/usr/lib/R/site-library/phytools/INDEX is in r-cran-phytools 0.6-44-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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tree
add.color.bar Add color bar to a plot
add.everywhere Add tip to all edges in a tree
add.random Add tips at random to the tree
add.simmap.legend Add legend to stochastically mapped tree
add.species.to.genus Add species to genus on a phylogeny or bind
simulated species subtrees to a backbone genus
tree
aic.w Computes AIC weights
allFurcTrees Generate all bi- and multifurcating unrooted
trees
anc.Bayes Bayesian ancestral character estimation
anc.ML Ancestral character estimation using likelihood
anc.trend Ancestral character estimation with a trend
ancThresh Ancestral character estimation under the
threshold model using Bayesian MCMC
anoletree Phylogeny of Greater Antillean anole ecomorph
species with mapped discrete character
applyBranchLengths Applies the branch lengths of a reference tree
to a target
as.multiPhylo Conversion to object of class '"multiPhylo"'
ave.rates Average the posterior rates
averageTree Compute an average tree from a set of trees and
related operations
bd Convert object of class "birthdeath" to raw
birth & death rates
bind.tip Attaches a new tip to a tree
bind.tree.simmap Attaches a new tip to a tree
bmPlot Simulates and visualizes discrete-time Brownian
evolution on a phylogeny
branching.diffusion Animation of branching random diffusion
brownie.lite Likelihood test for rate variation in a
continuous trait
brownieREML REML version of brownie.lite
cladelabels Add labels to subtrees of a plotted phylogeny
collapse.to.star Collapse a subtree to a star phylogeny
collapseTree Interactive tree visualizer
compare.chronograms Compares to chronograms with precisely matching
nodes in a visual manner
consensus.edges Compute consensus edges for a tree under some
criterion
contMap Map continuous trait evolution on the tree
cophylo Creates a co-phylogenetic plot
cospeciation Conducts a statistical test of cospeciation
between two trees
countSimmap Counts the number of character changes on a
SIMMAP style tree or set of trees
density.multiSimmap Computes a posterior distribution for the
number and types of changes on the tree
densityMap Plot posterior density of stochastic mapping on
a tree
densityTree Plots a posterior sample of trees
describe.simmap Summarizes a stochastic mapped tree or set of
trees
di2multi.simmap Collapse branches of zero length to polytomy in
stochastic map style tree
dotTree Creates a phylogenetic dot plot
drop.clade Drop a clade from a tree
drop.leaves Drop all the leaves (tips) from a tree
drop.tip.contMap Drop tip or tips from an object of class
"contMap" or "densityMap"
drop.tip.simmap Drop tips or extract clade from tree with
mapped discrete character
edgeProbs Compute the relative frequencies of state
changes along edges
estDiversity Estimate diversity at each node of the tree
evol.rate.mcmc Bayesian MCMC method for identifying
exceptional phenotypic diversification in a
phylogeny
evol.vcv Likelihood test for variation in the
evolutionary VCV matrix
evolvcv.lite Likelihood test for a shift in the evolutionary
correlation between traits
exhaustiveMP Exhaustive and branch & bound MP optimization
expand.clade Expands (or contracts) the tip-spacing of a
given clade or clades
expm Matrix exponential
export.as.xml Export trees & data in XML format
fancyTree Plots special types of phylogenetic trees
fastAnc (Reasonably) fast estimation of ML ancestral
states
fastBM (Reasonably) fast quantitative trait simulation
on phylogenies
fastMRCA Get the MRCA (or height above the root of the
MRCA) of a pair of tip taxa
findMRCA Get the MRCA of a set of taxa
fit.bd Fits birth-death (speciation/extinction) model
to reconstructed phylogeny
fitBayes Evolutionary model fitting with intraspecific
variability using Bayesian MCMC
fitDiversityModel Fit diversity-dependent phenotypic evolution
model
fitMk Fits Mk model
fitPagel Function to test for correlated evolution of
binary traits
force.ultrametric Forces a phylogenetic tree to be ultrametric
gammatest Gamma test of Pybus & Harvey (2000)
genSeq Simulate a DNA alignment on the tree under a
model
geo.legend Adds a geological (or other temporal) legend to
a plotted tree
get.treepos Internal functions
getCladesofSize Get all subtrees larger than or equal to a
specified size
getDescendants Get descendant node numbers
getExtant Returns a list of the extant or extinct
lineages in a tree containing
non-contemporaneous tips
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
labelnodes Function to interactively label nodes of a
plotted tree
ladderize.simmap Ladderize a tree with a mapped discrete
character
lambda.transform Lambda transformation of matrix
likMlambda Likelihood for joint lambda
linklabels Function to add tip labels to a plotted tree
with linking lines
locate.fossil Locate a fossil lineage in a tree using
continuous characters
locate.yeti Locate a cryptic, recently extinct, or missing
taxon on a tree
ls.tree Least squares branch lengths for a given tree
ltt Creates lineage-through-time plot (including
extinct lineages)
ltt95 Creates a (1-alpha)-percent CI for a set of
LTTs
make.era.map Create "era" map on a phylogenetic tree
make.simmap Simulate stochastic character maps on a
phylogenetic tree or trees
map.overlap Proportional overlap between two mapped
character histories on a tree
map.to.singleton Converts a mapped tree to a tree with singleton
nodes
mapped.states Returns a vector, matrix, or list of the mapped
states on a tree or set of trees
markChanges Add marked changes to a plotted tree with
mapped discrete character
matchNodes Matches nodes between two trees
mergeMappedStates Merge two or more mapped states into one state
midpoint.root Midpoint root a phylogeny
minRotate Rotates all nodes of the tree to minimize the
difference in order with a vector
minSplit Finding the minimum (median) split in the
posterior sample
modified.Grafen Computes modified Grafen edge lengths
mrp.supertree Matrix representation parsimony supertree
estimation
multi.mantel Multiple matrix regression (partial Mantel
test)
multiC Returns a list with phylogenetic VCV matrix for
each mapped state
multiRF Computes Robinson-Foulds distance between a set
of trees
nodeHeights Compute the heights above the root of each node
nodelabels.cophylo Add labels to a plotted "cophylo" object
optim.phylo.ls Phylogeny inference using the least squares
method
orderMappedEdge Order the columns of mapped.edge to match
across trees
paintSubTree Paint sub-trees with a discrete character
paste.tree Paste two trees together
pbtree Simulate pure-birth or birth-death stochastic
tree or trees
pgls.Ives Phylogenetic regression with intraspecific
sampling error
phenogram Plot phenogram (traitgram)
phyl.RMA Phylogenetic reduced major axis (RMA)
regression
phyl.cca Phylogenetic canonical correlation analysis
phyl.pairedttest Phylogenetic paired t-test
phyl.pca Phylogenetic principal components analysis
phyl.resid Phylogenetic size-correction via GLS regression
phyl.vcv Compute evolutionary VCV matrix for a tree &
dataset
phylANOVA Phylogenetic ANOVA and post-hoc tests
phylo.heatmap Creates a phylogenetic heat map
phylo.to.map Plot tree with tips linked to geographic
coordinates
phylo.toBackbone Converts tree to backbone or vice versa
phyloDesign Compute design matrix for least squares
analyses
phylomorphospace Creates phylomorphospace plot
phylomorphospace3d Creates tree-dimensional phylomorphospace plot
phylosig Compute phylogenetic signal with two methods
phytools-package phytools: Phylogenetic Tools for comparative
biology (and other things)
plot.backbonePhylo Plots backbone tree with triangles as clades
plotBranchbyTrait Plot branch colors by a quantitative trait or
value
plotSimmap Plot stochastic character mapped tree
plotThresh Tree plotting with posterior probabilities of
ancestral states from the threshold model
plotTree Plots rooted phylogenetic tree
plotTree.errorbars Plot a tree with error bars around divergence
dates
plotTree.wBars Plot a tree with bars at the tips
posterior.evolrate Analysis of the posterior sample from
evol.rate.mcmc
posthoc Generic post-hoc test
print.backbonePhylo Print method for backbone phylogeny
ratebystate Method for investigating the rate of one trait
as a function of the state of another
ratebytree Likelihood test for rate variation among trees
rateshift Find the temporal position of one or more rate
shifts
read.newick Robust Newick style tree reader
read.simmap Read SIMMAP style trees from file
reorder.backbonePhylo Reorders a backbone phylogeny
reorderSimmap Reorder edges of a simmap tree
rep.phylo Replicate a tree or set of trees
reroot Re-root a tree along an edge
rerootingMethod Get marginal ancestral state reconstructions by
re-rooting
rescaleSimmap Rescale SIMMAP style tree
resolveNode Compute all possible resolutions of a node or
all nodes in a multifurcating tree
rotateNodes Rotates a node or set of nodes in a
phylogenetic tree
roundBranches Rounds the branch lengths of a tree
roundPhylogram Plot a round phylogram
rstate Pick a random state according to a vector of
probabilities
sampleFrom Sample from a set of distributions
setMap Set color map for objects of class '"contMap"'
or '"densityMap"'
sim.corrs Multivariate Brownian simulation with multiple
correlations and rates
sim.history Simulate stochastic character history under
some model
sim.ratebystate Conduct simulation of state dependent rate
variation
sim.rates Brownian or OU simulation with multiple
evolutionary regimes
skewers Matrix comparison using the method of random
skewers
splitEdgeColor Split edge colors when descendant edges have
different mapped states
splitTree Split tree at a point
splitplotTree Plots a phylogeny in two columns
starTree Create star phylogeny
strahlerNumber Computes Strahler number for trees and nodes
threshBayes Threshold model using Bayesian MCMC
threshDIC Deviance Information Criterion from the
threshold model
threshState Computes value for a threshold character from a
liability and thresholds
to.matrix Convert a character vector to a binary matrix
treeSlice Slices the tree at a particular point and
returns all subtrees, or the tree rootward of
the point
untangle Attempts to untangle crossing branches for
plotting
vcvPhylo Calculates cophenetic (i.e., phylogenetic VCV)
matrix
write.simmap Write a stochastic character mapped tree to
file
writeAncestors Write a tree to file with ancestral states and
(optionally) CIs at nodes
writeNexus Write a tree to file in Nexus format
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