
posthoc.ratebytree Likelihood test for rate variation among trees, clades, or traits
print.backbonePhylo Print method for backbone phylogeny
print.cospeciation Conducts a statistical test of cospeciation between two trees
print.evol.rate.mcmc Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
print.fit.bd Fits birth-death (speciation/extinction) model to reconstructed phylogeny
print.fitDiversityModel Fit diversity-dependent phenotypic evolution model
print.summary.evol.rate.mcmc Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
project.phylomorphospace Creates phylomorphospace plot

-- R --

ratebystate Method for investigating the rate of one trait as a function of the state of another
ratebytree Likelihood test for rate variation among trees, clades, or traits
rateshift Find the temporal position of one or more rate shifts
read.newick Robust Newick style tree reader
read.simmap Read SIMMAP style trees from file
reorder.backbonePhylo Reorders a backbone phylogeny
reorderSimmap Reorder edges of a simmap tree
rep.multiPhylo Replicate a tree or set of trees
rep.phylo Replicate a tree or set of trees
repPhylo Replicate a tree or set of trees
reroot Re-root a tree along an edge
rerootingMethod Get marginal ancestral state reconstructions by re-rooting
rescaleSimmap Rescale SIMMAP style tree
resolveAllNodes Compute all possible resolutions of a node or all nodes in a multifurcating tree
resolveNode Compute all possible resolutions of a node or all nodes in a multifurcating tree
rootedge.to.singleton Converts a tree without singletons to a tree with singleton nodes
rotate.multi Rotates a node or set of nodes in a phylogenetic tree
rotateNodes Rotates a node or set of nodes in a phylogenetic tree
roundBranches Rounds the branch lengths of a tree
roundPhylogram Plot a round phylogram
rstate Pick a random state according to a vector of probabilities

-- S --

sampleFrom Sample from a set of distributions
scores Phylogenetic principal components analysis
scores.phyl.pca Phylogenetic principal components analysis
setMap Set color map for various phylogenetic objects of classes
setMap.contMap Set color map for various phylogenetic objects of classes
setMap.densityMap Set color map for various phylogenetic objects of classes
setMap.phyloScattergram Set color map for various phylogenetic objects of classes
sim.corrs Multivariate Brownian simulation with multiple correlations and rates
sim.ctt Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories
sim.history Simulate character history or a discrete character at the tips of the tree under some model
sim.Mk Simulate character history or a discrete character at the tips of the tree under some model
sim.multiCtt Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories
sim.multiMk Simulate character history or a discrete character at the tips of the tree under some model
sim.ratebystate Conduct simulation of state dependent rate variation
sim.rates Brownian or OU simulation with multiple evolutionary regimes
simBMphylo Creates a graphical illustration of Brownian motion evolution on a phylogeny
skewers Matrix comparison using the method of random skewers
splitEdgeColor Split edge colors when descendant edges have different mapped states
splitplotTree Plots a phylogeny in two columns
splitTree Split tree at a point
starTree Create star phylogeny
strahlerNumber Computes Strahler number for trees and nodes
summary.evol.rate.mcmc Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
summary.multiSimmap Summarizes a stochastic mapped tree or set of trees
summary.simmap Summarizes a stochastic mapped tree or set of trees

-- T --

threshBayes Threshold model using Bayesian MCMC
threshDIC Deviance Information Criterion from the threshold model
threshState Computes value for a threshold character from a liability and thresholds
tiplabels.cophylo Add labels to a plotted "cophylo" object
tipRotate Rotates all nodes of the tree to minimize the difference in order with a vector
to.matrix Convert a character vector to a binary matrix
tree.grow Creates an animation of a tree growing from left-to-right or upwards
treeSlice Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point

-- U --

untangle Attempts to untangle crossing branches for plotting

-- V --

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

-- W --

write.simmap Write a stochastic character mapped tree to file
writeAncestors Write a tree to file with ancestral states and (optionally) CIs at nodes
writeNexus Write a tree to file in Nexus format