R: Generating Random NMF Models

rnmf {NMF} | R Documentation

## Generating Random NMF Models

### Description

Generates NMF models with random values drawn from a uniform distribution. It returns an NMF model with basis and mixture coefficient matrices filled with random values. The main purpose of the function `rnmf` is to provide a common interface to generate random seeds used by the `nmf` function.

### Usage

      rnmf(x, target, ...)

      ## S4 method for signature 'NMF,numeric'
    rnmf(x, target, ncol = NULL,
        keep.names = TRUE, dist = runif)

      ## S4 method for signature 'ANY,matrix'
    rnmf(x, target, ...,
        dist = list(max = max(max(target, na.rm = TRUE), 1)),
        use.dimnames = TRUE)

      ## S4 method for signature 'numeric,missing'
    rnmf(x, target, ..., W, H,
        dist = runif)

      ## S4 method for signature 'missing,missing'
    rnmf(x, target, ..., W, H)

      ## S4 method for signature 'numeric,numeric'
    rnmf(x, target, ncol = NULL,
        ..., dist = runif)

      ## S4 method for signature 'formula,ANY'
    rnmf(x, target, ...,
        dist = runif)

### Arguments

`x` | an object that determines the rank, dimension and/or class of the generated NMF model, e.g. a numeric value or an object that inherits from class `NMF`. See the description of the specific methods for more details on the supported types.
`target` | optional specification of target dimensions. See section Methods for how this parameter is used by the different methods.
`...` | extra arguments to allow extensions and passed to the next method eventually down to `nmfModel`, where they are used to initialise slots that are specific to the instantiating NMF model.
`ncol` | single numeric value that specifies the number of columns of the coefficient matrix. Only used when `target` is a single numeric value.
`keep.names` | a logical that indicates if the dimension names of the original NMF object `x` should be conserved (`TRUE`) or discarded (`FALSE`).
`dist` | specification of the random distribution to use to draw the entries of the basis and coefficient matrices. It may be specified as: a `function` which must be a distribution function such as e.g. `runif` that is used to draw the entries of both the basis and coefficient matrices. It is passed in the `dist` argument of `rmatrix`. a `list` of arguments that are passed internally to `rmatrix`, via `do.call('rmatrix', dist)`. a `character` string that is partially matched to ‘basis’ or ‘coef’, that specifies which matrix in should be drawn randomly, the other remaining as in `x` – unchanged. a `list` with elements ‘basis’ and/or ‘coef’, which specify the `dist` argument separately for the basis and coefficient matrix respectively. These elements may be either a distribution function, or a list of arguments that are passed internally to `rmatrix`, via `do.call('rmatrix', dist$basis)` or `do.call('rmatrix', dist$coef)`.
`use.dimnames` | a logical that indicates whether the dimnames of the target matrix should be set on the returned NMF model.
`W` | value for the basis matrix. `data.frame` objects are converted into matrices with `as.matrix`.
`H` | value for the mixture coefficient matrix `data.frame` objects are converted into matrices with `as.matrix`.

### Details

If necessary, extensions of the standard NMF model or custom models must define a method "rnmf,<NMF.MODEL.CLASS>,numeric" for initialising their specific slots other than the basis and mixture coefficient matrices. In order to benefit from the complete built-in interface, the overloading methods should call the generic version using function `callNextMethod`, prior to set the values of the specific slots. See for example the method `rnmf` defined for `NMFOffset` models: `showMethods(rnmf, class='NMFOffset', include=TRUE))`.

For convenience, shortcut methods for working on `data.frame` objects directly are implemented. However, note that conversion of a `data.frame` into a `matrix` object may take some non-negligible time, for large datasets. If using this method or other NMF-related methods several times, consider converting your data `data.frame` object into a matrix once for good, when first loaded.

### Value

An NMF model, i.e. an object that inherits from class `NMF`.

### Methods

rnmf

  `signature(x = "NMFOffset", target = "numeric")`: Generates a random NMF model with offset, from class `NMFOffset`.

  The offset values are drawn from a uniform distribution between 0 and the maximum entry of the basis and coefficient matrices, which are drawn by the next suitable `rnmf` method, which is the workhorse method `rnmf,NMF,numeric`.

rnmf

  `signature(x = "NMF", target = "numeric")`: Generates a random NMF model of the same class and rank as another NMF model.

  This is the workhorse method that is eventually called by all other methods. It generates an NMF model of the same class and rank as `x`, compatible with the dimensions specified in `target`, that can be a single or 2-length numeric vector, to specify a square or rectangular target matrix respectively.

  The second dimension can also be passed via argument `ncol`, so that calling `rnmf(x, 20, 10, ...)` is equivalent to `rnmf(x, c(20, 10), ...)`, but easier to write.

  The entries are uniformly drawn between `0` and `max` (optionally specified in `...`) that defaults to 1.

  By default the dimnames of `x` are set on the returned NMF model. This behaviour is disabled with argument `keep.names=FALSE`. See `nmfModel`.

rnmf

  `signature(x = "ANY", target = "matrix")`: Generates a random NMF model compatible and consistent with a target matrix.

  The entries are uniformly drawn between `0` and `max(target)`. It is more or less a shortcut for: rnmf(x, dim(target), max=max(target), ...)

  It returns an NMF model of the same class as `x`.

rnmf

  `signature(x = "ANY", target = "data.frame")`: Shortcut for `rnmf(x, as.matrix(target))`.

rnmf

  `signature(x = "NMF", target = "missing")`: Generates a random NMF model of the same dimension as another NMF model.

  It is a shortcut for `rnmf(x, nrow(x), ncol(x), ...)`, which returns a random NMF model of the same class and dimensions as `x`.

rnmf

  `signature(x = "numeric", target = "missing")`: Generates a random NMF model of a given rank, with known basis and/or coefficient matrices.

  This methods allow to easily generate partially random NMF model, where one or both factors are known. Although the later case might seems strange, it makes sense for NMF models that have fit extra data, other than the basis and coefficient matrices, that are drawn by an `rnmf` method defined for their own class, which should internally call `rnmf,NMF,numeric` and let it draw the basis and coefficient matrices. (e.g. see `NMFOffset` and `rnmf,NMFOffset,numeric-method`).

  Depending on whether arguments `W` and/or `H` are missing, this method interprets `x` differently:

  - `W` provided, `H` missing: `x` is taken as the number of columns that must be drawn to build a random coefficient matrix (i.e. the number of columns in the target matrix).

  - `W` is missing, `H` is provided: `x` is taken as the number of rows that must be drawn to build a random basis matrix (i.e. the number of rows in the target matrix).

  - both `W` and `H` are provided: `x` is taken as the target rank of the model to generate.

  - Having both `W` and `H` missing produces an error, as the dimension of the model cannot be determined in this case.

  The matrices `W` and `H` are reduced if necessary and possible to be consistent with this value of the rank, by the internal call to `nmfModel`.

  All arguments in `...` are passed to the function `nmfModel` which is used to build an initial NMF model, that is in turn passed to `rnmf,NMF,numeric` with `dist=list(coef=dist)` or `dist=list(basis=dist)` when suitable. The type of NMF model to generate can therefore be specified in argument `model` (see `nmfModel` for other possible arguments).

  The returned NMF model, has a basis matrix equal to `W` (if not missing) and a coefficient matrix equal to `H` (if not missing), or drawn according to the specification provided in argument `dist` (see method `rnmf,NMF,numeric` for details on the supported values for `dist`).

rnmf

  `signature(x = "missing", target = "missing")`: Generates a random NMF model with known basis and coefficient matrices.

  This method is a shortcut for calling `rnmf,numeric,missing` with a suitable value for `x` (the rank), when both factors are known: codernmf(min(ncol(W), nrow(H)), ..., W=W, H=H).

  Arguments `W` and `H` are required. Note that calling this method only makes sense for NMF models that contains data to fit other than the basis and coefficient matrices, e.g. `NMFOffset`.

rnmf

  `signature(x = "numeric", target = "numeric")`: Generates a random standard NMF model of given dimensions.

  This is a shortcut for `rnmf(nmfModel(x, target, ncol, ...)), dist=dist)`. It generates a standard NMF model compatible with the dimensions passed in `target`, that can be a single or 2-length numeric vector, to specify a square or rectangular target matrix respectively. See `nmfModel`.

rnmf

  `signature(x = "formula", target = "ANY")`: Generate a random formula-based NMF model, using the method `nmfModel,formula,ANY-method`.

### See Also

`rmatrix`

Other NMF-interface: `basis`, `.basis`, `.basis<-`, `basis<-`, `coef`, `.coef`, `.coef<-`, `coef<-`, `coefficients`, `.DollarNames,NMF-method`, `loadings,NMF-method`, `misc`, `NMF-class`, `$<-,NMF-method`, `$,NMF-method`, `nmfModel`, `nmfModels`, `scoef`

### Examples

    #----------
    # rnmf,NMFOffset,numeric-method
    #----------
    # random NMF model with offset
    x <- rnmf(2, 3, model='NMFOffset')
    x
    offset(x)
    # from a matrix
    x <- rnmf(2, rmatrix(5,3, max=10), model='NMFOffset')
    offset(x)

    #----------
    # rnmf,NMF,numeric-method
    #----------
    ## random NMF of same class and rank as another model

    x <- nmfModel(3, 10, 5)
    x
    rnmf(x, 20) # square
    rnmf(x, 20, 13)
    rnmf(x, c(20, 13))

    # using another distribution
    rnmf(x, 20, dist=rnorm)

    # other than standard model
    y <- rnmf(3, 50, 10, model='NMFns')
    y

    #----------
    # rnmf,ANY,matrix-method
    #----------
    # random NMF compatible with a target matrix
    x <- nmfModel(3, 10, 5)
    y <- rmatrix(20, 13)
    rnmf(x, y) # rank of x
    rnmf(2, y) # rank 2

    #----------
    # rnmf,NMF,missing-method
    #----------
    ## random NMF from another model

    a <- nmfModel(3, 100, 20)
    b <- rnmf(a)

    #----------
    # rnmf,numeric,missing-method
    #----------
    # random NMF model with known basis matrix
    x <- rnmf(5, W=matrix(1:18, 6)) # 6 x 5 model with rank=3
    basis(x) # fixed
    coef(x) # random

    # random NMF model with known coefficient matrix
    x <- rnmf(5, H=matrix(1:18, 3)) # 5 x 6 model with rank=3
    basis(x) # random
    coef(x) # fixed

    # random model other than standard NMF
    x <- rnmf(5, H=matrix(1:18, 3), model='NMFOffset')
    basis(x) # random
    coef(x) # fixed
    offset(x) # random

    #----------
    # rnmf,missing,missing-method
    #----------
    # random model other than standard NMF
    x <- rnmf(W=matrix(1:18, 6), H=matrix(21:38, 3), model='NMFOffset')
    basis(x) # fixed
    coef(x) # fixed
    offset(x) # random

    #----------
    # rnmf,numeric,numeric-method
    #----------
    ## random standard NMF of given dimensions

    # generate a random NMF model with rank 3 that fits a 100x20 matrix
    rnmf(3, 100, 20)

    # generate a random NMF model with rank 3 that fits a 100x100 matrix
    rnmf(3, 100)

[Package NMF version 0.20.6 Index]