laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies
Version 2.4-1

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.

AuthorDan Rabosky, Klaus Schliep
Date of publication2013-09-04 14:58:43
MaintainerDan Rabosky <drabosky@umich.edu>
LicenseGPL (>= 2)
Version2.4-1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("laser")

Getting started

Package overview

Popular man pages

calcLHbd: Calculate Likelihood of Branching Times Under Birth-Death...
fitdAICrc: Test for Rate Variation Using delta-AICrc Test Statistic
fitdAICrc.batch: Generate Null Distribution of dAICrc
magsand: Estimate speciation rates for crown and stem groups
plotNodeNumbers.phylo: Plot phylogenetic tree with node numbers
plotRate: Plot speciation and extinction rates through time
yuleWindow: Fit Yule Model (Pure Birth) to Temporal Window of Branching...
See all...

All man pages Function index File listing

Man pages

agamids: Ultrametric Phylogeny of Australian Agamid Lizards
bd: Fit Rate-Constant Birth-Death Model to Branching Times
birthdeathSim: birthdeathSim
calcLHbd: Calculate Likelihood of Branching Times Under Birth-Death...
DensityDependent: Fit Density Dependent Speciation Model to Branching Times
fitContinuousBirthDeath: Fit model with continuous-time varying speciation/extinction...
fitdAICrc: Test for Rate Variation Using delta-AICrc Test Statistic
fitdAICrc.batch: Generate Null Distribution of dAICrc
gamStat: gamStat
getBtimes: Get Branching Times From Parenthetic-Format Tree ('Newick')
getBtimes.batch: Branching Times for Batch of Phylogenies
laser-internals: internal functions for package laser
laser-package: LASER
magsand: Estimate speciation rates for crown and stem groups
mccrTest: Conduct monte carlo constant rates (gamma statistic) test
plethodon: plethodon
plotLtt: plotLtt
plotNodeNumbers.phylo: Plot phylogenetic tree with node numbers
plotRate: Plot speciation and extinction rates through time
pureBirth: pureBirth
RandomTrees: Random Phylogenetic Trees
scaleBranchingtimes: Scale Branching Times
truncateTree: Truncate a Set of Branching Times
warblers: Branching times from phylogeny of North American Dendroica...
yule-n-rate: yule-n-rate
yuleSim: yuleSim
yuleWindow: Fit Yule Model (Pure Birth) to Temporal Window of Branching...

Functions

Files

laser
laser/NAMESPACE
laser/NEWS
laser/data
laser/data/agamids.txt.gz
laser/data/warblers.rda
laser/data/agamids.rda
laser/data/rtrees5.rda
laser/data/plethodon.rda
laser/data/warblers.txt.gz
laser/data/rtrees50.rda
laser/data/rtrees50.txt.gz
laser/data/rtrees5.txt.gz
laser/R
laser/R/yuleSim.R
laser/R/birthdeathSim.R
laser/R/calcLHbd.R
laser/R/gamStat.R
laser/R/getLikelihood.EXVAR.R
laser/R/lambda.stem.ci.R
laser/R/DDL.R
laser/R/pTt.BOTHVAR.R
laser/R/plotRate.R
laser/R/fitEXVAR.R
laser/R/gsr.R
laser/R/getLikelihood.BOTHVAR.R
laser/R/getSpeciationtimes.R
laser/R/fitSPVAR.R
laser/R/fitBOTHVAR.R
laser/R/pTt.EXVAR.R
laser/R/DDX.R
laser/R/rhoFxn.EXVAR.R
laser/R/getBtimes.R
laser/R/getBtimes.batch.R
laser/R/lambda.crown.ms01.R
laser/R/mccrTest.R
laser/R/lambdaFx.R
laser/R/combinations.R
laser/R/fitdAICrc.batch.R
laser/R/rhoFxn.SPVAR.R
laser/R/pureBirth.R
laser/R/getLikelihood.SPVAR.R
laser/R/bd.R
laser/R/lambda.stem.ms01.R
laser/R/plotLtt.R
laser/R/scaleBranchingtimes.R
laser/R/lamda.stem.ml.R
laser/R/yuleNrate.R
laser/R/muFx.R
laser/R/plotNodeNumbers.phylo.R
laser/R/rhoFxn.BOTHVAR.R
laser/R/yuleWindow.R
laser/R/truncateTree.R
laser/R/node.sons.R
laser/R/pTt.SPVAR.R
laser/R/checkbasal.R
laser/R/fitdAICrc.R
laser/R/yuleint2.R
laser/MD5
laser/DESCRIPTION
laser/man
laser/man/plethodon.Rd
laser/man/laser-package.Rd
laser/man/yule-n-rate.Rd
laser/man/fitdAICrc.Rd
laser/man/getBtimes.Rd
laser/man/birthdeathSim.Rd
laser/man/yuleSim.Rd
laser/man/plotRate.Rd
laser/man/fitContinuousBirthDeath.Rd
laser/man/bd.Rd
laser/man/DensityDependent.Rd
laser/man/mccrTest.Rd
laser/man/warblers.Rd
laser/man/pureBirth.Rd
laser/man/laser-internals.Rd
laser/man/fitdAICrc.batch.Rd
laser/man/RandomTrees.Rd
laser/man/agamids.Rd
laser/man/calcLHbd.Rd
laser/man/plotLtt.Rd
laser/man/magsand.Rd
laser/man/truncateTree.Rd
laser/man/plotNodeNumbers.phylo.Rd
laser/man/yuleWindow.Rd
laser/man/scaleBranchingtimes.Rd
laser/man/gamStat.Rd
laser/man/getBtimes.batch.Rd
laser documentation built on Jan. 15, 2017, 4:49 p.m.

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