TESS: 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.

AuthorSebastian Hoehna and Michael R. May
Date of publication2015-10-28 08:44:56
MaintainerSebastian Hoehna <Sebastian.Hoehna@gmail.com>
LicenseGPL-3
Version2.1.0

View on CRAN

Man pages

cettiidae: Cettiidae phylogeny from Alstroem et al. (2011)

conifers: Conifer phylogeny from Leslie et al. (2012)

mammalia: Dated family level mammalian phylogeny from Meredith et al....

tess.analysis: tess.analysis: Diversification rate estimation under an...

tess.likelihood: tess.likelihood: Probability density of a tree under a...

tess.likelihood.rateshift: tess.likelihood.rateshift: Probability density of a tree...

tess.mcmc: tess.mcmc: Markov chain Monte Carlo simulation using a...

tess.nTaxa.expected: tess.nTaxa.expected: The expected number of taxa at present...

TESS-package: Diversification rate estimation and fast simulation of...

tess.pathSampling: tess.pathSampling: Marginal likelihood estimation via...

tess.plot.multichain.diagnostics: tess.plot.multichain.diagnostics: Plotting the mcmc...

tess.plot.output: tess.plot.output: Plotting the output of a diversification...

tess.plot.singlechain.diagnostics: tess.plot.mcmc.diagnostics: Plotting the single chain mcmc...

tess.PosteriorPrediction: tess.PosteriorPrediction: Approximation of the posterior...

tess.PosteriorPredictiveTest: tess.PosteriorPredictiveTest: Approximation of the posterior...

tess.process.output: tess.process.output: Summarizing the output of a...

tess.sim.age: tess.sim.age: Simulate a reconstructed tree for a given age...

tess.sim.taxa: tess.sim.taxa.taxa: Simulate a reconstructed tree for a given...

tess.sim.taxa.age: tess.sim.taxa.taxa.age: Simulate a reconstructed tree for a...

tess.steppingStoneSampling: tess.steppingStoneSampling: Marginal likelihood estimation...

Functions

cettiidae Man page
conifers Man page
globalBiDe.analysis Man page
globalBiDe.output.summary Man page
mammalia Man page
TESS Man page
tess.analysis Man page
tess.likelihood Man page
tess.likelihood.rateshift Man page
tess.mcmc Man page
tess.nTaxa.expected Man page
TESS-package Man page
tess.pathSampling Man page
tess.plot.multichain.diagnostics Man page
tess.plot.output Man page
tess.plot.singlechain.diagnostics Man page
tess.PosteriorPrediction Man page
tess.PosteriorPredictiveTest Man page
tess.process.output Man page
tess.sim.age Man page
tess.sim.taxa Man page
tess.sim.taxa.age Man page
tess.steppingStoneSampling Man page

Files

TESS
TESS/inst
TESS/inst/CITATION
TESS/inst/doc
TESS/inst/doc/Bayesian_Diversification_Rate_Analysis.pdf
TESS/inst/doc/Bayesian_Diversification_Rate_Analysis.Rnw
TESS/inst/doc/Bayesian_Diversification_Rate_Analysis.R
TESS/src
TESS/src/mass_extinction_equations.cpp
TESS/src/RcppExports.cpp
TESS/NAMESPACE
TESS/NEWS
TESS/data
TESS/data/conifers.rda
TESS/data/mammalia.rda
TESS/data/cettiidae.rda
TESS/R
TESS/R/tess.sim.taxa.R TESS/R/tess.utilities.R TESS/R/tess.analysis.R TESS/R/tess.sim.taxa.age.R TESS/R/tess.plot.multichain.diagnostics.R TESS/R/tess.PathSampling.R TESS/R/tess.sim.age.R TESS/R/tess.plot.singlechain.diagnostics.R TESS/R/tess.equations.R TESS/R/tess.nTaxa.expected.R TESS/R/tess.likelihood.R TESS/R/tess.PosteriorPrediction.R TESS/R/tess.PosteriorPredictiveTest.R TESS/R/RcppExports.R TESS/R/tess.plot.output.R TESS/R/tess.likelihood.rateshift.R TESS/R/tess.SteppingStoneSampling.R TESS/R/tess.mcmc.R TESS/R/tess.process.output.R
TESS/vignettes
TESS/vignettes/ext_figures
TESS/vignettes/ext_figures/models.pdf
TESS/vignettes/ext_figures/BirthDeathShift.pdf
TESS/vignettes/ext_figures/birth-death-sketch.pdf
TESS/vignettes/ext_figures/ss.pdf
TESS/vignettes/ext_figures/diversified-sampling.pdf
TESS/vignettes/results
TESS/vignettes/results/marginalLikelihoodConstBD.rds
TESS/vignettes/results/comet_posterior_4.rds
TESS/vignettes/results/samplesUniform.rds
TESS/vignettes/results/comet_posterior_2.rds
TESS/vignettes/results/marginalLikelihoodDecrBD.rds
TESS/vignettes/results/marginalLikelihoodEpisodicBD.rds
TESS/vignettes/results/samplesEpisodicBD.rds
TESS/vignettes/results/comet_no_rateshifts.rds
TESS/vignettes/results/comet_posterior_3.rds
TESS/vignettes/results/samples_run_1.rds
TESS/vignettes/results/samples_run_good.rds
TESS/vignettes/results/comet_no_mass_extinctions.rds
TESS/vignettes/results/samplesConstBD.rds
TESS/vignettes/results/marginalLikelihoodMassExtinctionBD.rds
TESS/vignettes/results/samplesMassExtinctionBD.rds
TESS/vignettes/results/samples_run_2.rds
TESS/vignettes/results/samplesDiversified.rds
TESS/vignettes/results/samples_run_large.rds
TESS/vignettes/results/samples_run_small.rds
TESS/vignettes/results/comet_posterior_1.rds
TESS/vignettes/results/samplesDecrBD.rds
TESS/vignettes/results/tess_analysis.rds
TESS/vignettes/results/comet_hyperpriors.rds
TESS/vignettes/results/output_auto_stop.rds
TESS/vignettes/results/samples_run_auto_tuned.rds
TESS/vignettes/literature.bib
TESS/vignettes/Bayesian_Diversification_Rate_Analysis.Rnw
TESS/MD5
TESS/build
TESS/build/vignette.rds
TESS/DESCRIPTION
TESS/man
TESS/man/tess.mcmc.Rd TESS/man/tess.analysis.Rd TESS/man/tess.nTaxa.expected.Rd TESS/man/tess.plot.singlechain.diagnostics.Rd TESS/man/cettiidae.Rd TESS/man/tess.likelihood.rateshift.Rd TESS/man/mammalia.Rd TESS/man/conifers.Rd TESS/man/tess.process.output.Rd TESS/man/tess.sim.taxa.Rd TESS/man/tess.likelihood.Rd TESS/man/tess.steppingStoneSampling.Rd TESS/man/tess.PosteriorPredictiveTest.Rd TESS/man/tess.sim.age.Rd TESS/man/tess.PosteriorPrediction.Rd TESS/man/tess.sim.taxa.age.Rd TESS/man/TESS-package.Rd TESS/man/tess.plot.multichain.diagnostics.Rd TESS/man/tess.plot.output.Rd TESS/man/tess.pathSampling.Rd

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