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phytools (version 0.1-6)

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

27,917

Version

0.1-6

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

January 11th, 2012

Functions in phytools (0.1-6)

anc.Bayes

Bayesian ancestral character estimation

anc.ML

Ancestral character estimation using likelihood

fitBayes

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

posterior.evolrate

Analysis of the posterior sample from evol.rate.mcmc

vcvPhylo

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

splitTree

Split tree at a point

nodeHeights

Compute the heights above the root of each node

starTree

Create star phylogeny

phyloDesign

Compute design matrix for least squares analyses

add.everywhere

Add tip to all edges in a tree

paste.tree

Paste two trees together

phyl.pca

Phylogenetic principal components analysis

phyl.resid

Phylogenetic size-correction via GLS regression

treeSlice

Slices the tree at a particular point and returns all subtrees

brownie.lite

Likelihood test for rate variation

sim.rates

Brownian simulationn with multiple evolutionary rates

read.newick

Read Newick style tree

gammatest

Gamma test of Pybus & Harvey (2000)

minSplit

Finding the minimum (median) split in the posterior sample

pbtree

Simulate pure-birth stochastic tree or trees

write.simmap

Simulate stochastic character map on a phylogenetic tree

drop.clade

Drop clade from a tree

sim.history

Simulate stochastic character history under some model

phyl.cca

Phylogenetic canonical correlation analysis

reorderSimmap

Reorder edges of a simmap tree

phylosig

Compute phylogenetic signal with two methods

fastBM

Fast Brownian simulation

make.simmap

Simulate stochastic character map on a phylogenetic tree

phytools-package

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

phylomorphospace

Creates phylomorphospace plot

plotSimmap

Plot stochastic character mapped tree

read.simmap

Read SIMMAP style trees from file

sampleFrom

Sample from a set of distributions

phenogram

Plot phenogram (traitgram)

lambda.transform

Lambda transformation of matrix

anc.trend

Ancestral character estimation with a trend

allFurcTrees

Generate all bi- and multifurcating unrooted trees

evol.vcv

Likelihood test for variation in the evolutionary VCV matrix

fitDiversityModel

Fit diversity-dependent phenotypic evolution model

mrp.supertree

Matrix representation parsimony supertree estimation

evol.rate.mcmc

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

phyl.pairedttest

Phylogenetic paired t-test

make.era.map

Create "era" map on a phylogenetic tree

plotTree

Plots rooted phylogenetic tree

expm

Matrix exponential

estDiversity

Estimate diversity at each node of the tree

ltt

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

phyl.RMA

Phylogenetic reduced major axis (RMA) regression

phyl.vcv

Compute phylogenetic VCV matrix for a tree & dataset

rstate

Pick a random state according to a vector of probabilities

phylANOVA

Phylogenetic ANOVA and post-hoc tests

drop.tip.simmap

Drop tip from SIMMAP format tree

brownieREML

REML version of brownie.lite

ls.tree

Least squares branch lengths for a given tree

evolvcv.lite

Likelihood test for a shift in the evolutionary correlation between traits

map.overlap

Proportional overlap between two mapped character histories on a tree

optim.phylo.ls

Phylogeny inference using the least squares method

branching.diffusion

Animation of branching random diffusion

reroot

Re-root a tree along an edge

exhaustiveMP

Exhaustive and branch & bound MP optimization