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phytools (version 0.1-9)
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
12,126
Version
0.1-9
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
August 8th, 2012
Functions in phytools (0.1-9)
Search all functions
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
add.everywhere
Add tip to all edges in a tree
estDiversity
Estimate diversity at each node of the tree
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
fastBM
Fast Brownian simulation
ltt
Creates lineage-through-time plot (including extinct lineages)
read.simmap
Read SIMMAP style trees from file
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
phyl.pca
Phylogenetic principal components analysis
anc.trend
Ancestral character estimation with a trend
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
branching.diffusion
Animation of branching random diffusion
phyloDesign
Compute design matrix for least squares analyses
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
ls.tree
Least squares branch lengths for a given tree
phylANOVA
Phylogenetic ANOVA and post-hoc tests
exhaustiveMP
Exhaustive and branch & bound MP optimization
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
export.as.xml
Export trees & data in XML format
treeSlice
Slices the tree at a particular point and returns all subtrees
gammatest
Gamma test of Pybus & Harvey (2000)
write.simmap
Simulate stochastic character map on a phylogenetic tree
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
allFurcTrees
Generate all bi- and multifurcating unrooted trees
brownie.lite
Likelihood test for rate variation
pbtree
Simulate pure-birth stochastic tree or trees
mrp.supertree
Matrix representation parsimony supertree estimation
brownieREML
REML version of brownie.lite
findMRCA
Get the MRCA of a set of taxa
fastMRCA
Get the MRCA of a pair of tip taxa
make.simmap
Simulate stochastic character map on a phylogenetic tree
map.overlap
Proportional overlap between two mapped character histories on a tree
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
paste.tree
Paste two trees together
plotSimmap
Plot stochastic character mapped tree
plotTree
Plots rooted phylogenetic tree
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
sampleFrom
Sample from a set of distributions
phenogram
Plot phenogram (traitgram)
phylomorphospace3d
Creates phylomorphospace plot
anc.ML
Ancestral character estimation using likelihood
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
reorderSimmap
Reorder edges of a simmap tree
rescaleSimmap
Rescale SIMMAP style tree
sim.rates
Brownian simulation with multiple evolutionary rates
drop.tip.simmap
Drop tip from SIMMAP format tree
drop.clade
Drop clade from a tree
fancyTree
Plots special types of phylogenetic trees
getDescendants
Get descendant node numbers
pgls.Ives
Phylogenetic regression with intraspecific sampling error
phylosig
Compute phylogenetic signal with two methods
phyl.vcv
Compute phylogenetic VCV matrix for a tree & dataset
paintSubTree
Paint sub-trees with a discrete character
rstate
Pick a random state according to a vector of probabilities
phyl.resid
Phylogenetic size-correction via GLS regression
phylomorphospace
Creates phylomorphospace plot
expm
Matrix exponential
nodeHeights
Compute the heights above the root of each node
splitTree
Split tree at a point
optim.phylo.ls
Phylogeny inference using the least squares method
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
lambda.transform
Lambda transformation of matrix
sim.history
Simulate stochastic character history under some model
make.era.map
Create "era" map on a phylogenetic tree
read.newick
Read Newick style tree
phyl.pairedttest
Phylogenetic paired t-test
phyl.cca
Phylogenetic canonical correlation analysis
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
starTree
Create star phylogeny
minSplit
Finding the minimum (median) split in the posterior sample
anc.Bayes
Bayesian ancestral character estimation
reroot
Re-root a tree along an edge