Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (2.5-2) of this package.
Take me there.
phytools (version 0.1-7)
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
2.5-2
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
12,223
Version
0.1-7
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
February 27th, 2012
Functions in phytools (0.1-7)
Search all functions
drop.clade
Drop clade from a tree
fastBM
Fast Brownian simulation
make.era.map
Create "era" map on a phylogenetic tree
anc.Bayes
Bayesian ancestral character estimation
pbtree
Simulate pure-birth stochastic tree or trees
sampleFrom
Sample from a set of distributions
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
brownie.lite
Likelihood test for rate variation
map.overlap
Proportional overlap between two mapped character histories on a tree
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
phyl.vcv
Compute phylogenetic VCV matrix for a tree & dataset
exhaustiveMP
Exhaustive and branch & bound MP optimization
make.simmap
Simulate stochastic character map on a phylogenetic tree
nodeHeights
Compute the heights above the root of each node
phyloDesign
Compute design matrix for least squares analyses
phylomorphospace
Creates phylomorphospace plot
phyl.pairedttest
Phylogenetic paired t-test
read.newick
Read Newick style tree
brownieREML
REML version of brownie.lite
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
findMRCA
Get the MRCA of a set of taxa
allFurcTrees
Generate all bi- and multifurcating unrooted trees
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
paintSubTree
Paint sub-trees with a discrete character
sim.history
Simulate stochastic character history under some model
estDiversity
Estimate diversity at each node of the tree
ltt
Creates lineage-through-time plot (including extinct lineages)
mrp.supertree
Matrix representation parsimony supertree estimation
paste.tree
Paste two trees together
phyl.resid
Phylogenetic size-correction via GLS regression
phenogram
Plot phenogram (traitgram)
optim.phylo.ls
Phylogeny inference using the least squares method
rstate
Pick a random state according to a vector of probabilities
plotTree
Plots rooted phylogenetic tree
starTree
Create star phylogeny
read.simmap
Read SIMMAP style trees from file
lambda.transform
Lambda transformation of matrix
getDescendants
Get descendant node numbers
ls.tree
Least squares branch lengths for a given tree
sim.rates
Brownian simulation with multiple evolutionary rates
splitTree
Split tree at a point
reorderSimmap
Reorder edges of a simmap tree
anc.trend
Ancestral character estimation with a trend
anc.ML
Ancestral character estimation using likelihood
branching.diffusion
Animation of branching random diffusion
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
phylANOVA
Phylogenetic ANOVA and post-hoc tests
reroot
Re-root a tree along an edge
phylosig
Compute phylogenetic signal with two methods
write.simmap
Simulate stochastic character map on a phylogenetic tree
drop.tip.simmap
Drop tip from SIMMAP format tree
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
gammatest
Gamma test of Pybus & Harvey (2000)
treeSlice
Slices the tree at a particular point and returns all subtrees
phyl.pca
Phylogenetic principal components analysis
phyl.cca
Phylogenetic canonical correlation analysis
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
add.everywhere
Add tip to all edges in a tree
expm
Matrix exponential
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
minSplit
Finding the minimum (median) split in the posterior sample
plotSimmap
Plot stochastic character mapped tree