R: Apply Function for NMF Objects

nmfApply {NMF} | R Documentation

## Apply Function for NMF Objects

### Description

The function `nmfApply` provides exteneded `apply`-like functionality for objects of class `NMF`. It enables to easily apply a function over different margins of NMF models.

### Usage

      nmfApply(X, MARGIN, FUN, ..., simplify = TRUE,
        USE.NAMES = TRUE)

### Arguments

`X` | an object that has suitable `basis` and `coef` methods, e.g. an NMF model.
`MARGIN` | a single numeric (integer) value that specifies over which margin(s) the function `FUN` is applied. See section Details for a list of possible values.
`FUN` | a function to apply over the specified margins.
`...` | extra arguments passed to `FUN`
`simplify` | a logical only used when `MARGIN=3`, that indicates if `sapply` should try to simplify result if possible. Since this argument follows ‘...’ its name cannot be abbreviated.
`USE.NAMES` | a logical only used when `MARGIN=3`, that indicates if `sapply` should use the names of the basis components to name the results if present. Since this argument follows ‘...’ its name cannot be abbreviated.

### Details

The function `FUN` is applied via a call to `apply` or `sapply` according to the value of argument `MARGIN` as follows:

MARGIN=1

  apply `FUN` to each row of the basis matrix: `apply(basis(X), 1L, FUN, ...)`.

MARGIN=2

  apply `FUN` to each column of the coefficient matrix: `apply(coef(X), 2L, FUN, ...)`.

MARGIN=3

  apply `FUN` to each pair of associated basis component and basis profile: more or less `sapply(seq(nbasis(X)), function(i, ...) FUN(basis(X)[,i], coef(X)[i, ], ...), ...)`.

  In this case `FUN` must be have at least two arguments, to which are passed each basis components and basis profiles respectively – as numeric vectors.

MARGIN=4

  apply `FUN` to each column of the basis matrix, i.e. to each basis component: `apply(basis(X), 2L, FUN, ...)`.

MARGIN=5

  apply `FUN` to each row of the coefficient matrix: `apply(coef(X), 1L, FUN, ...)`.

### Value

a vector or a list. See `apply` and `sapply` for more details on the output format.

[Package NMF version 0.21.0 Index]