TESS: Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events
Version 2.1.0

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.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TESS")

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

TESS Man page
TESS-package Man page
cettiidae Man page
conifers Man page
equations_p1_rateshift_CPP Source code
equations_pSurvival_rateshift_CPP Source code
find.max Source code
first Source code
globalBiDe.analysis Man page
globalBiDe.output.summary Man page
last Source code
mammalia Man page
rejection.sample.simple Source code
tess.PosteriorPrediction Man page Source code
tess.PosteriorPredictiveTest Man page Source code
tess.analysis Man page Source code
tess.create.phylo Source code
tess.equations.nTaxa.expected.constant Source code
tess.equations.nTaxa.expected.fastApprox Source code
tess.equations.nTaxa.expected.reconstructed.constant Source code
tess.equations.nTaxa.expected.reconstructed.fastApprox Source code
tess.equations.p1.constant Source code
tess.equations.p1.fastApprox Source code
tess.equations.p1.rateshift Source code
tess.equations.pN.constant Source code
tess.equations.pN.fastApprox Source code
tess.equations.pN.rateshift Source code
tess.equations.pSurvival.constant Source code
tess.equations.pSurvival.fastApprox Source code
tess.equations.pSurvival.rateshift Source code
tess.equations.pWaiting.constant Source code
tess.likelihood Man page Source code
tess.likelihood.constant Source code
tess.likelihood.function Source code
tess.likelihood.rateshift Man page Source code
tess.mcmc Man page Source code
tess.nTaxa.expected Man page Source code
tess.ode.piecewise Source code
tess.pathSampling Man page Source code
tess.plot.multichain.diagnostics Man page Source code
tess.plot.output Man page Source code
tess.plot.singlechain.diagnostics Man page Source code
tess.prepare.pdf Source code
tess.process.output Man page Source code
tess.sim.age Man page Source code
tess.sim.age.constant Source code
tess.sim.age.function Source code
tess.sim.age.rateshift Source code
tess.sim.taxa Man page Source code
tess.sim.taxa.age Man page Source code
tess.sim.taxa.age.constant Source code
tess.sim.taxa.age.function Source code
tess.sim.taxa.age.rateshift Source code
tess.sim.taxa.constant Source code
tess.sim.taxa.function Source code
tess.steppingStoneSampling Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Bayesian_Diversification_Rate_Analysis.pdf
inst/doc/Bayesian_Diversification_Rate_Analysis.Rnw
inst/doc/Bayesian_Diversification_Rate_Analysis.R
src
src/mass_extinction_equations.cpp
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/conifers.rda
data/mammalia.rda
data/cettiidae.rda
R
R/tess.sim.taxa.R
R/tess.utilities.R
R/tess.analysis.R
R/tess.sim.taxa.age.R
R/tess.plot.multichain.diagnostics.R
R/tess.PathSampling.R
R/tess.sim.age.R
R/tess.plot.singlechain.diagnostics.R
R/tess.equations.R
R/tess.nTaxa.expected.R
R/tess.likelihood.R
R/tess.PosteriorPrediction.R
R/tess.PosteriorPredictiveTest.R
R/RcppExports.R
R/tess.plot.output.R
R/tess.likelihood.rateshift.R
R/tess.SteppingStoneSampling.R
R/tess.mcmc.R
R/tess.process.output.R
vignettes
vignettes/ext_figures
vignettes/ext_figures/models.pdf
vignettes/ext_figures/BirthDeathShift.pdf
vignettes/ext_figures/birth-death-sketch.pdf
vignettes/ext_figures/ss.pdf
vignettes/ext_figures/diversified-sampling.pdf
vignettes/results
vignettes/results/marginalLikelihoodConstBD.rds
vignettes/results/comet_posterior_4.rds
vignettes/results/samplesUniform.rds
vignettes/results/comet_posterior_2.rds
vignettes/results/marginalLikelihoodDecrBD.rds
vignettes/results/marginalLikelihoodEpisodicBD.rds
vignettes/results/samplesEpisodicBD.rds
vignettes/results/comet_no_rateshifts.rds
vignettes/results/comet_posterior_3.rds
vignettes/results/samples_run_1.rds
vignettes/results/samples_run_good.rds
vignettes/results/comet_no_mass_extinctions.rds
vignettes/results/samplesConstBD.rds
vignettes/results/marginalLikelihoodMassExtinctionBD.rds
vignettes/results/samplesMassExtinctionBD.rds
vignettes/results/samples_run_2.rds
vignettes/results/samplesDiversified.rds
vignettes/results/samples_run_large.rds
vignettes/results/samples_run_small.rds
vignettes/results/comet_posterior_1.rds
vignettes/results/samplesDecrBD.rds
vignettes/results/tess_analysis.rds
vignettes/results/comet_hyperpriors.rds
vignettes/results/output_auto_stop.rds
vignettes/results/samples_run_auto_tuned.rds
vignettes/literature.bib
vignettes/Bayesian_Diversification_Rate_Analysis.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/tess.mcmc.Rd
man/tess.analysis.Rd
man/tess.nTaxa.expected.Rd
man/tess.plot.singlechain.diagnostics.Rd
man/cettiidae.Rd
man/tess.likelihood.rateshift.Rd
man/mammalia.Rd
man/conifers.Rd
man/tess.process.output.Rd
man/tess.sim.taxa.Rd
man/tess.likelihood.Rd
man/tess.steppingStoneSampling.Rd
man/tess.PosteriorPredictiveTest.Rd
man/tess.sim.age.Rd
man/tess.PosteriorPrediction.Rd
man/tess.sim.taxa.age.Rd
man/TESS-package.Rd
man/tess.plot.multichain.diagnostics.Rd
man/tess.plot.output.Rd
man/tess.pathSampling.Rd
TESS documentation built on May 19, 2017, 5:57 p.m.