phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

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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; fitting a model in which a discrete character evolves under the threshold model; visualization of cospeciation; a simple statistical test for cospeciation between two trees. 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; computing a consensus tree under multiple methods, including via minimization of the distance to other trees in the set; a wide range of visualizations of trees; and a variety of other manipulations and analyses that phylogenetic biologists may find useful for their research.

Author
Liam J. Revell
Date of publication
2016-12-05 22:44:57
Maintainer
Liam J. Revell <liam.revell@umb.edu>
License
GPL (>= 2)
Version
0.5-64
URLs

View on CRAN

Man pages

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...
aic.w
Computes AIC weights
allFurcTrees
Generate all bi- and multifurcating unrooted trees
anc.Bayes
Bayesian ancestral character estimation
anc.ML
Ancestral character estimation using likelihood
ancThresh
Ancestral character estimation under the threshold model...
anc.trend
Ancestral character estimation with a trend
anoletree
Phylogeny of Greater Antillean anole ecomorph species with...
applyBranchLengths
Applies the branch lengths of a reference tree to a target
as.multiPhylo
Conversion to object of class '"multiPhylo"'
averageTree
Compute an average tree from a set of trees and related...
ave.rates
Average the posterior rates
bd
Convert object of class "birthdeath" to raw birth & death...
bind.tip
Attaches a new tip to a tree
bind.tree.simmap
Attaches a new tip to a tree
bmPlot
Simulates and visualizes discrete-time Brownian evolution on...
branching.diffusion
Animation of branching random diffusion
brownie.lite
Likelihood test for rate variation in a continuous trait
brownieREML
REML version of brownie.lite
cladelabels
Add labels to subtrees of a plotted phylogeny
collapse.to.star
Collapse a subtree to a star phylogeny
collapseTree
Interactive tree visualizer
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 SIMMAP style 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.simmap
Collapse branches of zero length to polytomy in stochastic...
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...
drop.tip.simmap
Drop tips or extract clade from tree with mapped discrete...
edgeProbs
Compute the relative frequencies of state changes along edges
estDiversity
Estimate diversity at each node of the tree
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic...
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation...
exhaustiveMP
Exhaustive and branch & bound MP optimization
expm
Matrix exponential
export.as.xml
Export trees & data in XML format
fancyTree
Plots special types of phylogenetic trees
fastAnc
Fast estimation of ML ancestral states
fastBM
Fast Brownian simulation
fastMRCA
Get the MRCA (or height above the root of the MRCA) of a pair...
findMRCA
Get the MRCA of a set of taxa
fitBayes
Evolutionary model fitting with intraspecific variability...
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
fitMk
Fits Mk model
fitPagel
Function to test for correlated evolution of binary traits
gammatest
Gamma test of Pybus & Harvey (2000)
genSeq
Simulate a DNA alignment on the tree under a model
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...
getSisters
Get the sister node number, label, or set of nodes for a node...
getStates
Get the states at nodes or tips from a mapped tree
ladderize.simmap
Ladderize a tree with a mapped discrete character
lambda.transform
Lambda transformation of matrix
likMlambda
Likelihood for joint lambda
locate.fossil
Locate a fossil lineage in a tree using continuous characters
locate.yeti
Locate a cryptic, recently extinct, or missing taxon on a...
ls.tree
Least squares branch lengths for a given tree
ltt
Creates lineage-through-time plot (including extinct...
ltt95
Creates a (1-alpha)-percent CI for a set of LTTs
make.era.map
Create "era" map on a phylogenetic tree
make.simmap
Simulate stochastic character maps on a phylogenetic tree or...
map.overlap
Proportional overlap between two mapped character histories...
mapped.states
Returns a vector, matrix, or list of the mapped states on a...
map.to.singleton
Converts a mapped tree to a tree with singleton nodes
markChanges
Add marked changes to a plotted tree with mapped discrete...
matchNodes
Matches nodes between two trees
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...
minSplit
Finding the minimum (median) split in the posterior sample
modified.Grafen
Computes modified Grafen edge lengths
mrp.supertree
Matrix representation parsimony supertree estimation
multiC
Returns a list with phylogenetic VCV matrix for each mapped...
multi.mantel
Multiple matrix regression (partial Mantel test)
multiRF
Computes Robinson-Foulds distance between a set of trees
nodeHeights
Compute the heights above the root of each node
nodelabels.cophylo
Add labels to a plotted "cophylo" object
optim.phylo.ls
Phylogeny inference using the least squares method
orderMappedEdge
Order the columns of mapped.edge to match across trees
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
phenogram
Plot phenogram (traitgram)
phylANOVA
Phylogenetic ANOVA and post-hoc tests
phyl.cca
Phylogenetic canonical correlation analysis
phyloDesign
Compute design matrix for least squares analyses
phylo.heatmap
Creates a phylogenetic heat map
phylomorphospace
Creates phylomorphospace plot
phylomorphospace3d
Creates tree-dimensional phylomorphospace plot
phylosig
Compute phylogenetic signal with two methods
phylo.toBackbone
Converts tree to backbone or vice versa
phylo.to.map
Plot tree with tips linked to geographic coordinates
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
phytools-package
phytools: Phylogenetic Tools for comparative biology (and...
plot.backbonePhylo
Plots backbone tree with triangles as clades
plotBranchbyTrait
Plot branch colors by a quantitative trait or value
plotSimmap
Plot stochastic character mapped tree
plotThresh
Tree plotting with posterior probabilities of ancestral...
plotTree
Plots rooted phylogenetic tree
plotTree.wBars
Plot a tree with bars at the tips
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
print.backbonePhylo
Print method for backbone phylogeny
ratebystate
Method for investigating the rate of one trait as a function...
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.phylo
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
resolveNode
Compute all possible resolutions of a node or all nodes in a...
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
sampleFrom
Sample from a set of distributions
setMap
Set color map for objects of class '"contMap"' or...
sim.corrs
Multivariate Brownian simulation with multiple correlations...
sim.history
Simulate stochastic character history under some model
sim.ratebystate
Conduct simulation of state dependent rate variation
sim.rates
Brownian simulation with multiple evolutionary rates
skewers
Matrix comparison using the method of random skewers
splitEdgeColor
Split edge colors when descendant edges have different mapped...
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
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...
to.matrix
Convert a character vector to a binary matrix
treeSlice
Slices the tree at a particular point and returns all...
untangle
Attempts to untangle crossing branches for plotting
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
writeAncestors
Write a tree to file with ancestral states and (optionally)...
writeNexus
Write a tree to file in Nexus format
write.simmap
Write a stochastic character mapped tree to file

Files in this package

phytools
phytools/inst
phytools/inst/CITATION
phytools/NAMESPACE
phytools/data
phytools/data/anoletree.rda
phytools/R
phytools/R/backbonePhylo.R
phytools/R/fitMk.R
phytools/R/read.newick.R
phytools/R/ls.consensus.R
phytools/R/paintSubTree.R
phytools/R/contMap.R
phytools/R/cophylo.R
phytools/R/plotBranchbyTrait.R
phytools/R/sim.rates.R
phytools/R/splitplotTree.R
phytools/R/anc.ML.R
phytools/R/add.species.to.genus.R
phytools/R/phyl.resid.R
phytools/R/make.simmap.R
phytools/R/locate.fossil.R
phytools/R/ratebystate.R
phytools/R/bmPlot.R
phytools/R/multi.mantel.R
phytools/R/phylo.heatmap.R
phytools/R/phylomorphospace.R
phytools/R/phyl.pairedttest.R
phytools/R/densityMap.R
phytools/R/rerootingMethod.R
phytools/R/estDiversity.R
phytools/R/fastAnc.R
phytools/R/phylANOVA.R
phytools/R/pgls.Ives.R
phytools/R/optim.phylo.ls.R
phytools/R/utilities.R
phytools/R/consensus.edges.R
phytools/R/rateshift.R
phytools/R/export.as.xml.R
phytools/R/add.everywhere.R
phytools/R/phyl.pca.R
phytools/R/ltt.R
phytools/R/add.random.R
phytools/R/mcmcLambda.R
phytools/R/densityTree.R
phytools/R/writeAncestors.R
phytools/R/collapseTree.R
phytools/R/fancyTree.R
phytools/R/pbtree.R
phytools/R/cospeciation.R
phytools/R/allFurcTrees.R
phytools/R/resolveNodes.R
phytools/R/phyl.cca.R
phytools/R/starTree.R
phytools/R/plotSimmap.R
phytools/R/ancThresh.R
phytools/R/plotTree.wBars.R
phytools/R/evol.rate.mcmc.R
phytools/R/mrp.supertree.R
phytools/R/phylo.to.map.R
phytools/R/write.simmap.R
phytools/R/mcmcBM.full.R
phytools/R/fastBM.R
phytools/R/exhaustiveMP.R
phytools/R/ltt95.R
phytools/R/sim.history.R
phytools/R/evol.vcv.R
phytools/R/phylosig.R
phytools/R/map.to.singleton.R
phytools/R/threshBayes.R
phytools/R/fitDiversityModel.R
phytools/R/fitPagel.R
phytools/R/treeSlice.R
phytools/R/phylomorphospace3d.R
phytools/R/evolvcv.lite.R
phytools/R/fitBayes.R
phytools/R/anc.Bayes.R
phytools/R/multiRF.R
phytools/R/branching.diffusion.R
phytools/R/read.simmap.R
phytools/R/map.overlap.R
phytools/R/skewers.R
phytools/R/phyl.RMA.R
phytools/R/drop.tip.simmap.R
phytools/R/phenogram.R
phytools/R/dotTree.R
phytools/R/writeNexus.R
phytools/R/brownieREML.R
phytools/R/strahlerNumber.R
phytools/R/sim.corrs.R
phytools/R/roundPhylogram.R
phytools/R/mcmcBM.R
phytools/R/make.era.map.R
phytools/R/anc.trend.R
phytools/R/brownie.lite.R
phytools/R/locate.yeti.R
phytools/MD5
phytools/DESCRIPTION
phytools/man
phytools/man/markChanges.Rd
phytools/man/nodeHeights.Rd
phytools/man/posterior.evolrate.Rd
phytools/man/cophylo.Rd
phytools/man/brownie.lite.Rd
phytools/man/add.simmap.legend.Rd
phytools/man/ave.rates.Rd
phytools/man/anc.Bayes.Rd
phytools/man/phylANOVA.Rd
phytools/man/paste.tree.Rd
phytools/man/branching.diffusion.Rd
phytools/man/fitDiversityModel.Rd
phytools/man/getCladesofSize.Rd
phytools/man/evol.rate.mcmc.Rd
phytools/man/cospeciation.Rd
phytools/man/locate.fossil.Rd
phytools/man/averageTree.Rd
phytools/man/countSimmap.Rd
phytools/man/ls.tree.Rd
phytools/man/writeAncestors.Rd
phytools/man/findMRCA.Rd
phytools/man/anc.trend.Rd
phytools/man/threshState.Rd
phytools/man/phyl.vcv.Rd
phytools/man/rateshift.Rd
phytools/man/bd.Rd
phytools/man/orderMappedEdge.Rd
phytools/man/splitTree.Rd
phytools/man/writeNexus.Rd
phytools/man/bmPlot.Rd
phytools/man/splitplotTree.Rd
phytools/man/applyBranchLengths.Rd
phytools/man/getSisters.Rd
phytools/man/add.species.to.genus.Rd
phytools/man/ladderize.simmap.Rd
phytools/man/getExtant.Rd
phytools/man/add.arrow.Rd
phytools/man/minRotate.Rd
phytools/man/plotTree.Rd
phytools/man/phyloDesign.Rd
phytools/man/sim.rates.Rd
phytools/man/rotateNodes.Rd
phytools/man/ltt95.Rd
phytools/man/contMap.Rd
phytools/man/di2multi.simmap.Rd
phytools/man/phyl.cca.Rd
phytools/man/sim.corrs.Rd
phytools/man/mrp.supertree.Rd
phytools/man/ltt.Rd
phytools/man/phylo.to.map.Rd
phytools/man/fancyTree.Rd
phytools/man/reroot.Rd
phytools/man/multi.mantel.Rd
phytools/man/map.overlap.Rd
phytools/man/roundPhylogram.Rd
phytools/man/edgeProbs.Rd
phytools/man/skewers.Rd
phytools/man/add.color.bar.Rd
phytools/man/add.everywhere.Rd
phytools/man/make.era.map.Rd
phytools/man/mergeMappedStates.Rd
phytools/man/sampleFrom.Rd
phytools/man/starTree.Rd
phytools/man/treeSlice.Rd
phytools/man/fitBayes.Rd
phytools/man/nodelabels.cophylo.Rd
phytools/man/locate.yeti.Rd
phytools/man/fastAnc.Rd
phytools/man/drop.leaves.Rd
phytools/man/plotSimmap.Rd
phytools/man/strahlerNumber.Rd
phytools/man/read.simmap.Rd
phytools/man/evol.vcv.Rd
phytools/man/print.backbonePhylo.Rd
phytools/man/bind.tip.Rd
phytools/man/ancThresh.Rd
phytools/man/matchNodes.Rd
phytools/man/phylomorphospace.Rd
phytools/man/consensus.edges.Rd
phytools/man/multiC.Rd
phytools/man/plot.backbonePhylo.Rd
phytools/man/phenogram.Rd
phytools/man/minSplit.Rd
phytools/man/densityMap.Rd
phytools/man/optim.phylo.ls.Rd
phytools/man/to.matrix.Rd
phytools/man/setMap.Rd
phytools/man/likMlambda.Rd
phytools/man/phyl.pca.Rd
phytools/man/untangle.Rd
phytools/man/sim.history.Rd
phytools/man/threshBayes.Rd
phytools/man/plotThresh.Rd
phytools/man/anoletree.Rd
phytools/man/splitEdgeColor.Rd
phytools/man/vcvPhylo.Rd
phytools/man/phylosig.Rd
phytools/man/read.newick.Rd
phytools/man/plotBranchbyTrait.Rd
phytools/man/export.as.xml.Rd
phytools/man/rerootingMethod.Rd
phytools/man/map.to.singleton.Rd
phytools/man/reorder.backbonePhylo.Rd
phytools/man/paintSubTree.Rd
phytools/man/phylo.heatmap.Rd
phytools/man/allFurcTrees.Rd
phytools/man/exhaustiveMP.Rd
phytools/man/write.simmap.Rd
phytools/man/phyl.pairedttest.Rd
phytools/man/threshDIC.Rd
phytools/man/make.simmap.Rd
phytools/man/multiRF.Rd
phytools/man/fastBM.Rd
phytools/man/reorderSimmap.Rd
phytools/man/phylo.toBackbone.Rd
phytools/man/aic.w.Rd
phytools/man/phytools-package.Rd
phytools/man/cladelabels.Rd
phytools/man/lambda.transform.Rd
phytools/man/modified.Grafen.Rd
phytools/man/mapped.states.Rd
phytools/man/as.multiPhylo.Rd
phytools/man/densityTree.Rd
phytools/man/fastMRCA.Rd
phytools/man/pgls.Ives.Rd
phytools/man/fitPagel.Rd
phytools/man/resolveNode.Rd
phytools/man/bind.tree.simmap.Rd
phytools/man/describe.simmap.Rd
phytools/man/drop.tip.contMap.Rd
phytools/man/midpoint.root.Rd
phytools/man/phylomorphospace3d.Rd
phytools/man/getStates.Rd
phytools/man/phyl.RMA.Rd
phytools/man/roundBranches.Rd
phytools/man/gammatest.Rd
phytools/man/genSeq.Rd
phytools/man/expm.Rd
phytools/man/phyl.resid.Rd
phytools/man/anc.ML.Rd
phytools/man/fitMk.Rd
phytools/man/rep.phylo.Rd
phytools/man/dotTree.Rd
phytools/man/estDiversity.Rd
phytools/man/rescaleSimmap.Rd
phytools/man/evolvcv.lite.Rd
phytools/man/rstate.Rd
phytools/man/pbtree.Rd
phytools/man/add.random.Rd
phytools/man/plotTree.wBars.Rd
phytools/man/ratebystate.Rd
phytools/man/brownieREML.Rd
phytools/man/sim.ratebystate.Rd
phytools/man/getDescendants.Rd
phytools/man/collapseTree.Rd
phytools/man/drop.clade.Rd
phytools/man/collapse.to.star.Rd
phytools/man/drop.tip.simmap.Rd