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phytools (version 0.4-05)

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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Version

Install

install.packages('phytools')

Monthly Downloads

12,223

Version

0.4-05

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

May 5th, 2014

Functions in phytools (0.4-05)

bind.tip

Attaches a new tip to a tree

expm

Matrix exponential

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

collapse.to.star

Collapse a subtree to a star phylogeny

export.as.xml

Export trees & data in XML format

genSeq

Simulate a DNA alignment on the tree under a model

add.color.bar

Add color bar to a plot

anc.trend

Ancestral character estimation with a trend

add.species.to.genus

Add species to genus on a phylogeny

ltt

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

ltt95

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

di2multi.simmap

Collapse branches of zero length to polytomy in stochastic map style tree

brownie.lite

Likelihood test for rate variation in a continuous trait

mergeMappedStates

Merge two or more mapped states into one state

applyBranchLengths

Applies the branch lengths of a reference tree to a target

describe.simmap

Summarizes a stochastic mapped tree or set of trees

fastBM

Fast Brownian simulation

multi.mantel

Multiple matrix regression (partial Mantel test)

ls.tree

Least squares branch lengths for a given tree

phyl.pairedttest

Phylogenetic paired t-test

matchNodes

Matches nodes between two trees

map.overlap

Proportional overlap between two mapped character histories on a tree

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

exhaustiveMP

Exhaustive and branch & bound MP optimization

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

phyl.resid

Phylogenetic size-correction via GLS regression

drop.clade

Drop a clade from a tree

brownieREML

REML version of brownie.lite

fancyTree

Plots special types of phylogenetic trees

plot.backbonePhylo

Plots backbone tree with triangles as clades

plotTree

Plots rooted phylogenetic tree

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

lambda.transform

Lambda transformation of matrix

rotateNodes

Rotates a node or set of nodes in a phylogenetic tree

branching.diffusion

Animation of branching random diffusion

minRotate

Rotates all nodes of the tree to minimize the difference in order with a vector

phylANOVA

Phylogenetic ANOVA and post-hoc tests

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

mrp.supertree

Matrix representation parsimony supertree estimation

minSplit

Finding the minimum (median) split in the posterior sample

phytools-package

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

ave.rates

Average the posterior rates

paintSubTree

Paint sub-trees with a discrete character

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

orderMappedEdge

Order the columns of mapped.edge to match across trees

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

nodeHeights

Compute the heights above the root of each node

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

anoletree

Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

phylo.to.map

Plot tree with tips linked to geographic coordinates

multiRF

Computes Robinson-Foulds distance between a set of trees

fastMRCA

Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa

countSimmap

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

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

anc.ML

Ancestral character estimation using likelihood

read.newick

Robust Newick style tree reader

getCladesofSize

Get all subtrees larger than or equal to a specified size

reorder.backbonePhylo

Reorders a backbone phylogeny

repPhylo

Replicate a tree into a list of trees

getDescendants

Get descendant node numbers

findMRCA

Get the MRCA of a set of taxa

sampleFrom

Sample from a set of distributions

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

splitTree

Split tree at a point

map.to.singleton

Converts a mapped tree to a tree with singleton nodes

make.era.map

Create "era" map on a phylogenetic tree

sim.rates

Brownian simulation with multiple evolutionary rates

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

allFurcTrees

Generate all bi- and multifurcating unrooted trees

skewers

Matrix comparison using the method of random skewers

read.simmap

Read SIMMAP style trees from file

reorderSimmap

Reorder edges of a simmap tree

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

cladelabels

Add labels to subtrees of a plotted phylogeny

getExtant

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

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

rescaleSimmap

Rescale SIMMAP style tree

getStates

Get the states at nodes or tips from a mapped tree

midpoint.root

Midpoint root a phylogeny

phenogram

Plot phenogram (traitgram)

optim.phylo.ls

Phylogeny inference using the least squares method

fastAnc

Fast estimation of ML ancestral states

phylomorphospace

Creates phylomorphospace plot

sim.ratebystate

Conduct simulation of state dependent rate variation

paste.tree

Paste two trees together

phylo.toBackbone

Converts tree to backbone or vice versa

roundPhylogram

Plot a round phylogram

phyl.cca

Phylogenetic canonical correlation analysis

plotSimmap

Plot stochastic character mapped tree

roundBranches

Rounds the branch lengths of a tree

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

phylosig

Compute phylogenetic signal with two methods

pbtree

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

rateshift

Find the temporal position of one or more rate shifts

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

rstate

Pick a random state according to a vector of probabilities

plotThresh

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

ratebystate

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

splitplotTree

Plots a phylogeny in two columns

reroot

Re-root a tree along an edge

to.matrix

Convert a character vector to a binary matrix

vcvPhylo

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

treeSlice

Slices the tree at a particular point and returns all subtrees

sim.history

Simulate stochastic character history under some model

writeAncestors

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

threshBayes

Threshold model using Bayesian MCMC

starTree

Create star phylogeny

writeNexus

Write a tree to file in Nexus format

strahlerNumber

Computes Strahler number for trees and nodes

phyloDesign

Compute design matrix for least squares analyses

anc.Bayes

Bayesian ancestral character estimation

densityMap

Plot posterior density of stochastic mapping on a tree

drop.leaves

Drop all the leaves (tips) from a tree

contMap

Map continuous trait evolution on the tree

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

estDiversity

Estimate diversity at each node of the tree

likMlambda

Likelihood for joint lambda

write.simmap

Write a stochastic character mapped tree to file

threshState

Computes value for a threshold character from a liability and thresholds

threshDIC

Deviance Information Criterion from the threshold model

getSisters

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

gammatest

Gamma test of Pybus & Harvey (2000)

phyl.pca

Phylogenetic principal components analysis

pgls.Ives

Phylogenetic regression with intraspecific sampling error

print.backbonePhylo

Print method for backbone phylogeny

untangle

Attempts to untangle crossing branches for plotting