Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events
Diversification rate estimation and fast simulation of reconstructed p...
tess.analysis: Diversification rate estimation under an episodic birth...
tess.likelihood.rateshift: Probability density of a tree under a tree-...
tess.likelihood: Probability density of a tree under a tree-wide time-...
tess.mcmc: Markov chain Monte Carlo simulation using a general Metropo...
tess.nTaxa.expected: The expected number of taxa at present of a tree ...
tess.pathSampling: Marginal likelihood estimation via Path-Sampling.
tess.plot.multichain.diagnostics: Plotting the mcmc diagnostics of a e...
tess.plot.output: Plotting the output of a diversification rate estima...
tess.plot.mcmc.diagnostics: Plotting the single chain mcmc diagnostics...
tess.PosteriorPrediction: Approximation of the posterior predictive di...
tess.PosteriorPredictiveTest: Approximation of the posterior predictiv...
tess.process.output: Summarizing the output of a diversification rate ...
tess.sim.age: Simulate a reconstructed tree for a given age under a gl...
tess.sim.taxa.taxa.age: Simulate a reconstructed tree for a given age ...
tess.sim.taxa.taxa: Simulate a reconstructed tree for a given number o...
tess.steppingStoneSampling: Marginal likelihood estimation via Steppin...
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.