tess.process.output {TESS}R Documentation

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.

Description

tess.process.output summarizes the output generated by a tess.analysis(...) run.

Usage

tess.process.output(dir,
                    tree=NULL,
                    numExpectedRateChanges=2,
                    numExpectedMassExtinctions=2,
                    burnin=0.25,
                    numIntervals=100,
                    criticalBayesFactors=c(2,6,10))

Arguments

dir

The directory from which the CoMET output will be read.

tree

The tree analyzed with CoMET in phylo format. By default, looks for a tree in the target directory.

numExpectedRateChanges

The number of expected diversification-rate changes.

numExpectedMassExtinctions

The number of expected mass-extinction events.

burnin

The fraction of samples that will be discarded as burnin.

numIntervals

The number of discrete intervals in which to break the tree.

criticalBayesFactors

The Bayes factor thresholds to use to assess significance of events.

Details

The output of a CoMET analysis is stored in a directory with different files containing the MCMC samples from the posterior distribution. For example, the tess.analysis function stores the times and survival probabilities of the mass-extinction events in a file. This function, converts the output by counting the number of events that fall into a given time-bin. This pre-processing of the output simplifies the plotting.

Value

This function returns a list with the following elements:

posterior

An object of class 'mcmc' that contains the trace of the model's posterior probability.

numSpeciationCategories

An object of class 'mcmc' that contains samples from the posterior distribution of the number of speciation categories (minimum 1, since this includes the initial speciation rate).

numExtinctionCategories

An object of class 'mcmc' that contains samples from the posterior distribution of the number of extinction categories (minimum 1, since this includes the initial extinction rate).

numMassExtinctions

An object of class 'mcmc' that contains samples from the posterior distribution of the number of mass-extinction events.

speciation rates

An object of class 'mcmc' that contains speciation rates sampled from the posterior distribution for each of numIntervals discrete time intervals. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

speciation change times

An object of class 'mcmc' that contains speciation-rate-change events sampled from the posterior distribution for each of numIntervals discrete time intervals. A value of 1 indicates an event was contained in the interval, 0 that no event was contained in the interval. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

speciation Bayes factors

A vector of class 'numeric' that contains the Bayes factor support for there being a speciation-rate-change event for each of numIntervals discrete time intervals. The ith element corresponds to the Bayes factor support for an event in the ith interval.

speciationRateChangeCriticalPosteriorProbabilities

A vector of posterior probabilities that correspond to critical Bayes factor thresholds (specified by the argument criticalBayesFactors). Element i is the posterior probability of a speciation-rate-change event in an interval needed to produce Bayes factor support of criticalBayesFactors[i].

extinction rates

An object of class 'mcmc' that contains extinction rates sampled from the posterior distribution for each of numIntervals discrete time intervals. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

extinction change times

An object of class 'mcmc' that contains extinction-rate-change events sampled from the posterior distribution for each of numIntervals discrete time intervals. A value of 1 indicates an event was contained in the interval, 0 that no event was contained in the interval. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

extinction Bayes factors

A vector of class 'numeric' that contains the Bayes factor support for there being a extinction-rate-change event for each of numIntervals discrete time intervals. The ith element corresponds to the Bayes factor support for an event in the ith interval.

extinctionRateChangeCriticalPosteriorProbabilities

A vector of posterior probabilities that correspond to critical Bayes factor thresholds (specified by the argument criticalBayesFactors). Element i is the posterior probability of a extinction-rate-change event in an interval needed to produce Bayes factor support of criticalBayesFactors[i].

net-diversification rates

An object of class 'mcmc' that contains net-diversification (speciation - extinction) rates sampled from the posterior distribution for each of numIntervals discrete time intervals. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

relative-extinction rates

An object of class 'mcmc' that contains relative-extinction (extinction / speciation) rates sampled from the posterior distribution for each of numIntervals discrete time intervals. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

mass extinction times

An object of class 'mcmc' that contains mass-extinction events sampled from the posterior distribution for each of numIntervals discrete time intervals. A value of 1 indicates an event was contained in the interval, 0 that no event was contained in the interval. Rows correspond to samples from the posterior distribution, columns correspond to intervals.

mass extinction Bayes factors

A vector of class 'numeric' that contains the Bayes factor support for there being a mass-extinction event for each of numIntervals discrete time intervals. The ith element corresponds to the Bayes factor support for an event in the ith interval.

massExtinctionCriticalPosteriorProbabilities

A vector of posterior probabilities that correspond to critical Bayes factor thresholds (specified by the argument criticalBayesFactors). Element i is the posterior probability of a mass-extinction event in an interval needed to produce Bayes factor support of criticalBayesFactors[i].

criticalBayesFactors

The critical Bayes factor values used for the Bayes factor tests (default 2 ln BF = {2,6,10}).

tree

The tree analyzed with CoMET (just in case).

intervals

The discrete intervals used to compute the interval-specific parameters.

Author(s)

Michael R. May

Examples

# Load the data, compute the sampling fraction rho
data(conifers)
totalConiferSpecies <- 630
sampledConiferSpecies <- conifers$Nnode+1
rho <- sampledConiferSpecies / totalConiferSpecies

# Run a tess analysis
tess.analysis(tree = conifers,
              initialSpeciationRate=c(1.0),
              initialExtinctionRate=c(0.5),
              empiricalHyperPriors = FALSE,
              numExpectedRateChanges = 2,
              numExpectedMassExtinctions = 2,
              samplingProbability = rho,
              MAX_ITERATIONS = 200,
              BURNIN=100)

# Process the output
coniferOutput <- tess.process.output(dir=getwd(),
                                     numExpectedRateChanges=2,
                                     numExpectedMassExtinctions=2)

# Plot the output
tess.plot.output(coniferOutput)



[Package TESS version 2.1.2 Index]