Likelihood Analysis of Speciation/Extinction Rates from Phylogenies


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Documentation for package ‘laser’ version 2.2

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laser-package LASER
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 Model
DDL Fit Density Dependent Speciation Model to Branching Times
DDX Fit Density Dependent Speciation Model to Branching Times
fitBOTHVAR Fit model with continuous-time varying speciation/extinction rates to phylogeny
fitdAICrc Test for Rate Variation Using delta-AICrc Test Statistic
fitdAICrc.batch Generate Null Distribution of dAICrc
fitEXVAR Fit model with continuous-time varying speciation/extinction rates to phylogeny
fitNDR_1rate Estimate diversification rate from combined taxonomic/phylogenetic data
fitNDR_2rate Fit 2-rate diversification model to combined phylogenetic/taxonomic data
fitSPVAR Fit model with continuous-time varying speciation/extinction rates to phylogeny
gamStat gamStat
getBtimes Get Branching Times From Parenthetic-Format Tree ('Newick')
getBtimes.batch Branching Times for Batch of Phylogenies
getTipdata Add species richness data to tips of phylogenetic tree
lambda.crown.ms01 Estimate speciation rates for crown and stem groups
lambda.stem.ci Estimate speciation rates for crown and stem groups
lambda.stem.ml Estimate speciation rates for crown and stem groups
lambda.stem.ms01 Estimate speciation rates for crown and stem groups
laser LASER
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
rtrees5 Random Phylogenetic Trees
rtrees50 Random Phylogenetic Trees
scaleBranchingtimes Scale Branching Times
skinkdiversity Species richness for Australian sphenomorphine skink genera
skinktree Phylogenetic tree of Australian sphenomorphine skink genera
truncateTree Truncate a Set of Branching Times
warblers Branching times from phylogeny of North American Dendroica warblers
yule-n-rate yule-n-rate
yule2rate yule-n-rate
yule3rate yule-n-rate
yule4rate yule-n-rate
yule5rate yule-n-rate
yuleSim yuleSim
yuleWindow Fit Yule Model (Pure Birth) to Temporal Window of Branching Times