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phytools (version 0.2-80)
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
0.2-80
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
May 31st, 2013
Functions in phytools (0.2-80)
Search functions
branching.diffusion
Animation of branching random diffusion
anoletree
Phylogeny of 100 Greater Antillean anole species with mapped discrete character
findMRCA
Get the MRCA of a set of taxa
orderMappedEdge
Order the columns of mapped.edge to match across trees
anc.trend
Ancestral character estimation with a trend
pbtree
Simulate pure-birth or birth-death stochastic tree or trees
pgls.Ives
Phylogenetic regression with intraspecific sampling error
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
brownie.lite
Likelihood test for rate variation in a continuous trait
fancyTree
Plots special types of phylogenetic trees
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
getStates
Get the states at nodes or tips from a mapped tree
densityMap
Plot posterior density of stochastic mapping on a tree
read.newick
Read Newick style tree
gammatest
Gamma test of Pybus & Harvey (2000)
threshState
Computes value for a threshold character from a liability and thresholds
plotTree
Plots rooted phylogenetic tree
splitTree
Split tree at a point
rstate
Pick a random state according to a vector of probabilities
rerootingMethod
Get marginal ancestral state reconstructions by re-rooting
threshBayes
Threshold model using Bayesian MCMC
to.matrix
Convert a character vector to a binary matrix
make.era.map
Create "era" map on a phylogenetic tree
threshDIC
Deviance Information Criterion from the threshold model
writeAncestors
Write a tree to file with ancestral states and (optionally) CIs at nodes
read.simmap
Read SIMMAP style trees from file
ltt
Creates lineage-through-time plot (including extinct lineages)
phylANOVA
Phylogenetic ANOVA and post-hoc tests
ls.tree
Least squares branch lengths for a given tree
optim.phylo.ls
Phylogeny inference using the least squares method
anc.Bayes
Bayesian ancestral character estimation
bind.tip
Attaches a new tip to a tree
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
export.as.xml
Export trees & data in XML format
plotSimmap
Plot stochastic character mapped tree
add.random
Add tips at random to the tree
applyBranchLengths
Applies the branch lengths of a reference tree to a target
phyl.cca
Phylogenetic canonical correlation analysis
ave.rates
Average the posterior rates
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
phyloDesign
Compute design matrix for least squares analyses
sim.ratebystate
Conduct simulation of state dependent rate variation
xkcdTree
Plot xkcd style tree
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
repPhylo
Replicate a tree into a list of trees
mrp.supertree
Matrix representation parsimony supertree estimation
treeSlice
Slices the tree at a particular point and returns all subtrees
allFurcTrees
Generate all bi- and multifurcating unrooted trees
getDescendants
Get descendant node numbers
lambda.transform
Lambda transformation of matrix
map.overlap
Proportional overlap between two mapped character histories on a tree
phylomorphospace
Creates phylomorphospace plot
ratebystate
Method for investigating the rate of one trait as a function of the state of another
fastMRCA
Get the MRCA of a pair of tip taxa
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
add.color.bar
Add color bar to a plot
expm
Matrix exponential
phyl.pca
Phylogenetic principal components analysis
plotThresh
Tree plotting with posterior probabilities of ancestral states from the threshold model
phylosig
Compute phylogenetic signal with two methods
phenogram
Plot phenogram (traitgram)
sampleFrom
Sample from a set of distributions
drop.clade
Drop a clade from a tree
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
getCladesofSize
Get all subtrees larger than or equal to a specified size
make.simmap
Simulate stochastic character maps on a phylogenetic tree or trees
nodeHeights
Compute the heights above the root of each node
paste.tree
Paste two trees together
reroot
Re-root a tree along an edge
sim.history
Simulate stochastic character history under some model
sim.rates
Brownian simulation with multiple evolutionary rates
add.everywhere
Add tip to all edges in a tree
anc.ML
Ancestral character estimation using likelihood
drop.tip.simmap
Drop tips or extract clade from tree with mapped discrete character
describe.simmap
Summarizes a stochastic mapped tree or set of trees
paintSubTree
Paint sub-trees with a discrete character
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
minSplit
Finding the minimum (median) split in the posterior sample
matchNodes
Matches nodes between two trees
splitplotTree
Plots a phylogeny in two columns
write.simmap
Write a stochastic character mapped tree to file
strahlerNumber
Computes Strahler number for trees and nodes
fastAnc
Fast estimation of ML ancestral states
ltt95
Creates a (1-$\alpha$)-percent CI for a set of LTTs
fastBM
Fast Brownian simulation
mergeMappedStates
Merge two or more mapped states into one state
multi.mantel
Multiple matrix regression (partial Mantel test)
phyl.resid
Phylogenetic size-correction via GLS regression
plotBranchbyTrait
Plot branch colors by a quantitative trait or value
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
starTree
Create star phylogeny
countSimmap
Counts the number of character changes on a SIMMAP style tree or set of trees
brownieREML
REML version of brownie.lite
contMap
Map continuous trait evolution on the tree
estDiversity
Estimate diversity at each node of the tree
exhaustiveMP
Exhaustive and branch & bound MP optimization
getSisters
Get the sister node number, label, or set of nodes for a node or tip
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
likMlambda
Likelihood for joint lambda
phyl.pairedttest
Phylogenetic paired t-test
phylomorphospace3d
Creates tree-dimensional phylomorphospace plot
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
roundBranches
Rounds the branch lengths of a tree
reorderSimmap
Reorder edges of a simmap tree
rescaleSimmap
Rescale SIMMAP style tree
untangle
Attempts to untangle crossing branches for plotting
writeNexus
Write a tree to file in Nexus format