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phytools (version 0.2-0)
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
15,321
Version
0.2-0
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
September 29th, 2012
Functions in phytools (0.2-0)
Search all functions
add.everywhere
Add tip to all edges in a tree
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
allFurcTrees
Generate all bi- and multifurcating unrooted trees
fancyTree
Plots special types of phylogenetic trees
brownie.lite
Likelihood test for rate variation
write.simmap
Write a stochastic character mapped tree to file
phyl.resid
Phylogenetic size-correction via GLS regression
estDiversity
Estimate diversity at each node of the tree
minSplit
Finding the minimum (median) split in the posterior sample
paintSubTree
Paint sub-trees with a discrete character
lambda.transform
Lambda transformation of matrix
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
read.newick
Read Newick style tree
anc.trend
Ancestral character estimation with a trend
exhaustiveMP
Exhaustive and branch & bound MP optimization
export.as.xml
Export trees & data in XML format
make.simmap
Simulate stochastic character map on a phylogenetic tree
phenogram
Plot phenogram (traitgram)
phylANOVA
Phylogenetic ANOVA and post-hoc tests
phyl.pairedttest
Phylogenetic paired t-test
threshBayes
Threshold model using Bayesian MCMC
plotSimmap
Plot stochastic character mapped tree
splitTree
Split tree at a point
sim.history
Simulate stochastic character history under some model
gammatest
Gamma test of Pybus & Harvey (2000)
ls.tree
Least squares branch lengths for a given tree
getDescendants
Get descendant node numbers
map.overlap
Proportional overlap between two mapped character histories on a tree
likMlambda
Likelihood for joint lambda
pgls.Ives
Phylogenetic regression with intraspecific sampling error
rescaleSimmap
Rescale SIMMAP style tree
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
branching.diffusion
Animation of branching random diffusion
brownieREML
REML version of brownie.lite
mrp.supertree
Matrix representation parsimony supertree estimation
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
phyl.pca
Phylogenetic principal components analysis
pbtree
Simulate pure-birth stochastic tree or trees
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
paste.tree
Paste two trees together
reroot
Re-root a tree along an edge
sampleFrom
Sample from a set of distributions
phyloDesign
Compute design matrix for least squares analyses
sim.rates
Brownian simulation with multiple evolutionary rates
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
anc.Bayes
Bayesian ancestral character estimation
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
fastMRCA
Get the MRCA of a pair of tip taxa
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
starTree
Create star phylogeny
phylomorphospace3d
Creates phylomorphospace plot
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
phylomorphospace
Creates phylomorphospace plot
findMRCA
Get the MRCA of a set of taxa
ltt
Creates lineage-through-time plot (including extinct lineages)
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
treeSlice
Slices the tree at a particular point and returns all subtrees
nodeHeights
Compute the heights above the root of each node
fastBM
Fast Brownian simulation
rstate
Pick a random state according to a vector of probabilities
plotTree
Plots rooted phylogenetic tree
drop.clade
Drop clade from a tree
expm
Matrix exponential
drop.tip.simmap
Drop tip from SIMMAP format tree
phylosig
Compute phylogenetic signal with two methods
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
read.simmap
Read SIMMAP style trees from file
anc.ML
Ancestral character estimation using likelihood
optim.phylo.ls
Phylogeny inference using the least squares method
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
phyl.cca
Phylogenetic canonical correlation analysis
reorderSimmap
Reorder edges of a simmap tree
make.era.map
Create "era" map on a phylogenetic tree