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phytools (version 0.2-20)
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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Install
install.packages('phytools')
Monthly Downloads
11,883
Version
0.2-20
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
February 17th, 2013
Functions in phytools (0.2-20)
Search functions
fastBM
Fast Brownian simulation
densityMap
Plot posterior density of stochastic mapping on a tree
branching.diffusion
Animation of branching random diffusion
fastMRCA
Get the MRCA of a pair of tip taxa
phylANOVA
Phylogenetic ANOVA and post-hoc tests
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
applyBranchLengths
Applies the branch lengths of a reference tree to a target
drop.clade
Drop clade from a tree
threshState
Computes value for a threshold character from a liability and thresholds
exhaustiveMP
Exhaustive and branch & bound MP optimization
map.overlap
Proportional overlap between two mapped character histories on a tree
splitplotTree
Plots a phylogeny in two columns
getDescendants
Get descendant node numbers
pbtree
Simulate pure-birth stochastic tree or trees
phyloDesign
Compute design matrix for least squares analyses
lambda.transform
Lambda transformation of matrix
rescaleSimmap
Rescale SIMMAP style tree
threshBayes
Threshold model using Bayesian MCMC
rstate
Pick a random state according to a vector of probabilities
phyl.cca
Phylogenetic canonical correlation analysis
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
gammatest
Gamma test of Pybus & Harvey (2000)
roundBranches
Rounds the branch lengths of a tree
getSisters
Get the sister node, label, or set of nodes for a node or tip
phyl.pairedttest
Phylogenetic paired t-test
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
treeSlice
Slices the tree at a particular point and returns all subtrees
threshDIC
Deviance Information Criterion from the threshold model
findMRCA
Get the MRCA of a set of taxa
anc.Bayes
Bayesian ancestral character estimation
likMlambda
Likelihood for joint lambda
nodeHeights
Compute the heights above the root of each node
pgls.Ives
Phylogenetic regression with intraspecific sampling error
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
reroot
Re-root a tree along an edge
optim.phylo.ls
Phylogeny inference using the least squares method
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
mrp.supertree
Matrix representation parsimony supertree estimation
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
plotTree
Plots rooted phylogenetic tree
starTree
Create star phylogeny
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
ltt
Creates lineage-through-time plot (including extinct lineages)
export.as.xml
Export trees & data in XML format
sampleFrom
Sample from a set of distributions
sim.rates
Brownian simulation with multiple evolutionary rates
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
allFurcTrees
Generate all bi- and multifurcating unrooted trees
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
reorderSimmap
Reorder edges of a simmap tree
phylosig
Compute phylogenetic signal with two methods
write.simmap
Write a stochastic character mapped tree to file
splitTree
Split tree at a point
bind.tip
Attaches a new tip to a tree
brownie.lite
Likelihood test for rate variation
read.simmap
Read SIMMAP style trees from file
phylomorphospace3d
Creates phylomorphospace plot
add.everywhere
Add tip to all edges in a tree
ave.rates
Average the posterior rates
expm
Matrix exponential
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
estDiversity
Estimate diversity at each node of the tree
add.random
Add tip to all edges in a tree
orderMappedEdge
Matches nodes between two trees
contMap
Map continuous trait evolution on the tree
ls.tree
Least squares branch lengths for a given tree
phyl.pca
Phylogenetic principal components analysis
multi.mantel
Multiple matrix regression (partial Mantel test)
minSplit
Finding the minimum (median) split in the posterior sample
read.newick
Read Newick style tree
writeNexus
Write a stochastic character mapped tree to file
phylomorphospace
Creates phylomorphospace plot
make.simmap
Simulate stochastic character map on a phylogenetic tree
anc.ML
Ancestral character estimation using likelihood
anc.trend
Ancestral character estimation with a trend
fancyTree
Plots special types of phylogenetic trees
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
make.era.map
Create "era" map on a phylogenetic tree
paintSubTree
Paint sub-trees with a discrete character
xkcdTree
Plot xkcd style tree
drop.tip.simmap
Drop tip from SIMMAP format tree
matchNodes
Matches nodes between two trees
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
phyl.resid
Phylogenetic size-correction via GLS regression
plotSimmap
Plot stochastic character mapped tree
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
brownieREML
REML version of brownie.lite
fastAnc
Fast estimation of ML ancestral states
plotThresh
Tree plotting with posterior probabilities of ancestral states from the threshold model
phenogram
Plot phenogram (traitgram)
sim.history
Simulate stochastic character history under some model
paste.tree
Paste two trees together