sparse.model.matrix {Matrix}R Documentation

Construct Sparse Design / Model Matrices

Description

Construct a sparse model or “design” matrix, form a formula and data frame (sparse.model.matrix) or a single factor (fac2sparse).

The fac2[Ss]parse() functions are utilities, also used internally in the principal user level function sparse.model.matrix().

Usage

sparse.model.matrix(object, data = environment(object),
		    contrasts.arg = NULL, xlev = NULL, transpose = FALSE,
		    drop.unused.levels = FALSE, row.names = TRUE,
		    verbose = FALSE, ...)

fac2sparse(from, to = c("d", "i", "l", "n", "z"),
	   drop.unused.levels = TRUE, giveCsparse = TRUE)
fac2Sparse(from, to = c("d", "i", "l", "n", "z"),
	   drop.unused.levels = TRUE, giveCsparse = TRUE,
	   factorPatt12, contrasts.arg = NULL)

Arguments

object

an object of an appropriate class. For the default method, a model formula or terms object.

data

a data frame created with model.frame. If another sort of object, model.frame is called first.

contrasts.arg
for sparse.model.matrix():

A list, whose entries are contrasts suitable for input to the contrasts replacement function and whose names are the names of columns of data containing factors.

for fac2Sparse():

character string or NULL or (coercable to) "sparseMatrix", specifying the contrasts to be applied to the factor levels.

xlev

to be used as argument of model.frame if data has no "terms" attribute.

transpose

logical indicating if the transpose should be returned; if the transposed is used anyway, setting transpose = TRUE is more efficient.

drop.unused.levels

should factors have unused levels dropped? The default for sparse.model.matrix has been changed to FALSE, 2010-07, for compatibility with R's standard (dense) model.matrix().

row.names

logical indicating if row names should be used.

verbose

logical or integer indicating if (and how much) progress output should be printed.

...

further arguments passed to or from other methods.

from

(for fac2sparse():) a factor.

to

a character indicating the “kind” of sparse matrix to be returned. The default, "d" is for double.

giveCsparse

(for fac2sparse():) logical indicating if the result must be a CsparseMatrix.

factorPatt12

logical vector, say fp, of length two; when fp[1] is true, return “contrasted” t(X); when fp[2] is true, the original (“dummy”) t(X), i.e, the result of fac2sparse().

Value

a sparse matrix, extending CsparseMatrix (for fac2sparse() if giveCsparse is true as per default; a TsparseMatrix, otherwise).

For fac2Sparse(), a list of length two, both components with the corresponding transposed model matrix, where the corresponding factorPatt12 is true.

Note that model.Matrix(*, sparse=TRUE) from package MatrixModels may be often be preferable to sparse.model.matrix() nowadays, as model.Matrix() returns modelMatrix objects with additional slots assign and contrasts which relate back to the variables used.

fac2sparse(), the basic workhorse of sparse.model.matrix(), returns the transpose (t) of the model matrix.

Author(s)

Doug Bates and Martin Maechler, with initial suggestions from Tim Hesterberg.

See Also

model.matrix in standard R's package stats.
model.Matrix which calls sparse.model.matrix or model.matrix depending on its sparse argument may be preferred to sparse.model.matrix.

as(f, "sparseMatrix") (see coerce(from = "factor", ..) in the class doc sparseMatrix) produces the transposed sparse model matrix for a single factor f (and no contrasts).

Examples

dd <- data.frame(a = gl(3,4), b = gl(4,1,12))# balanced 2-way
options("contrasts") # the default:  "contr.treatment"
sparse.model.matrix(~ a + b, dd)
sparse.model.matrix(~ -1+ a + b, dd)# no intercept --> even sparser
sparse.model.matrix(~ a + b, dd, contrasts = list(a="contr.sum"))
sparse.model.matrix(~ a + b, dd, contrasts = list(b="contr.SAS"))

## Sparse method is equivalent to the traditional one :
stopifnot(all(sparse.model.matrix(~ a + b, dd) ==
	      Matrix(model.matrix(~ a + b, dd), sparse=TRUE)),
	  all(sparse.model.matrix(~ 0+ a + b, dd) ==
	      Matrix(model.matrix(~ 0+ a + b, dd), sparse=TRUE)))


(ff <- gl(3,4,, c("X","Y", "Z")))
fac2sparse(ff) #  3 x 12 sparse Matrix of class "dgCMatrix"
##
##  X  1 1 1 1 . . . . . . . .
##  Y  . . . . 1 1 1 1 . . . .
##  Z  . . . . . . . . 1 1 1 1

## can also be computed via sparse.model.matrix():
f30 <- gl(3,0    )
f12 <- gl(3,0, 12)
stopifnot(
  all.equal(t( fac2sparse(ff) ),
	    sparse.model.matrix(~ 0+ff),
	    tolerance = 0, check.attributes=FALSE),
  is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),
  is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),
  is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),
  is(M <- fac2sparse(f12, drop=FALSE),"CsparseMatrix"), dim(M) == c(3,12)
 )
[Package Matrix version 1.2-12 Index]