Package: TESS 3.0.0

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.

Authors:Sebastian Hoehna and Michael R. May

TESS_3.0.0.tar.gz
TESS_3.0.0.zip(r-4.5)TESS_3.0.0.zip(r-4.4)TESS_3.0.0.zip(r-4.3)
TESS_3.0.0.tgz(r-4.4-x86_64)TESS_3.0.0.tgz(r-4.4-arm64)TESS_3.0.0.tgz(r-4.3-x86_64)TESS_3.0.0.tgz(r-4.3-arm64)
TESS_3.0.0.tar.gz(r-4.5-noble)TESS_3.0.0.tar.gz(r-4.4-noble)
TESS_3.0.0.tgz(r-4.4-emscripten)TESS_3.0.0.tgz(r-4.3-emscripten)
TESS.pdf |TESS.html✨
TESS/json (API)
NEWS

# Install 'TESS' in R:
install.packages('TESS', repos = c('https://hoehna.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hoehna/tess/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • cettiidae - Cettiidae phylogeny from Alstroem et al.
  • conifers - Conifer phylogeny from Leslie et al.
  • mammalia - Dated family level mammalian phylogeny from Meredith et al. (2011): Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification.

On CRAN:

5.93 score 2 stars 1 packages 94 scripts 316 downloads 359 mentions 21 exports 7 dependencies

Last updated 3 years agofrom:82ee22f7a6. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64ERRORNov 05 2024
R-4.5-linux-x86_64ERRORNov 05 2024
R-4.4-win-x86_64ERRORNov 05 2024
R-4.4-mac-x86_64ERRORNov 05 2024
R-4.4-mac-aarch64ERRORNov 05 2024
R-4.3-win-x86_64ERRORNov 05 2024
R-4.3-mac-x86_64ERRORNov 05 2024
R-4.3-mac-aarch64ERRORNov 05 2024

Exports:tess.analysistess.analysis.efbdtess.branching.timestess.likelihoodtess.likelihood.bdstptess.likelihood.ebdstptess.likelihood.efbdtess.likelihood.rateshifttess.mcmctess.nTaxa.expectedtess.pathSamplingtess.plot.multichain.diagnosticstess.plot.outputtess.plot.singlechain.diagnosticstess.PosteriorPredictiontess.PosteriorPredictiveTesttess.process.outputtess.sim.agetess.sim.taxatess.sim.taxa.agetess.steppingStoneSampling

Dependencies:apecodadeSolvedigestlatticenlmeRcpp

Readme and manuals

Help Manual

Help pageTopics
Diversification rate estimation and fast simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes including mass-extinction eventsTESS-package TESS
Cettiidae phylogeny from Alstroem et al. (2011)cettiidae
Conifer phylogeny from Leslie et al. (2012)conifers
Dated family level mammalian phylogeny from Meredith et al. (2011): Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification.mammalia
tess.analysis: Diversification rate estimation under an episodic birth-death process including mass-extinction events.globalBiDe.analysis tess.analysis
tess.analysis.efbdtess.analysis.efbd
Titletess.branching.times
tess.likelihood: Probability density of a tree under a tree-wide time-dependent birth-death processtess.likelihood
tess.likelihood.bdstptess.likelihood.bdstp
tess.likelihood.ebdstptess.likelihood.ebdstp
tess.likelihood.efbd: Probability density of a tree under a tree-wide time-dependent fossilized birth-death processtess.likelihood.efbd
tess.likelihood.rateshift: Probability density of a tree under a tree-wide time-dependent birth-death-shift processtess.likelihood.rateshift
tess.mcmc: Markov chain Monte Carlo simulation using a general Metropolis-Hastings algorithm.tess.mcmc
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.nTaxa.expected
tess.pathSampling: Marginal likelihood estimation via Path-Sampling.tess.pathSampling
tess.plot.multichain.diagnostics: Plotting the mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events.tess.plot.multichain.diagnostics
tess.plot.output: Plotting the output of a diversification rate estimation including mass-extinction events.tess.plot.output
tess.plot.mcmc.diagnostics: Plotting the single chain mcmc diagnostics of a episodic diversification rate analysis with mass-extinction events.tess.plot.singlechain.diagnostics
tess.PosteriorPrediction: Approximation of the posterior predictive distribution.tess.PosteriorPrediction
tess.PosteriorPredictiveTest: Approximation of the posterior predictive distribution.tess.PosteriorPredictiveTest
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.globalBiDe.output.summary tess.process.output
tess.sim.age: Simulate a reconstructed tree for a given age under a global, time-dependent birth-death process.tess.sim.age
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
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.sim.taxa.age
tess.steppingStoneSampling: Marginal likelihood estimation via Stepping-Stone-Sampling.tess.steppingStoneSampling