laser (version 2.4-1)

Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Description

laser implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time and whether rates vary among lineages.

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Version

Install

install.packages('laser')

Monthly Downloads

Version

2.4-1

License

GPL (>= 2)

Maintainer

Dan Rabosky

Last Published

September 4th, 2013

Functions in laser (2.4-1)

truncateTree

Truncate a Set of Branching Times

gamStat

Fit Rate-Constant Birth-Death Model to Branching Times

plotLtt

yuleWindow

Fit Yule Model (Pure Birth) to Temporal Window of Branching Times

birthdeathSim

laser-internals

internal functions for package laser

calcLHbd

Calculate Likelihood of Branching Times Under Birth-Death Model

Branching Times for Batch of Phylogenies

fitdAICrc

Test for Rate Variation Using delta-AICrc Test Statistic

plotNodeNumbers.phylo.Rd

Plot phylogenetic tree with node numbers

MagallonSanderson.Rd

Estimate speciation rates for crown and stem groups

agamids

Ultrametric Phylogeny of Australian Agamid Lizards

mccrTest.Rd

Conduct monte carlo constant rates (gamma statistic) test

yuleSim

fitdAICrc.batch

Generate Null Distribution of dAICrc

scaleBranchingtimes

Scale Branching Times

warblers

Branching times from phylogeny of North American Dendroica warblers

DensityDependent

Fit Density Dependent Speciation Model to Branching Times

getBtimes

Get Branching Times From Parenthetic-Format Tree ('Newick')

fitSPVAR

Fit model with continuous-time varying speciation/extinction rates to phylogeny

pureBirth

RandomTrees

Random Phylogenetic Trees

plotRate

Plot speciation and extinction rates through time

yule-n-rate