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phytools (version 0.1-5)
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
12,223
Version
0.1-5
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
December 18th, 2011
Functions in phytools (0.1-5)
Search all functions
estDiversity
Estimate diversity at each node of the tree
rstate
Pick a random state according to a vector of probabilities
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
treeSlice
Slices the tree at a particular point and returns all subtrees
phyloDesign
Compute design matrix for least squares analyses
phyl.vcv
Compute phylogenetic VCV matrix for a tree & dataset
starTree
Create star phylogeny
nodeHeights
Compute the heights above the root of each node
make.era.map
Create "era" map on a phylogenetic tree
phenogram
Plot phenogram (traitgram)
read.simmap
Read SIMMAP style trees from file
sim.history
Simulate stochastic character history under some model
map.overlap
Proportional overlap between two mapped character histories on a tree
anc.ML
Ancestral character estimation using likelihood
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
brownie.lite
Likelihood test for rate variation
allFurcTrees
Generate all bi- and multifurcating unrooted trees
make.simmap
Simulate stochastic character map on a phylogenetic tree
plotSimmap
Plot stochastic character mapped tree
phylosig
Compute phylogenetic signal with two methods
read.newick
Read Newick style tree
fastBM
Fast Brownian simulation
phyl.pairedttest
Phylogenetic paired t-test
drop.clade
Drop clade from a tree
optim.phylo.ls
Phylogeny inference using the least squares method
anc.trend
Ancestral character estimation with a trend
phyl.resid
Phylogenetic size-correction via GLS regression
add.everywhere
Add tip to all edges in a tree
anc.Bayes
Bayesian ancestral character estimation
brownieREML
REML version of brownie.lite
mrp.supertree
Matrix representation parsimony supertree estimation
ltt
Creates lineage-through-time plot (including extinct lineages)
gammatest
Gamma test of Pybus & Harvey (2000)
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
phyl.cca
Phylogenetic canonical correlation analysis
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
paste.tree
Paste two trees together
phylANOVA
Generate all bi- and multifurcating unrooted trees
write.simmap
Simulate stochastic character map on a phylogenetic tree
drop.tip.simmap
Drop tip from SIMMAP format tree
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
phyl.pca
Phylogenetic principal components analysis
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
minSplit
Finding the minimum (median) split in the posterior sample
plotTree
Plots rooted phylogenetic tree
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
ls.tree
Least squares branch lengths for a given tree
lambda.transform
Lambda transformation of matrix
phylomorphospace
Creates phylomorphospace plot
sim.rates
Brownian simulationn with multiple evolutionary rates
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
splitTree
Split tree at a point
expm
Matrix exponential
reroot
Re-root a tree along an edge
exhaustiveMP
Exhaustive and branch & bound MP optimization
branching.diffusion
Animation of branching random diffusion
reorderSimmap
Reorder edges of a simmap tree