Phylogenetic Tools for Comparative Biology (and Other Things)

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Documentation for package ‘phytools’ version 1.5-1

• DESCRIPTION file.

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A B C D E F G K L M N O P R S T U V W

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 Akaike 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
anole.data	Phylogenetic datasets
anoletree	Phylogenetic datasets
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"'
as.princomp	Phylogenetic principal components analysis
as.princomp.phyl.pca	Phylogenetic principal components analysis
as.Qmatrix	Convert a fitted M_k_ model to a Q-matrix
as.Qmatrix.fitMk	Convert a fitted M_k_ model to a Q-matrix
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	Binds two trees of class '"simmap"'
biplot.phyl.pca	Phylogenetic principal components analysis
bmPlot	Simulates and visualizes discrete-time Brownian evolution on a phylogeny
bonyfish.data	Phylogenetic datasets
bonyfish.tree	Phylogenetic datasets
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
cotangleplot	Creates a co-phylogenetic plot
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.anc.Bayes	Bayesian ancestral character estimation
density.mcmcMk	Fits extended M_k_ model for discrete character evolution
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.multiSimmap	Drop or keep tip or tips from an object of class "multiSimmap"
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 --

edge.widthMap	Map continuous trait evolution on the tree
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
fitHRM	Fits extended M_k_ model for discrete character evolution
fitMk	Fits extended M_k_ model for discrete character evolution
fitMk.parallel	Fits extended M_k_ model for discrete character evolution
fitmultiMk	Fits extended M_k_ model for discrete character evolution
fitPagel	Function to test for correlated evolution of binary traits
fitpolyMk	Fits extended M_k_ model for discrete character evolution
flatworm.data	Phylogenetic datasets
flatworm.tree	Phylogenetic datasets
force.ultrametric	Coerces 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
graph.polyMk	Fits extended M_k_ model for discrete character evolution
gtt	Creates lineage-through-time plot (including extinct lineages)

-- K --

keep.tip.contMap	Drop tip or tips from an object of class "contMap" or "densityMap"
keep.tip.densityMap	Drop tip or tips from an object of class "contMap" or "densityMap"
keep.tip.multiSimmap	Drop or keep tip or tips from an object of class "multiSimmap"
keep.tip.simmap	Drop tips or extract clade from tree with mapped discrete character

-- 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
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)
ltt.multiPhylo	Creates lineage-through-time plot (including extinct lineages)
ltt.multiSimmap	Creates lineage-through-time plot (including extinct lineages)
ltt.phylo	Creates lineage-through-time plot (including extinct lineages)
ltt.simmap	Creates lineage-through-time plot (including extinct lineages)
ltt95	Creates a (1-alpha)% 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
mammal.data	Phylogenetic datasets
mammal.tree	Phylogenetic datasets
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 extended M_k_ model for discrete character evolution
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
multirateBM	Function to fit a multi-rate Brownian evolution model
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.anc.Bayes	Bayesian ancestral character estimation
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 extended M_k_ model for discrete character evolution
plot.densityMap	Plot posterior density of stochastic mapping on a tree
plot.describe.simmap	Summarizes a stochastic mapped tree or set of trees
plot.edge.widthMap	Map continuous trait evolution on the tree
plot.expand.clade	Expands (or contracts) the tip-spacing of a given clade or clades
plot.fitHRM	Fits extended M_k_ model for discrete character evolution
plot.fitMk	Fits extended M_k_ model for discrete character evolution
plot.fitPagel	Function to test for correlated evolution of binary traits
plot.fitpolyMk	Fits extended M_k_ model for discrete character evolution
plot.gfit	Fits extended M_k_ model for discrete character evolution
plot.ltt95	Creates a (1-alpha)% CI for a set of LTTs
plot.mcmcMk	Fits extended M_k_ model for discrete character evolution
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.Qmatrix	Convert a fitted M_k_ model to a Q-matrix
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.Qmatrix	Convert a fitted M_k_ model to a Q-matrix
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	Newick or Nexus style tree reader
read.simmap	Read SIMMAP style trees from file
readNexus	Newick or Nexus style tree reader
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
rescale	Rescale phylogenetic objects of different types
rescale.multiSimmap	Rescale object of class '"simmap"'
rescale.simmap	Rescale object of class '"simmap"'
rescaleSimmap	Rescale object of class '"simmap"'
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, sigmoidal, or spline phylogram or cladogram
rstate	Pick a random state according to a vector of probabilities

-- S --

salamanders	Phylogenetic datasets
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.multirateBM_plot	Set color map for various phylogenetic objects of classes
setMap.phyloScattergram	Set color map for various phylogenetic objects of classes
sigmoidPhylogram	Plot a round, sigmoidal, or spline phylogram or cladogram
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
splinePhylogram	Plot a round, sigmoidal, or spline phylogram or cladogram
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
sunfish.data	Phylogenetic datasets
sunfish.tree	Phylogenetic datasets

-- 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
vertebrate.data	Phylogenetic datasets
vertebrate.tree	Phylogenetic datasets

-- W --

wasp.data	Phylogenetic datasets
wasp.trees	Phylogenetic datasets
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