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.


News

	CHANGES IN TESS VERSION 1.3.0 

NEW FEATURES

o Added the skyline birth-death model for piecewise constant rates

o Added the skyline birth-death model for piecewise linear rates

o Added a family level sampling birth-death model

o Added a reversible jump MCMC to estimate number of rate changes

o Added a reversible jump MCMC to estimate the number of mass-extinction events.

o ...

BUG FIXES

o ...

o ...


	CHANGES IN TESS VERSION 1.2.2 (not released)

NEW FEATURES

o Added a cut-off value for the maximum number of taxa simulated under simulations condition on the age of the tree.

BUG FIXES

o Corrected the likelihoods for diversified sampling.



	CHANGES IN TESS VERSION 1.2.1

BUG FIXES

o Corrected the likelihoods for mass-extinctions.

o Improved the likelihoods for large trees.



	CHANGES IN TESS VERSION 1.2.0

NEW FEATURES

o Included diversified sampling.

o Included age dependent sampling.




	CHANGES IN TESS VERSION 1.1.0

NEW FEATURES

o MCMC algorithm is available for any model.

o Posterior prediction is available for any model.

o A posterior predictive simulation function.




	CHANGES IN TESS VERSION 1.0.3

BUG FIXES

o globalBiDe.equations.pN had a missing constant factor.

o sim.globalBiDe.taxa.age.constant includes the sampling probability correctly.

OTHER CHANGES

o globalBiDe.likelihood uses now fast approximations too.

o sim.globalBiDe.taxa searches now for a reasonable range of the tmrca.



	CHANGES IN TESS VERSION 1.0.2

BUG FIXES

o likelihood for constant rates had a bug for incomplete taxon sampling.



	CHANGES IN TESS VERSION 1.0.1

BUG FIXES

o sim.globalBiDe.* had wrong ordering of speciation times.

Reference manual

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install.packages("TESS")

2.1.0 by Sebastian Hoehna, 3 years ago


Browse source code at https://github.com/cran/TESS


Authors: Sebastian Hoehna and Michael R. May


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL-3 license


Imports Rcpp

Depends on ape, coda, deSolve

Suggests knitr

Linking to Rcpp


Imported by RPANDA.

Suggested by nLTT.


See at CRAN