Standardize a Sparse Matrix in Triplet Format

Detect or standardize a TsparseMatrix with unsorted or duplicated \((i,j)\) pairs.

anyDuplicatedT(x, ...)
isUniqueT(x, byrow = FALSE, isT = is(x, "TsparseMatrix"))
asUniqueT(x, byrow = FALSE, isT = is(x, "TsparseMatrix"))
aggregateT(x)

Arguments

x

an R object. anyDuplicatedT and aggregateT require x inheriting from TsparseMatrix. asUniqueT requires x inheriting from Matrix and coerces x to TsparseMatrix if necessary.

...

optional arguments passed to the default method for generic function anyDuplicated.

byrow

a logical indicating if x should be sorted by row then by column.

isT

a logical indicating if x inherits from virtual class TsparseMatrix.

Value

anyDuplicatedT(x) returns the index of the first duplicated \((i,j)\) pair in x (0 if there are no duplicated pairs).

isUniqueT(x) returns TRUE if x is a TsparseMatrix with sorted, nonduplicated \((i,j)\) pairs and FALSE otherwise.

asUniqueT(x) returns the unique TsparseMatrix representation of x with sorted, nonduplicated \((i,j)\) pairs. Values corresponding to identical \((i,j)\) pairs are aggregated by addition, where in the logical case “addition” refers to logical OR.

aggregateT(x) aggregates without sorting.

See also

Virtual class TsparseMatrix.

Examples

example("dgTMatrix-class", echo=FALSE)
#> Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
#>   ..@ i       : int [1:9] 0 1 3 0 1 3 2 3 2
#>   ..@ j       : int [1:9] 0 0 0 2 2 2 4 5 6
#>   ..@ Dim     : int [1:2] 4 7
#>   ..@ Dimnames:List of 2
#>   .. ..$ : NULL
#>   .. ..$ : NULL
#>   ..@ x       : num [1:9] 1 2 4 9 10 12 19 24 27
#>   ..@ factors : list()
#> Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
#>   ..@ i       : int [1:5] 1 1 0 3 3
#>   ..@ j       : int [1:5] 2 2 4 0 0
#>   ..@ Dim     : int [1:2] 4 5
#>   ..@ Dimnames:List of 2
#>   .. ..$ : NULL
#>   .. ..$ : NULL
#>   ..@ x       : num [1:5] 10 20 30 40 50
#>   ..@ factors : list()
## -> 'T2'  with (i,j,x) slots of length 5 each
T2u <- asUniqueT(T2)
stopifnot(## They "are" the same (and print the same):
          all.equal(T2, T2u, tol=0),
          ## but not internally:
          anyDuplicatedT(T2)  == 2,
          anyDuplicatedT(T2u) == 0,
          length(T2 @x) == 5,
          length(T2u@x) == 3)

isUniqueT(T2 ) # FALSE
#> [1] FALSE
isUniqueT(T2u) # TRUE
#> [1] TRUE

T3 <- T2u
T3[1, c(1,3)] <- 10; T3[2, c(1,5)] <- 20
T3u <- asUniqueT(T3)
str(T3u) # sorted in 'j', and within j, sorted in i
#> Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
#>   ..@ i       : int [1:7] 0 1 3 0 1 0 1
#>   ..@ j       : int [1:7] 0 0 0 2 2 4 4
#>   ..@ Dim     : int [1:2] 4 5
#>   ..@ Dimnames:List of 2
#>   .. ..$ : NULL
#>   .. ..$ : NULL
#>   ..@ x       : num [1:7] 10 20 90 10 30 30 20
#>   ..@ factors : list()
stopifnot(isUniqueT(T3u))

## Logical l.TMatrix and n.TMatrix :
(L2 <- T2 > 0)
#> 4 x 5 sparse Matrix of class "lgTMatrix"
#>               
#> [1,] . . . . |
#> [2,] . . | . .
#> [3,] . . . . .
#> [4,] | . . . .
validObject(L2u <- asUniqueT(L2))
#> [1] TRUE
(N2 <- as(L2, "nMatrix"))
#> 4 x 5 sparse Matrix of class "ngTMatrix"
#>               
#> [1,] . . . . |
#> [2,] . . | . .
#> [3,] . . . . .
#> [4,] | . . . .
validObject(N2u <- asUniqueT(N2))
#> [1] TRUE
stopifnot(N2u@i == L2u@i, L2u@i == T2u@i,  N2@i == L2@i, L2@i == T2@i,
          N2u@j == L2u@j, L2u@j == T2u@j,  N2@j == L2@j, L2@j == T2@j)
# now with a nasty NA  [partly failed in Matrix 1.1-5]:
L.0N <- L.1N <- L2
L.0N@x[1:2] <- c(FALSE, NA)
L.1N@x[1:2] <- c(TRUE, NA)
validObject(L.0N)
#> [1] TRUE
validObject(L.1N)
#> [1] TRUE
(m.0N <- as.matrix(L.0N))
#>       [,1]  [,2]  [,3]  [,4]  [,5]
#> [1,] FALSE FALSE FALSE FALSE  TRUE
#> [2,] FALSE FALSE    NA FALSE FALSE
#> [3,] FALSE FALSE FALSE FALSE FALSE
#> [4,]  TRUE FALSE FALSE FALSE FALSE
(m.1N <- as.matrix(L.1N))
#>       [,1]  [,2]  [,3]  [,4]  [,5]
#> [1,] FALSE FALSE FALSE FALSE  TRUE
#> [2,] FALSE FALSE  TRUE FALSE FALSE
#> [3,] FALSE FALSE FALSE FALSE FALSE
#> [4,]  TRUE FALSE FALSE FALSE FALSE
stopifnot(identical(10L, which(is.na(m.0N))), !anyNA(m.1N))
symnum(m.0N)
#>               
#> [1,] . . . . |
#> [2,] . . ? . .
#> [3,] . . . . .
#> [4,] | . . . .
symnum(m.1N)
#>               
#> [1,] . . . . |
#> [2,] . . | . .
#> [3,] . . . . .
#> [4,] | . . . .