The R Project SVN R-packages

#### 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)
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'
m[-(4:7), 3:4]        # dito; the upper right corner of 'm'

## rows or columns only:
m[1,]     # first row, as simple numeric vector
m[,2]     # 2nd column
m[,1:2]   # sub matrix of first two columns
m[-(1:6),, drop=FALSE] # not the first 6 rows, i.e. only the 7th
m[integer(0),] #-> 0 x 4 Matrix
m[2:4, numeric(0)] #-> 3 x 0 Matrix

## 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"]
stopifnot(identical(mn["rc", "D"], mn[3,4]), mn[3,4] == 24,
          identical(mn[, "A"], mn[,1]), mn[,1] == 1:7,
          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,]

g10 <- m [ m > 10 ]
stopifnot(18 == length(g10))
## needs R >= 2.3.0 [Buglet in R(<= 2.2.1)'s possibleExtends()]:
stopifnot(10 == length(m[ m <= 10 ]))


### 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"))
str(mT <- as(m, "dgTMatrix"))
stopifnot(identical(mT, as(mC, "dgTMatrix")),
      identical(mC, as(mT, "dgCMatrix")))

mC[,1]
mC[1:2,]
mC[7,  drop = FALSE]
assert.EQ.mat(mC[1:2,], mm[1:2,])
stopifnot(all.equal(mC[,3],   mm[,3]))
assert.EQ.mat(mC[7, , drop=FALSE], mm[7, , drop=FALSE])

stopifnot(dim(mC[numeric(0), ]) == c(0,20), # used to give warnings
          dim(mC[, integer(0)]) == c(40,0),
          identical(mC[, integer(0)], mC[, FALSE]),
          identical(mC[7,  drop = FALSE],
                    mC[7,, drop = FALSE]))
validObject(print(mT[,c(2,4)]))
stopifnot(all.equal(mT[2,], mm[2,]),
          ## row or column indexing in combination with t() :
          identical(mT[2,], t(mT)[,2]),
          identical(mT[-2,], t(t(mT)[,-2])),
          identical(mT[c(2,5),], t(t(mT)[,c(2,5)]))
          )
assert.EQ.mat(mT[4,, drop = FALSE], mm[4,, drop = FALSE])
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'
      ## TODO: identical3() with as(mC[c(3,7), 2:4],"matrix"),
          ##       fails because of 'dimnames'
          identical(mm[c(3,7), 2:4], as(mT[c(3,7), 2:4],"matrix"))
          )

x.x <- crossprod(mC)
stopifnot(class(x.x) == "dsCMatrix",
          class(x.x. <- round(x.x / 10000)) == "dsCMatrix")
head(x.x.) # Note the *non*-structural 0's printed as "0"
## FIXME (once we require 2.4.x or higher):
##  tail(x.x., -2) # the last two lines

lx.x <- as(x.x, "lsCMatrix") # FALSE only for "structural" 0
if(FALSE) { ## FIXME: needs coercion  "lsCMatrix" to "lgTMatrix"
    lx.x[1:10, 1:10]
    lx.x[1:3, ]
}

## --- negative indices ----------
mc <- mC[1:5, 1:7]
mt <- mT[1:5, 1:7]
## sub matrix
assert.EQ.mat(mC[1:2, 0:3], mm[1:2, 0:3]) # test 0-index
stopifnot(identical(mc[-(3:5), 0:2], mC[1:2, 0:2]),
          identical(mt[-(3:5), 0:2], mT[1:2, 0:2]),
          identical(mC[2:3, 4],      mm[2:3, 4]))
assert.EQ.mat(mC[1:2,], mm[1:2,])
## 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,])

## Sub *Assignment* ---- now works (partially):
mt0 <- mt
mt[1, 4] <- -99
mt[2:3, 1:6] <- 0
mt
m2 <- mt+mt
m2[1,4] <- -200
m2[c(1,3), c(5:6,2)] <- 1:6
stopifnot(m2[1,4] == -200,
          as.vector(m2[c(1,3), c(5:6,2)]) == 1:6)
mt[,3] <- 30
mt[2:3,] <- 250
mt[1:5 %% 2 == 1, 3] <- 0
mt[3:1, 1:7 > 5] <- 0
mt

tt <- as(mt,"matrix")
ii <- c(0,2,5)
jj <- c(2:3,5)
tt[ii, jj] <- 1:6 # 0 is just "dropped"
mt[ii, jj] <- 1:6
assert.EQ.mat(mt, tt)

mt[1:5, 2:6]
as((mt0 - mt)[1:5,], "dsparseMatrix")# [1,5] and lines 2:3

mt[c(2,4), ] <- 0; stopifnot(as(mt[c(2,4), ],"matrix") == 0)
mt[2:3, 4:7] <- 33
validObject(mt)
mt

mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
mc[1,4] <-  00 ; stopifnot(mc[1,4] ==  00)
mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
mc[1:2,4:3] <- 4:1; stopifnot(as.matrix(mc[1:2,4:3]) == 4:1)

mc[-1, 3] <- -2:1 # 0 should not be entered; 'value' recycled
mt[-1, 3] <- -2:1
stopifnot(mc@x != 0, mt@x != 0,
          mc[-1,3] == -2:1, mt[-1,3] == -2:1) ##--> BUG -- fixed

ev <- 1:5 %% 2 == 0
mc[ev, 3] <- 0:1
if(FALSE)## FIXME
 stopifnot(mc[ev, 3] == 0:1) ##-> BUG  {very peculiar; the 2nd time it works ...}
validObject(mc)
mc # now shows a non-structural zeros
mc[ii, jj] <- 1:6
mc[c(2,5), c(3,5)] <- 3.2
validObject(mc)
(m. <- mc)
if(FALSE)## FIXME:
 mc[4,] <- 0 # -> error -- another Bug

H <- Hilbert(9)
Hc <- as(round(H, 3), "dsCMatrix")# a sparse matrix with no 0 ...
(trH <- tril(Hc[1:5, 1:5]))
stopifnot(is(trH, "triangularMatrix"), trH@uplo == "L")

i <- c(1:2, 4, 6:7); j <- c(2:4,6)
H[i,j] <- 0
(H. <- round(as(H, "sparseMatrix"), 3)[ , 2:7])
Hc. <- Hc
Hc.[i,j] <- 0 ## now "works", but setting "non-structural" 0s
stopifnot(as.matrix(Hc.[i,j]) == 0)
Hc.[, 1:6]

cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''