The function seed provides a single interface for
calling all seeding methods used to initialise NMF
computations. These methods at least set the basis and
coefficient matrices of the initial object to
valid nonnegative matrices. They will be used as a
starting point by any NMF algorithm that accept
initialisation.
IMPORTANT: this interface is still considered experimental and is subject to changes in future release.
seed(x, model, method, ...) # S4 method for matrix,NMF,NMFSeed
seed(x, model, method,
rng, ...)
# S4 method for ANY,ANY,function
seed(x, model, method, name,
...)
an NMFfit object.
target matrix one wants to approximate with NMF
specification of the NMF model, e.g., the factorization rank.
specification of a seeding method. See each method for details on the supported formats.
extra to allow extensions and passed down to the actual seeding method.
rng setting to use. If not missing the RNG
settings are set and restored on exit using
setRNG.
All arguments in ... are passed to teh seeding
strategy.
optional name of the seeding method for custom seeding strategies.
signature(x = "matrix", model = "NMF",
method = "NMFSeed"): This is the workhorse method that
seeds an NMF model object using a given seeding strategy
defined by an NMFSeed object, to fit a given
target matrix.
signature(x = "ANY", model = "ANY",
method = "function"): Seeds an NMF model using a custom
seeding strategy, defined by a function.
method must have signature (x='NMFfit',
y='matrix', ...), where x is the unseeded NMF
model and y is the target matrix to fit. It must
return an NMF object, that contains
the seeded NMF model.
signature(x = "ANY", model = "ANY",
method = "missing"): Seeds the model with the default
seeding method given by
nmf.getOption('default.seed')
signature(x = "ANY", model = "ANY",
method = "NULL"): Use NMF method 'none'.
signature(x = "ANY", model = "ANY",
method = "numeric"): Use method to set the RNG
with setRNG and use method “random”
to seed the NMF model.
Note that in this case the RNG settings are not restored. This is due to some internal technical reasons, and might change in future releases.
signature(x = "ANY", model = "ANY",
method = "character"): Use the registered seeding method
whose access key is method.
signature(x = "ANY", model = "list",
method = "NMFSeed"): Seed a model using the elements in
model to instantiate it with
nmfModel.
signature(x = "ANY", model = "numeric",
method = "NMFSeed"): Seeds a standard NMF model (i.e. of
class NMFstd) of rank model.