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.

Author
Sebastian Hoehna and Michael R. May
Date of publication
2015-10-28 08:44:56
Maintainer
Sebastian Hoehna <Sebastian.Hoehna@gmail.com>
License
GPL-3
Version
2.1.0

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...

Files in this package

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