laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

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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.

Author
Dan Rabosky, Klaus Schliep
Date of publication
2013-09-04 14:58:43
Maintainer
Dan Rabosky <drabosky@umich.edu>
License
GPL (>= 2)
Version
2.4-1

View on CRAN

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...

Files in this package

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