boa: Bayesian Output Analysis Program (BOA) for MCMC

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A menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of Markov chain Monte Carlo sampling output.

Author
Brian J. Smith [aut, cre]
Date of publication
2016-06-23 01:29:05
Maintainer
Brian J. Smith <brian-j-smith@uiowa.edu>
License
GPL-2
Version
1.1.8-2
URLs

View on CRAN

Man pages

boa.acf
Autocorrelation Function
boa.batchMeans
Batch Means
boa.chain
Session Lists of MCMC Sequences
boa.chain.add
Add MCMC Sequence
boa.chain.collapse
Concatenate MCMC Sequences
boa.chain.del
Delete MCMC Sequences
boa.chain.eval
Formulate New Parameter
boa.chain.gandr
Gelman and Rubin Convergence Diagnostics
boa.chain.import
Import MCMC Sequence
boa.chain.info
Information about MCMC Sequences
boa.chain.reset
Reset MCMC Sequences
boa.chain.subset
Subset MCMC Sequences
boa.chain.support
Set Support for Parameters
boa.getiter
Extract Iterations
boa.getparms
Extract Parameters
boa.geweke
Geweke Convergence Diagnostics
boa.gewekePwr
Geweke Spectral Density Estimation
boa.handw
Heidelberger and Welch Convergence Diagnostics
boa.hpd
Highest Probability Density Interval
boa.importASCII
Import ASCII Data
boa.importBUGS
Import BUGS Data
boa.importMatrix
Import ASCII Data
boa.init
Start Session
boa.iter
Extract Iteration Numbers
boa.license
Licensing Information
boa.load
Load Session
boa.menu
Interactive BOA Menu
boa.par
Global Parameters
boa.pardesc
Global Parameters Descriptions
boa.plot
Plot Parameters in MCMC Sequences
boa.plot.acf
Plot Autocorrelation Function
boa.plot.bandg
Plot Brooks and Gelman Multivariate Shrink Factors
boa.plot.close
Close Graphics Windows
boa.plot.density
Plot Density Functions
boa.plot.gandr
Plot Gelman and Rubin Shrink Factors
boa.plot.geweke
Plot Geweke Convergence Diagnostics
boa.plot.history
Plot Parameter Estimation Histories
boa.plot.open
Open Graphics Windows
boa.plot.par
Set Plotting Parameters
boa.plot.title
Add Plot Title
boa.plot.trace
Plot Trace Histories
boa.pnames
Extract Parameter Names
boa.print.acf
Print Autocorrelation Functions
boa.print.cor
Print Correlation Matrices
boa.print.gandr
Print Gelman and Rubin Convergence Diagnostics
boa.print.geweke
Print Geweke Convergence Diagnostics
boa.print.handw
Print Heidelberger and Welch Convergence Diagnostics
boa.print.hpd
Print Highest Probability Density Intervals
boa.print.info
Print Information about MCMC Sequences
boa.print.par
Print Global Parameters' Descriptions and Current Values
boa.print.randl
Print Raftery and Lewis Convergence Diagnostics
boa.print.stats
Print Summary Statistics
boa.quit
Quit Session
boa.randl
Raftery and Lewis Convergence Diagnostics
boa.save
Save Session
boa.sortiter
Sort by Iteration Numbers
boa.sortparms
Sort by Parameter Names
boa.stats
Summary Statistics
boa.transform
Transform Variables
boa.version
Version Information
colVars
Column Variances
line
BUGS Line Example

Files in this package

boa
boa/inst
boa/inst/CITATION
boa/NAMESPACE
boa/data
boa/data/line.rda
boa/R
boa/R/boa.getparms.R
boa/R/boa.license.R
boa/R/boa.importASCII.R
boa/R/boa.menu.analysis.R
boa/R/boa.transform.R
boa/R/boa.plot.title.R
boa/R/boa.chain.del.R
boa/R/colVars.R
boa/R/boa.plot.gandr.R
boa/R/boa.stats.R
boa/R/boa.chain.info.R
boa/R/boa.plot.geweke.R
boa/R/boa.plot.open.R
boa/R/boa.print.randl.R
boa/R/boa.chain.collapse.R
boa/R/boa.menu.plotdesc.R
boa/R/boa.print.stats.R
boa/R/boa.print.info.R
boa/R/boa.chain.subset.R
boa/R/boa.print.acf.R
boa/R/boa.randl.R
boa/R/boa.print.gandr.R
boa/R/boa.version.R
boa/R/boa.plot.par.R
boa/R/boa.print.handw.R
boa/R/boa.chain.import.R
boa/R/boa.plot.close.R
boa/R/boa.gewekePwr.R
boa/R/boa.acf.R
boa/R/boa.importMatrix.R
boa/R/boa.menu.window.R
boa/R/boa.getiter.R
boa/R/boa.plot.acf.R
boa/R/boa.menu.plot.R
boa/R/boa.menu.parms.R
boa/R/boa.menu.data.R
boa/R/boa.plot.R
boa/R/boa.print.geweke.R
boa/R/boa.menu.stats.R
boa/R/boa.chain.add.R
boa/R/boa.chain.eval.R
boa/R/boa.batchMeans.R
boa/R/boa.print.hpd.R
boa/R/boa.menu.import.R
boa/R/boa.hpd.R
boa/R/boa.sortparms.R
boa/R/boa.menu.plotcoda.R
boa/R/boa.chain.gandr.R
boa/R/boa.plot.history.R
boa/R/boa.print.cor.R
boa/R/boa.importBUGS.R
boa/R/boa.menu.file.R
boa/R/boa.plot.bandg.R
boa/R/boa.chain.support.R
boa/R/boa.pardesc.R
boa/R/spectrum0.R
boa/R/boa.geweke.R
boa/R/boa.handw.R
boa/R/boa.sortiter.R
boa/R/boa.getinput.R
boa/R/boa.chain.reset.R
boa/R/boa.print.par.R
boa/R/boa.plot.density.R
boa/R/boa.menu.par.R
boa/R/boa.core.R
boa/R/boa.menu.R
boa/R/boa.menu.coda.R
boa/R/boa.pnames.R
boa/R/boa.plot.trace.R
boa/R/boa.menu.chains.R
boa/R/boa.menu.setpar.R
boa/R/boa.iter.R
boa/MD5
boa/DESCRIPTION
boa/man
boa/man/boa.license.Rd
boa/man/boa.par.Rd
boa/man/boa.plot.close.Rd
boa/man/boa.print.cor.Rd
boa/man/boa.plot.density.Rd
boa/man/boa.print.handw.Rd
boa/man/boa.gewekePwr.Rd
boa/man/boa.sortiter.Rd
boa/man/boa.chain.support.Rd
boa/man/boa.plot.title.Rd
boa/man/boa.plot.Rd
boa/man/boa.print.gandr.Rd
boa/man/boa.plot.trace.Rd
boa/man/boa.print.geweke.Rd
boa/man/boa.chain.eval.Rd
boa/man/boa.plot.par.Rd
boa/man/boa.sortparms.Rd
boa/man/boa.plot.gandr.Rd
boa/man/boa.chain.subset.Rd
boa/man/boa.acf.Rd
boa/man/boa.importASCII.Rd
boa/man/boa.plot.open.Rd
boa/man/boa.getparms.Rd
boa/man/boa.geweke.Rd
boa/man/boa.init.Rd
boa/man/boa.plot.geweke.Rd
boa/man/boa.chain.collapse.Rd
boa/man/boa.quit.Rd
boa/man/boa.hpd.Rd
boa/man/boa.version.Rd
boa/man/boa.chain.del.Rd
boa/man/boa.chain.import.Rd
boa/man/boa.print.info.Rd
boa/man/boa.batchMeans.Rd
boa/man/boa.iter.Rd
boa/man/line.Rd
boa/man/boa.getiter.Rd
boa/man/boa.plot.acf.Rd
boa/man/boa.importMatrix.Rd
boa/man/boa.plot.history.Rd
boa/man/boa.save.Rd
boa/man/boa.print.hpd.Rd
boa/man/boa.transform.Rd
boa/man/boa.chain.Rd
boa/man/boa.stats.Rd
boa/man/boa.load.Rd
boa/man/colVars.Rd
boa/man/boa.print.acf.Rd
boa/man/boa.pardesc.Rd
boa/man/boa.chain.reset.Rd
boa/man/boa.chain.add.Rd
boa/man/boa.print.par.Rd
boa/man/boa.print.stats.Rd
boa/man/boa.menu.Rd
boa/man/boa.plot.bandg.Rd
boa/man/boa.chain.info.Rd
boa/man/boa.importBUGS.Rd
boa/man/boa.randl.Rd
boa/man/boa.pnames.Rd
boa/man/boa.chain.gandr.Rd
boa/man/boa.handw.Rd
boa/man/boa.print.randl.Rd