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phytools (version 1.9-16)

Phylogenetic Tools for Comparative Biology (and Other Things)

Description

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

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Version

Install

install.packages('phytools')

Monthly Downloads

27,917

Version

1.9-16

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/liamrevell/phytools

Maintainer

Liam Revell

Last Published

July 14th, 2023

Functions in phytools (1.9-16)

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

Phylogenetic datasets

Compute the parsimony score

Add tip to all edges in a tree

Bayesian ancestral character estimation

Conducts correlational D-test from stochastic mapping

Add tips at random to the tree

Conversion to object of class "multiPhylo"

Attaches a new tip to a tree

Add labels to subtrees of a plotted phylogeny

collapse.to.star

Collapse a subtree to a star phylogeny

Average the posterior rates

Computes Akaike weights

bind.tree.simmap

Binds two trees of class "simmap"

Creates a co-phylogenetic plot

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

Likelihood test for rate variation in a continuous trait

add.simmap.legend

Add legend to stochastically mapped tree

REML version of brownie.lite

Conducts a statistical test of cospeciation between two trees

drop.tip.contMap

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

Ancestral character estimation under the threshold model using Bayesian MCMC

Likelihood test for a shift in the evolutionary correlation between traits

Exhaustive and branch & bound MP optimization

Compute marginal ancestral states

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

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

Ancestral character estimation using likelihood

Simulates and visualizes discrete-time Brownian evolution on a phylogeny

Ancestral character estimation with a trend

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

drop.tip.multiSimmap

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

branching.diffusion

Animation of branching random diffusion

consensus.edges

Compute consensus edges for a tree under some criterion

applyBranchLengths

Applies the branch lengths of a reference tree to a target

Get the states at nodes or tips from a mapped tree

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

Convert a fitted Mk model to a Q-matrix

Locate a fossil lineage in a tree using continuous characters

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

Interactive tree visualizer

Drop a clade from a tree

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

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

Map continuous trait evolution on the tree

Simulate a DNA alignment on the tree under a model

Drop all the leaves (tips) from a tree

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

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

density.multiSimmap

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

drop.tip.simmap

Drop tips or extract clade from tree with mapped discrete character

compare.chronograms

Compares two chronograms with precisely matching nodes in a visual manner

Map continuous trait evolution on the tree

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

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

di2multi.simmap

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

Plot posterior density of stochastic mapping on a tree

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

Export trees & data in XML format

force.ultrametric

Coerces a phylogenetic tree to be ultrametric

Proportional overlap between two mapped character histories on a tree

Plots special types of phylogenetic trees

Creates a phylogenetic dot plot

map.to.singleton

Converts a tree without singletons to a tree with singleton nodes

Gamma test of Pybus & Harvey (2000)

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

Function to interactively label nodes of a plotted tree

Likelihood test for variation in the evolutionary variance-covariance matrix

nodelabels.cophylo

Add labels to a plotted "cophylo" object

(Reasonably) fast estimation of ML ancestral states

ladderize.simmap

Ladderize a tree with a mapped discrete character

Phylogeny inference using the least squares method

Plots a posterior sample of trees

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

describe.simmap

Summarizes a stochastic mapped tree or set of trees

Compute the relative frequencies of state changes along edges

Get the MRCA of a set of taxa

Least squares branch lengths for a given tree

Finding the minimum (median) split in the posterior sample

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

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

Get position or node of a plotted tree interactively

modified.Grafen

Computes modified Grafen edge lengths

Add marked changes to a plotted tree with mapped discrete character

Fits extended Mk model for discrete character evolution

Phylogenetic size-correction via GLS regression

Compute evolutionary VCV matrix for a tree & dataset

getCladesofSize

Get all subtrees larger than or equal to a specified size

phylo.toBackbone

Converts tree to backbone or vice versa

Function to test for correlated evolution of binary traits

Create "era" map on a phylogenetic tree

Midpoint root a phylogeny

Estimate diversity at each node of the tree

Simulate stochastic character maps on a phylogenetic tree or trees

(Reasonably) fast quantitative trait simulation on phylogenies

Compute design matrix for least squares analyses

Function to fit a multi-rate Brownian evolution model

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

Compute the heights above the root of each node

Matches nodes between two trees

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

Returns a list with phylogenetic VCV matrix for each mapped state

orderMappedEdge

Order the columns of mapped.edge to match across trees

Plots rooted phylogenetic tree

Paint sub-trees with a discrete character

plotTree.datamatrix

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

mergeMappedStates

Merge two or more mapped states into one state

Find the temporal position of one or more rate shifts

Newick or Nexus style tree reader

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

sim.ratebystate

Conduct simulation of state dependent rate variation

Get descendant node numbers

Phylogenetic ANOVA and post-hoc tests

Matrix representation parsimony supertree estimation

Multiple matrix regression (partial Mantel test)

Computes Robinson-Foulds distance between a set of trees

phyl.pairedttest

Phylogenetic paired t-test

Creates a phylogenetic heat map

Phylogenetic regression with intraspecific sampling error

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

Plot traitgram (phenogram)

lambda.transform

\(\lambda\) transformation of matrix

Phylogenetic principal components analysis

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

Generic post-hoc test

phylomorphospace

Creates phylomorphospace plot

plot.backbonePhylo

Plots backbone tree with triangles as clades

phylomorphospace3d

Creates three-dimensional phylomorphospace plot

Likelihood for joint \(\lambda\)

Phylogenetic reduced major axis (RMA) regression

Phylogenetic canonical correlation analysis

plotBranchbyTrait

Plot branch colors by a quantitative trait or value

Reorder edges of a "simmap" tree

Replicate a tree or set of trees

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

Paste two trees together

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

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

Rescale phylogenetic objects of different types

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

Rescale object of class "simmap"

Rounds the branch lengths of a tree

Plot a round, sigmoidal, or spline phylogram or cladogram

Split tree at a point

Rotates a node or set of nodes in a phylogenetic tree

Set color map for various phylogenetic objects of classes

Matrix comparison using the method of random skewers

Split edge colors when descendant edges have different mapped states

Plots a phylogeny in two columns

Computes value for a threshold character from a liability and thresholds

Multivariate Brownian simulation with multiple correlations and rates

Phylogenetic imputation for multivariate continuous character data

Compute phylogenetic signal with two methods

Threshold model using Bayesian MCMC

Deviance Information Criterion from the threshold model

Create star phylogeny

phytools-package

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

Plot tree with tips linked to geographic coordinates

Write a stochastic character mapped tree to file

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

Plot stochastic character mapped tree

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

plotTree.errorbars

Plot a tree with error bars around divergence dates

Computes Strahler number for trees and nodes

Convert a character vector to a binary matrix

Write a tree to file in Nexus format

Plot a tree with bars at the tips

print.backbonePhylo

Print method for backbone phylogeny

Compute the parsimony score

Read SIMMAP style trees from file

reorder.backbonePhylo

Reorders a backbone phylogeny

Pick a random state according to a vector of probabilities

Sample from a set of distributions

Brownian or OU simulation with multiple evolutionary regimes

Creates a graphical illustration of Brownian motion evolution on a phylogeny

Re-root a tree along an edge

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

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

rerootingMethod

Get marginal ancestral state reconstructions by re-rooting

Attempts to untangle crossing branches for plotting

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