⚠️There's a newer version (2.5-2) of this package.Take me there.

phytools (version 0.4-21)

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

12,223

Version

0.4-21

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

June 28th, 2014

Functions in phytools (0.4-21)

allFurcTrees

Generate all bi- and multifurcating unrooted trees

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

add.species.to.genus

Add species to genus on a phylogeny

make.simmap

Simulate stochastic character maps on a phylogenetic tree or trees

anc.Bayes

Bayesian ancestral character estimation

di2multi.simmap

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

countSimmap

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

add.random

Add tips at random to the tree

drop.clade

Drop a clade from a tree

add.simmap.legend

Add legend to stochastically mapped tree

branching.diffusion

Animation of branching random diffusion

ave.rates

Average the posterior rates

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

brownieREML

REML version of brownie.lite

findMRCA

Get the MRCA of a set of taxa

fancyTree

Plots special types of phylogenetic trees

bind.tip

Attaches a new tip to a tree

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

midpoint.root

Midpoint root a phylogeny

optim.phylo.ls

Phylogeny inference using the least squares method

applyBranchLengths

Applies the branch lengths of a reference tree to a target

getSisters

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

bmPlot

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

brownie.lite

Likelihood test for rate variation in a continuous trait

drop.leaves

Drop all the leaves (tips) from a tree

matchNodes

Matches nodes between two trees

densityMap

Plot posterior density of stochastic mapping on a tree

phyl.pairedttest

Phylogenetic paired t-test

minSplit

Finding the minimum (median) split in the posterior sample

estDiversity

Estimate diversity at each node of the tree

plot.backbonePhylo

Plots backbone tree with triangles as clades

sim.corrs

Multivariate Brownian simulation with multiple correlations and rates

ltt

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

anc.ML

Ancestral character estimation using likelihood

fastAnc

Fast estimation of ML ancestral states

add.everywhere

Add tip to all edges in a tree

repPhylo

Replicate a tree into a list of trees

getCladesofSize

Get all subtrees larger than or equal to a specified size

add.color.bar

Add color bar to a plot

anoletree

Phylogeny of Greater Antillean anole ecomorph species with mapped discrete character

ancThresh

Ancestral character estimation under the threshold model using Bayesian MCMC

fastBM

Fast Brownian simulation

phylosig

Compute phylogenetic signal with two methods

gammatest

Gamma test of Pybus & Harvey (2000)

likMlambda

Likelihood for joint lambda

export.as.xml

Export trees & data in XML format

anc.trend

Ancestral character estimation with a trend

collapse.to.star

Collapse a subtree to a star phylogeny

rstate

Pick a random state according to a vector of probabilities

threshState

Computes value for a threshold character from a liability and thresholds

phyl.pca

Phylogenetic principal components analysis

lambda.transform

Lambda transformation of matrix

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

minRotate

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

reroot

Re-root a tree along an edge

print.backbonePhylo

Print method for backbone phylogeny

phylANOVA

Phylogenetic ANOVA and post-hoc tests

getStates

Get the states at nodes or tips from a mapped tree

multiRF

Computes Robinson-Foulds distance between a set of trees

orderMappedEdge

Order the columns of mapped.edge to match across trees

make.era.map

Create "era" map on a phylogenetic tree

paintSubTree

Paint sub-trees with a discrete character

nodeHeights

Compute the heights above the root of each node

roundPhylogram

Plot a round phylogram

locate.yeti

Locate a cryptic, recently extinct, or missing taxon on a tree

multiC

Returns a list with phylogenetic VCV matrix for each mapped state

sampleFrom

Sample from a set of distributions

setMap

Set color map for objects of class "contMap" or "densityMap"

paste.tree

Paste two trees together

contMap

Map continuous trait evolution on the tree

sim.rates

Brownian simulation with multiple evolutionary rates

pgls.Ives

Phylogenetic regression with intraspecific sampling error

phyl.cca

Phylogenetic canonical correlation analysis

phyloDesign

Compute design matrix for least squares analyses

mergeMappedStates

Merge two or more mapped states into one state

exhaustiveMP

Exhaustive and branch & bound MP optimization

read.simmap

Read SIMMAP style trees from file

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

vcvPhylo

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

pbtree

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

getDescendants

Get descendant node numbers

phylo.to.map

Plot tree with tips linked to geographic coordinates

getExtant

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

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

ls.tree

Least squares branch lengths for a given tree

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

reorder.backbonePhylo

Reorders a backbone phylogeny

map.to.singleton

Converts a mapped tree to a tree with singleton nodes

plotThresh

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

phyl.resid

Phylogenetic size-correction via GLS regression

multi.mantel

Multiple matrix regression (partial Mantel test)

expm

Matrix exponential

untangle

Attempts to untangle crossing branches for plotting

roundBranches

Rounds the branch lengths of a tree

rateshift

Find the temporal position of one or more rate shifts

map.overlap

Proportional overlap between two mapped character histories on a tree

ratebystate

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

rotateNodes

Rotates a node or set of nodes in a phylogenetic tree

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

strahlerNumber

Computes Strahler number for trees and nodes

phenogram

Plot phenogram (traitgram)

to.matrix

Convert a character vector to a binary matrix

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

plotSimmap

Plot stochastic character mapped tree

writeNexus

Write a tree to file in Nexus format

plotTree

Plots rooted phylogenetic tree

plotTree.wBars

Plot a tree with bars at the tips

write.simmap

Write a stochastic character mapped tree to file

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

treeSlice

Slices the tree at a particular point and returns all subtrees

reorderSimmap

Reorder edges of a simmap tree

skewers

Matrix comparison using the method of random skewers

phylomorphospace

Creates phylomorphospace plot

phyl.vcv

Compute evolutionary VCV matrix for a tree & dataset

read.newick

Robust Newick style tree reader

starTree

Create star phylogeny

rescaleSimmap

Rescale SIMMAP style tree

splitTree

Split tree at a point

threshBayes

Threshold model using Bayesian MCMC

cladelabels

Add labels to subtrees of a plotted phylogeny

describe.simmap

Summarizes a stochastic mapped tree or set of trees

fastMRCA

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

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

genSeq

Simulate a DNA alignment on the tree under a model

ltt95

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

phytools-package

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

mrp.supertree

Matrix representation parsimony supertree estimation

phylo.toBackbone

Converts tree to backbone or vice versa

sim.history

Simulate stochastic character history under some model

sim.ratebystate

Conduct simulation of state dependent rate variation

threshDIC

Deviance Information Criterion from the threshold model

splitplotTree

Plots a phylogeny in two columns

writeAncestors

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