Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes

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Documentation for package ‘TESS’ version 1.2.0

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TESS-package Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes
cettiidae Cettiidae phylogeny from Alstroem et al. (2011)
globalBiDe.likelihood globalBiDe.likelihood: Probability density of a tree under a global, time-dependent birth-death process
globalBiDe.nTaxa.expected globalBiDe.nTaxa.expected: The expected number of taxa at present of a tree under a global, time-dependent birth-death process (E[N(T)])
mammalia Dated family level mammalian phylogeny from Meredith et al. (2011): Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification.
sim.globalBiDe.age sim.globalBiDe.age: Simulate a reconstructed tree for a given age under a global, time-dependent birth-death process.
sim.globalBiDe.taxa sim.globalBiDe.taxa.taxa: Simulate a reconstructed tree for a given number of taxa under a global, time-dependent birth-death process.
sim.globalBiDe.taxa.age sim.globalBiDe.taxa.taxa.age: Simulate a reconstructed tree for a given age and number of taxa under a global, time-dependent birth-death process.
TESS Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes
tess.mcmc tess.mcmc: Metropolis-Hastings algorithm.
tess.PosteriorPrediction tess.PosteriorPrediction: Approximation of the posterior predictive distribution.
tess.PosteriorPredictiveTest tess.PosteriorPredictiveTest: Approximation of the posterior predictive distribution.
tess.steppingStoneSampling tess.steppingStoneSampling: Marginal likelihood estimation via Stepping-Stone-Sampling.