Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

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Documentation for package ‘TESS’ version 2.1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

TESS-package	Diversification rate estimation and fast simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes including mass-extinction events
cettiidae	Cettiidae phylogeny from Alstroem et al. (2011)
conifers	Conifer phylogeny from Leslie et al. (2012)
globalBiDe.analysis	tess.analysis: Diversification rate estimation under an episodic birth-death process including mass-extinction events.
globalBiDe.output.summary	tess.process.output: Summarizing the output of a diversification rate estimation including mass-extinction events. See the tess.analysis function for more information on how such output is generated and the tess.plot.output how the output can be visualized. Also have a look at the vignette for more in detail description and examples.
mammalia	Dated family level mammalian phylogeny from Meredith et al. (2011): Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification.
TESS	Diversification rate estimation and fast simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes including mass-extinction events
tess.analysis	tess.analysis: Diversification rate estimation under an episodic birth-death process including mass-extinction events.
tess.likelihood	tess.likelihood: Probability density of a tree under a tree-wide time-dependent birth-death process
tess.likelihood.rateshift	tess.likelihood.rateshift: Probability density of a tree under a tree-wide time-dependent birth-death-shift process
tess.mcmc	tess.mcmc: Markov chain Monte Carlo simulation using a general Metropolis-Hastings algorithm.
tess.nTaxa.expected	tess.nTaxa.expected: The expected number of taxa at present of a tree under a global, time-dependent birth-death process ( E[ N(T) ] )
tess.pathSampling	tess.pathSampling: Marginal likelihood estimation via Path-Sampling.
tess.plot.multichain.diagnostics	tess.plot.multichain.diagnostics: Plotting the mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events.
tess.plot.output	tess.plot.output: Plotting the output of a diversification rate estimation including mass-extinction events.
tess.plot.singlechain.diagnostics	tess.plot.mcmc.diagnostics: Plotting the single chain mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events.
tess.PosteriorPrediction	tess.PosteriorPrediction: Approximation of the posterior predictive distribution.
tess.PosteriorPredictiveTest	tess.PosteriorPredictiveTest: Approximation of the posterior predictive distribution.
tess.process.output	tess.process.output: Summarizing the output of a diversification rate estimation including mass-extinction events. See the tess.analysis function for more information on how such output is generated and the tess.plot.output how the output can be visualized. Also have a look at the vignette for more in detail description and examples.
tess.sim.age	tess.sim.age: Simulate a reconstructed tree for a given age under a global, time-dependent birth-death process.
tess.sim.taxa	tess.sim.taxa.taxa: Simulate a reconstructed tree for a given number of taxa under a global, time-dependent birth-death process.
tess.sim.taxa.age	tess.sim.taxa.taxa.age: Simulate a reconstructed tree for a given age and number of taxa under a global, time-dependent birth-death process.
tess.steppingStoneSampling	tess.steppingStoneSampling: Marginal likelihood estimation via Stepping-Stone-Sampling.