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Design Issues in Matrix Package Development: 1 The Matrix Class Structures

1. The document discusses the class hierarchy and structure of matrices in the Matrix package, including diagonal matrices which have their own class. 2. It covers matrix transformations between classes using as() and coercion rules for changing matrix types, shapes, and storage formats while maintaining structure. 3. The session info provides details of the R version and packages used.

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37 views5 pages

Design Issues in Matrix Package Development: 1 The Matrix Class Structures

1. The document discusses the class hierarchy and structure of matrices in the Matrix package, including diagonal matrices which have their own class. 2. It covers matrix transformations between classes using as() and coercion rules for changing matrix types, shapes, and storage formats while maintaining structure. 3. The session info provides details of the R version and packages used.

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rojasleop
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Design Issues in Matrix package Development

Martin Maechler and Douglas Bates


R Core Development Team
[email protected], [email protected]

Spring 2008 (typeset on November 27, 2015)

Abstract
This is a (currently very incomplete) write-up of the many smaller
and larger design decisions we have made in organizing functionalities in
the Matrix package.
Classes: Theres a rich hierarchy of matrix classes, which you can
visualize as a set of trees whose inner (and upper) nodes are virtual
classes and only the leaves are non-virtual actual classes.
Functions and Methods:
- setAs()
- others

1 The Matrix class structures


Take Martins DSC 2007 talk to depict class hierarchy.

1.1 Diagonal Matrices


The class of diagonal matrices is worth mentioning for several reasons. First,
we have wanted such a class, because multiplication methods are particularly
simple with diagonal matrices. The typical constructor is Diagonal() whereas
the accessor (as for traditional matrices), diag() simply returns the vector of
diagonal entries:
> library(Matrix)
> (D4 <- Diagonal(4, 10*(1:4)))

4 x 4 diagonal matrix of class "ddiMatrix"


[,1] [,2] [,3] [,4]
[1,] 10 . . .
[2,] . 20 . .
[3,] . . 30 .
[4,] . . . 40

1
> str(D4)

Formal class 'ddiMatrix' [package "Matrix"] with 4 slots


..@ diag : chr "N"
..@ Dim : int [1:2] 4 4
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : num [1:4] 10 20 30 40

> diag(D4)

[1] 10 20 30 40

We can modify the diagonal in the traditional way (via method definition for
diag<-()):
> diag(D4) <- diag(D4) + 1:4
> D4

4 x 4 diagonal matrix of class "ddiMatrix"


[,1] [,2] [,3] [,4]
[1,] 11 . . .
[2,] . 22 . .
[3,] . . 33 .
[4,] . . . 44

Note that unit-diagonal matrices (the identity matrices of linear algebra)


with slot diag = "U" can have an empty x slot, very analogously to the unit-
diagonal triangular matrices:

> str(I3 <- Diagonal(3)) ## empty 'x' slot

Formal class 'ddiMatrix' [package "Matrix"] with 4 slots


..@ diag : chr "U"
..@ Dim : int [1:2] 3 3
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : num(0)

> getClass("diagonalMatrix") ## extending "denseMatrix"

Virtual Class "diagonalMatrix" [package "Matrix"]

Slots:

Name: diag Dim Dimnames

2
Class: character integer list

Extends:
Class "sparseMatrix", directly
Class "Matrix", by class "sparseMatrix", distance 2
Class "mMatrix", by class "Matrix", distance 3

Known Subclasses: "ddiMatrix", "ldiMatrix"

We have implemented diagonal matrices as dense rather than sparse matrices,


for the following reasons:
1. The diag()onal (vector) is the basic part of such a matrix, and this is
simply the x slot unless the diag slot is "U", the unit-diagonal case, which
is the identity matrix.

2. given 1), it does not make much sense to store where the matrix is non-
zero. This contrasts with all sparse matrix implementations, and hence
we did not want to call a diagonal matrix sparse.

2 Matrix Transformations
2.1 Coercions between Matrix classes
You may need to transform Matrix objects into specific shape (triangular,
symmetric), content type (double, logical, . . . ) or storage structure (dense
or sparse). Every useR should use as(x, <superclass>) to this end, where
<superclass> is a virtual Matrix super class, such as "triangularMatrix"
"dMatrix", or "sparseMatrix".
In other words, the user should not coerce directly to a specific desired class
such as "dtCMatrix", even though that may occasionally work as well.
Here is a set of rules to which the Matrix developers and the users should
typically adhere:

Rule 1 : as(M, "matrix") should work for all Matrix objects M.


Rule 2 : Matrix(x) should also work for matrix like objects x and always
return a classed Matrix.
Applied to a "matrix" object m, M. <- Matrix(m) can be considered a
kind of inverse of m <- as(M, "matrix"). For sparse matrices however,
M. well be a CsparseMatrix, and it is often more structured than M, e.g.,
> (M <- spMatrix(4,4, i=1:4, j=c(3:1,4), x=c(4,1,4,8))) # dgTMatrix

4 x 4 sparse Matrix of class "dgTMatrix"

[1,] . . 4 .

3
[2,] . 1 . .
[3,] 4 . . .
[4,] . . . 8

> m <- as(M, "matrix")


> (M. <- Matrix(m)) # dsCMatrix (i.e. *symmetric*)

4 x 4 sparse Matrix of class "dsCMatrix"

[1,] . . 4 .
[2,] . 1 . .
[3,] 4 . . .
[4,] . . . 8

Rule 3 : All the following coercions to virtual matrix classes should work:

1. as(m, "dMatrix")
2. as(m, "lMatrix")
3. as(m, "nMatrix")
4. as(m, "denseMatrix")
5. as(m, "sparseMatrix")
6. as(m, "generalMatrix")
whereas the next ones should work under some assumptions:

1. as(m1, "triangularMatrix")
should work when m1 is a triangular matrix, i.e. the upper or lower
triangle of m1 contains only zeros.
2. as(m2, "symmetricMatrix") should work when m2 is a symmetric
matrix in the sense of isSymmetric(m2) returning TRUE. Note that
this is typically equivalent to something like isTRUE(all.equal(m2,
t(m2))), i.e., the lower and upper triangle of the matrix have to be
equal up to small numeric fuzz.

3 Session Info
> toLatex(sessionInfo())

R version 3.2.2 Patched (2015-11-26 r69707), x86_64-pc-linux-gnu

Locale: LC_CTYPE=de_CH.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8,


LC_COLLATE=C, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=de_CH.UTF-8,
LC_PAPER=de_CH.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C,
LC_MEASUREMENT=de_CH.UTF-8, LC_IDENTIFICATION=C

4
Base packages: base, datasets, grDevices, graphics, methods, stats, utils
Other packages: Matrix 1.2-3
Loaded via a namespace (and not attached): grid 3.2.2, lattice 0.20-33,
tools 3.2.2

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