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phytools (version 0.2-1)
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
0.2-1
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
November 13th, 2012
Functions in phytools (0.2-1)
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anc.ML
Ancestral character estimation using likelihood
anc.trend
Ancestral character estimation with a trend
phyl.cca
Phylogenetic canonical correlation analysis
fastMRCA
Get the MRCA of a pair of tip taxa
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
brownieREML
REML version of brownie.lite
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
findMRCA
Get the MRCA of a set of taxa
make.era.map
Create "era" map on a phylogenetic tree
map.overlap
Proportional overlap between two mapped character histories on a tree
phyloDesign
Compute design matrix for least squares analyses
write.simmap
Write a stochastic character mapped tree to file
xkcdTree
Plot xkcd style tree
starTree
Create star phylogeny
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
expm
Matrix exponential
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
densityMap
Plot posterior density of stochastic mapping on a tree
likMlambda
Likelihood for joint lambda
phylomorphospace
Creates phylomorphospace plot
estDiversity
Estimate diversity at each node of the tree
threshBayes
Threshold model using Bayesian MCMC
rstate
Pick a random state according to a vector of probabilities
add.everywhere
Add tip to all edges in a tree
drop.tip.simmap
Drop tip from SIMMAP format tree
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
getDescendants
Get descendant node numbers
nodeHeights
Compute the heights above the root of each node
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
optim.phylo.ls
Phylogeny inference using the least squares method
export.as.xml
Export trees & data in XML format
exhaustiveMP
Exhaustive and branch & bound MP optimization
drop.clade
Drop clade from a tree
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
read.simmap
Read SIMMAP style trees from file
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
matchNodes
Matches nodes between two trees
anc.Bayes
Bayesian ancestral character estimation
fastAnc
Fast estimation of ML ancestral states
pgls.Ives
Phylogenetic regression with intraspecific sampling error
minSplit
Finding the minimum (median) split in the posterior sample
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
allFurcTrees
Generate all bi- and multifurcating unrooted trees
mrp.supertree
Matrix representation parsimony supertree estimation
ltt
Creates lineage-through-time plot (including extinct lineages)
gammatest
Gamma test of Pybus & Harvey (2000)
phenogram
Plot phenogram (traitgram)
fastBM
Fast Brownian simulation
threshDIC
Deviance Information Criterion from the threshold model
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
plotSimmap
Plot stochastic character mapped tree
phyl.resid
Phylogenetic size-correction via GLS regression
branching.diffusion
Animation of branching random diffusion
writeNexus
Write a stochastic character mapped tree to file
make.simmap
Simulate stochastic character map on a phylogenetic tree
fancyTree
Plots special types of phylogenetic trees
lambda.transform
Lambda transformation of matrix
brownie.lite
Likelihood test for rate variation
phylosig
Compute phylogenetic signal with two methods
ls.tree
Least squares branch lengths for a given tree
multi.mantel
Multiple matrix regression (partial Mantel test)
paste.tree
Paste two trees together
phyl.pairedttest
Phylogenetic paired t-test
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
phylomorphospace3d
Creates phylomorphospace plot
sim.rates
Brownian simulation with multiple evolutionary rates
phylANOVA
Phylogenetic ANOVA and post-hoc tests
rescaleSimmap
Rescale SIMMAP style tree
reorderSimmap
Reorder edges of a simmap tree
sim.history
Simulate stochastic character history under some model
paintSubTree
Paint sub-trees with a discrete character
reroot
Re-root a tree along an edge
sampleFrom
Sample from a set of distributions
phyl.pca
Phylogenetic principal components analysis
read.newick
Read Newick style tree
contMap
Map continuous trait evolution on the tree
pbtree
Simulate pure-birth stochastic tree or trees
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
splitTree
Split tree at a point
plotTree
Plots rooted phylogenetic tree
treeSlice
Slices the tree at a particular point and returns all subtrees