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[matrix] Annotation of /pkg/tests/indexing.R
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Annotation of /pkg/tests/indexing.R

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1 : maechler 1710 ## For both 'Extract' ("[") and 'Replace' ("[<-") Method testing
2 : maechler 687
3 :     library(Matrix)
4 :    
5 : maechler 907 source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
6 : maechler 687
7 : maechler 873 ### Dense Matrices
8 :    
9 : maechler 1673 m <- Matrix(1:28 +0, nrow = 7)
10 :     validObject(m)
11 : maechler 873 stopifnot(identical(m, m[]),
12 :     identical(m[2, 3], 16), # simple number
13 :     identical(m[2, 3:4], c(16,23))) # simple numeric of length 2
14 : maechler 687
15 : maechler 873 m[2, 3:4, drop=FALSE] # sub matrix of class 'dgeMatrix'
16 :     m[-(4:7), 3:4] # dito; the upper right corner of 'm'
17 : maechler 687
18 : maechler 873 ## rows or columns only:
19 :     m[1,] # first row, as simple numeric vector
20 :     m[,2] # 2nd column
21 :     m[,1:2] # sub matrix of first two columns
22 :     m[-(1:6),, drop=FALSE] # not the first 6 rows, i.e. only the 7th
23 : maechler 1331 m[integer(0),] #-> 0 x 4 Matrix
24 :     m[2:4, numeric(0)] #-> 3 x 0 Matrix
25 : maechler 687
26 : maechler 873 ## logical indexing
27 :     stopifnot(identical(m[2,3], m[(1:nrow(m)) == 2, (1:ncol(m)) == 3]),
28 :     identical(m[2,], m[(1:nrow(m)) == 2, ]),
29 :     identical(m[,3:4], m[, (1:4) >= 3]))
30 :    
31 : maechler 886 ## dimnames indexing:
32 :     mn <- m
33 :     dimnames(mn) <- list(paste("r",letters[1:nrow(mn)],sep=""),
34 :     LETTERS[1:ncol(mn)])
35 :     mn["rd", "D"]
36 : maechler 1226 stopifnot(identical(mn["rc", "D"], mn[3,4]), mn[3,4] == 24,
37 :     identical(mn[, "A"], mn[,1]), mn[,1] == 1:7,
38 : maechler 886 identical(mn[c("re", "rb"), "B"], mn[c(5,2), 2])
39 :     )
40 : maechler 873
41 : maechler 886 mo <- m
42 :     m[2,3] <- 100
43 :     m[1:2, 4] <- 200
44 :     m[, 1] <- -1
45 :     m[1:3,]
46 :    
47 : maechler 1673 m. <- as.matrix(m)
48 :    
49 :     ## m[ cbind(i,j) ] indexing:
50 :     ij <- cbind(1:6, 2:3)
51 :     stopifnot(identical(m[ij], m.[ij]))
52 :    
53 : maechler 1599 ## testing operations on logical Matrices rather more than indexing:
54 : maechler 1226 g10 <- m [ m > 10 ]
55 :     stopifnot(18 == length(g10))
56 : maechler 1362 stopifnot(10 == length(m[ m <= 10 ]))
57 : maechler 1599 sel <- (20 < m) & (m < 150)
58 : maechler 1655 sel.<- (20 < m.)& (m.< 150)
59 : maechler 1599 nsel <-(20 >= m) | (m >= 150)
60 : maechler 1575 (ssel <- as(sel, "sparseMatrix"))
61 :     stopifnot(is(sel, "lMatrix"), is(ssel, "lsparseMatrix"),
62 : maechler 1655 identical3(as.mat(sel.), as.mat(sel), as.mat(ssel)),
63 :     identical3(!sel, !ssel, nsel), # !<sparse> is typically dense
64 : maechler 1599 identical3(m[ sel], m[ ssel], as.matrix(m)[as.matrix( ssel)]),
65 :     identical3(m[!sel], m[!ssel], as.matrix(m)[as.matrix(!ssel)])
66 : maechler 1575 )
67 : maechler 873
68 : maechler 1575 ## more sparse Matrices --------------------------------------
69 : maechler 873
70 : maechler 687 m <- 1:800
71 :     set.seed(101) ; m[sample(800, 600)] <- 0
72 :     m <- Matrix(m, nrow = 40)
73 :     mm <- as(m, "matrix")
74 :     dimnames(mm) <- NULL ## << workaround: as(<sparse>, "matrix") has NULL dimnames
75 :     str(mC <- as(m, "dgCMatrix"))
76 :     str(mT <- as(m, "dgTMatrix"))
77 :     stopifnot(identical(mT, as(mC, "dgTMatrix")),
78 :     identical(mC, as(mT, "dgCMatrix")))
79 :    
80 :     mC[,1]
81 :     mC[1:2,]
82 : maechler 925 mC[7, drop = FALSE]
83 : maechler 1226 assert.EQ.mat(mC[1:2,], mm[1:2,])
84 : maechler 1799
85 :     ## *repeated* indices - did not work at all ...
86 :     i <- rep(8:10,2)
87 :     j <- c(2:4, 4:3)
88 :     assert.EQ.mat(mC[i,], mm[i,])
89 :     assert.EQ.mat(mC[,j], mm[,j])
90 :     if(FALSE) ## FIXME
91 :     assert.EQ.mat(mC[i,j], mm[i,j])
92 :    
93 : maechler 1673 stopifnot(all.equal(mC[,3], mm[,3]),
94 :     identical(mC[ij], mm[ij]))
95 : maechler 1226 assert.EQ.mat(mC[7, , drop=FALSE], mm[7, , drop=FALSE])
96 :    
97 : maechler 1331 stopifnot(dim(mC[numeric(0), ]) == c(0,20), # used to give warnings
98 :     dim(mC[, integer(0)]) == c(40,0),
99 :     identical(mC[, integer(0)], mC[, FALSE]),
100 :     identical(mC[7, drop = FALSE],
101 : maechler 925 mC[7,, drop = FALSE]))
102 : maechler 1269 validObject(print(mT[,c(2,4)]))
103 :     stopifnot(all.equal(mT[2,], mm[2,]),
104 :     ## row or column indexing in combination with t() :
105 :     identical(mT[2,], t(mT)[,2]),
106 :     identical(mT[-2,], t(t(mT)[,-2])),
107 :     identical(mT[c(2,5),], t(t(mT)[,c(2,5)]))
108 :     )
109 : maechler 1226 assert.EQ.mat(mT[4,, drop = FALSE], mm[4,, drop = FALSE])
110 : maechler 687 stopifnot(identical3(mm[,1], mC[,1], mT[,1]),
111 :     identical3(mm[3,], mC[3,], mT[3,]),
112 :     identical3(mT[2,3], mC[2,3], 0),
113 :     identical(mT[], mT),
114 : maechler 1665 identical4( mm[c(3,7), 2:4], as.mat( m[c(3,7), 2:4]),
115 :     as.mat(mT[c(3,7), 2:4]), as.mat(mC[c(3,7), 2:4]))
116 : bates 1367 )
117 : maechler 687
118 : maechler 1331 x.x <- crossprod(mC)
119 :     stopifnot(class(x.x) == "dsCMatrix",
120 : maechler 1673 class(x.x. <- round(x.x / 10000)) == "dsCMatrix",
121 :     identical(x.x[cbind(2:6, 2:6)],
122 :     diag(x.x [2:6, 2:6])))
123 : maechler 1331 head(x.x.) # Note the *non*-structural 0's printed as "0"
124 : maechler 1575 tail(x.x., -3) # all but the first three lines
125 : maechler 1331
126 :     lx.x <- as(x.x, "lsCMatrix") # FALSE only for "structural" 0
127 : maechler 1665 (l10 <- lx.x[1:10, 1:10])# "lsC"
128 :     (l3 <- lx.x[1:3, ])
129 :     m.x <- as(x.x, "matrix")
130 :     stopifnot(class(l10) == "lsCMatrix", # symmetric indexing -> symmetric !
131 :     identical(as.mat(lx.x), m.x != 0),
132 :     identical(as.logical(lx.x), as.logical(m.x)),
133 :     identical(as.mat(l10), m.x[1:10, 1:10] != 0),
134 :     identical(as.mat(l3 ), m.x[1:3, ] != 0)
135 :     )
136 : maechler 1331
137 : maechler 1705 ## used to fail
138 :     n <- 5 ## or much larger
139 :     sm <- new("dsTMatrix", i=as.integer(1),j=as.integer(1),
140 :     Dim=as.integer(c(n,n)), x = 1)
141 :     (cm <- as(sm, "CsparseMatrix"))
142 :     sm[2,]
143 :     stopifnot(sm[2,] == c(0:1, rep.int(0,ncol(sm)-2)),
144 :     sm[2,] == cm[2,],
145 :     sm[,3] == sm[3,],
146 :     all(sm[,-(1:3)] == t(sm[-(1:3),])), # all(<lge.>)
147 :     all(sm[,-(1:3)] == 0)
148 :     )
149 : maechler 1665
150 : maechler 1710 ### Diagonal -- Sparse:
151 :     m0 <- Diagonal(5)
152 :     (m1 <- as(m0, "sparseMatrix")) # dtTMatrix
153 :     (m2 <- as(m0, "CsparseMatrix")) # dtCMatrix (with an irrelevant warning)
154 : maechler 1799 m1g <- as(m1, "generalMatrix")
155 :     stopifnot(is(m1g, "dgTMatrix"))
156 :     assert.EQ.mat(m2[1:3,], diag(5)[1:3,])
157 :     assert.EQ.mat(m2[,c(4,1)], diag(5)[,c(4,1)])
158 :     stopifnot(identical(m2[1:3,], as(m1[1:3,], "CsparseMatrix")),
159 :     identical(Matrix:::uniqTsparse(m1[, c(4,2)]),
160 :     Matrix:::uniqTsparse(as(m2[, c(4,2)], "TsparseMatrix")))
161 :     )## failed in 0.9975-11
162 : maechler 1705
163 : maechler 1710 M <- m0; M[1,] <- 0
164 :     stopifnot(identical(M, Diagonal(x=c(0, rep(1,4)))))
165 :     M <- m0; M[,3] <- 3 ; M ; stopifnot(is(M, "sparseMatrix"), M[,3] == 3)
166 :     validObject(M)
167 :     M <- m0; M[1:3, 3] <- 0 ;M
168 :     T <- m0; T[1:3, 3] <- 10
169 :     stopifnot(identical(M, Diagonal(x=c(1,1, 0, 1,1))),
170 :     is(T, "triangularMatrix"), identical(T[,3], c(10,10,10,0,0)))
171 :    
172 :     M <- m1; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
173 :     M <- m1; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
174 :     validObject(M)
175 :     M <- m1; M[1:3, 3] <- 0 ;M
176 :     assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
177 :     T <- m1; T[1:3, 3] <- 10; validObject(T)
178 :     stopifnot(is(T, "dtTMatrix"), identical(T[,3], c(10,10,10,0,0)))
179 :    
180 :     M <- m2; M[1,] <- 0 ; M ; assert.EQ.mat(M, diag(c(0,rep(1,4))), tol=0)
181 :     M <- m2; M[,3] <- 3 ; stopifnot(is(M,"sparseMatrix"), M[,3] == 3)
182 :     validObject(M)
183 :     M <- m2; M[1:3, 3] <- 0 ;M
184 :     assert.EQ.mat(M, diag(c(1,1, 0, 1,1)), tol=0)
185 :     T <- m2; T[1:3, 3] <- 10; validObject(T)
186 :     stopifnot(is(T, "dtCMatrix"), identical(T[,3], c(10,10,10,0,0)))
187 :    
188 :    
189 : maechler 925 ## --- negative indices ----------
190 :     mc <- mC[1:5, 1:7]
191 :     mt <- mT[1:5, 1:7]
192 :     ## sub matrix
193 : maechler 1226 assert.EQ.mat(mC[1:2, 0:3], mm[1:2, 0:3]) # test 0-index
194 : maechler 925 stopifnot(identical(mc[-(3:5), 0:2], mC[1:2, 0:2]),
195 : maechler 1226 identical(mt[-(3:5), 0:2], mT[1:2, 0:2]),
196 :     identical(mC[2:3, 4], mm[2:3, 4]))
197 :     assert.EQ.mat(mC[1:2,], mm[1:2,])
198 : maechler 925 ## sub vector
199 :     stopifnot(identical4(mc[-(1:4), ], mC[5, 1:7],
200 :     mt[-(1:4), ], mT[5, 1:7]))
201 :     stopifnot(identical4(mc[-(1:4), -(2:4)], mC[5, c(1,5:7)],
202 :     mt[-(1:4), -(2:4)], mT[5, c(1,5:7)]))
203 :    
204 :     ## mixing of negative and positive must give error
205 :     assertError(mT[-1:1,])
206 :    
207 : maechler 1226 ## Sub *Assignment* ---- now works (partially):
208 :     mt0 <- mt
209 :     mt[1, 4] <- -99
210 :     mt[2:3, 1:6] <- 0
211 :     mt
212 :     m2 <- mt+mt
213 :     m2[1,4] <- -200
214 :     m2[c(1,3), c(5:6,2)] <- 1:6
215 :     stopifnot(m2[1,4] == -200,
216 :     as.vector(m2[c(1,3), c(5:6,2)]) == 1:6)
217 :     mt[,3] <- 30
218 :     mt[2:3,] <- 250
219 :     mt[1:5 %% 2 == 1, 3] <- 0
220 :     mt[3:1, 1:7 > 5] <- 0
221 :     mt
222 : maechler 1215
223 : maechler 1226 tt <- as(mt,"matrix")
224 :     ii <- c(0,2,5)
225 :     jj <- c(2:3,5)
226 :     tt[ii, jj] <- 1:6 # 0 is just "dropped"
227 :     mt[ii, jj] <- 1:6
228 :     assert.EQ.mat(mt, tt)
229 : maechler 1215
230 : maechler 1226 mt[1:5, 2:6]
231 :     as((mt0 - mt)[1:5,], "dsparseMatrix")# [1,5] and lines 2:3
232 :    
233 : maechler 1315 mt[c(2,4), ] <- 0; stopifnot(as(mt[c(2,4), ],"matrix") == 0)
234 : maechler 1226 mt[2:3, 4:7] <- 33
235 :     validObject(mt)
236 :     mt
237 :    
238 : maechler 1315 mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
239 :     mc[1,4] <- 00 ; stopifnot(mc[1,4] == 00)
240 :     mc[1,4] <- -99 ; stopifnot(mc[1,4] == -99)
241 :     mc[1:2,4:3] <- 4:1; stopifnot(as.matrix(mc[1:2,4:3]) == 4:1)
242 :    
243 : maechler 1226 mc[-1, 3] <- -2:1 # 0 should not be entered; 'value' recycled
244 :     mt[-1, 3] <- -2:1
245 : maechler 1315 stopifnot(mc@x != 0, mt@x != 0,
246 : maechler 1707 mc[-1,3] == -2:1, mt[-1,3] == -2:1) ## failed earlier
247 : maechler 1315
248 : maechler 1707 mc0 <- mc
249 : maechler 1724 mt0 <- as(mc0, "TsparseMatrix")
250 :     m0 <- as(mc0, "matrix")
251 : maechler 1707 set.seed(1)
252 : maechler 1724 for(i in 1:50) {
253 :     mc <- mc0; mt <- mt0 ; m <- m0
254 : maechler 1707 ev <- 1:5 %% 2 == round(runif(1))# 0 or 1
255 :     j <- sample(ncol(mc), 1 + round(runif(1)))
256 :     nv <- rpois(sum(ev) * length(j), lambda = 1)
257 :     mc[ev, j] <- nv
258 : maechler 1724 m[ev, j] <- nv
259 :     mt[ev, j] <- nv
260 :     if(i %% 10 == 1) print(mc[ev,j, drop = FALSE])
261 :     stopifnot(as.vector(mc[ev, j]) == nv, ## failed earlier...
262 :     as.vector(mt[ev, j]) == nv)
263 :     validObject(mc) ; assert.EQ.mat(mc, m)
264 :     validObject(mt) ; assert.EQ.mat(mt, m)
265 : maechler 1707 }
266 :    
267 :     mc # no longer has non-structural zeros
268 : maechler 1226 mc[ii, jj] <- 1:6
269 :     mc[c(2,5), c(3,5)] <- 3.2
270 :     validObject(mc)
271 : maechler 1600 m. <- mc
272 :     mc[4,] <- 0
273 :     mc
274 : maechler 1226
275 : maechler 1331 H <- Hilbert(9)
276 : maechler 1374 Hc <- as(round(H, 3), "dsCMatrix")# a sparse matrix with no 0 ...
277 :     (trH <- tril(Hc[1:5, 1:5]))
278 :     stopifnot(is(trH, "triangularMatrix"), trH@uplo == "L")
279 : maechler 1331
280 : maechler 1374 i <- c(1:2, 4, 6:7); j <- c(2:4,6)
281 :     H[i,j] <- 0
282 : maechler 1331 (H. <- round(as(H, "sparseMatrix"), 3)[ , 2:7])
283 :     Hc. <- Hc
284 : maechler 1374 Hc.[i,j] <- 0 ## now "works", but setting "non-structural" 0s
285 :     stopifnot(as.matrix(Hc.[i,j]) == 0)
286 : maechler 1331 Hc.[, 1:6]
287 :    
288 : maechler 1724 ## an example that failed for a long time
289 : maechler 1673 sy3 <- new("dsyMatrix", Dim = as.integer(c(2, 2)), x = c(14, -1, 2, -7))
290 : maechler 1825 validObject(dm <- kronecker(Diagonal(2), sy3))# now sparse with new kronecker
291 :     dm <- Matrix(as.matrix(dm))# -> "dsyMatrix"
292 : maechler 1673 (s2 <- as(dm, "sparseMatrix"))
293 :     validObject(st <- as(s2, "TsparseMatrix"))
294 : maechler 1725 stopifnot(is(s2, "symmetricMatrix"),
295 :     is(st, "symmetricMatrix"))
296 : maechler 1673 validObject(s.32 <- st[1:3,1:2]) ## 3 x 2 - and *not* dsTMatrix
297 :     validObject(s2.32 <- s2[1:3,1:2])
298 :     I <- c(1,4:3)
299 :     stopifnot(is(s2.32, "generalMatrix"),
300 :     is(s.32, "generalMatrix"),
301 :     identical(as.mat(s.32), as.mat(s2.32)),
302 :     identical3(dm[1:3,-1], asD(s2[1:3,-1]), asD(st[1:3,-1])),
303 :     identical4(2, dm[4,3], s2[4,3], st[4,3]),
304 :     identical3(diag(dm), diag(s2), diag(st)),
305 :     is((cI <- s2[I,I]), "dsCMatrix"),
306 :     is((tI <- st[I,I]), "dsTMatrix"),
307 :     identical4(as.mat(dm)[I,I], as.mat(dm[I,I]), as.mat(tI), as.mat(cI))
308 :     )
309 :    
310 :     ## now sub-assign and check for consistency
311 :     ## symmetric subassign should keep symmetry
312 :     st[I,I] <- 0; validObject(st); stopifnot(is(st,"symmetricMatrix"))
313 :     s2[I,I] <- 0; validObject(s2); stopifnot(is(s2,"symmetricMatrix"))
314 : maechler 1724 ##
315 : maechler 1673 m <- as.mat(st)
316 :     m[2:1,2:1] <- 4:1
317 :     st[2:1,2:1] <- 4:1
318 :     s2[2:1,2:1] <- 4:1
319 :     stopifnot(identical(m, as.mat(st)),
320 :     1:4 == as.vector(s2[1:2,1:2]),
321 :     identical(m, as.mat(s2)))
322 :    
323 : maechler 1724 ## now a slightly different situation for 's2' (had bug)
324 :     s2 <- as(dm, "sparseMatrix")
325 :     s2[I,I] <- 0; diag(s2)[2:3] <- -(1:2)
326 :     stopifnot(is(s2,"symmetricMatrix"), diag(s2) == c(0:-2,0))
327 :     t2 <- as(s2, "TsparseMatrix")
328 :     m <- as.mat(s2)
329 :     s2[2:1,2:1] <- 4:1
330 :     t2[2:1,2:1] <- 4:1
331 :     m[2:1,2:1] <- 4:1
332 :     assert.EQ.mat(t2, m)
333 :     assert.EQ.mat(s2, m)
334 :     ## and the same (for a different s2 !)
335 :     s2[2:1,2:1] <- 4:1
336 :     t2[2:1,2:1] <- 4:1
337 :     assert.EQ.mat(t2, m)# ok
338 :     assert.EQ.mat(s2, m)# failed in 0.9975-8
339 :    
340 :    
341 : maechler 1673 ## m[cbind(i,j)] <- value:
342 :     m.[ cbind(3:5, 1:3) ] <- 1:3
343 :     stopifnot(m.[3,1] == 1, m.[4,2] == 2)
344 :     x.x[ cbind(2:6, 2:6)] <- 12:16
345 :     validObject(x.x)
346 :     stopifnot(class(x.x) == "dsCMatrix",
347 :     12:16 == as.mat(x.x)[cbind(2:6, 2:6)])
348 : maechler 1725 (ne1 <- (mc - m.) != 0)
349 :     stopifnot(identical(ne1, 0 != abs(mc - m.)))
350 :     (ge <- m. >= mc) # contains "=" -> result is dense
351 :     ne. <- mc != m. # was wrong (+ warning)
352 :     stopifnot(identical(!(m. < mc), m. >= mc),
353 :     identical(m. < mc, as(!ge, "sparseMatrix")),
354 :     identical(ne., Matrix:::drop0(ne1)))
355 : maechler 1673
356 : maechler 1751 (M3 <- Matrix(upper.tri(matrix(, 3, 3)))) # ltC; indexing used to fail
357 :     T3 <- as(M3, "TsparseMatrix")
358 :     stopifnot(identical(drop(M3), M3),
359 :     identical4(drop(M3[,2, drop = FALSE]), M3[,2, drop = TRUE],
360 :     drop(T3[,2, drop = FALSE]), T3[,2, drop = TRUE]),
361 :     is(T3, "triangularMatrix"),
362 :     !is(T3[,2, drop=FALSE], "triangularMatrix")
363 :     )
364 : maechler 1725
365 : maechler 1226 cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''

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