R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 beta (2005-09-27 r35689)
ISBN 3-900051-07-0

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> #### For both 'Extract' ("[") and 'Replace' ("[<-") Method testing
> 
> library(Matrix)
> 
> source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
> 
> ### Dense Matrices
> 
> m <- Matrix(1:28, nrow = 7)
> validObject(m) ; m@x <- as.double(m@x) ; validObject(m)
[1] TRUE
[1] TRUE
> stopifnot(identical(m, m[]),
+           identical(m[2, 3],  16), # simple number
+           identical(m[2, 3:4], c(16,23))) # simple numeric of length 2
> 
> m[2, 3:4, drop=FALSE] # sub matrix of class 'dgeMatrix'
1 x 2 Matrix of class "dgeMatrix"
     [,1] [,2]
[1,]   16   23
> m[-(4:7), 3:4]        # dito; the upper right corner of 'm'
3 x 2 Matrix of class "dgeMatrix"
     [,1] [,2]
[1,]   15   22
[2,]   16   23
[3,]   17   24
> 
> ## rows or columns only:
> m[1,]     # first row, as simple numeric vector
[1]  1  8 15 22
> m[,2]     # 2nd column
[1]  8  9 10 11 12 13 14
> m[,1:2]   # sub matrix of first two columns
7 x 2 Matrix of class "dgeMatrix"
     [,1] [,2]
[1,]    1    8
[2,]    2    9
[3,]    3   10
[4,]    4   11
[5,]    5   12
[6,]    6   13
[7,]    7   14
> m[-(1:6),, drop=FALSE] # not the first 6 rows, i.e. only the 7th
1 x 4 Matrix of class "dgeMatrix"
     [,1] [,2] [,3] [,4]
[1,]    7   14   21   28
> 
> ## logical indexing
> stopifnot(identical(m[2,3], m[(1:nrow(m)) == 2, (1:ncol(m)) == 3]),
+           identical(m[2,], m[(1:nrow(m)) == 2, ]),
+           identical(m[,3:4], m[, (1:4) >= 3]))
> 
> ## dimnames indexing:
> mn <- m
> dimnames(mn) <- list(paste("r",letters[1:nrow(mn)],sep=""),
+                      LETTERS[1:ncol(mn)])
> mn["rd", "D"]
[1] 25
> stopifnot(identical(mn["rc", "D"], mn[3,4]),
+           identical(mn[, "A"], mn[,1]),
+           identical(mn[c("re", "rb"), "B"], mn[c(5,2), 2])
+           )
> 
> mo <- m
> m[2,3] <- 100
> m[1:2, 4] <- 200
> m[, 1] <- -1
> m[1:3,]
3 x 4 Matrix of class "dgeMatrix"
     [,1] [,2] [,3] [,4]
[1,]   -1    8   15  200
[2,]   -1    9  100  200
[3,]   -1   10   17   24
> 
> ## TODO: more --- particularly once we have "m > 10" working!
> 
> 
> ### Sparse Matrices
> 
> m <- 1:800
> set.seed(101) ; m[sample(800, 600)] <- 0
> m <- Matrix(m, nrow = 40)
> mm <- as(m, "matrix")
> dimnames(mm) <- NULL ## << workaround: as(<sparse>, "matrix") has NULL dimnames
> str(mC <- as(m, "dgCMatrix"))
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
  ..@ p       : int [1:21] 0 8 22 28 37 41 50 63 71 81 ...
  ..@ Dim     : int [1:2] 40 20
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ factors : list()
  ..@ x       : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
> str(mT <- as(m, "dgTMatrix"))
Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:200] 2 6 11 21 24 29 37 38 1 4 ...
  ..@ j       : int [1:200] 0 0 0 0 0 0 0 0 1 1 ...
  ..@ Dim     : int [1:2] 40 20
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ factors : list()
  ..@ x       : num [1:200] 3 7 12 22 25 30 38 39 42 45 ...
> stopifnot(identical(mT, as(mC, "dgTMatrix")),
+ 	  identical(mC, as(mT, "dgCMatrix")))
> 
> mC[,1]
 [1]  0  0  3  0  0  0  7  0  0  0  0 12  0  0  0  0  0  0  0  0  0 22  0  0 25
[26]  0  0  0  0 30  0  0  0  0  0  0  0 38 39  0
> mC[1:2,]
2 x 20 sparse Matrix of class "dgCMatrix"
                                                               
[1,] . .  . 121 . .   241 . . . . 441 .   .   561 . 641 . .   .
[2,] . 42 . .   . 202 .   . . . . .   482 522 .   . .   . 722 .
> mC[7,  drop = FALSE]
1 x 20 sparse Matrix of class "dgCMatrix"
                                                      
[1,] 7 . . . . . . 287 . . 407 . 487 527 . . . . 727 .
> stopifnot(identical(mC[7,  drop = FALSE],
+                     mC[7,, drop = FALSE]))
> mT[,c(2,4)]
40 x 2 sparse Matrix of class "dgTMatrix"
            
 [1,] .  121
 [2,] 42 .  
 [3,] .  .  
 [4,] .  .  
 [5,] 45 .  
 [6,] .  .  
 [7,] .  .  
 [8,] .  128
 [9,] .  129
[10,] 50 .  
[11,] .  .  
[12,] 52 132
[13,] .  133
[14,] .  .  
[15,] 55 .  
[16,] .  .  
[17,] .  .  
[18,] .  138
[19,] .  .  
[20,] .  .  
[21,] .  141
[22,] .  142
[23,] 63 .  
[24,] .  .  
[25,] 65 .  
[26,] .  .  
[27,] 67 .  
[28,] 68 .  
[29,] .  .  
[30,] .  .  
[31,] 71 .  
[32,] 72 .  
[33,] .  .  
[34,] 74 .  
[35,] .  .  
[36,] 76 .  
[37,] .  .  
[38,] .  .  
[39,] .  159
[40,] 80 .  
> mT[1,]
 [1]   0   0   0 121   0   0 241   0   0   0   0 441   0   0 561   0 641   0   0
[20]   0
> mT[4, drop = FALSE]
1 x 20 sparse Matrix of class "dgTMatrix"
                                                      
[1,] . . . . . . . . 324 . . . 484 524 564 . . . . 764
> stopifnot(identical3(mm[,1], mC[,1], mT[,1]),
+ 	  identical3(mm[3,], mC[3,], mT[3,]),
+ 	  identical3(mT[2,3], mC[2,3], 0),
+ 	  identical(mT[], mT),
+ 	  ## TODO: identical4() with  m[c(3,7), 2:4] - fail because of 'dimnames'
+ 	  identical3(as(mC[c(3,7), 2:4],"matrix"), mm[c(3,7), 2:4],
+ 		     as(mT[c(3,7), 2:4],"matrix")))
> 
> ## --- negative indices ----------
> mc <- mC[1:5, 1:7]
> mt <- mT[1:5, 1:7]
> ## sub matrix
> stopifnot(identical(mc[-(3:5), 0:2], mC[1:2, 0:2]),
+           identical(mt[-(3:5), 0:2], mT[1:2, 0:2]))
> ## sub vector
> stopifnot(identical4(mc[-(1:4), ], mC[5, 1:7],
+                      mt[-(1:4), ], mT[5, 1:7]))
> stopifnot(identical4(mc[-(1:4), -(2:4)], mC[5, c(1,5:7)],
+                      mt[-(1:4), -(2:4)], mT[5, c(1,5:7)]))
> 
> ## mixing of negative and positive must give error
> assertError(mT[-1:1,])
> 
> ## At least these now give a nicely understandable error:
> try(mT[1, 4] <- -99)
Error in "[<-"(`*tmp*`, 1, 4, value = -99) : 
	not-yet-implemented 'Matrix[<-' method
> try(mT[2:3, ] <- 0)
Error in "[<-"(`*tmp*`, 2:3, , value = 0) : 
	not-yet-implemented 'Matrix[<-' method
>