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phytools (version 0.1-0)
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
0.1-0
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
October 17th, 2011
Functions in phytools (0.1-0)
Search all functions
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
reroot
Re-root a tree along an edge
lambda.transform
Lambda transformation of matrix
make.simmap
Simulate stochastic character map on a phylogenetic tree
phyl.pca
Phylogenetic principal components analysis
optim.phylo.ls
Phylogeny inference using the least squares method
phylANOVA
Generate all bi- and multifurcating unrooted trees
phylomorphospace
Creates phylomorphospace plot
sim.rates
Brownian simulationn with multiple evolutionary rates
drop.tip.simmap
Drop tip from SIMMAP format tree
phyloDesign
Compute design matrix for least squares analyses
read.newick
Read Newick style tree
nodeHeights
Compute the heights above the root of each node
ltt
Creates lineage-through-time plot (including extinct lineages)
read.simmap
Read SIMMAP style trees from file
paste.tree
Paste two trees together
brownie.lite
Likelihood test for rate variation
starTree
Create star phylogeny
plotTree
Plots rooted phylogenetic tree
plotSimmap
Plot stochastic character mapped tree
treeSlice
Slices the tree at a particular point and returns all subtrees
add.everywhere
Add tip to all edges in a tree
exhaustiveMP
Exhaustive and branch & bound MP optimization
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
reorderSimmap
Reorder edges of a simmap tree
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
estDiversity
Estimate diversity at each node of the tree
fastBM
Fast Brownian simulation
phyl.vcv
Compute phylogenetic VCV matrix for a tree & dataset
mrp.supertree
Matrix representation parsimony supertree estimation
map.overlap
Ancestral character estimation with a trend
phyl.cca
Phylogenetic canonical correlation analysis
rstate
Pick a random state according to a vector of probabilities
anc.trend
Ancestral character estimation with a trend
drop.clade
Drop clade from a tree
write.simmap
Simulate stochastic character map on a phylogenetic tree
expm
Matrix exponential
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
splitTree
Split tree at a point
allFurcTrees
Generate all bi- and multifurcating unrooted trees
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
branching.diffusion
Animation of branching random diffusion
ls.tree
Least squares branch lengths for a given tree
phyl.pairedttest
Phylogenetic paired t-test
phyl.resid
Phylogenetic size-correction via GLS regression
gammatest
Gamma test of Pybus & Harvey (2000)
minSplit
Finding the minimum (median) split in the posterior sample
phylosig
Compute phylogenetic signal with two methods
sim.history
Simulate stochastic character history under some model