unpackedMatrix-class: Virtual Class '"unpackedMatrix"' of Unpacked Dense Matrices
In Matrix: Sparse and Dense Matrix Classes and Methods

unpackedMatrix-class

R Documentation

Virtual Class `"unpackedMatrix"` of Unpacked Dense Matrices

Description

Class "unpackedMatrix" is the virtual class of dense matrices in "unpacked" format, storing all m*n elements of an m-by-n matrix. It is used to define common methods for efficient subsetting, transposing, etc. of its proper subclasses: currently "[dln]geMatrix" (unpacked general), "[dln]syMatrix" (unpacked symmetric), "[dln]trMatrix" (unpacked triangular), and subclasses of these, such as "dpoMatrix".

Slots

Dim, Dimnames:: as all Matrix objects.

Extends

Class "denseMatrix", directly. Class "Matrix", by class "denseMatrix", distance 2.

Methods

pack: signature(x = "unpackedMatrix"): ...
unpack: signature(x = "unpackedMatrix"): ...
isSymmetric: signature(object = "unpackedMatrix"): ...
isTriangular: signature(object = "unpackedMatrix"): ...
isDiagonal: signature(object = "unpackedMatrix"): ...
t: signature(x = "unpackedMatrix"): ...
diag: signature(x = "unpackedMatrix"): ...
diag<-: signature(x = "unpackedMatrix"): ...

Author(s)

Mikael Jagan

Examples

showClass("unpackedMatrix")
showMethods(classes = "unpackedMatrix")


showClass("ngeMatrix")
## "lgeMatrix" is really more relevant


showClass("lgeMatrix")
str(new("lgeMatrix"))
set.seed(1)
(lM <- Matrix(matrix(rnorm(28), 4,7) > 0))# a simple random lgeMatrix
set.seed(11)
(lC <- Matrix(matrix(rnorm(28), 4,7) > 0))# a simple random lgCMatrix
as(lM, "CsparseMatrix")


(s0 <- new("nsyMatrix"))

(M2 <- Matrix(c(TRUE, NA, FALSE, FALSE), 2, 2)) # logical dense (ltr)
(sM <- M2 & t(M2))                       # -> "lge"
class(sM <- as(sM, "nMatrix"))           # -> "nge"
     (sM <- as(sM, "symmetricMatrix"))   # -> "nsy"
str(sM <- as(sM, "packedMatrix")) # -> "nsp", i.e., packed symmetric


(M2 <- Matrix(c(TRUE, NA, FALSE, FALSE), 2, 2)) # logical dense (ltr)
str(M2)
# can
(sM <- M2 | t(M2)) # "lge"
as(sM, "symmetricMatrix")
str(sM <- as(sM, "packedMatrix")) # packed symmetric


## Only upper triangular part matters (when uplo == "U" as per default)
(sy2 <- new("dsyMatrix", Dim = as.integer(c(2,2)), x = c(14, NA,32,77)))
str(t(sy2)) # uplo = "L", and the lower tri. (i.e. NA is replaced).

chol(sy2) #-> "Cholesky" matrix
(sp2 <- pack(sy2)) # a "dspMatrix"

## Coercing to dpoMatrix gives invalid object:
sy3 <- new("dsyMatrix", Dim = as.integer(c(2,2)), x = c(14, -1, 2, -7))
try(as(sy3, "dpoMatrix")) # -> error: not positive definite


## 4x4 example
m <- matrix(0,4,4); m[upper.tri(m)] <- 1:6
(sym <- m+t(m)+diag(11:14, 4))
(S1 <- pack(sym))
(S2 <- t(S1))
stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :
str(S1)
S2@x


showClass("ntrMatrix")

str(new("ntpMatrix"))
(nutr <- as(upper.tri(matrix(, 4, 4)), "ndenseMatrix"))
str(nutp <- pack(nutr)) # packed matrix: only 10 = 4*(4+1)/2 entries
!nutp # the logical negation (is *not* logical triangular !)
## but this one is:
stopifnot(all.equal(nutp, pack(!!nutp)))


showClass("ltrMatrix")

str(new("ltpMatrix"))
(lutr <- as(upper.tri(matrix(, 4, 4)), "ldenseMatrix"))
str(lutp <- pack(lutr)) # packed matrix: only 10 = 4*(4+1)/2 entries
!lutp # the logical negation (is *not* logical triangular !)
## but this one is:
stopifnot(all.equal(lutp, pack(!!lutp)))


(m <- rbind(2:3, 0:-1))
(M <- as(m, "generalMatrix"))

(T <- as(M, "triangularMatrix")) # formally upper triangular
(T2 <- as(t(M), "triangularMatrix"))
stopifnot(T@uplo == "U", T2@uplo == "L", identical(T2, t(T)))

m <- matrix(0,4,4); m[upper.tri(m)] <- 1:6
(t1 <- Matrix(m+diag(,4)))
str(t1p <- pack(t1))
(t1pu <- diagN2U(t1p))
stopifnot(exprs = {
   inherits(t1 , "dtrMatrix"); validObject(t1)
   inherits(t1p, "dtpMatrix"); validObject(t1p)
   inherits(t1pu,"dtCMatrix"); validObject(t1pu)
   t1pu@x == 1:6
   all(t1pu == t1p)
   identical((t1pu - t1)@x, numeric())# sparse all-0
})

Matrix documentation built on Aug. 13, 2024, 3:01 p.m.