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phytools (version 0.2-30)
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
0.2-30
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
March 20th, 2013
Functions in phytools (0.2-30)
Search functions
make.simmap
Simulate stochastic character map on a phylogenetic tree
applyBranchLengths
Applies the branch lengths of a reference tree to a target
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
reorderSimmap
Reorder edges of a simmap tree
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
writeNexus
Write a stochastic character mapped tree to file
allFurcTrees
Generate all bi- and multifurcating unrooted trees
sampleFrom
Sample from a set of distributions
getDescendants
Get descendant node numbers
ls.tree
Least squares branch lengths for a given tree
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
nodeHeights
Compute the heights above the root of each node
rstate
Pick a random state according to a vector of probabilities
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
matchNodes
Matches nodes between two trees
read.newick
Read Newick style tree
fastAnc
Fast estimation of ML ancestral states
phyl.pca
Phylogenetic principal components analysis
phyl.resid
Phylogenetic size-correction via GLS regression
plotThresh
Tree plotting with posterior probabilities of ancestral states from the threshold model
getSisters
Get the sister node, label, or set of nodes for a node or tip
map.overlap
Proportional overlap between two mapped character histories on a tree
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
multi.mantel
Multiple matrix regression (partial Mantel test)
optim.phylo.ls
Phylogeny inference using the least squares method
roundBranches
Rounds the branch lengths of a tree
paste.tree
Paste two trees together
brownieREML
REML version of brownie.lite
ltt
Creates lineage-through-time plot (including extinct lineages)
rescaleSimmap
Rescale SIMMAP style tree
sim.rates
Brownian simulation with multiple evolutionary rates
drop.clade
Drop clade from a tree
pbtree
Simulate pure-birth stochastic tree or trees
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
pgls.Ives
Phylogenetic regression with intraspecific sampling error
likMlambda
Likelihood for joint lambda
paintSubTree
Paint sub-trees with a discrete character
orderMappedEdge
Order the columns of mapped.edge to match across trees
treeSlice
Slices the tree at a particular point and returns all subtrees
untangle
Attempts to untangle crossing branches for plotting
add.random
Add tips at random to the tree
findMRCA
Get the MRCA of a set of taxa
mrp.supertree
Matrix representation parsimony supertree estimation
threshBayes
Threshold model using Bayesian MCMC
splitplotTree
Plots a phylogeny in two columns
add.color.bar
Add color bar to a plot
drop.tip.simmap
Drop tip from SIMMAP format tree
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
phyl.pairedttest
Phylogenetic paired t-test
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
threshDIC
Deviance Information Criterion from the threshold model
countSimmap
Counts the number of character changes on a SIMMAP style tree or set of trees
fancyTree
Plots special types of phylogenetic trees
gammatest
Gamma test of Pybus & Harvey (2000)
phyl.cca
Phylogenetic canonical correlation analysis
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
brownie.lite
Likelihood test for rate variation
anc.trend
Ancestral character estimation with a trend
repPhylo
Replicate a tree into a list of trees
plotBranchbyTrait
Plot branch colors by a quantitative trait or value
threshState
Computes value for a threshold character from a liability and thresholds
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
add.everywhere
Add tip to all edges in a tree
export.as.xml
Export trees & data in XML format
minSplit
Finding the minimum (median) split in the posterior sample
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
sim.ratebystate
Conduct simulation of state dependent rate variation
read.simmap
Read SIMMAP style trees from file
splitTree
Split tree at a point
estDiversity
Estimate diversity at each node of the tree
branching.diffusion
Animation of branching random diffusion
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
fastMRCA
Get the MRCA of a pair of tip taxa
bind.tip
Attaches a new tip to a tree
densityMap
Plot posterior density of stochastic mapping on a tree
phylANOVA
Phylogenetic ANOVA and post-hoc tests
phylosig
Compute phylogenetic signal with two methods
sim.history
Simulate stochastic character history under some model
ave.rates
Average the posterior rates
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
phenogram
Plot phenogram (traitgram)
plotSimmap
Plot stochastic character mapped tree
write.simmap
Write a stochastic character mapped tree to file
xkcdTree
Plot xkcd style tree
anc.ML
Ancestral character estimation using likelihood
phylomorphospace3d
Creates phylomorphospace plot
ratebystate
Method for investigating the rate of one trait as a function of the state of another
reroot
Re-root a tree along an edge
contMap
Map continuous trait evolution on the tree
fastBM
Fast Brownian simulation
exhaustiveMP
Exhaustive and branch & bound MP optimization
make.era.map
Create "era" map on a phylogenetic tree
phylomorphospace
Creates phylomorphospace plot
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
expm
Matrix exponential
anc.Bayes
Bayesian ancestral character estimation
lambda.transform
Lambda transformation of matrix
phyloDesign
Compute design matrix for least squares analyses
plotTree
Plots rooted phylogenetic tree
writeAncestors
Write a tree to file with ancestral states and (optionally) CIs at nodes
starTree
Create star phylogeny