NMF Package Specific Options
NMF Package Specific Options
nmf.options sets/get single or multiple options,
that are specific to the NMF package. It behaves in the
same way as options.
nmf.getOption returns the value of a single
option, that is specific to the NMF package. It behaves
in the same way as getOption.
nmf.resetOptions reset all NMF specific options to
their default values.
nmf.printOptions prints all NMF specific options
along with their default values, in a relatively compact
way.
nmf.options(...) nmf.getOption(x, default = NULL) nmf.resetOptions(..., ALL = FALSE) nmf.printOptions()
... |
option specifications. For For |
ALL |
logical that indicates if options that are not part of the default set of options should be removed. Note that in pkgmaker <= 0.9 this argument is only taken into account when no other argument is present. This is fixed in version 0.9.1. |
x |
a character string holding an option name. |
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. |
Default number of cores to use to perform
parallel NMF computations. Note that this option is
effectively used only if the global option 'cores'
is not set. Moreover, the number of cores can also be set
at runtime, in the call to nmf, via
arguments .pbackend or .options (see
nmf for more details).
Default NMF algorithm used by
the nmf function when argument method is
missing. The value should the key of one of the
registered NMF algorithms or a valid specification of an
NMF algorithm. See ?nmfAlgorithm.
Default seeding method used by the
nmf function when argument seed is missing.
The value should the key of one of the registered seeding
methods or a vallid specification of a seeding method.
See ?nmfSeed.
Toggle default residual tracking. When
TRUE, the nmf function compute and store
the residual track in the result – if not otherwise
specified in argument .options. Note that tracking
may significantly slow down the computations.
Number of iterations between two
points in the residual track. This option is relevant
only when residual tracking is enabled. See ?nmf.
this is a symbolic link to option
track for backward compatibility.
Default loop/parallel foreach backend
used by the nmf function when argument
.pbackend is missing. Currently the following
values are supported: 'par' for multicore,
'seq' for sequential, NA for standard
sapply (i.e. do not use a foreach loop),
NULL for using the currently registered foreach
backend.
this is a symbolic link to option
pbackend for backward compatibility.
Interval/frequency (in number of runs) at which garbage collection is performed.
Default level of verbosity.
Toogles debug mode. In this mode the console output may be very – very – messy, and is aimed at debugging only.
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.
# 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()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.