RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (2.1-1) of this package.
Take me there.
phytools (version 0.4-21)
Phylogenetic Tools for comparative biology (and other things)
Description
phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.
Copy Link
Copy
Link to current version
Version
Version
2.1-1
2.0-3
1.9-16
1.5-1
1.2-0
1.0-3
1.0-1
0.7-90
0.7-80
0.7-70
0.7-47
0.7-20
0.6-99
0.6-60
0.6-44
0.6-20
0.6-00
0.5-64
0.5-38
0.5-20
0.5-10
0.5-00
0.4-60
0.4-56
0.4-45
0.4-31
0.4-21
0.4-05
0.3-93
0.3-72.1
0.3-10
0.2-90
0.2-80
0.2-70
0.2-50
0.2-40
0.2-30
0.2-20
0.2-1
0.2-0
0.1-9
0.1-8
0.1-7
0.1-6
0.1-5
0.1-2
0.1-0
0.0-8
Down Chevron
Install
install.packages('phytools')
Monthly Downloads
11,883
Version
0.4-21
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
June 28th, 2014
Functions in phytools (0.4-21)
Search functions
allFurcTrees
Generate all bi- and multifurcating unrooted trees
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
add.species.to.genus
Add species to genus on a phylogeny
make.simmap
Simulate stochastic character maps on a phylogenetic tree or trees
anc.Bayes
Bayesian ancestral character estimation
di2multi.simmap
Collapse branches of zero length to polytomy in stochastic map style tree
countSimmap
Counts the number of character changes on a SIMMAP style tree or set of trees
add.random
Add tips at random to the tree
drop.clade
Drop a clade from a tree
add.simmap.legend
Add legend to stochastically mapped tree
branching.diffusion
Animation of branching random diffusion
ave.rates
Average the posterior rates
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
brownieREML
REML version of brownie.lite
findMRCA
Get the MRCA of a set of taxa
fancyTree
Plots special types of phylogenetic trees
bind.tip
Attaches a new tip to a tree
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
midpoint.root
Midpoint root a phylogeny
optim.phylo.ls
Phylogeny inference using the least squares method
applyBranchLengths
Applies the branch lengths of a reference tree to a target
getSisters
Get the sister node number, label, or set of nodes for a node or tip
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
brownie.lite
Likelihood test for rate variation in a continuous trait
drop.leaves
Drop all the leaves (tips) from a tree
matchNodes
Matches nodes between two trees
densityMap
Plot posterior density of stochastic mapping on a tree
phyl.pairedttest
Phylogenetic paired t-test
minSplit
Finding the minimum (median) split in the posterior sample
estDiversity
Estimate diversity at each node of the tree
plot.backbonePhylo
Plots backbone tree with triangles as clades
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
ltt
Creates lineage-through-time plot (including extinct lineages)
anc.ML
Ancestral character estimation using likelihood
fastAnc
Fast estimation of ML ancestral states
add.everywhere
Add tip to all edges in a tree
repPhylo
Replicate a tree into a list of trees
getCladesofSize
Get all subtrees larger than or equal to a specified size
add.color.bar
Add color bar to a plot
anoletree
Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
fastBM
Fast Brownian simulation
phylosig
Compute phylogenetic signal with two methods
gammatest
Gamma test of Pybus & Harvey (2000)
likMlambda
Likelihood for joint lambda
export.as.xml
Export trees & data in XML format
anc.trend
Ancestral character estimation with a trend
collapse.to.star
Collapse a subtree to a star phylogeny
rstate
Pick a random state according to a vector of probabilities
threshState
Computes value for a threshold character from a liability and thresholds
phyl.pca
Phylogenetic principal components analysis
lambda.transform
Lambda transformation of matrix
phylomorphospace3d
Creates tree-dimensional phylomorphospace plot
minRotate
Rotates all nodes of the tree to minimize the difference in order with a vector
reroot
Re-root a tree along an edge
print.backbonePhylo
Print method for backbone phylogeny
phylANOVA
Phylogenetic ANOVA and post-hoc tests
getStates
Get the states at nodes or tips from a mapped tree
multiRF
Computes Robinson-Foulds distance between a set of trees
orderMappedEdge
Order the columns of mapped.edge to match across trees
make.era.map
Create "era" map on a phylogenetic tree
paintSubTree
Paint sub-trees with a discrete character
nodeHeights
Compute the heights above the root of each node
roundPhylogram
Plot a round phylogram
locate.yeti
Locate a cryptic, recently extinct, or missing taxon on a tree
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
sampleFrom
Sample from a set of distributions
setMap
Set color map for objects of class
"contMap"
or
"densityMap"
paste.tree
Paste two trees together
contMap
Map continuous trait evolution on the tree
sim.rates
Brownian simulation with multiple evolutionary rates
pgls.Ives
Phylogenetic regression with intraspecific sampling error
phyl.cca
Phylogenetic canonical correlation analysis
phyloDesign
Compute design matrix for least squares analyses
mergeMappedStates
Merge two or more mapped states into one state
exhaustiveMP
Exhaustive and branch & bound MP optimization
read.simmap
Read SIMMAP style trees from file
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
pbtree
Simulate pure-birth or birth-death stochastic tree or trees
getDescendants
Get descendant node numbers
phylo.to.map
Plot tree with tips linked to geographic coordinates
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
ls.tree
Least squares branch lengths for a given tree
plotBranchbyTrait
Plot branch colors by a quantitative trait or value
reorder.backbonePhylo
Reorders a backbone phylogeny
map.to.singleton
Converts a mapped tree to a tree with singleton nodes
plotThresh
Tree plotting with posterior probabilities of ancestral states from the threshold model
phyl.resid
Phylogenetic size-correction via GLS regression
multi.mantel
Multiple matrix regression (partial Mantel test)
expm
Matrix exponential
untangle
Attempts to untangle crossing branches for plotting
roundBranches
Rounds the branch lengths of a tree
rateshift
Find the temporal position of one or more rate shifts
map.overlap
Proportional overlap between two mapped character histories on a tree
ratebystate
Method for investigating the rate of one trait as a function of the state of another
rotateNodes
Rotates a node or set of nodes in a phylogenetic tree
rerootingMethod
Get marginal ancestral state reconstructions by re-rooting
strahlerNumber
Computes Strahler number for trees and nodes
phenogram
Plot phenogram (traitgram)
to.matrix
Convert a character vector to a binary matrix
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
plotSimmap
Plot stochastic character mapped tree
writeNexus
Write a tree to file in Nexus format
plotTree
Plots rooted phylogenetic tree
plotTree.wBars
Plot a tree with bars at the tips
write.simmap
Write a stochastic character mapped tree to file
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
treeSlice
Slices the tree at a particular point and returns all subtrees
reorderSimmap
Reorder edges of a simmap tree
skewers
Matrix comparison using the method of random skewers
phylomorphospace
Creates phylomorphospace plot
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
read.newick
Robust Newick style tree reader
starTree
Create star phylogeny
rescaleSimmap
Rescale SIMMAP style tree
splitTree
Split tree at a point
threshBayes
Threshold model using Bayesian MCMC
cladelabels
Add labels to subtrees of a plotted phylogeny
describe.simmap
Summarizes a stochastic mapped tree or set of trees
fastMRCA
Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
drop.tip.simmap
Drop tips or extract clade from tree with mapped discrete character
genSeq
Simulate a DNA alignment on the tree under a model
ltt95
Creates a (1-$\alpha$)-percent CI for a set of LTTs
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
mrp.supertree
Matrix representation parsimony supertree estimation
phylo.toBackbone
Converts tree to backbone or vice versa
sim.history
Simulate stochastic character history under some model
sim.ratebystate
Conduct simulation of state dependent rate variation
threshDIC
Deviance Information Criterion from the threshold model
splitplotTree
Plots a phylogeny in two columns
writeAncestors
Write a tree to file with ancestral states and (optionally) CIs at nodes