Package contains various functions for phylogenetic analysis. This functionality is concentrated in the phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian and ML ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple Brownian rates and correlations; visualizing discrete and continuous character evolution using colors or projections into trait space; identifying the location of a change in the rate of character evolution on the tree; fast Brownian motion simulation and simulation under several other models of continuous trait evolution; fitting a model of correlated binary trait evolution; locating the position of a fossil or an recently extinct lineage on a tree using continuous character data with ML; plotting lineage accumulation through time, including across multiple trees (such as a Bayesian posterior sample); conducting an analysis called stochastic character mapping, in which character histories for a discrete trait are sampled from their posterior probability distribution under a model; conducting a multiple (i.e., partial) Mantel test; fitting a phylogenetic regression model with error in predictor and response variables; conducting a phylogenetic principal components analysis, a phylogenetic regression, a reduced major axis regression, a phylogenetic canonical correlation analysis, and a phylogenetic ANOVA; projecting a tree onto a geographic map; simulating discrete character histories on the tree; fitting a model in which a discrete character evolves under the threshold model; visualization of cospeciation; a simple statistical test for cospeciation between two trees. In addition to this phylogenetic comparative method functionality, the package also contains functions for a wide range of other purposes in phylogenetic biology. For instance, functionality in this package includes (but is not restricted to): adding taxa to a tree (including randomly, everywhere, or automatically to genera); generating all bi- and multi-furcating trees for a set of taxa; reducing a phylogeny to its backbone tree; dropping tips or adding tips to special types of phylogenetic trees; exporting a tree as an XML file; converting a tree with a mapped character to a tree with singleton nodes and one character state per edge; estimating a phylogeny using the least squares method; simulating birth-death trees under a range of conditions; rerooting trees; computing a consensus tree under multiple methods, including via minimization of the distance to other trees in the set; a wide range of visualizations of trees; and a variety of other manipulations and analyses that phylogenetic biologists may find useful for their research.
|Author||Liam J. Revell|
|Date of publication||2016-12-05 22:44:57|
|Maintainer||Liam J. Revell <email@example.com>|
|License||GPL (>= 2)|
add.arrow: Add an arrow pointing to a tip or node on the 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...
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
ancThresh: Ancestral character estimation under the threshold model...
anc.trend: Ancestral character estimation with a trend
anoletree: Phylogeny of Greater Antillean anole ecomorph species with...
applyBranchLengths: Applies the branch lengths of a reference tree to a target
as.multiPhylo: Conversion to object of class '"multiPhylo"'
averageTree: Compute an average tree from a set of trees and related...
ave.rates: Average the posterior rates
bd: Convert object of class "birthdeath" to raw birth & death...
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...
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
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...
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...
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...
drop.tip.simmap: Drop tips or extract clade from tree with mapped discrete...
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...
evol.vcv: Likelihood test for variation in the evolutionary VCV matrix
evolvcv.lite: Likelihood test for a shift in the evolutionary correlation...
exhaustiveMP: Exhaustive and branch & bound MP optimization
expm: Matrix exponential
export.as.xml: Export trees & data in XML format
fancyTree: Plots special types of phylogenetic trees
fastAnc: Fast estimation of ML ancestral states
fastBM: Fast Brownian simulation
fastMRCA: Get the MRCA (or height above the root of the MRCA) of a pair...
findMRCA: Get the MRCA of a set of taxa
fitBayes: Evolutionary model fitting with intraspecific variability...
fitDiversityModel: Fit diversity-dependent phenotypic evolution model
fitMk: Fits Mk model
fitPagel: Function to test for correlated evolution of binary traits
gammatest: Gamma test of Pybus & Harvey (2000)
genSeq: Simulate a DNA alignment on the tree under a model
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...
getSisters: Get the sister node number, label, or set of nodes for a node...
getStates: Get the states at nodes or tips from a mapped tree
ladderize.simmap: Ladderize a tree with a mapped discrete character
lambda.transform: Lambda transformation of matrix
likMlambda: Likelihood for joint lambda
locate.fossil: Locate a fossil lineage in a tree using continuous characters
locate.yeti: Locate a cryptic, recently extinct, or missing taxon on a...
ls.tree: Least squares branch lengths for a given tree
ltt: Creates lineage-through-time plot (including extinct...
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...
map.overlap: Proportional overlap between two mapped character histories...
mapped.states: Returns a vector, matrix, or list of the mapped states on a...
map.to.singleton: Converts a mapped tree to a tree with singleton nodes
markChanges: Add marked changes to a plotted tree with mapped discrete...
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...
minSplit: Finding the minimum (median) split in the posterior sample
modified.Grafen: Computes modified Grafen edge lengths
mrp.supertree: Matrix representation parsimony supertree estimation
multiC: Returns a list with phylogenetic VCV matrix for each mapped...
multi.mantel: Multiple matrix regression (partial Mantel test)
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)
phylANOVA: Phylogenetic ANOVA and post-hoc tests
phyl.cca: Phylogenetic canonical correlation analysis
phyloDesign: Compute design matrix for least squares analyses
phylo.heatmap: Creates a phylogenetic heat map
phylomorphospace: Creates phylomorphospace plot
phylomorphospace3d: Creates tree-dimensional phylomorphospace plot
phylosig: Compute phylogenetic signal with two methods
phylo.toBackbone: Converts tree to backbone or vice versa
phylo.to.map: Plot tree with tips linked to geographic coordinates
phyl.pairedttest: Phylogenetic paired t-test
phyl.pca: Phylogenetic principal components analysis
phyl.resid: Phylogenetic size-correction via GLS regression
phyl.RMA: Phylogenetic reduced major axis (RMA) regression
phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset
phytools-package: phytools: Phylogenetic Tools for comparative biology (and...
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...
plotTree: Plots rooted phylogenetic tree
plotTree.wBars: Plot a tree with bars at the tips
posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc
print.backbonePhylo: Print method for backbone phylogeny
ratebystate: Method for investigating the rate of one trait as a function...
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...
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...
sim.corrs: Multivariate Brownian simulation with multiple correlations...
sim.history: Simulate stochastic character history under some model
sim.ratebystate: Conduct simulation of state dependent rate variation
sim.rates: Brownian simulation with multiple evolutionary rates
skewers: Matrix comparison using the method of random skewers
splitEdgeColor: Split edge colors when descendant edges have different mapped...
splitplotTree: Plots a phylogeny in two columns
splitTree: Split tree at a point
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...
to.matrix: Convert a character vector to a binary matrix
treeSlice: Slices the tree at a particular point and returns all...
untangle: Attempts to untangle crossing branches for plotting
vcvPhylo: Calculates cophenetic (i.e., phylogenetic VCV) matrix
writeAncestors: Write a tree to file with ancestral states and (optionally)...
writeNexus: Write a tree to file in Nexus format
write.simmap: Write a stochastic character mapped tree to file