`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-class`

for more
details.

`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`

.

`.coef`

and `.coef<-`

are low-level S4 generics
that simply return/set coefficient data in an object,
leaving some common processing to be performed in
`coef`

and `coef<-`

.

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).

basis(object, ...) S4 (NMF) `basis`(object, all = TRUE, ...) .basis(object, ...) basis(object) <- value .basis(object) <- value S4 (NMF) `loadings`(x) coef(object, ...) S4 (NMF) `coef`(object, all = TRUE, ...) .coef(object, ...) coef(object) <- value .coef(object) <- value coefficients(object, ...) S4 (NMF) `coefficients`(object, all = TRUE, ...) scoef(object, ...) S4 (NMF) `scoef`(object, scale = 1) S4 (matrix) `scoef`(object, scale = 1)

- object
- an object from which to extract the factor
matrices, typically an object of class
`NMF-class`

. - ...
- extra arguments to allow extension and passed
to the low-level access functions
`.coef`

and`.basis`

. - all
- a logical that indicates whether the complete
matrix factor should be returned (
`TRUE`

) or only the non-fixed part. This is relevant only for formula-based NMF models that include fixed basis or coefficient terms. - value
- replacement value
- scale
- scaling factor, which indicates to the value the columns of the coefficient matrix should sum up to.
- x
- an object of class
`"factanal"`

or`"princomp"`

or the`loadings`

component of such an object.

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-class`

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.

`coef`

and `coef<-`

are S4 methods defined for
the corresponding generic functions from package
`stats`

(See coef). Similarly to
`basis`

and `basis<-`

, they are defined for the
top virtual class `NMF-class`

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
`signature(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
`signature(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
`signature(object = "NMF")`

: Pure virtual method for objects of class`NMF-class`

, that should be overloaded by sub-classes, and throws an error if called. - .basis
`signature(object = "NMFstd")`

: Get the basis matrix in standard NMF modelsThis function returns slot

`W`

of`object`

. - .basis
`signature(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<-
`signature(object = "NMF", value = "matrix")`

: Pure virtual method for objects of class`NMF-class`

, that should be overloaded by sub-classes, and throws an error if called. - .basis<-
`signature(object = "NMFstd", value = "matrix")`

: Set the basis matrix in standard NMF modelsThis function sets slot

`W`

of`object`

. - .basis<-
`signature(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. - basis<-
`signature(object = "ANY")`

: Default methods that calls`.basis<-`

and check the validity of the updated object. - coef
`signature(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
`signature(object = "NMF")`

: Pure virtual method for objects of class`NMF-class`

, that should be overloaded by sub-classes, and throws an error if called. - .coef
`signature(object = "NMFstd")`

: Get the mixture coefficient matrix in standard NMF modelsThis function returns slot

`H`

of`object`

. - .coef
`signature(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<-
`signature(object = "NMF", value = "matrix")`

: Pure virtual method for objects of class`NMF-class`

, that should be overloaded by sub-classes, and throws an error if called. - .coef<-
`signature(object = "NMFstd", value = "matrix")`

: Set the mixture coefficient matrix in standard NMF modelsThis function sets slot

`H`

of`object`

. - .coef<-
`signature(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. - coef<-
`signature(object = "ANY")`

: Default methods that calls`.coef<-`

and check the validity of the updated object. - coefficients
`signature(object = "NMF")`

: Alias to`coef,NMF`

, therefore also pure virtual. - loadings
`signature(x = "NMF")`

: Method loadings for NMF ModelsThe method

`loadings`

is identical to`basis`

, but do not accept any extra argument.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`

).

`.DollarNames,NMF-method`

,
`misc`

, `NMF-class`

,
`$<-,NMF-method`

, `$,NMF-method`

,
`nmfModel`

, `nmfModels`

,
`rnmf`