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

## Documentation for package ‘TESS’ version 2.1.0

- 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.