R: Fitted Matrix in NMF Models

fitted {NMF} | R Documentation

## Fitted Matrix in NMF Models

### Description

Computes the estimated target matrix based on a given NMF model. The estimation depends on the underlying NMF model. For example in the standard model V ~ W H, the target matrix is estimated by the matrix product W H. In other models, the estimate may depend on extra parameters/matrix (cf. Non-smooth NMF in `NMFns-class`).

### Usage

      fitted(object, ...)

      ## S4 method for signature 'NMFstd'
    fitted(object, W, H, ...)

      ## S4 method for signature 'NMFOffset'
    fitted(object, W, H,
        offset = object@offset)

      ## S4 method for signature 'NMFns'
    fitted(object, W, H, S, ...)

### Arguments

`object` | an object that inherit from class `NMF`
`...` | extra arguments to allow extension
`W` | a matrix to use in the computation as the basis matrix in place of `basis(object)`. It must be compatible with the coefficient matrix used in the computation (i.e. number of columns in `W` = number of rows in `H`).
`H` | a matrix to use in the computation as the coefficient matrix in place of `coef(object)`. It must be compatible with the basis matrix used in the computation (i.e. number of rows in `H` = number of columns in `W`).
`offset` | offset vector
`S` | smoothing matrix to use instead of `smoothing(object)` It must be a square matrix compatible with the basis and coefficient matrices used in the computation.

### Details

This function is a S4 generic function imported from fitted in the package stats. It is implemented as a pure virtual method for objects of 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.

### Value

the target matrix estimate as fitted by the model `object`

### Methods

fitted

  `signature(object = "NMF")`: Pure virtual method for objects of class `NMF`, that should be overloaded by sub-classes, and throws an error if called.

fitted

  `signature(object = "NMFstd")`: Compute the target matrix estimate in standard NMF models.

  The estimate matrix is computed as the product of the two matrix slots `W` and `H`:

  V ~ W H

fitted

  `signature(object = "NMFOffset")`: Computes the target matrix estimate for an NMFOffset object.

  The estimate is computed as:

  W H + offset

fitted

  `signature(object = "NMFns")`: Compute estimate for an NMFns object, according to the Nonsmooth NMF model (cf. `NMFns-class`).

  Extra arguments in `...` are passed to method `smoothing`, and are typically used to pass a value for `theta`, which is used to compute the smoothing matrix instead of the one stored in `object`.

fitted

  `signature(object = "NMFfit")`: Computes and return the estimated target matrix from an NMF model fitted with function `nmf`.

  It is a shortcut for `fitted(fit(object), ...)`, dispatching the call to the `fitted` method of the actual NMF model.

### Examples

    # random standard NMF model
    x <- rnmf(3, 10, 5)
    all.equal(fitted(x), basis(x) %*% coef(x))

[Package NMF version 0.21.0 Index]