Hashmat-class {Cardinal} | R Documentation

## Sparse Matrix Class Using Lists as Hash Tables

### Description

The Hashmat class implements compressed sparse column (CSC) style matrices using R `list` objects as the columns. The implementation is unique in that it allows re-assignment of the keys describing the rows, allowing for arbitrary re-ordering of rows and row-wise elements. This is useful for storing sparse signals, such as processed spectra.

### Usage

    ## Instance creation
    Hashmat(data = NA, nrow = 1, ncol = 1, byrow=FALSE,
        dimnames = NULL, ...)

    ## Additional methods documented below

### Arguments

`data` | A `matrix` or a `vector`. If `data` is a `matrix`, then a sparse matrix is construced from matrix directly and other arguments (except for `dimnames`) are ignored. If `data` is a `vector`, then the behavior is the same as for ordinary matrix construction.
`nrow` | The number of rows in the sparse matrix.
`ncol` | The number of columns in the sparse matrix.
`byrow` | If 'FALSE', the matrix is filled by columns. If 'TRUE', it is filled by rows.
`dimnames` | The 'dimnames' giving the dimension names for the matrix, analogous to the 'dimnames' attribute of an ordinary R matrix. This must be a list of length 2 or `NULL`.
`...` | Additional arguments passed to the constructor.

### Slots

`data`:

  A `list` with vectors corresponding columns of the sparse matrix, whose elements are its non-zero elements.

`keys`:

  A `character` vector providing the keys that determine the rows of the non-zero elements of the matrix.

`dim`:

  A length 2 integer vector analogous to the 'dim' attribute of an ordinary R matrix.

`dimnames`:

  A length 2 `list` analogous to the 'dimnames' attribute of an ordinary R matrix.

`.__classVersion__`:

  A `Versions` object describing the version of the class used to created the instance. Intended for developer use.

### Extends

`Versioned`

### Creating Objects

`Hashmat` instances are usually created through `Hashmat()`.

### Methods

Class-specific methods:

`pData(object)`, `pData(object)<-`:

  Access or set the list of `numeric` vectors storing the column-vectors of the sparse matrix directly.

`keys(object)`, `keys(object)<-`:

  Access of set the keys for the row elements. If this is a `character`, it sets the `keys` slot directly, and hence the 'dim' is also changed. If this is a `list`, then the list should have length equal to the number of rows, and each element should be an `integer` vector of length equal to the number of non-zero row elements for the respective column. The vectors are used to index the `keys` slot and set the key names of the vectors, and hence change or reorder the row elements.

Standard generic methods:

`combine(x, y, ...)`:

  Combines two Hashmat objects. See the `combine` method for matrices for details of how the Hashmat sparse matrices are combined. The behavior is identical, except when filling in missing elements in non-shared rows and columns, the resulting Hashmat object will have zeroes instead of NAs.

`dim(x), dim(x) <- value`:

  Return or set the dimensions of the sparse matrix.

`dimnames(x), dimnames(x) <- value`:

  Return or set the 'dimnames' of the sparse matrix.

`colnames(x), colnames(x) <- value`:

  Return or set the column names of the sparse matrix.

`rownames(x), rownames(x) <- value`:

  Return or set the row names of the sparse matrix.

`ncol`:

  Return the number of columns in the sparse matrix.

`nrow`:

  Return the number of columns in the sparse matrix.

`cbind`:

  Combine sparse matrices by columns. The keys used to resolve the rows must match between matrices.

`rbind`:

  Not allowed for sparse matrices. (Always returns an error.)

`Hashmat[i, j, ..., drop], Hashmat[i, j, ...] <- value`:

  Access and assign elements in the sparse matrix. A Hashmat sparse matrix can be indexed like an ordinary R matrix. Note however that linear indexing is not supported. Use `drop = NULL` to return a subset of the same class as the object.

### Author(s)

Kylie A. Bemis

### See Also

`matrix`, `Binmat`, `SImageSet`

### Examples

    ## Create an Hashmat object
    Hashmat()

    ## Using a list of elements and keys
    dmat1 <- diag(3)
    smat1 <- Hashmat(dmat1)
    all.equal(smat1[], dmat1, check.attr=FALSE)

    ## Filling an empty sparse matrix
    smat2 <- Hashmat(nrow=1000, ncol=1000)
    smat2[500,] <- rep(1, 1000)

    dmat2 <- matrix(nrow=1000, ncol=1000)
    dmat2[500,] <- rep(1, 1000)

    print(object.size(dmat2), units="Mb")
    print(object.size(smat2), units="Mb") # Much smaller

    all.equal(dmat2[500,], smat2[500,], , check.attr=FALSE)

[Package Cardinal version 1.12.1 Index]