# TESS v2.1.0

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

Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.

## Functions in TESS

 Name Description tess.plot.output tess.plot.output: Plotting the output of a diversification rate estimation including mass-extinction events. mammalia Dated family level mammalian phylogeny from Meredith et al. (2011): Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification. 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.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.plot.multichain.diagnostics tess.plot.multichain.diagnostics: Plotting the mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events. tess.pathSampling tess.pathSampling: Marginal likelihood estimation via Path-Sampling. 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) tess.analysis tess.analysis: Diversification rate estimation under an episodic birth-death process including mass-extinction events. tess.mcmc tess.mcmc: Markov chain Monte Carlo simulation using a general Metropolis-Hastings algorithm. tess.PosteriorPrediction tess.PosteriorPrediction: Approximation of the posterior predictive distribution. tess.PosteriorPredictiveTest tess.PosteriorPredictiveTest: Approximation of the posterior predictive distribution. tess.sim.age tess.sim.age: Simulate a reconstructed tree for a given age under a global, time-dependent birth-death process. tess.steppingStoneSampling tess.steppingStoneSampling: Marginal likelihood estimation via Stepping-Stone-Sampling. 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 conifers Conifer phylogeny from Leslie et al. (2012) 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.plot.singlechain.diagnostics tess.plot.mcmc.diagnostics: Plotting the single chain mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events. No Results!

## Vignettes of TESS

 Name ext_figures/BirthDeathShift.pdf ext_figures/birth-death-sketch.pdf ext_figures/diversified-sampling.pdf ext_figures/models.pdf ext_figures/ss.pdf results/comet_hyperpriors.rds results/comet_no_mass_extinctions.rds results/comet_no_rateshifts.rds results/comet_posterior_1.rds results/comet_posterior_2.rds results/comet_posterior_3.rds results/comet_posterior_4.rds results/marginalLikelihoodConstBD.rds results/marginalLikelihoodDecrBD.rds results/marginalLikelihoodEpisodicBD.rds results/marginalLikelihoodMassExtinctionBD.rds results/output_auto_stop.rds results/samplesConstBD.rds results/samplesDecrBD.rds results/samplesDiversified.rds results/samplesEpisodicBD.rds results/samplesMassExtinctionBD.rds results/samplesUniform.rds results/samples_run_1.rds results/samples_run_2.rds results/samples_run_auto_tuned.rds results/samples_run_good.rds results/samples_run_large.rds results/samples_run_small.rds results/tess_analysis.rds Bayesian_Diversification_Rate_Analysis.Rnw literature.bib No Results!