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. | |
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Vignettes of TESS
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Details
| Type | Package |
| Date | 2015-10-23 |
| License | GPL-3 |
| LinkingTo | Rcpp |
| VignetteBuilder | knitr |
| NeedsCompilation | yes |
| Packaged | 2015-10-28 02:42:07 UTC; hoehna |
| Repository | CRAN |
| Date/Publication | 2015-10-28 08:44:56 |
| depends | ape , coda , deSolve |
| suggests | knitr |
| imports | Rcpp (>= 0.11.0) |
| Contributors | Michael May, Sebastian Hoehna |
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