is_nonzero: is_nonzero() and the nz*() functions

In Bioconductor/SparseArray: High-performance sparse data representation and manipulation in R

is_nonzero() and the nz*() functions

Description

A set of functions for direct manipulation of the nonzero elements of an array-like object.

Usage

is_nonzero(x)

nzcount(x)
nzwhich(x, arr.ind=FALSE)
nzvals(x)
nzvals(x) <- value

sparsity(x)

Arguments

x	Typically (but not necessarily) an array-like object that is sparse, like a SparseArray derivative, or a dg[C|R]Matrix or lg[C|R]Matrix object from the Matrix package. However, x can also be an ordinary matrix or array, or any matrix-like or array-like object.
arr.ind	If arr.ind=FALSE (the default), the indices of the nonzero array elements are returned in a numeric vector (a.k.a. L-index). Otherwise, they're returned in an ordinary matrix (a.k.a. M-index). See ?Lindex in the S4Arrays package for more information about L-index and M-index, and how to convert from one to the other. Note that using arr.ind=TRUE won't work if nzcount(x) is >= .Machine$integer.max (= 2^31), because, in that case, the returned M-index would need to be a matrix with more rows than what is supported by base R.
value	A vector, typically of length nzcount(x) (or 1) and type type(x).

Details

nzcount(x) and nzwhich(x) are equivalent to, but typically more efficient than, sum(is_nonzero(x)) and which(is_nonzero(x)), respectively.

nzvals(x) is equivalent to, but typically more efficient than, x[nzwhich(x)] (or x[is_nonzero(x)]).

nzvals(x) <- value replaces the values of the nonzero array elements in x with the supplied values. It's equivalent to, but typically more efficient than, x[nzwhich(x)] <- value.

Note that nzvals(x) <- nzvals(x) is guaranteed to be a no-op.

Value

is_nonzero(): An array-like object of type() "logical" and same dimensions as the input object.

nzcount(): The number of nonzero array elements in x.

nzwhich(): The indices of the nonzero array elements in x, either as an L-index (if arr.ind is FALSE) or as an M-index (if arr.ind is TRUE). Note that the indices are returned sorted in strictly ascending order.

nzvals(): A vector of the same type() as x and containing the values of the nonzero array elements in x. Note that the returned vector is guaranteed to be parallel to nzwhich(x).

sparsity(x): The ratio between the number of zero-valued elements in array-like object x and its total number of elements (length(x) or prod(dim(x))). More precisely, sparsity(x) is 1 - nzcount(x)/length(x).

See Also

• is_nonna for is_nonna() and nna*() functions nnacount(), nnawhich(), etc...

• SparseArray objects.

• S4 classes dgCMatrix, lgCMatrix, and ngCMatrix defined in the Matrix package.

• Ordinary array objects in base R.

• base::which in base R.

Examples

a <- array(rpois(120, lambda=0.3), dim=c(5, 12, 2))

is_nonzero(a)

## Get the number of nonzero array elements in 'a':
nzcount(a)

## nzwhich() returns the indices of the nonzero array elements in 'a'.
## Either as a "L-index" i.e. an integer (or numeric) vector of
## length 'nzcount(a)' containing "linear indices":
nzidx <- nzwhich(a)
length(nzidx)
head(nzidx)

## Or as an "M-index" i.e. an integer matrix with 'nzcount(a)' rows
## and one column per dimension where the rows represent "array indices"
## (a.k.a. "array coordinates"):
Mnzidx <- nzwhich(a, arr.ind=TRUE)
dim(Mnzidx)

## Each row in the matrix is an n-tuple representing the "array
## coordinates" of a nonzero element in 'a':
head(Mnzidx)
tail(Mnzidx)

## Extract the values of the nonzero array elements in 'a' and return
## them in a vector "parallel" to 'nzwhich(a)':
a_nzvals <- nzvals(a)  # equivalent to 'a[nzwhich(a)]'
length(a_nzvals)
head(a_nzvals)

nzvals(a) <- log1p(nzvals(a))
a

## Sanity checks:
stopifnot(
  identical(nzidx, which(a != 0)),
  identical(Mnzidx, which(a != 0, arr.ind=TRUE, useNames=FALSE)),
  identical(nzvals(a), a[nzidx]),
  identical(nzvals(a), a[Mnzidx]),
  identical(`nzvals<-`(a, nzvals(a)), a)
)

Bioconductor/SparseArray documentation built on Nov. 14, 2024, 6:22 p.m.