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phytools (version 0.1-2)
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
0.1-2
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
November 27th, 2011
Functions in phytools (0.1-2)
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anc.trend
Ancestral character estimation with a trend
anc.Bayes
Bayesian ancestral character estimation
make.era.map
Create "era" map on a phylogenetic tree
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
ltt
Creates lineage-through-time plot (including extinct lineages)
allFurcTrees
Generate all bi- and multifurcating unrooted trees
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
drop.clade
Drop clade from a tree
fastBM
Fast Brownian simulation
phyl.vcv
Compute phylogenetic VCV matrix for a tree & dataset
optim.phylo.ls
Phylogeny inference using the least squares method
phyloDesign
Compute design matrix for least squares analyses
sim.rates
Brownian simulationn with multiple evolutionary rates
write.simmap
Simulate stochastic character map on a phylogenetic tree
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
read.simmap
Read SIMMAP style trees from file
drop.tip.simmap
Drop tip from SIMMAP format tree
brownieREML
REML version of brownie.lite
mrp.supertree
Matrix representation parsimony supertree estimation
paste.tree
Paste two trees together
phylANOVA
Generate all bi- and multifurcating unrooted trees
phyl.resid
Phylogenetic size-correction via GLS regression
treeSlice
Slices the tree at a particular point and returns all subtrees
plotSimmap
Plot stochastic character mapped tree
starTree
Create star phylogeny
sim.history
Simulate stochastic character history under some model
expm
Matrix exponential
gammatest
Gamma test of Pybus & Harvey (2000)
read.newick
Read Newick style tree
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
plotTree
Plots rooted phylogenetic tree
phylomorphospace
Creates phylomorphospace plot
add.everywhere
Add tip to all edges in a tree
lambda.transform
Lambda transformation of matrix
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
ls.tree
Least squares branch lengths for a given tree
map.overlap
Ancestral character estimation with a trend
minSplit
Finding the minimum (median) split in the posterior sample
phyl.pairedttest
Phylogenetic paired t-test
reorderSimmap
Reorder edges of a simmap tree
branching.diffusion
Animation of branching random diffusion
brownie.lite
Likelihood test for rate variation
nodeHeights
Compute the heights above the root of each node
phyl.pca
Phylogenetic principal components analysis
phylosig
Compute phylogenetic signal with two methods
rstate
Pick a random state according to a vector of probabilities
reroot
Re-root a tree along an edge
exhaustiveMP
Exhaustive and branch & bound MP optimization
make.simmap
Simulate stochastic character map on a phylogenetic tree
splitTree
Split tree at a point
estDiversity
Estimate diversity at each node of the tree
phyl.cca
Phylogenetic canonical correlation analysis
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix