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
= 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.
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 = <>
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 = form, the variables specified by the
names in the arguments are modified.