laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

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

View on CRAN

Functions

agamids Man page
bd Man page
birthdeathSim} \title{ birthdeathSim } \description{ Simulate Man page
calcLHbd Man page
checkbasal Man page
combinations Man page
DDL Man page
DDX Man page
fitBOTHVAR Man page
fitdAICrc Man page
fitdAICrc.batch Man page
fitEXVAR Man page
fitSPVAR Man page
gamStat Man page
getBtimes Man page
getBtimes.batch Man page
getLikelihood.BOTHVAR Man page
getLikelihood.EXVAR Man page
getLikelihood.SPVAR Man page
getSpeciationtimes Man page
gsr Man page
Ibd Man page
IDDL Man page
IDDX Man page
IpureBirth Man page
Iyule2rate Man page
Iyule3rate Man page
lambda.crown.ms01 Man page
lambdaFx Man page
lambda.stem.ci Man page
lambda.stem.ml Man page
lambda.stem.ms01 Man page
laser Man page
laser-internals Man page
laser-package Man page
mccrTest Man page
muFx Man page
node.sons Man page
plethodon Man page
plotLtt Man page
plotNodeNumbers.phylo Man page
plotRate Man page
pTt.BOTHVAR Man page
pTt.EXVAR Man page
pTt.SPVAR Man page
pureBirth Man page
rhoFxn.BOTHVAR Man page
rhoFxn.EXVAR Man page
rhoFxn.SPVAR Man page
rtrees5 Man page
rtrees50 Man page
scaleBranchingtimes Man page
truncateTree Man page
warblers Man page
yule2rate Man page
yule3rate Man page
yule4rate Man page
yule5rate Man page
yuleint2 Man page
yuleint2New Man page
yule-n-rate Man page
yuleSim Man page
yuleWindow Man page

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

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