Description Usage Arguments Details Methods (by generic) See Also Examples
basis
and basis<-
are S4 generic functions which respectively
extract and set the matrix of basis components of an NMF model
(i.e. the first matrix factor).
The methods .basis
, .coef
and their replacement versions
are implemented as pure virtual methods for the interface class
NMF
, meaning that concrete NMF models must provide a
definition for their corresponding class (i.e. sub-classes of
class NMF
).
See NMF
for more details.
The method loadings
is identical to basis
, but do
not accept any extra argument.
coef
and coef<-
respectively extract and set the
coefficient matrix of an NMF model (i.e. the second matrix factor).
For example, in the case of the standard NMF model V ~ W H,
the method coef
will return the matrix H.
Methods coefficients
and coefficients<-
are
simple aliases for methods coef
and coef<-
respectively.
scoef
is similar to coef
, but returns the mixture
coefficient matrix of an NMF model, with the columns scaled so that they
sum up to a given value (1 by default).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | basis(object, ...)
## S4 method for signature 'ANY'
basis(object, ...)
## S4 method for signature 'NMF'
basis(object, ..., all = TRUE)
.basis(object, ...)
basis(object, ...) <- value
## S4 replacement method for signature 'NMF'
basis(object, ..., use.dimnames = TRUE) <- value
.basis(object, ...) <- value
## S4 method for signature 'NMF'
loadings(x)
coef(object, ...)
## S4 method for signature 'NMF'
coef(object, ..., all = TRUE)
.coef(object, ...)
coef(object, ...) <- value
## S4 replacement method for signature 'NMF'
coef(object, ..., use.dimnames = TRUE) <- value
.coef(object, ...) <- value
coefficients(object, ...)
## S4 method for signature 'NMF'
coefficients(object, ..., all = TRUE)
scoef(object, ...)
## S4 method for signature 'matrix'
scoef(object, scale = 1)
## S4 method for signature 'NMFfitXn'
coef(object, ...)
## S4 method for signature 'NMFfitXn'
basis(object, ...)
|
object |
an object from which to extract the factor matrices, typically an
object of class |
... |
extra arguments to allow extension and passed to the low-level
access functions Note that these throw an error if used in replacement functions . |
all |
a logical that indicates whether the complete matrix factor
should be returned ( |
value |
replacement value |
use.dimnames |
logical that indicates if the object's dim names should be set using those from the new value, or left unchanged – after truncating them to fit new dimensions if necessary. This is useful to only set the entries of a factor. |
x |
an object of class NMF |
scale |
scaling factor, which indicates to the value the columns of the coefficient matrix should sum up to. |
For example, in the case of the standard NMF model V ~ W H,
the method basis
will return the matrix W.
basis
and basis<-
are defined for the top
virtual class NMF
only, and rely internally on the low-level
S4 generics .basis
and .basis<-
respectively that effectively
extract/set the coefficient data.
These data are post/pre-processed, e.g., to extract/set only their
non-fixed terms or check dimension compatibility.
The method loadings
is provided to standardise the NMF interface
against the one defined in the stats
package,
and emphasises the similarities between NMF and PCA or factorial analysis
(see loadings
).
coef
and coef<-
are S4 methods defined for the corresponding
generic functions from package stats
(See stats::coef).
Similarly to basis
and basis<-
, they are defined for the top
virtual class NMF
only, and rely internally on the S4
generics .coef
and .coef<-
respectively that effectively
extract/set the coefficient data.
These data are post/pre-processed, e.g., to extract/set only their
non-fixed terms or check dimension compatibility.
.basis:
.basis(object = NMF)
: Pure virtual method for objects of class NMF
, that
should be overloaded by sub-classes, and throws an error if called.
.basis(object = NMFstd)
: Get the basis matrix in standard NMF models
This function returns slot W
of object
.
.basis(object = NMFfit)
: Returns the basis matrix from an NMF model fitted with
function nmf
.
It is a shortcut for .basis(fit(object), ...)
, dispatching the call to
the .basis
method of the actual NMF model.
.basis<-:
.basis<-(object = NMF,value = mMatrix)
: Pure virtual method for objects of class NMF
, that
should be overloaded by sub-classes, and throws an error if called.
.basis<-(object = NMFstd,value = array)
: Set the basis matrix in standard NMF models
This function sets slot W
of object
.
.basis<-(object = NMFstd,value = mMatrix)
: Replaces a slice of the basis array.
.basis<-(object = NMFfit,value = matrix)
: Sets the the basis matrix of an NMF model fitted with
function nmf
.
It is a shortcut for .basis(fit(object)) <- value
, dispatching the call to
the .basis<-
method of the actual NMF model.
It is not meant to be used by the user, except when developing
NMF algorithms, to update the basis matrix of the seed object before
returning it.
.coef:
.coef(object = NMF)
: Pure virtual method for objects of class NMF
, that
should be overloaded by sub-classes, and throws an error if called.
.coef(object = NMFstd)
: Get the mixture coefficient matrix in standard NMF models, which
is stored in slot H
of object
.
.coef(object = NMFfit)
: Returns the the coefficient matrix from an NMF model fitted with
function nmf
.
It is a shortcut for .coef(fit(object), ...)
, dispatching the call to
the .coef
method of the actual NMF model.
.coef<-:
.coef<-(object = NMF,value = mMatrix)
: Pure virtual method for objects of class NMF
, that
should be overloaded by sub-classes, and throws an error if called.
.coef<-(object = NMFstd,value = array)
: Set the mixture coefficient matrix in standard NMF models
This function sets slot H
of object
.
.coef<-(object = NMFstd,value = mMatrix)
: Replaces a slice of the coefficent array.
.coef<-(object = NMFfit,value = matrix)
: Sets the the coefficient matrix of an NMF model fitted with
function nmf
.
It is a shortcut for .coef(fit(object)) <- value
, dispatching the call to
the .coef<-
method of the actual NMF model.
It is not meant to be used by the user, except when developing
NMF algorithms, to update the coefficient matrix in the seed object before
returning it.
basis:
basis(object = ANY)
: Default method returns the value of S3 slot or attribute 'basis'
.
It returns NULL
if none of these are set.
Arguments ...
are not used by this method.
basis(object = NMFfitXn)
: Returns the basis matrix of the best fit amongst all the fits stored in
object
.
It is a shortcut for basis(fit(object))
.
basis<-:
basis<-(object = NMF)
: Default methods that calls .basis<-
and check the validity of the
updated object.
coef:
coef(object = NMFfitXn)
: Returns the coefficient matrix of the best fit amongst all the fits stored in
object
.
It is a shortcut for coef(fit(object))
.
coef<-:
coef<-(object = NMF)
: Default methods that calls .coef<-
and check the validity of the
updated object.
coefficients:
coefficients(object = NMF)
: Alias to coef,NMF
, therefore also pure virtual.
Other NMF-interface:
NMF-class
,
nmfModel()
,
rnmf()
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