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\name{options-NMF}
\alias{nmf.getOption}
\alias{nmf.options}
\alias{nmf.printOptions}
\alias{nmf.resetOptions}
\alias{options-NMF}
\title{NMF Package Specific Options}
\usage{
nmf.options(...)
nmf.getOption(x, default = NULL)
nmf.resetOptions(..., ALL = FALSE)
nmf.printOptions()
}
\arguments{
\item{...}{option specifications. For \code{nmf.options}
this can be named arguments or a single unnamed argument
that is a named list (see \code{\link{options}}.
For \code{nmf.resetOptions}, this must be the names of
the options to reset. Note that \pkg{pkgmaker} version >=
0.9.1 is required for this to work correctly, when
options other than the default ones have been set after
the package is loaded.}
\item{ALL}{logical that indicates if options that are not
part of the default set of options should be removed.
Note that in \pkg{pkgmaker <= 0.9} this argument is only
taken into account when no other argument is present.
This is fixed in version 0.9.1.}
\item{x}{a character string holding an option name.}
\item{default}{if the specified option is not set in the
options list, this value is returned. This facilitates
retrieving an option and checking whether it is set and
setting it separately if not.}
}
\description{
NMF Package Specific Options
\code{nmf.options} sets/get single or multiple options,
that are specific to the NMF package. It behaves in the
same way as \code{\link[base]{options}}.
\code{nmf.getOption} returns the value of a single
option, that is specific to the NMF package. It behaves
in the same way as \code{\link[base]{getOption}}.
\code{nmf.resetOptions} reset all NMF specific options to
their default values.
\code{nmf.printOptions} prints all NMF specific options
along with their default values, in a relatively compact
way.
}
\section{Available options}{
\describe{
\item{cores}{Default number of cores to use to perform
parallel NMF computations. Note that this option is
effectively used only if the global option \code{'cores'}
is not set. Moreover, the number of cores can also be set
at runtime, in the call to \code{\link{nmf}}, via
arguments \code{.pbackend} or \code{.options} (see
\code{\link{nmf}} for more details).}
\item{default.algorithm}{Default NMF algorithm used by
the \code{nmf} function when argument \code{method} is
missing. The value should the key of one of the
registered NMF algorithms or a valid specification of an
NMF algorithm. See \code{?nmfAlgorithm}.}
\item{default.seed}{Default seeding method used by the
\code{nmf} function when argument \code{seed} is missing.
The value should the key of one of the registered seeding
methods or a vallid specification of a seeding method.
See \code{?nmfSeed}.}
\item{track}{Toggle default residual tracking. When
\code{TRUE}, the \code{nmf} function compute and store
the residual track in the result -- if not otherwise
specified in argument \code{.options}. Note that tracking
may significantly slow down the computations.}
\item{track.interval}{Number of iterations between two
points in the residual track. This option is relevant
only when residual tracking is enabled. See \code{?nmf}.}
\item{error.track}{this is a symbolic link to option
\code{track} for backward compatibility.}
\item{pbackend}{Default loop/parallel foreach backend
used by the \code{nmf} function when argument
\code{.pbackend} is missing. Currently the following
values are supported: \code{'par'} for multicore,
\code{'seq'} for sequential, \code{NA} for standard
\code{sapply} (i.e. do not use a foreach loop),
\code{NULL} for using the currently registered foreach
backend.}
\item{parallel.backend}{this is a symbolic link to option
\code{pbackend} for backward compatibility.}
\item{gc}{Interval/frequency (in number of runs) at which
garbage collection is performed.}
\item{verbose}{Default level of verbosity.}
\item{debug}{Toogles debug mode. In this mode the console
output may be very -- very -- messy, and is aimed at
debugging only.}
\item{maxIter}{ Default maximum number of iteration to
use (default NULL). This option is for internal/technical
usage only, to globally speed up examples or tests of NMF
algorithms. To be used with care at one's own risk... It
is documented here so that advanced users are aware of
its existence, and can avoid possible conflict with their
own custom options. } } % end description
}
\examples{
\dontshow{# roxygen generated flag
options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
}
# show all NMF specific options
nmf.printOptions()
# get some options
nmf.getOption('verbose')
nmf.getOption('pbackend')
# set new values
nmf.options(verbose=TRUE)
nmf.options(pbackend='mc', default.algorithm='lee')
nmf.printOptions()
# reset to default
nmf.resetOptions()
nmf.printOptions()
}
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