boa.par {boa}

Global Parameters

Description

Displays and sets the global parameters stored internally for use during a BOA session.

Usage

boa.par(...)

Arguments

...

A list may be given as the only argument, or a character string given as the only argument, or any number of arguments may be in the <name> = <value> form, or no argument at all may be given.

Value

If no arguments are supplied, a list of the current values is returned. If a character string is given, the current value of the named variable is returned. Otherwise, a list of the named variables and their old values is returned, but not printed.

Parameter Names and Default Values

acf.lags = c(1, 5, 10, 50)

Numeric vector of lags at which to estimate the autocorrelation function.

alpha = 0.05

Type I error rate used for all statistical tests and confidence intervals.

ASCIIext = ".txt"

Character string giving the filename extension used when importing ASCII files.

bandwidth = function(x) 0.5 * diff(range(x)) / (log(length(x)) + 1)

Function for computing the bandwidth used in estimating the density functions for parameters. This should take one argument which is a numeric vector of data on which density estimation is to be performed. A constant bandwidth may be specified by having this function return the desired constant.

batch.size = 50

Number of iterations to include in each batch when computing batch means and lag-1 batch autocorrelations. The batch size has the single largest impact on the time required to compute summary statistics. The computation time is decreased dramatically as the batch size increases. Consequently, users may want to increase the value of this variable for long MCMC sequences.

dev = <<see below>>

Character string giving the name of the function that creates graphics windows on the current platform. For Unix systems this is either "motif", "openlook", or "X11". The default is "motif" for the UNIX S-PLUS, "win.graph" for Windows S-PLUS, "X11" for UNIX R, and "windows" for Windows R.

dev.list = numeric(0)

Numeric vector containing the active graphics windows in use by the program. This is automatically maintained by the program, user should not directly modify this variable.

gandr.bins = 20

Number of line segments within the MCMC sequence at which to plot the Gelman and Rubin shrink factors.

gandr.win = 0.50

Proportion of iterations to include in the Brooks, Gelman, and Rubin Statistics.

geweke.bins = 10

Number of line segments within the MCMC sequence at which to plot the Geweke convergence diagnostics.

geweke.first = 0.1

Proportion of iterations to include in the first window when computing the Geweke convergence diagnostics.

geweke.last = 0.5

Proportion of iterations to include in the last window when computing the Geweke convergence diagnostics.

handw.error = 0.1

Accuracy of the posterior estimates when computing the Heidleberger and Welch convergence diagnostics.

kernel = "gaussian"

Character string giving the type of window used in estimating the density functions for parameters. Other choices are "cosine", "rectangular", or "triangular".

legend = TRUE

Logical value indicating that a legend be included in the plots.

path = ""

Character string giving the directory path in which the raw data files are stored. The default may be used if the files are located in the current working directory. The specified path should not end with a slash(es).

par = list()

List specifying graphics parameters passed to the par function for the construction of new plots.

plot.mfdim = c(3, 2)

Numeric vector giving the maximum number of rows and columns, respectively, of plots to include in a single graphics window.

plot.new = F

Logical value indicating that a new graphics window be automatically opened upon successive calls to boa.plot(). Otherwise, previous graphics windows will be closed.

plot.onelink = FALSE

Logical value indicating that each plot should include only one MCMC sequence. Otherwise, all sequences are displayed on the same plot.

quantiles = c(0.025, 0.5, 0.975)

Vector of probabilities at which to compute the quantiles. Values must be between 0 and 1.

randl.error = 0.005

Desired amount of error in estimating the quantile specified in the Raftery and Lewis convergence diagnostics.

randl.delta = 0.001

Delta valued used in computing the Raftery and Lewis convergence diagnostics.

randl.q = 0.025

Quantile to be estimated in computing the Raftery and Lewis convergence diagnostics.

title = TRUE

Logical value indicating that a title be added to the plots.

Side Effects

When variables are set, boa.par() modifies the internal list .boa.par. If boa.par() is called with either a list as the single argument, or with one or more arguments in the <name> = <value> form, the variables specified by the names in the arguments are modified.

Author(s)

Brian J. Smith