Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (2.4-4) of this package.
Take me there.
phytools (version 0.0-8)
Phylogenetic Tools for comparative biology (and other things)
Description
phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.
Copy Link
Link to current version
Version
Version
2.4-4
2.3-0
2.1-1
2.0-3
1.9-16
1.5-1
1.2-0
1.0-3
1.0-1
0.7-90
0.7-80
0.7-70
0.7-47
0.7-20
0.6-99
0.6-60
0.6-44
0.6-20
0.6-00
0.5-64
0.5-38
0.5-20
0.5-10
0.5-00
0.4-60
0.4-56
0.4-45
0.4-31
0.4-21
0.4-05
0.3-93
0.3-72.1
0.3-10
0.2-90
0.2-80
0.2-70
0.2-50
0.2-40
0.2-30
0.2-20
0.2-1
0.2-0
0.1-9
0.1-8
0.1-7
0.1-6
0.1-5
0.1-2
0.1-0
0.0-8
Install
install.packages('phytools')
Monthly Downloads
12,126
Version
0.0-8
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
August 20th, 2011
Functions in phytools (0.0-8)
Search all functions
allFurcTrees
Generate all bi- and multifurcating unrooted trees
nodeHeights
Estimate diversity at each node of the tree
phyl.resid
Phylogenetic size-correction via GLS regression
reroot
Re-root a tree along an edge
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
write.simmap
Simulate stochastic character map on a phylogenetic tree
reorderSimmap
Reorder edges of a simmap tree
anc.trend
Ancestral character estimation with a trend
minSplit
Finding the minimum (median) split in the posterior sample
compute.ancestor.nodes
Compute all ancestral nodes
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
fastBM
Fast Brownian simulation
starTree
Create star phylogeny
add.everywhere
Add tip to all edges in a tree
drop.tip.simmap
Drop tip from SIMMAP format tree
mrp.supertree
Matrix representation parsimony supertree estimation
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
plotTree
Plots rooted phylogenetic tree
phyl.pairedttest
Phylogenetic paired t-test
likelihood
Likelihood of evolutionary vcv matrix, for a particular lambda
ave.rates
Compute weighted average evolutionary rates
exhaustiveMP
Exhaustive and branch & bound MP optimization
phylANOVA
Generate all bi- and multifurcating unrooted trees
rstate
Pick a random state according to a vector of probabilities
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
lambda.transform
Lambda transformation of matrix
expm
Matrix exponential
gammatest
Gamma test of Pybus & Harvey (2000)
phylosig
Compute phylogenetic signal with two methods
phylomorphospace
Creates phylomorphospace plot
splitTree
Split tree at a point
add.to.branches.and.nodes
Add tip to branches and nodes of the tree
phyl.pca
Phylogenetic principal components analysis
whichorder
Which order are the edges of the tree
read.newick
Read Newick style tree
optim.phylo.ls
Phylogeny inference using the least squares method
tTests
Generate all bi- and multifurcating unrooted trees
brownie.lite
Likelihood test for rate variation
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
paste.tree
Paste tree
branch.and.bound
Perform branch & bound parsimony search
map.overlap
Ancestral character estimation with a trend
make.simmap
Simulate stochastic character map on a phylogenetic tree
phyl.vcv
Internal function
ltt
Creates lineage-through-time plot (including extinct lineages)
plotSimmap
Plot stochastic character mapped tree
drop.clade
Drop clade from a tree
read.simmap
Read SIMMAP style trees from file
likelihood.lambda
Likelihood of lambda transformation
phyloDesign
Compute design matrix for least squares analyses
branching.diffusion
Animation of branching random diffusion
exhaustive.search
Exhaustive MP search
estDiversity
Estimate diversity at each node of the tree
ls.tree
Least squares branch lengths for a given tree
treeSlice
Slices the tree at a particular point and returns all subtrees
fitDiversityModel
Fit diversity-dependent phenotypic evolution model