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[matrix] Annotation of /pkg/Matrix/R/diagMatrix.R
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Annotation of /pkg/Matrix/R/diagMatrix.R

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1 : maechler 1617 #### All methods for "diagonalMatrix" and its subclasses,
2 :     #### currently "ddiMatrix", "ldiMatrix"
3 :    
4 : maechler 1109 ## Purpose: Constructor of diagonal matrices -- ~= diag() ,
5 :     ## but *not* diag() extractor!
6 :     Diagonal <- function(n, x = NULL)
7 :     {
8 : mmaechler 2820 ## Allow Diagonal(4), Diagonal(x=1:5), and Diagonal(4, TRUE)
9 : mmaechler 2863 n <- if(missing(n)) length(x) else {
10 : maechler 1575 stopifnot(length(n) == 1, n == as.integer(n), n >= 0)
11 : mmaechler 2863 as.integer(n)
12 : maechler 1109 }
13 :    
14 : maechler 1654 if(missing(x)) ## unit diagonal matrix
15 : maechler 1575 new("ddiMatrix", Dim = c(n,n), diag = "U")
16 : maechler 1109 else {
17 : maechler 2128 lx <- length(x)
18 : mmaechler 2820 lx.1 <- lx == 1L
19 :     stopifnot(lx.1 || lx == n) # but keep 'x' short for now
20 : maechler 1575 if(is.logical(x))
21 :     cl <- "ldiMatrix"
22 :     else if(is.numeric(x)) {
23 :     cl <- "ddiMatrix"
24 :     x <- as.numeric(x)
25 :     }
26 :     else if(is.complex(x)) {
27 :     cl <- "zdiMatrix" # will not yet work
28 :     } else stop("'x' has invalid data type")
29 : mmaechler 2820 if(lx.1 && !is.na(x) && x == 1) # cheap check for uni-diagonal..
30 :     new(cl, Dim = c(n,n), diag = "U")
31 :     else
32 :     new(cl, Dim = c(n,n), diag = "N",
33 :     x = if(lx.1) rep.int(x,n) else x)
34 : maechler 1109 }
35 :     }
36 :    
37 : mmaechler 2840 .sparseDiagonal <- function(n, x = 1, uplo = "U",
38 : mmaechler 2508 shape = if(missing(cols)) "t" else "g",
39 : mmaechler 2840 unitri, kind,
40 :     cols = if(n) 0:(n - 1L) else integer(0))
41 : mmaechler 2508 {
42 : maechler 2144 stopifnot(n == (n. <- as.integer(n)), (n <- n.) >= 0)
43 : mmaechler 2840 if(!(mcols <- missing(cols)))
44 : mmaechler 2508 stopifnot(0 <= (cols <- as.integer(cols)), cols < n)
45 :     m <- length(cols)
46 :     if(missing(kind))
47 :     kind <-
48 :     if(is.double(x)) "d"
49 :     else if(is.logical(x)) "l"
50 :     else { ## for now
51 :     storage.mode(x) <- "double"
52 :     "d"
53 :     }
54 :     else stopifnot(any(kind == c("d","l","n")))
55 : mmaechler 2226 stopifnot(is.character(shape), nchar(shape) == 1,
56 :     any(shape == c("t","s","g"))) # triangular / symmetric / general
57 : mmaechler 2840 if((missing(unitri) || unitri) && shape == "t" &&
58 :     (mcols || cols == 0:(n-1L)) &&
59 :     ((any(kind == c("l", "n")) && allTrue(x)) ||
60 :     ( kind == "d" && allTrue(x == 1)))) { ## uni-triangular
61 :     new(paste0(kind,"tCMatrix"), Dim = c(n,n),
62 :     uplo = uplo, diag = "U", p = rep.int(0L, n+1L))
63 :     }
64 :     else if(kind == "n") {
65 : mmaechler 2508 if(shape == "g")
66 :     new("ngCMatrix", Dim = c(n,m), i = cols, p = 0:m)
67 :     else new(paste0("n", shape, "CMatrix"), Dim = c(n,m), uplo = uplo,
68 :     i = cols, p = 0:m)
69 :     }
70 : mmaechler 2840 else { ## kind != "n" -- have x slot :
71 :     if((lx <- length(x)) == 1) x <- rep.int(x, m)
72 :     else if(lx != m) stop("length(x) must be either 1 or #{cols}")
73 :     if(shape == "g")
74 :     new(paste0(kind, "gCMatrix"), Dim = c(n,m),
75 :     x = x, i = cols, p = 0:m)
76 :     else new(paste0(kind, shape, "CMatrix"), Dim = c(n,m), uplo = uplo,
77 :     x = x, i = cols, p = 0:m)
78 :     }
79 : maechler 2144 }
80 :    
81 : mmaechler 2226 ## Pkg 'spdep' had (relatively slow) versions of this as_dsCMatrix_I()
82 :     .symDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
83 :     .sparseDiagonal(n, x, uplo, shape = "s")
84 :    
85 : mmaechler 2608 # instead of diagU2N(as(Diagonal(n), "CsparseMatrix")), diag = "N" in any case:
86 : mmaechler 2840 .trDiagonal <- function(n, x = 1, uplo = "U", unitri=TRUE)
87 :     .sparseDiagonal(n, x, uplo, shape = "t", unitri=unitri)
88 : mmaechler 2226
89 :    
90 : mmaechler 2764 ## This is modified from a post of Bert Gunter to R-help on 1 Sep 2005.
91 :     ## Bert's code built on a post by Andy Liaw who most probably was influenced
92 :     ## by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002
93 :     ## who posted his bdiag() function written in December 1995.
94 : mmaechler 2209 if(FALSE)##--- no longer used:
95 : mmaechler 2206 .bdiag <- function(lst) {
96 : mmaechler 2764 ## block-diagonal matrix [a dgTMatrix] from list of matrices
97 : mmaechler 2206 stopifnot(is.list(lst), length(lst) >= 1)
98 : mmaechler 2813 dims <- vapply(lst, dim, 1L, USE.NAMES=FALSE)
99 : maechler 1617 ## make sure we had all matrices:
100 :     if(!(is.matrix(dims) && nrow(dims) == 2))
101 :     stop("some arguments are not matrices")
102 : maechler 1845 csdim <- rbind(rep.int(0L, 2),
103 : mmaechler 2206 apply(dims, 1, cumsum))
104 :     r <- new("dgTMatrix")
105 :     r@Dim <- as.integer(csdim[nrow(csdim),])
106 : maechler 1617 add1 <- matrix(1:0, 2,2)
107 : mmaechler 2206 for(i in seq_along(lst)) {
108 : maechler 1617 indx <- apply(csdim[i:(i+1),] + add1, 2, function(n) n[1]:n[2])
109 :     if(is.null(dim(indx))) ## non-square matrix
110 : mmaechler 2206 r[indx[[1]],indx[[2]]] <- lst[[i]]
111 : maechler 1617 else ## square matrix
112 : mmaechler 2206 r[indx[,1], indx[,2]] <- lst[[i]]
113 : maechler 1617 }
114 : mmaechler 2206 r
115 : maechler 1617 }
116 : mmaechler 2209 ## expand(<mer>) needed something like bdiag() for lower-triangular
117 :     ## (Tsparse) Matrices; hence Doug Bates provided a much more efficient
118 :     ## implementation for those; now extended and generalized:
119 : mmaechler 2206 .bdiag <- function(lst) {
120 : mmaechler 2209 ## block-diagonal matrix [a dgTMatrix] from list of matrices
121 : mmaechler 2206 stopifnot(is.list(lst), (nl <- length(lst)) >= 1)
122 : maechler 1617
123 : mmaechler 2891 Tlst <- lapply(lapply(lst, as_Csp2), # includes "diagU2N"
124 : mmaechler 2209 as, "TsparseMatrix")
125 : mmaechler 2206 if(nl == 1) return(Tlst[[1]])
126 :     ## else
127 : mmaechler 2813 i_off <- c(0L, cumsum(vapply(Tlst, nrow, 1L)))
128 :     j_off <- c(0L, cumsum(vapply(Tlst, ncol, 1L)))
129 : mmaechler 2209
130 : mmaechler 2813 clss <- vapply(Tlst, class, "")
131 : mmaechler 2741 typ <- substr(clss, 2, 2)
132 :     knd <- substr(clss, 1, 1)
133 :     sym <- typ == "s" # symmetric ones
134 :     tri <- typ == "t" # triangular ones
135 :     use.n <- any(is.n <- knd == "n")
136 :     if(use.n && !(use.n <- all(is.n))) {
137 : mmaechler 2209 Tlst[is.n] <- lapply(Tlst[is.n], as, "lMatrix")
138 : mmaechler 2741 knd [is.n] <- "l"
139 :     }
140 :     use.l <- !use.n && all(knd == "l")
141 : mmaechler 2209 if(all(sym)) { ## result should be *symmetric*
142 : mmaechler 2813 uplos <- vapply(Tlst, slot, ".", "uplo") ## either "U" or "L"
143 : mmaechler 2209 tLU <- table(uplos)# of length 1 or 2 ..
144 :     if(length(tLU) == 1) { ## all "U" or all "L"
145 :     useU <- uplos[1] == "U"
146 :     } else { ## length(tLU) == 2, counting "L" and "U"
147 :     useU <- diff(tLU) >= 0
148 :     if(useU && (hasL <- tLU[1] > 0))
149 :     Tlst[hasL] <- lapply(Tlst[hasL], t)
150 :     else if(!useU && (hasU <- tLU[2] > 0))
151 :     Tlst[hasU] <- lapply(Tlst[hasU], t)
152 :     }
153 :     if(use.n) { ## return nsparseMatrix :
154 :     r <- new("nsTMatrix")
155 :     } else {
156 : mmaechler 2741 r <- new(paste0(if(use.l) "l" else "d", "sTMatrix"))
157 : mmaechler 2209 r@x <- unlist(lapply(Tlst, slot, "x"))
158 :     }
159 :     r@uplo <- if(useU) "U" else "L"
160 :     }
161 : mmaechler 2813 else if(all(tri) && { ULs <- vapply(Tlst, slot, ".", "uplo")## "U" or "L"
162 : mmaechler 2209 all(ULs[1L] == ULs[-1L]) } ## all upper or all lower
163 :     ){ ## *triangular* result
164 :    
165 :     if(use.n) { ## return nsparseMatrix :
166 :     r <- new("ntTMatrix")
167 :     } else {
168 : mmaechler 2741 r <- new(paste0(if(use.l) "l" else "d", "tTMatrix"))
169 : mmaechler 2209 r@x <- unlist(lapply(Tlst, slot, "x"))
170 :     }
171 :     r@uplo <- ULs[1L]
172 :     }
173 :     else {
174 :     if(any(sym))
175 :     Tlst[sym] <- lapply(Tlst[sym], as, "generalMatrix")
176 :     if(use.n) { ## return nsparseMatrix :
177 :     r <- new("ngTMatrix")
178 :     } else {
179 : mmaechler 2741 r <- new(paste0(if(use.l) "l" else "d", "gTMatrix"))
180 : mmaechler 2209 r@x <- unlist(lapply(Tlst, slot, "x"))
181 :     }
182 :     }
183 :     r@Dim <- c(i_off[nl+1], j_off[nl + 1])
184 :     r@i <- unlist(lapply(1:nl, function(k) Tlst[[k]]@i + i_off[k]))
185 :     r@j <- unlist(lapply(1:nl, function(k) Tlst[[k]]@j + j_off[k]))
186 :     r
187 : mmaechler 2206 }
188 :    
189 :     bdiag <- function(...) {
190 :     if((nA <- nargs()) == 0) return(new("dgCMatrix"))
191 :     if(nA == 1 && !is.list(...))
192 :     return(as(..., "CsparseMatrix"))
193 :     alis <- if(nA == 1 && is.list(..1)) ..1 else list(...)
194 :     if(length(alis) == 1)
195 :     return(as(alis[[1]], "CsparseMatrix"))
196 :    
197 :     ## else : two or more arguments
198 :     as(.bdiag(alis), "CsparseMatrix")
199 :     }
200 :    
201 : mmaechler 3023 setMethod("tril", "diagonalMatrix", function(x, k = 0, ...)
202 :     if(k >= 0) x else .setZero(x, paste0(.M.kind(x), "tCMatrix")))
203 : mmaechler 2206
204 : mmaechler 3023 setMethod("triu", "diagonalMatrix", function(x, k = 0, ...)
205 :     if(k <= 0) x else .setZero(x, paste0(.M.kind(x), "tCMatrix")))
206 :    
207 :    
208 :    
209 : maechler 2136 .diag2tT <- function(from, uplo = "U", kind = .M.kind(from)) {
210 :     ## to triangular Tsparse
211 : maechler 1845 i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L
212 : mmaechler 2778 new(paste0(kind, "tTMatrix"),
213 : maechler 1654 diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
214 : maechler 2128 uplo = uplo,
215 : maechler 1654 x = from@x, # <- ok for diag = "U" and "N" (!)
216 :     i = i, j = i)
217 :     }
218 : maechler 1109
219 : maechler 2136 .diag2sT <- function(from, uplo = "U", kind = .M.kind(from)) {
220 :     ## to symmetric Tsparse
221 : maechler 2128 n <- from@Dim[1]
222 :     i <- seq_len(n) - 1L
223 : mmaechler 2778 new(paste0(kind, "sTMatrix"),
224 : maechler 1845 Dim = from@Dim, Dimnames = from@Dimnames,
225 : maechler 2128 i = i, j = i, uplo = uplo,
226 :     x = if(from@diag == "N") from@x else ## "U"-diag
227 :     rep.int(switch(kind,
228 :     "d" = 1.,
229 :     "l" =,
230 :     "n" = TRUE,
231 :     ## otherwise
232 : mmaechler 2863 stop(gettextf("%s kind not yet implemented",
233 :     sQuote(kind)), domain=NA)),
234 :     n))
235 : maechler 1845 }
236 :    
237 : mmaechler 2998 ## diagonal -> triangular, upper / lower depending on "partner" 'x':
238 : maechler 2144 diag2tT.u <- function(d, x, kind = .M.kind(d))
239 :     .diag2tT(d, uplo = if(is(x,"triangularMatrix")) x@uplo else "U", kind)
240 : maechler 2128
241 : mmaechler 2175 ## diagonal -> sparse {triangular OR symmetric} (upper / lower) depending on "partner":
242 :     diag2Tsmart <- function(d, x, kind = .M.kind(d)) {
243 :     clx <- getClassDef(class(x))
244 :     if(extends(clx, "symmetricMatrix"))
245 :     .diag2sT(d, uplo = x@uplo, kind)
246 :     else
247 :     .diag2tT(d, uplo = if(extends(clx,"triangularMatrix")) x@uplo else "U", kind)
248 :     }
249 : maechler 2136
250 : mmaechler 2814 ## FIXME: should not be needed {when ddi* is dsparse* etc}:
251 :     setMethod("is.finite", signature(x = "diagonalMatrix"),
252 :     function(x) is.finite(.diag2tT(x)))
253 :     setMethod("is.infinite", signature(x = "diagonalMatrix"),
254 :     function(x) is.infinite(.diag2tT(x)))
255 : mmaechler 2175
256 : maechler 2136 ## In order to evade method dispatch ambiguity warnings,
257 :     ## and because we can save a .M.kind() call, we use this explicit
258 :     ## "hack" instead of signature x = "diagonalMatrix" :
259 :     ##
260 :     ## ddi*:
261 : mmaechler 2922 di2tT <- function(from) .diag2tT(from, "U", "d")
262 :     setAs("ddiMatrix", "triangularMatrix", di2tT)
263 :     ##_no_longer_ setAs("ddiMatrix", "sparseMatrix", di2tT)
264 : maechler 1805 ## needed too (otherwise <dense> -> Tsparse is taken):
265 : mmaechler 2922 setAs("ddiMatrix", "TsparseMatrix", di2tT)
266 :     setAs("ddiMatrix", "dsparseMatrix", di2tT)
267 : maechler 2136 setAs("ddiMatrix", "CsparseMatrix",
268 :     function(from) as(.diag2tT(from, "U", "d"), "CsparseMatrix"))
269 : mmaechler 2998 setAs("ddiMatrix", "symmetricMatrix", function(from) .diag2sT(from, "U", "d"))
270 : maechler 2136 ##
271 :     ## ldi*:
272 : mmaechler 2922 di2tT <- function(from) .diag2tT(from, "U", "l")
273 :     setAs("ldiMatrix", "triangularMatrix", di2tT)
274 :     ##_no_longer_ setAs("ldiMatrix", "sparseMatrix", di2tT)
275 : maechler 2136 ## needed too (otherwise <dense> -> Tsparse is taken):
276 : mmaechler 2922 setAs("ldiMatrix", "TsparseMatrix", di2tT)
277 :     setAs("ldiMatrix", "lsparseMatrix", di2tT)
278 : maechler 2136 setAs("ldiMatrix", "CsparseMatrix",
279 :     function(from) as(.diag2tT(from, "U", "l"), "CsparseMatrix"))
280 : mmaechler 2998 setAs("ldiMatrix", "symmetricMatrix", function(from) .diag2sT(from, "U", "l"))
281 : mmaechler 2922 rm(di2tT)
282 : maechler 1654
283 : maechler 2128 setAs("diagonalMatrix", "nMatrix",
284 :     function(from) {
285 :     n <- from@Dim[1]
286 :     i <- if(from@diag == "U") integer(0) else which(isN0(from@x)) - 1L
287 :     new("ntTMatrix", i = i, j = i, diag = from@diag,
288 :     Dim = from@Dim, Dimnames = from@Dimnames)
289 :     })
290 :    
291 : mmaechler 2237 setAs("diagonalMatrix", "nsparseMatrix", function(from) as(from, "nMatrix"))
292 : maechler 2128
293 : mmaechler 2998 ##' A version of diag(x,n) which *does* preserve the mode of x, where diag() "fails"
294 : mmaechler 2175 mkDiag <- function(x, n) {
295 :     y <- matrix(as0(mod=mode(x)), n,n)
296 : mmaechler 2820 if (n > 0) y[1L + 0:(n - 1L) * (n + 1)] <- x
297 : mmaechler 2175 y
298 :     }
299 : mmaechler 2998 ## NB: diag(x,n) is really faster for n >= 20, and even more for large n
300 :     ## --> using diag() where possible, ==> .ddi2mat()
301 : mmaechler 2175
302 : mmaechler 2998 .diag2mat <- function(from)
303 :     ## want "ldiMatrix" -> <logical> "matrix" (but integer -> <double> for now)
304 :     mkDiag(if(from@diag == "U") as1(from@x) else from@x, n = from@Dim[1])
305 : maechler 1109
306 : mmaechler 2998 .ddi2mat <- function(from)
307 :     base::diag(if(from@diag == "U") as1(from@x) else from@x, nrow = from@Dim[1])
308 :    
309 :     setAs("ddiMatrix", "matrix", .ddi2mat)
310 :     ## the non-ddi diagonalMatrix -- only "ldiMatrix" currently:
311 :     setAs("diagonalMatrix", "matrix", .diag2mat)
312 :    
313 : maechler 2098 setMethod("as.vector", signature(x = "diagonalMatrix", mode="missing"),
314 :     function(x, mode) {
315 :     n <- x@Dim[1]
316 : mmaechler 2175 mod.x <- mode(x@x)
317 :     r <- vector(mod.x, length = n^2)
318 : maechler 2098 if(n)
319 : mmaechler 2820 r[1 + 0:(n - 1L) * (n + 1)] <-
320 : mmaechler 2175 if(x@diag == "U") as1(mod=mod.x) else x@x
321 : maechler 2098 r
322 :     })
323 :    
324 : maechler 1654 setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
325 : maechler 2128 function(from) as(as(from, "CsparseMatrix"), "generalMatrix"))
326 : maechler 1174
327 : mmaechler 2268 setAs("diagonalMatrix", "denseMatrix",
328 :     function(from) as(as(from, "CsparseMatrix"), "denseMatrix"))
329 :    
330 : mmaechler 2877 ..diag.x <- function(m) rep.int(as1(m@x), m@Dim[1])
331 :     .diag.x <- function(m) if(m@diag == "U") rep.int(as1(m@x), m@Dim[1]) else m@x
332 : maechler 1655
333 :     .diag.2N <- function(m) {
334 :     if(m@diag == "U") m@diag <- "N"
335 :     m
336 :     }
337 :    
338 : maechler 1174 setAs("ddiMatrix", "dgeMatrix",
339 : mmaechler 2183 function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
340 :     setAs("ddiMatrix", "ddenseMatrix",
341 :     function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
342 :     setAs("ldiMatrix", "ldenseMatrix",
343 :     function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
344 : maechler 1174
345 : mmaechler 2183
346 : maechler 1109 setAs("matrix", "diagonalMatrix",
347 :     function(from) {
348 : maechler 1295 d <- dim(from)
349 : maechler 1109 if(d[1] != (n <- d[2])) stop("non-square matrix")
350 :     if(any(from[row(from) != col(from)] != 0))
351 : mmaechler 2863 stop("matrix with non-zero off-diagonals cannot be coerced to \"diagonalMatrix\"")
352 : maechler 1295 x <- diag(from)
353 :     if(is.logical(x)) {
354 :     cl <- "ldiMatrix"
355 : mmaechler 2341 uni <- allTrue(x) ## uni := {is it unit-diagonal ?}
356 : maechler 1295 } else {
357 :     cl <- "ddiMatrix"
358 : mmaechler 2341 uni <- allTrue(x == 1)
359 : maechler 1295 storage.mode(x) <- "double"
360 : maechler 1575 } ## TODO: complex
361 : maechler 1295 new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
362 :     x = if(uni) x[FALSE] else x)
363 : maechler 1109 })
364 :    
365 :     ## ``generic'' coercion to diagonalMatrix : build on isDiagonal() and diag()
366 :     setAs("Matrix", "diagonalMatrix",
367 :     function(from) {
368 : mmaechler 2341 d <- dim(from)
369 : maechler 1109 if(d[1] != (n <- d[2])) stop("non-square matrix")
370 : mmaechler 2341 if(!isDiagonal(from)) stop("matrix is not diagonal")
371 :     ## else:
372 :     x <- diag(from)
373 :     if(is.logical(x)) {
374 :     cl <- "ldiMatrix"
375 :     uni <- allTrue(x)
376 :     } else {
377 :     cl <- "ddiMatrix"
378 :     uni <- allTrue(x == 1)
379 :     storage.mode(x) <- "double"
380 :     } ## TODO: complex
381 :     new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
382 :     x = if(uni) x[FALSE] else x)
383 : maechler 1109 })
384 :    
385 : maechler 1708
386 : mmaechler 2185 setMethod("diag", signature(x = "diagonalMatrix"),
387 :     function(x = 1, nrow, ncol) .diag.x(x))
388 : maechler 1708
389 : maechler 2098 subDiag <- function(x, i, j, ..., drop) {
390 : mmaechler 2508 x <- as(x, "CsparseMatrix") ## << was "TsparseMatrix" (Csparse is faster now)
391 : maechler 1799 x <- if(missing(i))
392 :     x[, j, drop=drop]
393 :     else if(missing(j))
394 : mmaechler 2363 if(nargs() == 4) x[i, , drop=drop] else x[i, drop=drop]
395 : maechler 1799 else
396 :     x[i,j, drop=drop]
397 : maechler 2120 if(isS4(x) && isDiagonal(x)) as(x, "diagonalMatrix") else x
398 : maechler 1799 }
399 :    
400 :     setMethod("[", signature(x = "diagonalMatrix", i = "index",
401 :     j = "index", drop = "logical"), subDiag)
402 :     setMethod("[", signature(x = "diagonalMatrix", i = "index",
403 : mmaechler 2363 j = "missing", drop = "logical"),
404 :     function(x, i, j, ..., drop) {
405 :     na <- nargs()
406 :     Matrix.msg("diag[i,m,l] : nargs()=", na, .M.level = 2)
407 :     if(na == 4)
408 :     subDiag(x, i=i, , drop=drop)
409 :     else subDiag(x, i=i, drop=drop)
410 :     })
411 : maechler 1799 setMethod("[", signature(x = "diagonalMatrix", i = "missing",
412 :     j = "index", drop = "logical"),
413 : maechler 2098 function(x, i, j, ..., drop) subDiag(x, j=j, drop=drop))
414 : maechler 1799
415 : maechler 1617 ## When you assign to a diagonalMatrix, the result should be
416 : maechler 1708 ## diagonal or sparse ---
417 :     ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch
418 : maechler 2098 ## Only(?) current bug: x[i] <- value is wrong when i is *vector*
419 :     replDiag <- function(x, i, j, ..., value) {
420 : mmaechler 2811 x <- as(x, "CsparseMatrix")# was "Tsparse.." till 2012-07
421 : maechler 1710 if(missing(i))
422 :     x[, j] <- value
423 : maechler 2098 else if(missing(j)) { ## x[i , ] <- v *OR* x[i] <- v
424 :     na <- nargs()
425 :     ## message("diagnosing replDiag() -- nargs()= ", na)
426 :     if(na == 4)
427 :     x[i, ] <- value
428 :     else if(na == 3)
429 :     x[i] <- value
430 : mmaechler 2863 else stop(gettextf("Internal bug: nargs()=%d; please report",
431 :     na), domain=NA)
432 : maechler 2098 } else
433 : maechler 1710 x[i,j] <- value
434 :     if(isDiagonal(x)) as(x, "diagonalMatrix") else x
435 :     }
436 : maechler 1617
437 : maechler 1710 setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
438 :     j = "index", value = "replValue"), replDiag)
439 : maechler 2098
440 : maechler 1710 setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
441 :     j = "missing", value = "replValue"),
442 : maechler 2098 function(x,i,j, ..., value) {
443 :     ## message("before replDiag() -- nargs()= ", nargs())
444 :     if(nargs() == 3)
445 :     replDiag(x, i=i, value=value)
446 :     else ## nargs() == 4 :
447 :     replDiag(x, i=i, , value=value)
448 :     })
449 :    
450 : mmaechler 2877 setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
451 :     j = "index", value = "replValue"),
452 :     function(x,i,j, ..., value) replDiag(x, j=j, value=value))
453 :    
454 :     ## x[] <- value :
455 :     setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
456 :     j = "missing", value = "ANY"),
457 :     function(x,i,j, ..., value)
458 :     {
459 :     if(all0(value)) { # be faster
460 :     r <- new(paste0(.M.kindC(getClassDef(class(x))),"tTMatrix"))# of all "0"
461 :     r@Dim <- x@Dim
462 :     r@Dimnames <- x@Dimnames
463 :     r
464 :     } else { ## typically non-sense: assigning to full sparseMatrix
465 :     x[TRUE] <- value
466 :     x
467 :     }
468 :     })
469 :    
470 :    
471 : mmaechler 2192 setReplaceMethod("[", signature(x = "diagonalMatrix",
472 :     i = "matrix", # 2-col.matrix
473 : maechler 2096 j = "missing", value = "replValue"),
474 : maechler 2098 function(x,i,j, ..., value) {
475 : maechler 2096 if(ncol(i) == 2) {
476 :     if(all((ii <- i[,1]) == i[,2])) { # replace in diagonal only
477 : mmaechler 2192 if(x@diag == "U") {
478 :     one <- as1(x@x)
479 :     if(any(value != one | is.na(value))) {
480 :     x@diag <- "N"
481 :     x@x <- rep.int(one, x@Dim[1])
482 : mmaechler 2811 } else return(x)
483 : mmaechler 2192 }
484 : maechler 2096 x@x[ii] <- value
485 :     x
486 :     } else { ## no longer diagonal, but remain sparse:
487 : mmaechler 2239 x <- as(x, "TsparseMatrix")
488 : maechler 2096 x[i] <- value
489 :     x
490 :     }
491 :     }
492 :     else { # behave as "base R": use as if vector
493 :     x <- as(x, "matrix")
494 :     x[i] <- value
495 :     Matrix(x)
496 :     }
497 :     })
498 :    
499 : maechler 1710
500 : mmaechler 2877 ## value = "sparseMatrix":
501 : mmaechler 2207 setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
502 : mmaechler 2239 value = "sparseMatrix"),
503 : mmaechler 2207 function (x, i, j, ..., value)
504 :     callGeneric(x=x, , j=j, value = as(value, "sparseVector")))
505 :     setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
506 : mmaechler 2239 value = "sparseMatrix"),
507 : mmaechler 2207 function (x, i, j, ..., value)
508 :     callGeneric(x=x, i=i, , value = as(value, "sparseVector")))
509 :     setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
510 : mmaechler 2239 value = "sparseMatrix"),
511 : mmaechler 2207 function (x, i, j, ..., value)
512 :     callGeneric(x=x, i=i, j=j, value = as(value, "sparseVector")))
513 : maechler 1710
514 : mmaechler 2877 ## value = "sparseVector":
515 : mmaechler 2207 setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
516 :     value = "sparseVector"),
517 :     replDiag)
518 :     setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
519 :     value = "sparseVector"),
520 :     replDiag)
521 :     setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
522 :     value = "sparseVector"),
523 :     replDiag)
524 :    
525 :    
526 : maechler 1109 setMethod("t", signature(x = "diagonalMatrix"),
527 :     function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })
528 :    
529 : mmaechler 2904 setMethod("isDiagonal", "diagonalMatrix", function(object) TRUE)
530 : mmaechler 3015 setMethod("isTriangular", "diagonalMatrix", function(object, upper=NA, ...) TRUE)
531 : mmaechler 2904 setMethod("isSymmetric", "diagonalMatrix", function(object, ...) TRUE)
532 : maechler 1109
533 : maechler 2112 setMethod("symmpart", signature(x = "diagonalMatrix"), function(x) x)
534 : mmaechler 3023 setMethod("skewpart", signature(x = "diagonalMatrix"), function(x) .setZero(x))
535 : maechler 2112
536 : maechler 2133 setMethod("chol", signature(x = "ddiMatrix"),
537 :     function(x, pivot, ...) {
538 : mmaechler 2183 if(x@diag == "U") return(x)
539 :     ## else
540 : maechler 2133 if(any(x@x < 0))
541 :     stop("chol() is undefined for diagonal matrix with negative entries")
542 : maechler 1654 x@x <- sqrt(x@x)
543 :     x
544 :     })
545 :     ## chol(L) is L for logical diagonal:
546 : maechler 2133 setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot, ...) x)
547 : maechler 1654
548 : mmaechler 2175 setMethod("determinant", signature(x = "diagonalMatrix", logarithm = "logical"),
549 : mmaechler 2185 function(x, logarithm, ...) mkDet(.diag.x(x), logarithm))
550 : mmaechler 2175
551 : mmaechler 2183 setMethod("norm", signature(x = "diagonalMatrix", type = "character"),
552 :     function(x, type, ...) {
553 :     if((n <- x@Dim[1]) == 0) return(0) # as for "sparseMatrix"
554 :     type <- toupper(substr(type[1], 1, 1))
555 :     isU <- (x@diag == "U") # unit-diagonal
556 :     if(type == "F") sqrt(if(isU) n else sum(x@x^2))
557 :     else { ## norm == "I","1","O","M" :
558 :     if(isU) 1 else max(abs(x@x))
559 :     }
560 :     })
561 :    
562 :    
563 :    
564 : maechler 1109 ## Basic Matrix Multiplication {many more to add}
565 : maechler 1654 ## ---------------------
566 :     ## Note that "ldi" logical are treated as numeric
567 : maechler 1109 diagdiagprod <- function(x, y) {
568 : mmaechler 2633 dimCheck(x,y)
569 : maechler 1109 if(x@diag != "U") {
570 : maechler 1654 if(y@diag != "U") {
571 :     nx <- x@x * y@x
572 :     if(is.numeric(nx) && !is.numeric(x@x))
573 :     x <- as(x, "dMatrix")
574 :     x@x <- as.numeric(nx)
575 :     }
576 :     return(x)
577 : maechler 1109 } else ## x is unit diagonal
578 : mmaechler 2912 return(y)
579 : maechler 1109 }
580 :    
581 : maechler 1654 setMethod("%*%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
582 : maechler 1109 diagdiagprod, valueClass = "ddiMatrix")
583 :    
584 : maechler 1654 formals(diagdiagprod) <- alist(x=, y=x)
585 :     setMethod("crossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
586 : maechler 1109 diagdiagprod, valueClass = "ddiMatrix")
587 : maechler 1654 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
588 : maechler 1109 diagdiagprod, valueClass = "ddiMatrix")
589 : maechler 1654 setMethod("crossprod", signature(x = "diagonalMatrix", y = "missing"),
590 :     diagdiagprod, valueClass = "ddiMatrix")
591 :     setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "missing"),
592 :     diagdiagprod, valueClass = "ddiMatrix")
593 : maechler 1109
594 :    
595 : mmaechler 2998 ## analogous to matdiagprod() below:
596 : maechler 1109 diagmatprod <- function(x, y) {
597 : mmaechler 2183 ## x is diagonalMatrix
598 : mmaechler 2998 if(x@Dim[2] != nrow(y)) stop("non-matching dimensions")
599 :     Matrix(if(x@diag == "U") y else x@x * y)
600 : maechler 1109 }
601 :     setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),
602 : maechler 1654 diagmatprod)
603 : mmaechler 2183 ## sneaky .. :
604 : maechler 1109 formals(diagmatprod) <- alist(x=, y=NULL)
605 : mmaechler 2998 setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"), diagmatprod)
606 : maechler 1109
607 : mmaechler 2183 diagGeprod <- function(x, y) {
608 : mmaechler 2998 if(x@Dim[2] != y@Dim[1]) stop("non-matching dimensions")
609 : maechler 1109 if(x@diag != "U")
610 :     y@x <- x@x * y@x
611 :     y
612 :     }
613 : mmaechler 2183 setMethod("%*%", signature(x= "diagonalMatrix", y= "dgeMatrix"), diagGeprod)
614 :     setMethod("%*%", signature(x= "diagonalMatrix", y= "lgeMatrix"), diagGeprod)
615 :     formals(diagGeprod) <- alist(x=, y=NULL)
616 : maechler 1109 setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),
617 : mmaechler 2183 diagGeprod, valueClass = "dgeMatrix")
618 :     setMethod("crossprod", signature(x = "diagonalMatrix", y = "lgeMatrix"),
619 :     diagGeprod)
620 : maechler 1109
621 : mmaechler 2998 ## analogous to diagmatprod() above:
622 : mmaechler 2183 matdiagprod <- function(x, y) {
623 :     dx <- dim(x)
624 : mmaechler 2998 if(dx[2] != y@Dim[1]) stop("non-matching dimensions")
625 : mmaechler 2183 Matrix(if(y@diag == "U") x else x * rep(y@x, each = dx[1]))
626 :     }
627 : mmaechler 2998 setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"), matdiagprod)
628 : mmaechler 2183 formals(matdiagprod) <- alist(x=, y=NULL)
629 : mmaechler 2998 setMethod("tcrossprod",signature(x = "matrix", y = "diagonalMatrix"), matdiagprod)
630 :     setMethod("crossprod", signature(x = "matrix", y = "diagonalMatrix"),
631 :     function(x, y=NULL) {
632 :     dx <- dim(x)
633 :     if(dx[1] != y@Dim[1]) stop("non-matching dimensions")
634 :     Matrix(t(rep.int(y@x, dx[2]) * x))
635 :     })
636 : maechler 1109
637 : mmaechler 2183 gediagprod <- function(x, y) {
638 :     dx <- dim(x)
639 : mmaechler 2998 if(dx[2] != y@Dim[1]) stop("non-matching dimensions")
640 : mmaechler 2183 if(y@diag == "N")
641 :     x@x <- x@x * rep(y@x, each = dx[1])
642 :     x
643 :     }
644 :     setMethod("%*%", signature(x= "dgeMatrix", y= "diagonalMatrix"), gediagprod)
645 :     setMethod("%*%", signature(x= "lgeMatrix", y= "diagonalMatrix"), gediagprod)
646 :     formals(gediagprod) <- alist(x=, y=NULL)
647 :     setMethod("tcrossprod", signature(x = "dgeMatrix", y = "diagonalMatrix"),
648 :     gediagprod)
649 :     setMethod("tcrossprod", signature(x = "lgeMatrix", y = "diagonalMatrix"),
650 :     gediagprod)
651 : maechler 1109
652 : maechler 1295 ## crossprod {more of these}
653 : maechler 1109
654 : maechler 1295 ## tcrossprod --- all are not yet there: do the dense ones here:
655 : maechler 1109
656 : mmaechler 2183 setMethod("%*%", signature(x = "diagonalMatrix", y = "denseMatrix"),
657 :     function(x, y) if(x@diag == "U") y else x %*% as(y, "generalMatrix"))
658 :     setMethod("%*%", signature(x = "denseMatrix", y = "diagonalMatrix"),
659 :     function(x, y) if(y@diag == "U") x else as(x, "generalMatrix") %*% y)
660 :    
661 :    
662 : maechler 1295 ## FIXME:
663 :     ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),
664 :     ## function(x, y = NULL) {
665 :     ## })
666 : maechler 1109
667 : mmaechler 2912 ##' @param x CsparseMatrix
668 :     ##' @param y diagonalMatrix
669 :     ##' @return x %*% y
670 : dmbates 2417 Cspdiagprod <- function(x, y) {
671 : mmaechler 2998 m <- ncol(x <- .Call(Csparse_diagU2N, x))
672 :     if(m != y@Dim[1]) stop("non-matching dimensions")
673 : mmaechler 2912 if(y@diag == "N") { ## otherwise: y == Diagonal(n) : multiplication is identity
674 : mmaechler 2674 if(!all(y@x[1L] == y@x[-1L]) && is(x, "symmetricMatrix"))
675 :     x <- as(x, "generalMatrix")
676 : mmaechler 2998 ind <- rep.int(seq_len(m), x@p[-1] - x@p[-m-1L])
677 : mmaechler 2674 x@x <- x@x * y@x[ind]
678 : mmaechler 2978 if(.hasSlot(x, "factors") && length(x@factors)) {# drop cashed ones
679 : mmaechler 2912 ## instead of dropping all factors, be smart about some
680 :     ## TODO ......
681 :     x@factors <- list()
682 :     }
683 : mmaechler 2674 }
684 : dmbates 2417 x
685 :     }
686 : maechler 1109
687 : mmaechler 2912 ##' @param x diagonalMatrix
688 :     ##' @param y CsparseMatrix
689 :     ##' @return x %*% y
690 : dmbates 2417 diagCspprod <- function(x, y) {
691 : mmaechler 2998 y <- .Call(Csparse_diagU2N, y)
692 :     if(x@Dim[2] != y@Dim[1]) stop("non-matching dimensions")
693 : mmaechler 2984 if(x@diag == "N") {
694 : mmaechler 2674 if(!all(x@x[1L] == x@x[-1L]) && is(y, "symmetricMatrix"))
695 :     y <- as(y, "generalMatrix")
696 :     y@x <- y@x * x@x[y@i + 1L]
697 : mmaechler 2978 if(.hasSlot(y, "factors") && length(yf <- y@factors)) {
698 : mmaechler 2912 ## TODO
699 :     if(FALSE) { ## instead of dropping all factors, be smart about some
700 :     keep <- character()
701 :     if(any(iLU <- names(yf) == "LU")) {
702 :     keep <- "LU"
703 :     }
704 :     y@factors <- yf[keep]
705 :     } else y@factors <- list() ## for now
706 :     }
707 : mmaechler 2674 }
708 : dmbates 2417 y
709 :     }
710 :    
711 :     setMethod("crossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
712 :     function(x, y = NULL) diagCspprod(x, y))
713 :    
714 : maechler 1799 setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
715 : dmbates 2417 function(x, y = NULL) diagCspprod(x, as(y, "CsparseMatrix")))
716 : maechler 1295
717 : dmbates 2417 ## Prefer calling diagCspprod to Cspdiagprod if going to transpose anyway
718 :     ## x'y == (y'x)'
719 :     setMethod("crossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
720 :     function(x, y = NULL) t(diagCspprod(y, x)))
721 :    
722 : maechler 1799 setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
723 : dmbates 2417 function(x, y = NULL) t(diagCspprod(y, as(x, "Csparsematrix"))))
724 : maechler 1799
725 : dmbates 2417 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
726 :     function(x, y = NULL) diagCspprod(x, t(y)))
727 :    
728 : maechler 1799 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
729 : dmbates 2417 function(x, y = NULL) diagCspprod(x, t(as(y, "CsparseMatrix"))))
730 : maechler 1799
731 : dmbates 2417 setMethod("tcrossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
732 :     function(x, y = NULL) Cspdiagprod(x, y))
733 :    
734 : maechler 1799 setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
735 : dmbates 2417 function(x, y = NULL) Cspdiagprod(as(x, "CsparseMatrix"), y))
736 : mmaechler 2472
737 : dmbates 2417 setMethod("%*%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
738 :     function(x, y) diagCspprod(x, y))
739 : maechler 1799
740 : mmaechler 2912 ## instead of "sparseMatrix", use: [RT]sparse.. ("closer" in method dispatch)
741 :     for(cl in c("TsparseMatrix", "RsparseMatrix")) {
742 :    
743 : maechler 1799 setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
744 : dmbates 2417 function(x, y) diagCspprod(as(x, "CsparseMatrix"), y))
745 : mmaechler 2472
746 : mmaechler 2183 setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),
747 : dmbates 2417 function(x, y) Cspdiagprod(as(x, "CsparseMatrix"), y))
748 : mmaechler 2912 }
749 : dmbates 2417
750 : maechler 1799 setMethod("%*%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
751 : dmbates 2417 function(x, y) Cspdiagprod(x, y))
752 :    
753 : maechler 1799 ## TODO: Write tests in ./tests/ which ensure that many "ops" with diagonal*
754 :     ## do indeed work by going through sparse (and *not* ddense)!
755 :    
756 :     setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),
757 :     function(a, b, ...) {
758 :     a@x <- 1/ a@x
759 :     a@Dimnames <- a@Dimnames[2:1]
760 :     a
761 :     })
762 :    
763 :     solveDiag <- function(a, b, ...) {
764 : mmaechler 2633 if(a@Dim[1] != nrow(b))
765 : maechler 1799 stop("incompatible matrix dimensions")
766 :     ## trivially invert a 'in place' and multiply:
767 :     a@x <- 1/ a@x
768 :     a@Dimnames <- a@Dimnames[2:1]
769 :     a %*% b
770 :     }
771 :     setMethod("solve", signature(a = "diagonalMatrix", b = "matrix"),
772 :     solveDiag)
773 :     setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),
774 :     solveDiag)
775 :    
776 : maechler 2106 ## Schur() ---> ./eigen.R
777 : maechler 1799
778 :    
779 :    
780 : mmaechler 2175 ###---------------- <Ops> (<Arith>, <Logic>, <Compare> ) ----------------------
781 : maechler 1295
782 : maechler 1655 ## Use function for several signatures, in order to evade
783 : mmaechler 2175 diagOdiag <- function(e1,e2) {
784 :     ## result should also be diagonal _ if possible _
785 : maechler 1655 r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
786 : mmaechler 2175 ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
787 :     r00 <- callGeneric(if(is.numeric(e1@x)) 0 else FALSE,
788 :     if(is.numeric(e2@x)) 0 else FALSE)
789 :     if(is0(r00)) { ## r00 == 0 or FALSE --- result *is* diagonal
790 : mmaechler 2814 if(is.numeric(r)) { # "double" *or* "integer"
791 : mmaechler 2175 if(is.numeric(e2@x)) {
792 :     e2@x <- r; return(.diag.2N(e2)) }
793 :     if(!is.numeric(e1@x))
794 :     ## e.g. e1, e2 are logical;
795 :     e1 <- as(e1, "dMatrix")
796 : mmaechler 2814 if(!is.double(r)) r <- as.double(r)
797 : mmaechler 2175 }
798 :     else if(is.logical(r))
799 :     e1 <- as(e1, "lMatrix")
800 : mmaechler 2863 else stop(gettextf("intermediate 'r' is of type %s",
801 :     typeof(r)), domain=NA)
802 : mmaechler 2175 e1@x <- r
803 :     .diag.2N(e1)
804 : maechler 1655 }
805 : mmaechler 2175 else { ## result not diagonal, but at least symmetric:
806 : mmaechler 2496 ## e.g., m == m
807 : mmaechler 2175 isNum <- (is.numeric(r) || is.numeric(r00))
808 :     isLog <- (is.logical(r) || is.logical(r00))
809 : mmaechler 2496 Matrix.msg("exploding <diag> o <diag> into dense matrix", .M.level = 2)
810 : mmaechler 2175 d <- e1@Dim
811 :     n <- d[1]
812 :     stopifnot(length(r) == n)
813 : mmaechler 2814 if(isNum && !is.double(r)) r <- as.double(r)
814 : mmaechler 2175 xx <- as.vector(matrix(rbind(r, matrix(r00,n,n)), n,n))
815 :     newcl <-
816 : mmaechler 2811 paste0(if(isNum) "d" else if(isLog) {
817 : mmaechler 2175 if(!any(is.na(r)) && !any(is.na(r00))) "n" else "l"
818 : mmaechler 2811 } else stop("not yet implemented .. please report"), "syMatrix")
819 : mmaechler 2175
820 :     new(newcl, Dim = e1@Dim, Dimnames = e1@Dimnames, x = xx)
821 :     }
822 : maechler 1655 }
823 :    
824 : mmaechler 2175 ### This would be *the* way, but we get tons of "ambiguous method dispatch"
825 : mmaechler 2185 ## we use this hack instead of signature x = "diagonalMatrix" :
826 :     diCls <- names(getClass("diagonalMatrix")@subclasses)
827 : mmaechler 2175 if(FALSE) {
828 : maechler 1655 setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
829 :     diagOdiag)
830 : mmaechler 2175 } else { ## These are just for method disambiguation:
831 :     for(c1 in diCls)
832 :     for(c2 in diCls)
833 :     setMethod("Ops", signature(e1 = c1, e2 = c2), diagOdiag)
834 :     }
835 : maechler 1655
836 : mmaechler 2493 ## diagonal o triangular |--> triangular
837 :     ## diagonal o symmetric |--> symmetric
838 : maechler 1845 ## {also when other is sparse: do these "here" --
839 :     ## before conversion to sparse, since that loses "diagonality"}
840 : mmaechler 2811 diagOtri <- function(e1,e2) {
841 :     ## result must be triangular
842 :     r <- callGeneric(d1 <- .diag.x(e1), diag(e2)) # error if not "compatible"
843 :     ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
844 :     e1.0 <- if(.n1 <- is.numeric(d1 )) 0 else FALSE
845 :     r00 <- callGeneric(e1.0, if(.n2 <- is.numeric(e2[0])) 0 else FALSE)
846 :     if(is0(r00)) { ## r00 == 0 or FALSE --- result *is* triangular
847 :     diag(e2) <- r
848 :     ## check what happens "in the triangle"
849 :     e2.2 <- if(.n2) 2 else TRUE
850 :     if(!callGeneric(e1.0, e2.2) == e2.2) { # values "in triangle" can change:
851 :     n <- dim(e2)[1L]
852 :     it <- indTri(n, upper = (e2@uplo == "U"))
853 :     e2[it] <- callGeneric(e1.0, e2[it])
854 :     }
855 :     e2
856 :     }
857 :     else { ## result not triangular ---> general
858 :     rr <- as(e2, "generalMatrix")
859 :     diag(rr) <- r
860 :     rr
861 :     }
862 :     }
863 : maechler 1845
864 : mmaechler 2811
865 :     setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "triangularMatrix"),
866 :     diagOtri)
867 :     ## For the reverse, Ops == "Arith" | "Compare" | "Logic"
868 :     ## 'Arith' := '"+"', '"-"', '"*"', '"^"', '"%%"', '"%/%"', '"/"'
869 :     setMethod("Arith", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
870 :     function(e1,e2)
871 :     { ## this must only trigger for *dense* e1
872 :     switch(.Generic,
873 :     "+" = .Call(dtrMatrix_addDiag, as(e1,"dtrMatrix"), .diag.x(e2)),
874 :     "-" = .Call(dtrMatrix_addDiag, as(e1,"dtrMatrix"), - .diag.x(e2)),
875 :     "*" = {
876 :     n <- e2@Dim[1L]
877 :     d2 <- if(e2@diag == "U") { # unit-diagonal
878 :     d <- rep.int(as1(e2@x), n)
879 :     e2@x <- d
880 :     e2@diag <- "N"
881 :     d
882 :     } else e2@x
883 :     e2@x <- diag(e1) * d2
884 :     e2
885 :     },
886 :     "^" = { ## will be dense ( as <ANY> ^ 0 == 1 ):
887 :     e1 ^ as(e2, "denseMatrix")
888 :     },
889 :     ## otherwise:
890 :     callGeneric(e1, diag2Tsmart(e2,e1)))
891 :     })
892 :    
893 :     ## Compare --> 'swap' (e.g. e1 < e2 <==> e2 > e1 ):
894 :     setMethod("Compare", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
895 :     .Cmp.swap)
896 :     ## '&' and "|' are commutative:
897 :     setMethod("Logic", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
898 :     function(e1,e2) callGeneric(e2, e1))
899 :    
900 : maechler 1655 ## For almost everything else, diag* shall be treated "as sparse" :
901 : maechler 1295 ## These are cheap implementations via coercion
902 :    
903 : maechler 2144 ## For disambiguation --- define this for "sparseMatrix" , then for "ANY";
904 :     ## and because we can save an .M.kind() call, we use this explicit
905 :     ## "hack" for all diagonalMatrix *subclasses* instead of just "diagonalMatrix" :
906 :     ##
907 :     ## ddi*:
908 :     setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "sparseMatrix"),
909 : mmaechler 2175 function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
910 : maechler 2144 setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ddiMatrix"),
911 : mmaechler 2175 function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
912 : maechler 2144 ## ldi*
913 :     setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "sparseMatrix"),
914 : mmaechler 2175 function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
915 : maechler 2144 setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ldiMatrix"),
916 : mmaechler 2175 function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
917 : maechler 1654
918 : mmaechler 2820 ## Ops: Arith --> numeric : "dMatrix"
919 :     ## Compare --> logical
920 :     ## Logic --> logical: "lMatrix"
921 : mmaechler 2175
922 : mmaechler 2820 ## Other = "numeric" : stay diagonal if possible
923 : mmaechler 2175 ## ddi*: Arith: result numeric, potentially ddiMatrix
924 : mmaechler 2813 for(arg2 in c("numeric","logical"))
925 :     setMethod("Arith", signature(e1 = "ddiMatrix", e2 = arg2),
926 : maechler 2144 function(e1,e2) {
927 : mmaechler 2820 n <- e1@Dim[1]
928 : maechler 2144 f0 <- callGeneric(0, e2)
929 : mmaechler 2945 if(all0(f0)) { # remain diagonal
930 : maechler 2157 L1 <- (le <- length(e2)) == 1L
931 : mmaechler 2820 if(e1@diag == "U") {
932 :     if(any((r <- callGeneric(1, e2)) != 1)) {
933 :     e1@diag <- "N"
934 :     e1@x[seq_len(n)] <- r # possibly recycling r
935 :     } ## else: result = e1 (is "U" diag)
936 :     } else {
937 : maechler 2144 r <- callGeneric(e1@x, e2)
938 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
939 :     e1@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
940 :     }
941 :     e1
942 :     } else
943 :     callGeneric(diag2tT.u(e1,e2, "d"), e2)
944 : maechler 2144 })
945 : maechler 1655
946 : mmaechler 2813 for(arg1 in c("numeric","logical"))
947 :     setMethod("Arith", signature(e1 = arg1, e2 = "ddiMatrix"),
948 : maechler 2144 function(e1,e2) {
949 : mmaechler 2820 n <- e2@Dim[1]
950 : maechler 2144 f0 <- callGeneric(e1, 0)
951 : mmaechler 2945 if(all0(f0)) { # remain diagonal
952 : maechler 2157 L1 <- (le <- length(e1)) == 1L
953 : mmaechler 2820 if(e2@diag == "U") {
954 :     if(any((r <- callGeneric(e1, 1)) != 1)) {
955 :     e2@diag <- "N"
956 :     e2@x[seq_len(n)] <- r # possibly recycling r
957 :     } ## else: result = e2 (is "U" diag)
958 :     } else {
959 : maechler 2144 r <- callGeneric(e1, e2@x)
960 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
961 :     e2@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
962 :     }
963 :     e2
964 :     } else
965 :     callGeneric(e1, diag2tT.u(e2,e1, "d"))
966 : maechler 2144 })
967 : mmaechler 2175
968 :     ## ldi* Arith --> result numeric, potentially ddiMatrix
969 : mmaechler 2813 for(arg2 in c("numeric","logical"))
970 :     setMethod("Arith", signature(e1 = "ldiMatrix", e2 = arg2),
971 : mmaechler 2175 function(e1,e2) {
972 : mmaechler 2820 n <- e1@Dim[1]
973 : mmaechler 2175 f0 <- callGeneric(0, e2)
974 : mmaechler 2945 if(all0(f0)) { # remain diagonal
975 : mmaechler 2175 L1 <- (le <- length(e2)) == 1L
976 : mmaechler 2984 E <- copyClass(e1, "ddiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
977 : mmaechler 2820 ## storage.mode(E@x) <- "double"
978 :     if(e1@diag == "U") {
979 :     if(any((r <- callGeneric(1, e2)) != 1)) {
980 :     E@diag <- "N"
981 :     E@x[seq_len(n)] <- r # possibly recycling r
982 :     } ## else: result = E (is "U" diag)
983 :     } else {
984 : mmaechler 2175 r <- callGeneric(e1@x, e2)
985 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
986 :     E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
987 : mmaechler 2814 }
988 : mmaechler 2820 E
989 :     } else
990 :     callGeneric(diag2tT.u(e1,e2, "l"), e2)
991 : mmaechler 2175 })
992 :    
993 : mmaechler 2813 for(arg1 in c("numeric","logical"))
994 :     setMethod("Arith", signature(e1 = arg1, e2 = "ldiMatrix"),
995 : mmaechler 2175 function(e1,e2) {
996 : mmaechler 2820 n <- e2@Dim[1]
997 : mmaechler 2175 f0 <- callGeneric(e1, 0)
998 : mmaechler 2945 if(all0(f0)) { # remain diagonal
999 : mmaechler 2175 L1 <- (le <- length(e1)) == 1L
1000 : mmaechler 2984 E <- copyClass(e2, "ddiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
1001 : mmaechler 2820 ## storage.mode(E@x) <- "double"
1002 :     if(e2@diag == "U") {
1003 :     if(any((r <- callGeneric(e1, 1)) != 1)) {
1004 :     E@diag <- "N"
1005 :     E@x[seq_len(n)] <- r # possibly recycling r
1006 :     } ## else: result = E (is "U" diag)
1007 :     } else {
1008 : mmaechler 2175 r <- callGeneric(e1, e2@x)
1009 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1010 :     E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1011 : mmaechler 2814 }
1012 : mmaechler 2820 E
1013 :     } else
1014 :     callGeneric(e1, diag2tT.u(e2,e1, "l"))
1015 : mmaechler 2175 })
1016 :    
1017 : mmaechler 2820 ## ddi*: for "Ops" without "Arith": <Compare> or <Logic> --> result logical, potentially ldi
1018 :     ##
1019 :     ## Note that ("numeric", "ddiMatrix") is simply swapped, e.g.,
1020 :     if(FALSE) {
1021 :     selectMethod("<", c("numeric","lMatrix"))# Compare
1022 :     selectMethod("&", c("numeric","lMatrix"))# Logic
1023 :     } ## so we don't need to define a method here :
1024 :    
1025 : mmaechler 2813 for(arg2 in c("numeric","logical"))
1026 :     setMethod("Ops", signature(e1 = "ddiMatrix", e2 = arg2),
1027 : mmaechler 2175 function(e1,e2) {
1028 : mmaechler 2820 n <- e1@Dim[1]
1029 : mmaechler 2175 f0 <- callGeneric(0, e2)
1030 : mmaechler 2945 if(all0(f0)) { # remain diagonal
1031 : mmaechler 2175 L1 <- (le <- length(e2)) == 1L
1032 : mmaechler 2984 E <- copyClass(e1, "ldiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
1033 : mmaechler 2820 ## storage.mode(E@x) <- "logical"
1034 :     if(e1@diag == "U") {
1035 :     if(any((r <- callGeneric(1, e2)) != 1)) {
1036 :     E@diag <- "N"
1037 :     E@x[seq_len(n)] <- r # possibly recycling r
1038 :     } ## else: result = E (is "U" diag)
1039 :     } else {
1040 : mmaechler 2175 r <- callGeneric(e1@x, e2)
1041 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1042 :     E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1043 : mmaechler 2814 }
1044 : mmaechler 2820 E
1045 :     } else
1046 :     callGeneric(diag2tT.u(e1,e2, "d"), e2)
1047 : mmaechler 2175 })
1048 :    
1049 : mmaechler 2820 ## ldi*: for "Ops" without "Arith": <Compare> or <Logic> --> result logical, potentially ldi
1050 : mmaechler 2813 for(arg2 in c("numeric","logical"))
1051 :     setMethod("Ops", signature(e1 = "ldiMatrix", e2 = arg2),
1052 : maechler 2144 function(e1,e2) {
1053 : mmaechler 2820 n <- e1@Dim[1]
1054 : maechler 2144 f0 <- callGeneric(FALSE, e2)
1055 : mmaechler 2945 if(all0(f0)) { # remain diagonal
1056 : maechler 2157 L1 <- (le <- length(e2)) == 1L
1057 : mmaechler 2820
1058 :     if(e1@diag == "U") {
1059 :     if(any((r <- callGeneric(TRUE, e2)) != 1)) {
1060 :     e1@diag <- "N"
1061 :     e1@x[seq_len(n)] <- r # possibly recycling r
1062 :     } ## else: result = e1 (is "U" diag)
1063 :     } else {
1064 : maechler 2144 r <- callGeneric(e1@x, e2)
1065 : mmaechler 2820 ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1066 :     e1@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1067 :     }
1068 :     e1
1069 :     } else
1070 :     callGeneric(diag2tT.u(e1,e2, "l"), e2)
1071 : maechler 2144 })
1072 : maechler 1655
1073 : maechler 2144
1074 :     ## Not {"sparseMatrix", "numeric} : {"denseMatrix", "matrix", ... }
1075 : mmaechler 2196 for(other in c("ANY", "Matrix", "dMatrix")) {
1076 :     ## ddi*:
1077 :     setMethod("Ops", signature(e1 = "ddiMatrix", e2 = other),
1078 : mmaechler 2493 function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
1079 : mmaechler 2196 setMethod("Ops", signature(e1 = other, e2 = "ddiMatrix"),
1080 : mmaechler 2493 function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
1081 : mmaechler 2196 ## ldi*:
1082 :     setMethod("Ops", signature(e1 = "ldiMatrix", e2 = other),
1083 : mmaechler 2493 function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
1084 : mmaechler 2196 setMethod("Ops", signature(e1 = other, e2 = "ldiMatrix"),
1085 : mmaechler 2493 function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
1086 : mmaechler 2196 }
1087 : mmaechler 2331
1088 :     ## Direct subclasses of "denseMatrix": currently ddenseMatrix, ldense... :
1089 :     dense.subCl <- local({ dM.scl <- getClass("denseMatrix")@subclasses
1090 : mmaechler 2813 names(dM.scl)[vapply(dM.scl, slot, 0, "distance") == 1] })
1091 : mmaechler 2268 for(DI in diCls) {
1092 : mmaechler 2814 dMeth <- if(extends(DI, "dMatrix"))
1093 :     function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2)
1094 :     else # "lMatrix", the only other kind for now
1095 :     function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2)
1096 : mmaechler 2331 for(c2 in c(dense.subCl, "Matrix")) {
1097 : mmaechler 2814 for(Fun in c("*", "&")) {
1098 : mmaechler 2268 setMethod(Fun, signature(e1 = DI, e2 = c2),
1099 :     function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
1100 :     setMethod(Fun, signature(e1 = c2, e2 = DI),
1101 :     function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
1102 :     }
1103 : mmaechler 2814 setMethod("^", signature(e1 = c2, e2 = DI),
1104 :     function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
1105 :     for(Fun in c("%%", "%/%", "/")) ## 0 <op> 0 |--> NaN for these.
1106 :     setMethod(Fun, signature(e1 = DI, e2 = c2), dMeth)
1107 : mmaechler 2175 }
1108 :     }
1109 : maechler 2144
1110 : mmaechler 3002 ## Group methods "Math", "Math2" in --> ./Math.R
1111 :    
1112 : mmaechler 2175 ### "Summary" : "max" "min" "range" "prod" "sum" "any" "all"
1113 : mmaechler 2345 ### ---------- the last 4: separately here
1114 : mmaechler 2175 for(cl in diCls) {
1115 :     setMethod("any", cl,
1116 :     function (x, ..., na.rm) {
1117 :     if(any(x@Dim == 0)) FALSE
1118 :     else if(x@diag == "U") TRUE else any(x@x, ..., na.rm = na.rm)
1119 :     })
1120 : mmaechler 2341 setMethod("all", cl, function (x, ..., na.rm) {
1121 :     n <- x@Dim[1]
1122 :     if(n >= 2) FALSE
1123 :     else if(n == 0 || x@diag == "U") TRUE
1124 :     else all(x@x, ..., na.rm = na.rm)
1125 :     })
1126 :     setMethod("prod", cl, function (x, ..., na.rm) {
1127 :     n <- x@Dim[1]
1128 :     if(n >= 2) 0
1129 :     else if(n == 0 || x@diag == "U") 1
1130 :     else ## n == 1, diag = "N" :
1131 :     prod(x@x, ..., na.rm = na.rm)
1132 :     })
1133 : mmaechler 2175
1134 :     setMethod("sum", cl,
1135 :     function(x, ..., na.rm) {
1136 :     r <- sum(x@x, ..., na.rm = na.rm)# double or integer, correctly
1137 :     if(x@diag == "U" && !is.na(r)) r + x@Dim[1] else r
1138 :     })
1139 :     }
1140 :    
1141 :     ## The remaining ones are max, min, range :
1142 :    
1143 :     setMethod("Summary", "ddiMatrix",
1144 :     function(x, ..., na.rm) {
1145 :     if(any(x@Dim == 0)) callGeneric(numeric(0), ..., na.rm=na.rm)
1146 :     else if(x@diag == "U")
1147 :     callGeneric(x@x, 0, 1, ..., na.rm=na.rm)
1148 :     else callGeneric(x@x, 0, ..., na.rm=na.rm)
1149 :     })
1150 :     setMethod("Summary", "ldiMatrix",
1151 :     function(x, ..., na.rm) {
1152 :     if(any(x@Dim == 0)) callGeneric(logical(0), ..., na.rm=na.rm)
1153 :     else if(x@diag == "U")
1154 :     callGeneric(x@x, FALSE, TRUE, ..., na.rm=na.rm)
1155 :     else callGeneric(x@x, FALSE, ..., na.rm=na.rm)
1156 :     })
1157 :    
1158 :    
1159 :    
1160 : maechler 1109 ## similar to prTriang() in ./Auxiliaries.R :
1161 :     prDiag <-
1162 :     function(x, digits = getOption("digits"), justify = "none", right = TRUE)
1163 :     {
1164 :     cf <- array(".", dim = x@Dim, dimnames = x@Dimnames)
1165 :     cf[row(cf) == col(cf)] <-
1166 :     sapply(diag(x), format, digits = digits, justify = justify)
1167 :     print(cf, quote = FALSE, right = right)
1168 :     invisible(x)
1169 :     }
1170 :    
1171 : mmaechler 2237 ## somewhat consistent with "print" for sparseMatrix :
1172 :     setMethod("print", signature(x = "diagonalMatrix"), prDiag)
1173 :    
1174 : maechler 1109 setMethod("show", signature(object = "diagonalMatrix"),
1175 : maechler 1592 function(object) {
1176 :     d <- dim(object)
1177 :     cl <- class(object)
1178 : mmaechler 2203 cat(sprintf('%d x %d diagonal matrix of class "%s"',
1179 : maechler 1592 d[1], d[2], cl))
1180 : mmaechler 2203 if(d[1] < 50) {
1181 :     cat("\n")
1182 :     prDiag(object)
1183 :     } else {
1184 :     cat(", with diagonal entries\n")
1185 :     show(diag(object))
1186 :     invisible(object)
1187 :     }
1188 : maechler 1592 })
1189 : mmaechler 2813
1190 : mmaechler 2998 rm(arg1, arg2, other, DI, Fun, cl, c1, c2,
1191 : mmaechler 2898 dense.subCl, diCls)# not used elsewhere
1192 : mmaechler 2820
1193 :     setMethod("summary", signature(object = "diagonalMatrix"),
1194 :     function(object, ...) {
1195 :     d <- dim(object)
1196 :     r <- summary(object@x, ...)
1197 :     attr(r, "header") <-
1198 :     sprintf('%d x %d diagonal Matrix of class "%s"',
1199 :     d[1], d[2], class(object))
1200 :     ## use ole' S3 technology for such a simple case
1201 :     class(r) <- c("diagSummary", class(r))
1202 :     r
1203 :     })
1204 :    
1205 :     print.diagSummary <- function (x, ...) {
1206 :     cat(attr(x, "header"),"\n")
1207 :     class(x) <- class(x)[-1]
1208 :     print(x, ...)
1209 :     invisible(x)
1210 :     }

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