Learn R Programming

⚠️There's a newer version (2.3-0) of this package.Take me there.

phytools (version 0.7-70)

Phylogenetic Tools for Comparative Biology (and Other Things)

Description

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Copy Link

Version

Install

install.packages('phytools')

Monthly Downloads

10,483

Version

0.7-70

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/liamrevell/phytools

Maintainer

Last Published

September 19th, 2020

Functions in phytools (0.7-70)

Bayesian ancestral character estimation

add.simmap.legend

Add legend to stochastically mapped tree

Add tips at random to the tree

Add an arrow pointing to a tip or node on the tree

Add color bar to a plot

add.species.to.genus

Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree

Generate all bi- and multifurcating unrooted trees

Computes AIC weights

Add tip to all edges in a tree

Conducts correlational D-test from stochastic mapping

Ancestral character estimation using likelihood

Phylogenetic datasets

Ancestral character estimation under the threshold model using Bayesian MCMC

Convert a fitted Mk model to a Q-matrix

applyBranchLengths

Applies the branch lengths of a reference tree to a target

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

branching.diffusion

Animation of branching random diffusion

bind.tree.simmap

Attaches a new tip to a tree

REML version of brownie.lite

Likelihood test for rate variation in a continuous trait

Attaches a new tip to a tree

Ancestral character estimation with a trend

Compute an average tree from a set of trees and related operations

Average the posterior rates

Conversion to object of class "multiPhylo"

density.multiSimmap

Computes a posterior distribution for the number and types of changes on the tree

Plot posterior density of stochastic mapping on a tree

Plots a posterior sample of trees

describe.simmap

Summarizes a stochastic mapped tree or set of trees

Add labels to subtrees of a plotted phylogeny

consensus.edges

Compute consensus edges for a tree under some criterion

Map continuous trait evolution on the tree

Convert object of class "birthdeath" to raw birth & death rates

Creates a co-phylogenetic plot

Conducts a statistical test of cospeciation between two trees

Interactive tree visualizer

collapse.to.star

Collapse a subtree to a star phylogeny

di2multi.simmap

Collapse or resolve polytomies in a tree with a character painted on the edges

compare.chronograms

Compares two chronograms with precisely matching nodes in a visual manner

Creates a phylogenetic dot plot

Drop a clade from a tree

Drop all the leaves (tips) from a tree

Counts the number of character changes on a object of class "simmap" or "multiSimmap"

Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories

Exhaustive and branch & bound MP optimization

Likelihood test for a shift in the evolutionary correlation between traits

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

Map continuous trait evolution on the tree

Estimate diversity at each node of the tree

Compute the relative frequencies of state changes along edges

drop.tip.contMap

Drop tip or tips from an object of class "contMap" or "densityMap"

(Reasonably) fast quantitative trait simulation on phylogenies

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

drop.tip.multiPhylo

Drop tip or tips from an object of class "multiPhylo" or "multiSimmap"

Plots special types of phylogenetic trees

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

Simulate a DNA alignment on the tree under a model

Likelihood test for variation in the evolutionary variance-covariance matrix

(Reasonably) fast estimation of ML ancestral states

Adds a geological (or other temporal) legend to a plotted tree

lambda.transform

\(\lambda\) transformation of matrix

Likelihood for joint \(\lambda\)

Expands (or contracts) the tip-spacing of a given clade or clades

Function to test for correlated evolution of binary traits

force.ultrametric

Forces a phylogenetic tree to be ultrametric

Gamma test of Pybus & Harvey (2000)

Export trees & data in XML format

Function to interactively label nodes of a plotted tree

ladderize.simmap

Ladderize a tree with a mapped discrete character

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

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

Get the states at nodes or tips from a mapped tree

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

Least squares branch lengths for a given tree

Proportional overlap between two mapped character histories on a tree

mergeMappedStates

Merge two or more mapped states into one state

Matches nodes between two trees

map.to.singleton

Converts a tree without singletons to a tree with singleton nodes

Phylogeny inference using the least squares method

Phylogenetic ANOVA and post-hoc tests

Get the MRCA of a set of taxa

Compute evolutionary VCV matrix for a tree & dataset

orderMappedEdge

Order the columns of mapped.edge to match across trees

Matrix representation parsimony supertree estimation

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

Plot stochastic character mapped tree

Fits birth-death (speciation/extinction) model to reconstructed phylogeny

plotTree.errorbars

Plot a tree with error bars around divergence dates

plotTree.datamatrix

Plot a tree with a discrete character data matrix at the tips

Read SIMMAP style trees from file

Rotates a node or set of nodes in a phylogenetic tree

Multiple matrix regression (partial Mantel test)

reorder.backbonePhylo

Reorders a backbone phylogeny

Rounds the branch lengths of a tree

Get descendant node numbers

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

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

Deviance Information Criterion from the threshold model

Phylogenetic regression with intraspecific sampling error

Function to add tip labels to a plotted tree with linking lines

Phylogenetic principal components analysis

Locate a fossil lineage in a tree using continuous characters

Finding the minimum (median) split in the posterior sample

Phylogenetic size-correction via GLS regression

modified.Grafen

Computes modified Grafen edge lengths

Computes value for a threshold character from a liability and thresholds

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

getCladesofSize

Get all subtrees larger than or equal to a specified size

Returns a list with phylogenetic VCV matrix for each mapped state

Get position or node of a plotted tree interactively

Write a stochastic character mapped tree to file

Phylogenetic canonical correlation analysis

Computes Robinson-Foulds distance between a set of trees

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

phylomorphospace

Creates phylomorphospace plot

Plots rooted phylogenetic tree

Compute design matrix for least squares analyses

Find the temporal position of one or more rate shifts

phyl.pairedttest

Phylogenetic paired t-test

phylo.toBackbone

Converts tree to backbone or vice versa

Plot tree with tips linked to geographic coordinates

Robust Newick style tree reader

Create "era" map on a phylogenetic tree

Multivariate Brownian simulation with multiple correlations and rates

Simulate character history or a discrete character at the tips of the tree under some model

Midpoint root a phylogeny

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

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

Simulate stochastic character maps on a phylogenetic tree or trees

Creates a graphical illustration of Brownian motion evolution on a phylogeny

Paint sub-trees with a discrete character

Slices the tree at a particular point and returns all subtrees, or the tree rootward of the point

Matrix comparison using the method of random skewers

Attempts to untangle crossing branches for plotting

Plot phenogram (traitgram)

Paste two trees together

Phylogenetic reduced major axis (RMA) regression

phytools-package

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

plot.backbonePhylo

Plots backbone tree with triangles as clades

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

Plot a tree with bars at the tips

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

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

Returns a vector, matrix, or list of the mapped states on a tree or set of trees

Add marked changes to a plotted tree with mapped discrete character

Compute the heights above the root of each node

Sample from a set of distributions

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

Re-root a tree along an edge

nodelabels.cophylo

Add labels to a plotted "cophylo" object

Likelihood test for rate variation among trees, clades, or traits

Rescale SIMMAP style tree

Compute all possible resolutions of a node or all nodes in a multifurcating tree

sim.ratebystate

Conduct simulation of state dependent rate variation

Creates a phylogenetic heat map

Phylogenetic imputation for multivariate continuous character data

Computes Strahler number for trees and nodes

Set color map for various phylogenetic objects of classes

phylomorphospace3d

Creates tree-dimensional phylomorphospace plot

Brownian or OU simulation with multiple evolutionary regimes

Compute phylogenetic signal with two methods

Generic post-hoc test

Plot a round phylogram

Reorder edges of a simmap tree

Split edge colors when descendant edges have different mapped states

print.backbonePhylo

Print method for backbone phylogeny

Replicate a tree or set of trees

Pick a random state according to a vector of probabilities

Write a tree to file in Nexus format

Threshold model using Bayesian MCMC

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

Plots a phylogeny in two columns

Split tree at a point

Create star phylogeny

Convert a character vector to a binary matrix

Creates an animation of a tree growing from left-to-right or upwards