tess.plot.singlechain.diagnostics: tess.plot.mcmc.diagnostics: Plotting the single chain mcmc...

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

Description

tess.plot.singlechain.diagnostics plots MCMC diagnostics for the output generated by a tess.process.output(...) command. Fore more examples see the vignette.

Usage

tess.plot.singlechain.diagnostics(output,
                                      parameters=c("speciation rates",
                                                   "speciation shift times",
                                                   "extinction rates",
                                                   "extinction shift times",
                                                   "net-diversification rates",
                                                   "relative-extinction rates",
                                                   "mass extinction times"),
                                      diagnostics=c("ESS","geweke"),
                                      ess.crit=c(100,200),
                                      geweke.crit=0.05,
                                      correction="bonferroni",
                                      xlab="million years ago",
                                      col=NULL,
                                      xaxt="n",
                                      yaxt="s",
                                      pch=19,
                                      ...)

Arguments

output	The processed output for plotting.
parameters	Which parameters to diagnose. See details for a complete description.
diagnostics	Which diagnostics to use. Options are "ESS" and "geweke".
ess.crit	Two values which correspond to low ESS threshold and acceptable ESS threshold. Default values are 100 and 200.
geweke.crit	The p-value cutoff for Geweke's diagnostic. Default is the canonical 0.05.
correction	What type of multiple-correction method to use. Options are "bonferroni" and "sidak".
xlab	The label of the x-axis. By default, millions of years.
col	Colors used for printing. Must be of same length as fig.types.
xaxt	The type of x-axis to plot. By default, no x-axis is plotted (recommended).
yaxt	The type of y-axis to plot.
pch	The type of points to draw (if points are drawn).
...	Arguments delegated to plot()

Details

This function generates visual summaries of single-chain MCMC diagnostics for the CoMET analysis in the output object. The argument parameters specifies the aspects of the model to summarize. Valid options are:

• speciation rates: Plots the interval-specific speciation rates.

• speciation shift times: Plots the posterior probability of at least one speciation-rate shift for each interval.

• extinction rates: Plots the interval-specific extinction rates.

• extinction shift times: Plots the posterior probability of at least one extinction-rate shift for each interval.

• net-diversification ratesPlots the interval-specific net-diversification rates.

• relative-extinction ratesPlots the interval-specific relative-extinction rates.

• mass extinction times: Plots the posterior probability of at least one mass-extinction event for each interval.

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.singlechain.diagnostics(coniferOutput)

hoehna/TESS documentation built on Feb. 3, 2022, 5:59 a.m.