⚠️There's a newer version (2.4-4) of this package.Take me there.

phytools (version 0.3-72.1)

Phylogenetic Tools for comparative biology (and other things)

Description

phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.

Copy Link

Version

Install

install.packages('phytools')

Monthly Downloads

11,829

Version

0.3-72.1

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

March 3rd, 2014

Functions in phytools (0.3-72.1)

applyBranchLengths

Applies the branch lengths of a reference tree to a target

anc.ML

Ancestral character estimation using likelihood

bind.tip

Attaches a new tip to a tree

add.simmap.legend

Add legend to stochastically mapped tree

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

collapse.to.star

Collapse a subtree to a star phylogeny

pgls.Ives

Phylogenetic regression with intraspecific sampling error

anc.trend

Ancestral character estimation with a trend

brownie.lite

Likelihood test for rate variation in a continuous trait

ave.rates

Average the posterior rates

allFurcTrees

Generate all bi- and multifurcating unrooted trees

describe.simmap

Summarizes a stochastic mapped tree or set of trees

drop.clade

Drop a clade from a tree

phylANOVA

Phylogenetic ANOVA and post-hoc tests

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

brownieREML

REML version of brownie.lite

add.color.bar

Add color bar to a plot

read.simmap

Read SIMMAP style trees from file

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

reorder.backbonePhylo

Reorders a backbone phylogeny

fancyTree

Plots special types of phylogenetic trees

estDiversity

Estimate diversity at each node of the tree

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

findMRCA

Get the MRCA of a set of taxa

roundBranches

Rounds the branch lengths of a tree

getCladesofSize

Get all subtrees larger than or equal to a specified size

fastMRCA

Get the MRCA of a pair of tip taxa

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

ltt

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

gammatest

Gamma test of Pybus & Harvey (2000)

phenogram

Plot phenogram (traitgram)

map.to.singleton

Converts a mapped tree to a tree with singleton nodes

phylo.to.map

Plot tree with tips linked to geographic coordinates

matchNodes

Matches nodes between two trees

drop.leaves

Drop all the leaves (tips) from a tree

plot.backbonePhylo

Plots backbone tree with triangles as clades

phylo.toBackbone

Converts tree to backbone or vice versa

export.as.xml

Export trees & data in XML format

pbtree

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

untangle

Attempts to untangle crossing branches for plotting

map.overlap

Proportional overlap between two mapped character histories on a tree

read.newick

Robust Newick style tree reader

exhaustiveMP

Exhaustive and branch & bound MP optimization

getStates

Get the states at nodes or tips from a mapped tree

optim.phylo.ls

Phylogeny inference using the least squares method

plotThresh

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

plotTree

Plots rooted phylogenetic tree

lambda.transform

Lambda transformation of matrix

ltt95

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

rotateNodes

Rotates a node or set of nodes in a phylogenetic tree

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

phyl.resid

Phylogenetic size-correction via GLS regression

nodeHeights

Compute the heights above the root of each node

phytools-package

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

minSplit

Finding the minimum (median) split in the posterior sample

multiRF

Computes Robinson-Foulds distance between a set of trees

write.simmap

Write a stochastic character mapped tree to file

phylomorphospace

Creates phylomorphospace plot

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

phyl.pairedttest

Phylogenetic paired t-test

threshState

Computes value for a threshold character from a liability and thresholds

ratebystate

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

sim.rates

Brownian simulation with multiple evolutionary rates

rescaleSimmap

Rescale SIMMAP style tree

splitplotTree

Plots a phylogeny in two columns

anoletree

Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character

phylosig

Compute phylogenetic signal with two methods

splitTree

Split tree at a point

vcvPhylo

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

writeNexus

Write a tree to file in Nexus format

starTree

Create star phylogeny

writeAncestors

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

repPhylo

Replicate a tree into a list of trees

threshBayes

Threshold model using Bayesian MCMC

paintSubTree

Paint sub-trees with a discrete character

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

treeSlice

Slices the tree at a particular point and returns all subtrees

getSisters

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

reorderSimmap

Reorder edges of a simmap tree

phyloDesign

Compute design matrix for least squares analyses

sim.history

Simulate stochastic character history under some model

add.random

Add tips at random to the tree

fastBM

Fast Brownian simulation

getExtant

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

ls.tree

Least squares branch lengths for a given tree

expm

Matrix exponential

multi.mantel

Multiple matrix regression (partial Mantel test)

orderMappedEdge

Order the columns of mapped.edge to match across trees

print.backbonePhylo

Print method for backbone phylogeny

reroot

Re-root a tree along an edge

rstate

Pick a random state according to a vector of probabilities

contMap

Map continuous trait evolution on the tree

densityMap

Plot posterior density of stochastic mapping on a tree

getDescendants

Get descendant node numbers

likMlambda

Likelihood for joint lambda

sampleFrom

Sample from a set of distributions

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

paste.tree

Paste two trees together

sim.ratebystate

Conduct simulation of state dependent rate variation

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

add.everywhere

Add tip to all edges in a tree

anc.Bayes

Bayesian ancestral character estimation

branching.diffusion

Animation of branching random diffusion

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

countSimmap

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

make.era.map

Create "era" map on a phylogenetic tree

threshDIC

Deviance Information Criterion from the threshold model

xkcdTree

Plot xkcd style tree

fastAnc

Fast estimation of ML ancestral states

mergeMappedStates

Merge two or more mapped states into one state

minRotate

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

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

phyl.cca

Phylogenetic canonical correlation analysis

mrp.supertree

Matrix representation parsimony supertree estimation

strahlerNumber

Computes Strahler number for trees and nodes

to.matrix

Convert a character vector to a binary matrix

genSeq

Simulate a DNA alignment on the tree under a model

plotSimmap

Plot stochastic character mapped tree

phyl.pca

Phylogenetic principal components analysis