Coerce a matrix-like objects to dgCMatrix (sparse matrix)

Source: R/misc.r

This helper function allows easy coercion to sparse matrix objects from the Matrix package, dgCMatrix.

as_dgCMatrix(x, make.dimnames = TRUE, ...)

as.dgCMatrix(x, make.dimnames = TRUE, ...)

as_spmat(x, make.dimnames = TRUE, ...)

# Default S3 method
as_dgCMatrix(x, make.dimnames = TRUE, ...)

# S3 method for class 'diffnet'
as_dgCMatrix(x, make.dimnames = TRUE, ...)

# S3 method for class 'array'
as_dgCMatrix(x, make.dimnames = TRUE, ...)

# S3 method for class 'igraph'
as_dgCMatrix(x, make.dimnames = TRUE, ...)

# S3 method for class 'network'
as_dgCMatrix(x, make.dimnames = TRUE, ...)

# S3 method for class 'list'
as_dgCMatrix(x, make.dimnames = TRUE, ...)

Arguments

x

An object to be coerced into a sparse matrix.

make.dimnames

Logical scalar. When TRUE, it makes sure that the returned object has dimnames.

...

Further arguments passed to the method.

Value

Either a list with dgCMatrix objects or a dgCMatrix object.

Details

In the case of the igraph and network methods, ... is passed to as_adj and as.matrix.network respectively.

Examples


set.seed(1231)
x <- rgraph_er(10)

# From matrix object
as_dgCMatrix(as.matrix(x))
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘1’, ‘2’, ‘3’ ... ]]
#>                       
#> 1  . . . . . . . . . .
#> 2  . . . . . . . . . .
#> 3  . . . . . . . . . .
#> 4  . . . . . . . . . .
#> 5  . . . . . . . . . .
#> 6  . . . . . . . . . .
#> 7  . . . . . . . . . .
#> 8  . . . . . . . . . .
#> 9  . . . . . . . . . .
#> 10 . . . . 1 . . . . .

# From a network object
as_dgCMatrix(network::as.network(as.matrix(x)))
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘1’, ‘2’, ‘3’ ... ]]
#>                       
#> 1  . . . . . . . . . .
#> 2  . . . . . . . . . .
#> 3  . . . . . . . . . .
#> 4  . . . . . . . . . .
#> 5  . . . . . . . . . .
#> 6  . . . . . . . . . .
#> 7  . . . . . . . . . .
#> 8  . . . . . . . . . .
#> 9  . . . . . . . . . .
#> 10 . . . . 1 . . . . .

# From igraph object
as_dgCMatrix(igraph::graph_from_adjacency_matrix(x))
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘1’, ‘2’, ‘3’ ... ]]
#>                       
#> 1  . . . . . . . . . .
#> 2  . . . . . . . . . .
#> 3  . . . . . . . . . .
#> 4  . . . . . . . . . .
#> 5  . . . . . . . . . .
#> 6  . . . . . . . . . .
#> 7  . . . . . . . . . .
#> 8  . . . . . . . . . .
#> 9  . . . . . . . . . .
#> 10 . . . . 1 . . . . .

# From array
myarray <- array(dim=c(10,10,2))
myarray[,,1] <- as.matrix(x)
myarray[,,2] <- as.matrix(x)

myarray
#> , , 1
#> 
#>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#>  [1,]    0    0    0    0    0    0    0    0    0     0
#>  [2,]    0    0    0    0    0    0    0    0    0     0
#>  [3,]    0    0    0    0    0    0    0    0    0     0
#>  [4,]    0    0    0    0    0    0    0    0    0     0
#>  [5,]    0    0    0    0    0    0    0    0    0     0
#>  [6,]    0    0    0    0    0    0    0    0    0     0
#>  [7,]    0    0    0    0    0    0    0    0    0     0
#>  [8,]    0    0    0    0    0    0    0    0    0     0
#>  [9,]    0    0    0    0    0    0    0    0    0     0
#> [10,]    0    0    0    0    1    0    0    0    0     0
#> 
#> , , 2
#> 
#>       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#>  [1,]    0    0    0    0    0    0    0    0    0     0
#>  [2,]    0    0    0    0    0    0    0    0    0     0
#>  [3,]    0    0    0    0    0    0    0    0    0     0
#>  [4,]    0    0    0    0    0    0    0    0    0     0
#>  [5,]    0    0    0    0    0    0    0    0    0     0
#>  [6,]    0    0    0    0    0    0    0    0    0     0
#>  [7,]    0    0    0    0    0    0    0    0    0     0
#>  [8,]    0    0    0    0    0    0    0    0    0     0
#>  [9,]    0    0    0    0    0    0    0    0    0     0
#> [10,]    0    0    0    0    1    0    0    0    0     0
#> 
as_dgCMatrix(myarray)
#> $`1`
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘1’, ‘2’, ‘3’ ... ]]
#>                       
#> 1  . . . . . . . . . .
#> 2  . . . . . . . . . .
#> 3  . . . . . . . . . .
#> 4  . . . . . . . . . .
#> 5  . . . . . . . . . .
#> 6  . . . . . . . . . .
#> 7  . . . . . . . . . .
#> 8  . . . . . . . . . .
#> 9  . . . . . . . . . .
#> 10 . . . . 1 . . . . .
#> 
#> $`2`
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘1’, ‘2’, ‘3’ ... ]]
#>                       
#> 1  . . . . . . . . . .
#> 2  . . . . . . . . . .
#> 3  . . . . . . . . . .
#> 4  . . . . . . . . . .
#> 5  . . . . . . . . . .
#> 6  . . . . . . . . . .
#> 7  . . . . . . . . . .
#> 8  . . . . . . . . . .
#> 9  . . . . . . . . . .
#> 10 . . . . 1 . . . . .
#> 

# From a diffnet object
ans <- as_dgCMatrix(medInnovationsDiffNet)
str(ans)
#> List of 18
#>  $ 1 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 2 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 3 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 4 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 5 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 6 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 7 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 8 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 9 :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 10:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 11:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 12:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 13:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 14:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 15:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 16:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 17:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()
#>  $ 18:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:294] 47 8 13 15 28 32 34 32 37 9 ...
#>   .. ..@ p       : int [1:126] 0 1 1 7 9 12 12 14 15 15 ...
#>   .. ..@ Dim     : int [1:2] 125 125
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. .. ..$ : chr [1:125] "1001" "1002" "1003" "1004" ...
#>   .. ..@ x       : num [1:294] 2 1 1 1 1 1 3 1 2 1 ...
#>   .. ..@ factors : list()