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phytools (version 0.3-10)

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

12,126

Version

0.3-10

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

July 16th, 2013

Functions in phytools (0.3-10)

applyBranchLengths

Applies the branch lengths of a reference tree to a target

describe.simmap

Summarizes a stochastic mapped tree or set of trees

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

getSisters

Get the sister node number, label, or set of nodes for a node or tip

ratebystate

Method for investigating the rate of one trait as a function of the state of another

estDiversity

Estimate diversity at each node of the tree

densityMap

Plot posterior density of stochastic mapping on a tree

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

rescaleSimmap

Rescale SIMMAP style tree

collapse.to.star

Collapse a subtree to a star phylogeny

allFurcTrees

Generate all bi- and multifurcating unrooted trees

plotThresh

Tree plotting with posterior probabilities of ancestral states from the threshold model

anc.trend

Ancestral character estimation with a trend

fancyTree

Plots special types of phylogenetic trees

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

fastBM

Fast Brownian simulation

phylomorphospace

Creates phylomorphospace plot

phyl.pca

Phylogenetic principal components analysis

multi.mantel

Multiple matrix regression (partial Mantel test)

phyloDesign

Compute design matrix for least squares analyses

drop.clade

Drop a clade from a tree

branching.diffusion

Animation of branching random diffusion

brownieREML

REML version of brownie.lite

ltt95

Creates a (1-$\alpha$)-percent CI for a set of LTTs

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

matchNodes

Matches nodes between two trees

anc.Bayes

Bayesian ancestral character estimation

pgls.Ives

Phylogenetic regression with intraspecific sampling error

phytools-package

phytools: Phylogenetic Tools for comparative biology (and other things)

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

add.simmap.legend

Add legend to stochastically mapped tree

read.newick

Robust Newick style tree reader

rotateNodes

Rotates a node or set of nodes in a phylogenetic tree

getCladesofSize

Get all subtrees larger than or equal to a specified size

optim.phylo.ls

Phylogeny inference using the least squares method

treeSlice

Slices the tree at a particular point and returns all subtrees

threshState

Computes value for a threshold character from a liability and thresholds

getStates

Get the states at nodes or tips from a mapped tree

expm

Matrix exponential

map.overlap

Proportional overlap between two mapped character histories on a tree

anoletree

Phylogeny of 100 Greater Antillean anole species with mapped discrete character

add.color.bar

Add color bar to a plot

make.era.map

Create "era" map on a phylogenetic tree

exhaustiveMP

Exhaustive and branch & bound MP optimization

phyl.pairedttest

Phylogenetic paired t-test

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

add.random

Add tips at random to the tree

countSimmap

Counts the number of character changes on a SIMMAP style tree or set of trees

starTree

Create star phylogeny

repPhylo

Replicate a tree into a list of trees

likMlambda

Likelihood for joint lambda

threshBayes

Threshold model using Bayesian MCMC

orderMappedEdge

Order the columns of mapped.edge to match across trees

mrp.supertree

Matrix representation parsimony supertree estimation

phylosig

Compute phylogenetic signal with two methods

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

sim.ratebystate

Conduct simulation of state dependent rate variation

writeAncestors

Write a tree to file with ancestral states and (optionally) CIs at nodes

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

gammatest

Gamma test of Pybus & Harvey (2000)

ls.tree

Least squares branch lengths for a given tree

minSplit

Finding the minimum (median) split in the posterior sample

lambda.transform

Lambda transformation of matrix

phyl.resid

Phylogenetic size-correction via GLS regression

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

plotTree

Plots rooted phylogenetic tree

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

ave.rates

Average the posterior rates

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

plotSimmap

Plot stochastic character mapped tree

vcvPhylo

Calculates cophenetic (i.e., phylogenetic VCV) matrix

add.everywhere

Add tip to all edges in a tree

bind.tip

Attaches a new tip to a tree

contMap

Map continuous trait evolution on the tree

fastAnc

Fast estimation of ML ancestral states

export.as.xml

Export trees & data in XML format

ltt

Creates lineage-through-time plot (including extinct lineages)

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

mergeMappedStates

Merge two or more mapped states into one state

paste.tree

Paste two trees together

phyl.cca

Phylogenetic canonical correlation analysis

phylANOVA

Phylogenetic ANOVA and post-hoc tests

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

read.simmap

Read SIMMAP style trees from file

reorderSimmap

Reorder edges of a simmap tree

untangle

Attempts to untangle crossing branches for plotting

brownie.lite

Likelihood test for rate variation in a continuous trait

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

anc.ML

Ancestral character estimation using likelihood

getDescendants

Get descendant node numbers

fastMRCA

Get the MRCA of a pair of tip taxa

findMRCA

Get the MRCA of a set of taxa

getExtant

Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips

paintSubTree

Paint sub-trees with a discrete character

nodeHeights

Compute the heights above the root of each node

pbtree

Simulate pure-birth or birth-death stochastic tree or trees

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

reroot

Re-root a tree along an edge

rstate

Pick a random state according to a vector of probabilities

phenogram

Plot phenogram (traitgram)

splitplotTree

Plots a phylogeny in two columns

writeNexus

Write a tree to file in Nexus format

splitTree

Split tree at a point

strahlerNumber

Computes Strahler number for trees and nodes

sampleFrom

Sample from a set of distributions

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

threshDIC

Deviance Information Criterion from the threshold model

roundBranches

Rounds the branch lengths of a tree

sim.history

Simulate stochastic character history under some model

sim.rates

Brownian simulation with multiple evolutionary rates

write.simmap

Write a stochastic character mapped tree to file

xkcdTree

Plot xkcd style tree

to.matrix

Convert a character vector to a binary matrix