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laser (version 2.1)

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

21

Version

2.1

License

GPL 2 or later

Maintainer

Dan Rabosky

Last Published

February 15th, 2017

Functions in laser (2.1)

DensityDependent

Fit Density Dependent Speciation Model to Branching Times
bd

Fit Rate-Constant Birth-Death Model to Branching Times
agamids

Ultrametric Phylogeny of Australian Agamid Lizards
calcLHbd

Calculate Likelihood of Branching Times Under Birth-Death Model
fitSPVAR

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

Random Phylogenetic Trees
laser-internals

internal functions for package laser
Rate-Variable Birth Death

Fit Rate-Variable Diversification Model With Extinction to Branching Times
getBtimes.batch

Branching Times for Batch of Phylogenies
fitdAICrc

Test for Rate Variation Using delta-AICrc Test Statistic
fitNDR_2rate.Rd

Fit 2-rate diversification model to combined phylogenetic/taxonomic data
pureBirth

pureBirth
yule-n-rate

yule-n-rate
skinkdiversity

Species richness for Australian sphenomorphine skink genera
yuleSim

yuleSim
MagallonSanderson.Rd

Estimate speciation rates for crown and stem groups
warblers

Branching times from phylogeny of North American Dendroica warblers
plotRate

Plot speciation and extinction rates through time
fitNDR_1rate.Rd

Estimate diversification rate from combined taxonomic/phylogenetic data
plethodon

plethodon
getTipdata.Rd

Add species richness data to tips of phylogenetic tree
getBtimes

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

Phylogenetic tree of Australian sphenomorphine skink genera
truncateTree

Truncate a Set of Branching Times
plotNodeNumbers.phylo.Rd

Plot phylogenetic tree with node numbers
laser-package

LASER
yuleWindow

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

Conduct monte carlo constant rates (gamma statistic) test
gamStat

gamStat
scaleBranchingtimes

Scale Branching Times
plotLtt

plotLtt