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phytools (version 0.4-31)
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
11,883
Version
0.4-31
License
GPL (>= 2)
Maintainer
Liam Revell
Last Published
August 26th, 2014
Functions in phytools (0.4-31)
Search functions
add.everywhere
Add tip to all edges in a tree
expm
Matrix exponential
branching.diffusion
Animation of branching random diffusion
anoletree
Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character
multi.mantel
Multiple matrix regression (partial Mantel test)
add.species.to.genus
Add species to genus on a phylogeny
mergeMappedStates
Merge two or more mapped states into one state
drop.clade
Drop a clade from a tree
nodeHeights
Compute the heights above the root of each node
brownieREML
REML version of brownie.lite
midpoint.root
Midpoint root a phylogeny
anc.Bayes
Bayesian ancestral character estimation
add.random
Add tips at random to the tree
phytools-package
phytools: Phylogenetic Tools for comparative biology (and other things)
fancyTree
Plots special types of phylogenetic trees
anc.ML
Ancestral character estimation using likelihood
ave.rates
Average the posterior rates
gammatest
Gamma test of Pybus & Harvey (2000)
print.backbonePhylo
Print method for backbone phylogeny
getDescendants
Get descendant node numbers
phyl.pairedttest
Phylogenetic paired t-test
drop.leaves
Drop all the leaves (tips) from a tree
multiC
Returns a list with phylogenetic VCV matrix for each mapped state
sim.rates
Brownian simulation with multiple evolutionary rates
anc.trend
Ancestral character estimation with a trend
rateshift
Find the temporal position of one or more rate shifts
fastBM
Fast Brownian simulation
rstate
Pick a random state according to a vector of probabilities
contMap
Map continuous trait evolution on the tree
fitBayes
Evolutionary model fitting with intraspecific variability using Bayesian MCMC
collapse.to.star
Collapse a subtree to a star phylogeny
phyl.pca
Phylogenetic principal components analysis
findMRCA
Get the MRCA of a set of taxa
locate.yeti
Locate a cryptic, recently extinct, or missing taxon on a tree
paintSubTree
Paint sub-trees with a discrete character
evol.rate.mcmc
Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny
densityMap
Plot posterior density of stochastic mapping on a tree
likMlambda
Likelihood for joint lambda
orderMappedEdge
Order the columns of mapped.edge to match across trees
evol.vcv
Likelihood test for variation in the evolutionary VCV matrix
allFurcTrees
Generate all bi- and multifurcating unrooted trees
exhaustiveMP
Exhaustive and branch & bound MP optimization
fitDiversityModel
Fit diversity-dependent phenotypic evolution model
genSeq
Simulate a DNA alignment on the tree under a model
export.as.xml
Export trees & data in XML format
pbtree
Simulate pure-birth or birth-death stochastic tree or trees
phyloDesign
Compute design matrix for least squares analyses
phyl.cca
Phylogenetic canonical correlation analysis
ancThresh
Ancestral character estimation under the threshold model using Bayesian MCMC
getExtant
Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips
drop.tip.simmap
Drop tips or extract clade from tree with mapped discrete character
countSimmap
Counts the number of character changes on a SIMMAP style tree or set of trees
cladelabels
Add labels to subtrees of a plotted phylogeny
add.color.bar
Add color bar to a plot
add.simmap.legend
Add legend to stochastically mapped tree
bind.tip
Attaches a new tip to a tree
di2multi.simmap
Collapse branches of zero length to polytomy in stochastic map style tree
lambda.transform
Lambda transformation of matrix
make.era.map
Create "era" map on a phylogenetic tree
drop.tip.contMap
Drop tip or tips from an object of class "contMap" or "densityMap"
phylo.to.map
Plot tree with tips linked to geographic coordinates
bmPlot
Simulates and visualizes discrete-time Brownian evolution on a phylogeny
multiRF
Computes Robinson-Foulds distance between a set of trees
brownie.lite
Likelihood test for rate variation in a continuous trait
roundPhylogram
Plot a round phylogram
matchNodes
Matches nodes between two trees
getCladesofSize
Get all subtrees larger than or equal to a specified size
plot.backbonePhylo
Plots backbone tree with triangles as clades
phenogram
Plot phenogram (traitgram)
read.newick
Robust Newick style tree reader
plotThresh
Tree plotting with posterior probabilities of ancestral states from the threshold model
repPhylo
Replicate a tree into a list of trees
estDiversity
Estimate diversity at each node of the tree
ltt
Creates lineage-through-time plot (including extinct lineages)
skewers
Matrix comparison using the method of random skewers
mrp.supertree
Matrix representation parsimony supertree estimation
ratebystate
Method for investigating the rate of one trait as a function of the state of another
phylo.toBackbone
Converts tree to backbone or vice versa
ltt95
Creates a (1-$\alpha$)-percent CI for a set of LTTs
sim.ratebystate
Conduct simulation of state dependent rate variation
describe.simmap
Summarizes a stochastic mapped tree or set of trees
evolvcv.lite
Likelihood test for a shift in the evolutionary correlation between traits
fastAnc
Fast estimation of ML ancestral states
pgls.Ives
Phylogenetic regression with intraspecific sampling error
sim.corrs
Multivariate Brownian simulation with multiple correlations and rates
strahlerNumber
Computes Strahler number for trees and nodes
vcvPhylo
Calculates cophenetic (i.e., phylogenetic VCV) matrix
phyl.resid
Phylogenetic size-correction via GLS regression
phyl.vcv
Compute evolutionary VCV matrix for a tree & dataset
plotBranchbyTrait
Plot branch colors by a quantitative trait or value
rotateNodes
Rotates a node or set of nodes in a phylogenetic tree
posterior.evolrate
Analysis of the posterior sample from evol.rate.mcmc
sampleFrom
Sample from a set of distributions
plotTree
Plots rooted phylogenetic tree
splitplotTree
Plots a phylogeny in two columns
threshBayes
Threshold model using Bayesian MCMC
fastMRCA
Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa
reorderSimmap
Reorder edges of a simmap tree
starTree
Create star phylogeny
rerootingMethod
Get marginal ancestral state reconstructions by re-rooting
reorder.backbonePhylo
Reorders a backbone phylogeny
splitTree
Split tree at a point
read.simmap
Read SIMMAP style trees from file
reroot
Re-root a tree along an edge
phylosig
Compute phylogenetic signal with two methods
minSplit
Finding the minimum (median) split in the posterior sample
rescaleSimmap
Rescale SIMMAP style tree
untangle
Attempts to untangle crossing branches for plotting
treeSlice
Slices the tree at a particular point and returns all subtrees
write.simmap
Write a stochastic character mapped tree to file
ls.tree
Least squares branch lengths for a given tree
getSisters
Get the sister node number, label, or set of nodes for a node or tip
getStates
Get the states at nodes or tips from a mapped tree
setMap
Set color map for objects of class
"contMap"
or
"densityMap"
map.to.singleton
Converts a mapped tree to a tree with singleton nodes
paste.tree
Paste two trees together
roundBranches
Rounds the branch lengths of a tree
sim.history
Simulate stochastic character history under some model
to.matrix
Convert a character vector to a binary matrix
threshDIC
Deviance Information Criterion from the threshold model
phylomorphospace3d
Creates tree-dimensional phylomorphospace plot
writeNexus
Write a tree to file in Nexus format
writeAncestors
Write a tree to file with ancestral states and (optionally) CIs at nodes
map.overlap
Proportional overlap between two mapped character histories on a tree
applyBranchLengths
Applies the branch lengths of a reference tree to a target
make.simmap
Simulate stochastic character maps on a phylogenetic tree or trees
phyl.RMA
Phylogenetic reduced major axis (RMA) regression
minRotate
Rotates all nodes of the tree to minimize the difference in order with a vector
phylANOVA
Phylogenetic ANOVA and post-hoc tests
optim.phylo.ls
Phylogeny inference using the least squares method
plotSimmap
Plot stochastic character mapped tree
plotTree.wBars
Plot a tree with bars at the tips
phylomorphospace
Creates phylomorphospace plot
threshState
Computes value for a threshold character from a liability and thresholds