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Maximum likelihood-based methods for analyzing lineage diversification rates
● Data Source:
CranContrib
● Keywords: package
● Alias: laser, laser-package
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Fits multi-rate variants of the pure birth (Yule) model to branching times derived from phylogenetic data. For example, the yule2rate model assumes that the clade has diversified under speciation rate r1 until some time st, at which point the speciation rate shifts to a new rate r2. The shift point(s) are found by optimizing parameters and computing likelihoods for a set of possible shift times and selecting the parameter combinations giving the maximum log-likelihood.
● Data Source:
CranContrib
● Keywords: models
● Alias: yule-n-rate, yule2rate, yule3rate, yule4rate, yule5rate
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fitdAICrc
(Package: laser) :
Test for Rate Variation Using delta-AICrc Test Statistic
Fits a specified set of rate-variable and rate-constant variants of the birth-death model to branching times from phylogenetic data. The test statistic dAICrc is the difference in AIC scores between the best rate-constant and rate-variable models.
● Data Source:
CranContrib
● Keywords: htest, models
● Alias: fitdAICrc
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getBtimes
(Package: laser) :
Get Branching Times From Parenthetic-Format Tree ('Newick')
Reads a file containing an ultrametric tree in parenthetic format and returns a numeric vector of branching times, sorted from earliest to most recent.
● Data Source:
CranContrib
● Keywords: IO, manip
● Alias: getBtimes
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Simulate Branching Times Under the birth-death model and/or with incomplete sampling
● Data Source:
CranContrib
● Keywords: datagen
● Alias: birthdeathSim
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Simulate Branching Times Under the Pure Birth Model
● Data Source:
CranContrib
● Keywords: datagen
● Alias: yuleSim
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plotRate
(Package: laser) :
Plot speciation and extinction rates through time
Plots diversification rates through time estimated from fits of exponential speciation and extinction models (Rabosky & Lovette 2008).
● Data Source:
CranContrib
● Keywords: models
● Alias: plotRate
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fitSPVAR
(Package: laser) :
Fit model with continuous-time varying speciation/extinction rates to phylogeny
Functions that fit time-varying speciation and extinction models to branching times derived from phylogenetic data. fitSPVAR fits a model with an exponentially declining speciation rate through time and constant extinction. fitEXVAR fits a model with exponentially increasing extinction and constant speciation. fitBOTHVAR fits a model where both speciation and extinction rates can vary through time.
● Data Source:
CranContrib
● Keywords: models
● Alias: fitBOTHVAR, fitEXVAR, fitSPVAR
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bd
(Package: laser) :
Fit Rate-Constant Birth-Death Model to Branching Times
Finds maximum likelihood estimates of the net diversification rate r (speciation rate S minus the extinction rate E) and the extinction fraction a = E/S, using branching times derived from an ultrametric phylogenetic tree.
● Data Source:
CranContrib
● Keywords: models
● Alias: bd
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DensityDependent
(Package: laser) :
Fit Density Dependent Speciation Model to Branching Times
Functions that fit density-dependent speciation rate models to branching times derived from phylogenetic data. DDX and DDL fit exponential and logistic variants of the density-dependent speciation rate model.
● Data Source:
CranContrib
● Keywords: models
● Alias: DDL, DDX
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