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Diff of /pkg/Matrix/R/diagMatrix.R

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pkg/R/diagMatrix.R revision 2096, Fri Dec 7 17:44:44 2007 UTC pkg/Matrix/R/diagMatrix.R revision 3069, Thu Mar 26 10:00:49 2015 UTC
# Line 5  Line 5 
5  ##          but *not* diag() extractor!  ##          but *not* diag() extractor!
6  Diagonal <- function(n, x = NULL)  Diagonal <- function(n, x = NULL)
7  {  {
8      ## Allow  Diagonal(4)  and  Diagonal(x=1:5)      ## Allow  Diagonal(4), Diagonal(x=1:5), and  Diagonal(4, TRUE)
9      if(missing(n))      n <- if(missing(n)) length(x) else {
         n <- length(x)  
     else {  
10          stopifnot(length(n) == 1, n == as.integer(n), n >= 0)          stopifnot(length(n) == 1, n == as.integer(n), n >= 0)
11          n <- as.integer(n)          as.integer(n)
12      }      }
13    
14      if(missing(x)) ## unit diagonal matrix      if(missing(x)) ## unit diagonal matrix
15          new("ddiMatrix", Dim = c(n,n), diag = "U")          new("ddiMatrix", Dim = c(n,n), diag = "U")
16      else {      else {
17          stopifnot(length(x) == n)          lx <- length(x)
18            lx.1 <- lx == 1L
19            stopifnot(lx.1 || lx == n) # but keep 'x' short for now
20          if(is.logical(x))          if(is.logical(x))
21              cl <- "ldiMatrix"              cl <- "ldiMatrix"
22          else if(is.numeric(x)) {          else if(is.numeric(x)) {
# Line 26  Line 26 
26          else if(is.complex(x)) {          else if(is.complex(x)) {
27              cl <- "zdiMatrix"  # will not yet work              cl <- "zdiMatrix"  # will not yet work
28          } else stop("'x' has invalid data type")          } else stop("'x' has invalid data type")
29          new(cl, Dim = c(n,n), diag = "N", x = x)          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      }      }
35  }  }
36    
37  ### This is modified from a post of Bert Gunter to R-help on  1 Sep 2005.  .sparseDiagonal <- function(n, x = 1, uplo = "U",
38  ### Bert's code built on a post by Andy Liaw who most probably was influenced                              shape = if(missing(cols)) "t" else "g",
39  ### by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002                              unitri, kind,
40  ### who posted his bdiag() function written in December 1995.                              cols = if(n) 0:(n - 1L) else integer(0))
41    {
42        stopifnot(n == (n. <- as.integer(n)), (n <- n.) >= 0)
43        if(!(mcols <- missing(cols)))
44            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        stopifnot(is.character(shape), nchar(shape) == 1,
56                  any(shape == c("t","s","g"))) # triangular / symmetric / general
57        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            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        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    }
80    
81  bdiag <- function(...) {  ## Pkg 'spdep' had (relatively slow) versions of this as_dsCMatrix_I()
82      if(nargs() == 0) return(new("dgCMatrix"))  .symDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
83      ## else :      .sparseDiagonal(n, x, uplo, shape = "s")
84      mlist <- if (nargs() == 1) as.list(...) else list(...)  
85      dims <- sapply(mlist, dim)  # instead of   diagU2N(as(Diagonal(n), "CsparseMatrix")), diag = "N" in any case:
86    .trDiagonal <- function(n, x = 1, uplo = "U", unitri=TRUE)
87        .sparseDiagonal(n, x, uplo, shape = "t", unitri=unitri)
88    
89    
90    ## 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    if(FALSE)##--- no longer used:
95    .bdiag <- function(lst) {
96        ## block-diagonal matrix [a dgTMatrix] from list of matrices
97        stopifnot(is.list(lst), length(lst) >= 1)
98        dims <- vapply(lst, dim, 1L, USE.NAMES=FALSE)
99      ## make sure we had all matrices:      ## make sure we had all matrices:
100      if(!(is.matrix(dims) && nrow(dims) == 2))      if(!(is.matrix(dims) && nrow(dims) == 2))
101          stop("some arguments are not matrices")          stop("some arguments are not matrices")
102      csdim <- rbind(rep.int(0L, 2),      csdim <- rbind(rep.int(0L, 2),
103                     apply(sapply(mlist, dim), 1, cumsum))                     apply(dims, 1, cumsum))
104      ret <- new("dgTMatrix", Dim = as.integer(csdim[nrow(csdim),]))      r <- new("dgTMatrix")
105        r@Dim <- as.integer(csdim[nrow(csdim),])
106      add1 <- matrix(1:0, 2,2)      add1 <- matrix(1:0, 2,2)
107      for(i in seq_along(mlist)) {      for(i in seq_along(lst)) {
108          indx <- apply(csdim[i:(i+1),] + add1, 2, function(n) n[1]:n[2])          indx <- apply(csdim[i:(i+1),] + add1, 2, function(n) n[1]:n[2])
109          if(is.null(dim(indx))) ## non-square matrix          if(is.null(dim(indx))) ## non-square matrix
110              ret[indx[[1]],indx[[2]]] <- mlist[[i]]              r[indx[[1]],indx[[2]]] <- lst[[i]]
111          else ## square matrix          else ## square matrix
112              ret[indx[,1],indx[,2]] <- mlist[[i]]              r[indx[,1], indx[,2]] <- lst[[i]]
113      }      }
114      ## slightly debatable if we really should return Csparse.. :      r
     as(ret, "CsparseMatrix")  
115  }  }
116    ## 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    .bdiag <- function(lst) {
120        ## block-diagonal matrix [a dgTMatrix] from list of matrices
121        stopifnot(is.list(lst), (nl <- length(lst)) >= 1)
122    
123        Tlst <- lapply(lapply(lst, as_Csp2), # includes "diagU2N"
124                       as, "TsparseMatrix")
125        if(nl == 1) return(Tlst[[1]])
126        ## else
127        i_off <- c(0L, cumsum(vapply(Tlst, nrow, 1L)))
128        j_off <- c(0L, cumsum(vapply(Tlst, ncol, 1L)))
129    
130        clss <- vapply(Tlst, class, "")
131        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            Tlst[is.n] <- lapply(Tlst[is.n], as, "lMatrix")
138            knd [is.n] <- "l"
139        }
140        use.l <- !use.n && all(knd == "l")
141        if(all(sym)) { ## result should be *symmetric*
142            uplos <- vapply(Tlst, slot, ".", "uplo") ## either "U" or "L"
143            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                r <- new(paste0(if(use.l) "l" else "d", "sTMatrix"))
157                r@x <- unlist(lapply(Tlst, slot, "x"))
158            }
159            r@uplo <- if(useU) "U" else "L"
160        }
161        else if(all(tri) && { ULs <- vapply(Tlst, slot, ".", "uplo")##  "U" or "L"
162                              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                r <- new(paste0(if(use.l) "l" else "d", "tTMatrix"))
169                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                r <- new(paste0(if(use.l) "l" else "d", "gTMatrix"))
180                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    }
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    setMethod("tril", "diagonalMatrix", function(x, k = 0, ...)
202        if(k >= 0) x else .setZero(x, paste0(.M.kind(x), "tCMatrix")))
203    
204  diag2tT <- function(from) {  setMethod("triu", "diagonalMatrix", function(x, k = 0, ...)
205        if(k <= 0) x else  .setZero(x, paste0(.M.kind(x), "tCMatrix")))
206    
207    
208    
209    .diag2tT <- function(from, uplo = "U", kind = .M.kind(from)) {
210        ## to triangular Tsparse
211      i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L      i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L
212      new(paste(.M.kind(from), "tTMatrix", sep=''),      new(paste0(kind, "tTMatrix"),
213          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
214            uplo = uplo,
215          x = from@x, # <- ok for diag = "U" and "N" (!)          x = from@x, # <- ok for diag = "U" and "N" (!)
216          i = i, j = i)          i = i, j = i)
217  }  }
218    
219  diag2sT <- function(from) { # to symmetric Tsparse  .diag2sT <- function(from, uplo = "U", kind = .M.kind(from)) {
220      i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L      ## to symmetric Tsparse
221      new(paste(.M.kind(from), "sTMatrix", sep=''),      n <- from@Dim[1]
222        i <- seq_len(n) - 1L
223        new(paste0(kind, "sTMatrix"),
224          Dim = from@Dim, Dimnames = from@Dimnames,          Dim = from@Dim, Dimnames = from@Dimnames,
225          x = from@x, i = i, j = i)          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                           stop(gettextf("%s kind not yet implemented",
233                                         sQuote(kind)), domain=NA)),
234                    n))
235    }
236    
237    ## diagonal -> triangular,  upper / lower depending on "partner" 'x':
238    diag2tT.u <- function(d, x, kind = .M.kind(d))
239        .diag2tT(d, uplo = if(is(x,"triangularMatrix")) x@uplo else "U", kind)
240    
241    ## 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    
250  setAs("diagonalMatrix", "triangularMatrix", diag2tT)  ## FIXME: should not be needed {when ddi* is dsparse* etc}:
251  setAs("diagonalMatrix", "sparseMatrix", diag2tT)  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    
256    ## 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    di2tT <- function(from) .diag2tT(from, "U", "d")
262    setAs("ddiMatrix", "triangularMatrix", di2tT)
263    ##_no_longer_ setAs("ddiMatrix", "sparseMatrix", di2tT)
264  ## needed too (otherwise <dense> -> Tsparse is taken):  ## needed too (otherwise <dense> -> Tsparse is taken):
265  setAs("diagonalMatrix", "TsparseMatrix", diag2tT)  setAs("ddiMatrix", "TsparseMatrix", di2tT)
266  ## is better than this:  setAs("ddiMatrix", "dsparseMatrix", di2tT)
267  ## setAs("diagonalMatrix", "sparseMatrix",  setAs("ddiMatrix", "CsparseMatrix",
268  ##       function(from)        function(from) as(.diag2tT(from, "U", "d"), "CsparseMatrix"))
269  ##        as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))  setAs("ddiMatrix", "symmetricMatrix", function(from) .diag2sT(from, "U", "d"))
270  setAs("diagonalMatrix", "CsparseMatrix",  ##
271        function(from) as(diag2tT(from), "CsparseMatrix"))  ## ldi*:
272    di2tT <- function(from) .diag2tT(from, "U", "l")
273  setAs("diagonalMatrix", "symmetricMatrix", diag2sT)  setAs("ldiMatrix", "triangularMatrix", di2tT)
274    ##_no_longer_ setAs("ldiMatrix", "sparseMatrix", di2tT)
275    ## needed too (otherwise <dense> -> Tsparse is taken):
276    setAs("ldiMatrix", "TsparseMatrix", di2tT)
277    setAs("ldiMatrix", "lsparseMatrix", di2tT)
278    setAs("ldiMatrix", "CsparseMatrix",
279          function(from) as(.diag2tT(from, "U", "l"), "CsparseMatrix"))
280    setAs("ldiMatrix", "symmetricMatrix", function(from) .diag2sT(from, "U", "l"))
281    rm(di2tT)
282    
283  setAs("diagonalMatrix", "matrix",  setAs("diagonalMatrix", "nMatrix",
284        function(from) {        function(from) {
285            n <- from@Dim[1]            i <- if(from@diag == "U") integer(0) else which(isN0(from@x)) - 1L
286            diag(x = if(from@diag == "U") { if(is.numeric(from@x)) 1. else TRUE            new("ntTMatrix", i = i, j = i, diag = from@diag,
287                                       } else from@x,                Dim = from@Dim, Dimnames = from@Dimnames)
                nrow = n, ncol = n)  
288        })        })
289    
290  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:  setAs("diagonalMatrix", "nsparseMatrix", function(from) as(from, "nMatrix"))
       function(from) as(from, paste(.M.kind(from), "gCMatrix", sep='')))  
291    
292  .diag.x <- function(m) {  ##' A version of diag(x,n) which *does* preserve the mode of x, where diag() "fails"
293      if(m@diag == "U")  mkDiag <- function(x, n) {
294          rep.int(if(is.numeric(m@x)) 1. else TRUE,      y <- matrix(as0(mod=mode(x)), n,n)
295                  m@Dim[1])      if (n > 0) y[1L + 0:(n - 1L) * (n + 1)] <- x
296      else m@x      y
 }  
   
 .diag.2N <- function(m) {  
     if(m@diag == "U") m@diag <- "N"  
     m  
297  }  }
298    ## NB: diag(x,n) is really faster for n >= 20, and even more for large n
299    ## --> using diag() where possible, ==> .ddi2mat()
300    
301  ## given the above, the following  4  coercions should be all unneeded;  .diag2mat <- function(from)
302  ## we prefer triangular to general:      ## want "ldiMatrix" -> <logical> "matrix"  (but integer -> <double> for now)
303  setAs("ddiMatrix", "dgTMatrix",      mkDiag(if(from@diag == "U") as1(from@x) else from@x, n = from@Dim[1])
304        function(from) {  
305            .Deprecated("as(, \"sparseMatrix\")")  .ddi2mat <- function(from)
306            n <- from@Dim[1]      base::diag(if(from@diag == "U") as1(from@x) else from@x, nrow = from@Dim[1])
307            i <- seq_len(n) - 1L  
308            new("dgTMatrix", i = i, j = i, x = .diag.x(from),  setAs("ddiMatrix", "matrix", .ddi2mat)
309                Dim = c(n,n), Dimnames = from@Dimnames) })  ## the non-ddi diagonalMatrix -- only "ldiMatrix" currently:
310    setAs("diagonalMatrix", "matrix", .diag2mat)
311    
312    setMethod("as.vector", signature(x = "diagonalMatrix", mode="missing"),
313              function(x, mode) {
314                  n <- x@Dim[1]
315                  mod.x <- mode(x@x)
316                  r <- vector(mod.x, length = n^2)
317                  if(n)
318                      r[1 + 0:(n - 1L) * (n + 1)] <-
319                          if(x@diag == "U") as1(mod=mod.x) else x@x
320                  r
321              })
322    
323  setAs("ddiMatrix", "dgCMatrix",  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
324        function(from) as(as(from, "sparseMatrix"), "dgCMatrix"))        function(from) as(as(from, "CsparseMatrix"), "generalMatrix"))
325    
326  setAs("ldiMatrix", "lgTMatrix",  setAs("diagonalMatrix", "denseMatrix",
327        function(from) {        function(from) as(as(from, "CsparseMatrix"), "denseMatrix"))
           .Deprecated("as(, \"sparseMatrix\")")  
           n <- from@Dim[1]  
           if(from@diag == "U") { # unit-diagonal  
               x <- rep.int(TRUE, n)  
               i <- seq_len(n) - 1L  
           } else { # "normal"  
               nz <- nz.NA(from@x, na. = TRUE)  
               x <- from@x[nz]  
               i <- which(nz) - 1L  
           }  
           new("lgTMatrix", i = i, j = i, x = x,  
               Dim = c(n,n), Dimnames = from@Dimnames) })  
328    
329  setAs("ldiMatrix", "lgCMatrix",  ..diag.x <- function(m)                   rep.int(as1(m@x), m@Dim[1])
330        function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))  .diag.x  <- function(m) if(m@diag == "U") rep.int(as1(m@x), m@Dim[1]) else m@x
331    
332    .diag.2N <- function(m) {
333        if(m@diag == "U") m@diag <- "N"
334        m
335    }
336    
 if(FALSE) # now have faster  "ddense" -> "dge"  
337  setAs("ddiMatrix", "dgeMatrix",  setAs("ddiMatrix", "dgeMatrix",
338        function(from) as(as(from, "matrix"), "dgeMatrix"))        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
339    setAs("ddiMatrix", "ddenseMatrix",
340          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
341    setAs("ldiMatrix", "ldenseMatrix",
342          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
343    
344    
345  setAs("matrix", "diagonalMatrix",  setAs("matrix", "diagonalMatrix",
346        function(from) {        function(from) {
347            d <- dim(from)            d <- dim(from)
348            if(d[1] != (n <- d[2])) stop("non-square matrix")            if(d[1] != (n <- d[2])) stop("non-square matrix")
349            if(any(from[row(from) != col(from)] != 0))            if(any(from[row(from) != col(from)] != 0))
350                stop("has non-zero off-diagonal entries")                stop("matrix with non-zero off-diagonals cannot be coerced to \"diagonalMatrix\"")
351            x <- diag(from)            x <- diag(from)
352            if(is.logical(x)) {            if(is.logical(x)) {
353                cl <- "ldiMatrix"                cl <- "ldiMatrix"
354                uni <- all(x)                uni <- allTrue(x) ## uni := {is it unit-diagonal ?}
355            } else {            } else {
356                cl <- "ddiMatrix"                cl <- "ddiMatrix"
357                uni <- all(x == 1)                uni <- allTrue(x == 1)
358                storage.mode(x) <- "double"                storage.mode(x) <- "double"
359            } ## TODO: complex            } ## TODO: complex
360            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
# Line 174  Line 371 
371            x <- diag(from)            x <- diag(from)
372            if(is.logical(x)) {            if(is.logical(x)) {
373                cl <- "ldiMatrix"                cl <- "ldiMatrix"
374                uni <- all(x)                uni <- allTrue(x)
375            } else {            } else {
376                cl <- "ddiMatrix"                cl <- "ddiMatrix"
377                uni <- all(x == 1)                uni <- allTrue(x == 1)
378                storage.mode(x) <- "double"                storage.mode(x) <- "double"
379            }            } ## TODO: complex
380            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
381                x = if(uni) x[FALSE] else x)                x = if(uni) x[FALSE] else x)
382        })        })
# Line 188  Line 385 
385  setMethod("diag", signature(x = "diagonalMatrix"),  setMethod("diag", signature(x = "diagonalMatrix"),
386            function(x = 1, nrow, ncol) .diag.x(x))            function(x = 1, nrow, ncol) .diag.x(x))
387    
388    subDiag <- function(x, i, j, ..., drop) {
389  subDiag <- function(x, i, j, drop) {      x <- as(x, "CsparseMatrix") ## << was "TsparseMatrix" (Csparse is faster now)
     x <- as(x, "sparseMatrix")  
390      x <- if(missing(i))      x <- if(missing(i))
391          x[, j, drop=drop]          x[, j, drop=drop]
392      else if(missing(j))      else if(missing(j))
393          x[i, , drop=drop]          if(nargs() == 4) x[i, , drop=drop] else x[i, drop=drop]
394      else      else
395          x[i,j, drop=drop]          x[i,j, drop=drop]
396      if(isDiagonal(x)) as(x, "diagonalMatrix") else x      if(isS4(x) && isDiagonal(x)) as(x, "diagonalMatrix") else x
397  }  }
398    
399  setMethod("[", signature(x = "diagonalMatrix", i = "index",  setMethod("[", signature(x = "diagonalMatrix", i = "index",
400                           j = "index", drop = "logical"), subDiag)                           j = "index", drop = "logical"), subDiag)
401  setMethod("[", signature(x = "diagonalMatrix", i = "index",  setMethod("[", signature(x = "diagonalMatrix", i = "index",
402                          j = "missing", drop = "logical"),                          j = "missing", drop = "logical"),
403            function(x, i, drop) subDiag(x, i=i, drop=drop))            function(x, i, j, ..., drop) {
404                  na <- nargs()
405                  Matrix.msg("diag[i,m,l] : nargs()=", na, .M.level = 2)
406                  if(na == 4)
407                       subDiag(x, i=i, , drop=drop)
408                  else subDiag(x, i=i,   drop=drop)
409              })
410  setMethod("[", signature(x = "diagonalMatrix", i = "missing",  setMethod("[", signature(x = "diagonalMatrix", i = "missing",
411                           j = "index", drop = "logical"),                           j = "index", drop = "logical"),
412            function(x, j, drop) subDiag(x, j=j, drop=drop))            function(x, i, j, ..., drop) subDiag(x, j=j, drop=drop))
413    
414  ## When you assign to a diagonalMatrix, the result should be  ## When you assign to a diagonalMatrix, the result should be
415  ## diagonal or sparse ---  ## diagonal or sparse ---
416  ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch  ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch
417  replDiag <- function(x, i, j, value) {  ## Only(?) current bug:  x[i] <- value  is wrong when  i is *vector*
418      x <- as(x, "sparseMatrix")  replDiag <- function(x, i, j, ..., value) {
419      message(sprintf("diagnosing replDiag() -- nargs() = %d\n", nargs()))      x <- as(x, "CsparseMatrix")# was "Tsparse.." till 2012-07
420      if(missing(i))      if(missing(i))
421          x[, j] <- value          x[, j] <- value
422      else if(missing(j))      else if(missing(j)) { ##  x[i , ] <- v  *OR*   x[i] <- v
423            na <- nargs()
424    ##         message("diagnosing replDiag() -- nargs()= ", na)
425            if(na == 4)
426          x[i, ] <- value          x[i, ] <- value
427      else          else if(na == 3)
428                x[i] <- value
429            else stop(gettextf("Internal bug: nargs()=%d; please report",
430                               na), domain=NA)
431        } else
432          x[i,j] <- value          x[i,j] <- value
433      if(isDiagonal(x)) as(x, "diagonalMatrix") else x      if(isDiagonal(x)) as(x, "diagonalMatrix") else x
434  }  }
435    
436  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
437                                  j = "index", value = "replValue"), replDiag)                                  j = "index", value = "replValue"), replDiag)
438    
439  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
440                                  j = "missing", value = "replValue"),                                  j = "missing", value = "replValue"),
441                   function(x, i, value) replDiag(x, i=i, value=value))                   function(x,i,j, ..., value) {
442  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "matrix", # 2-col.matrix                       ## message("before replDiag() -- nargs()= ", nargs())
443                         if(nargs() == 3)
444                             replDiag(x, i=i, value=value)
445                         else ## nargs() == 4 :
446                             replDiag(x, i=i, , value=value)
447                     })
448    
449    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
450                                    j = "index", value = "replValue"),
451                     function(x,i,j, ..., value) replDiag(x, j=j, value=value))
452    
453    ## x[] <- value :
454    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
455                                    j = "missing", value = "ANY"),
456                     function(x,i,j, ..., value)
457                 {
458                  if(all0(value)) { # be faster
459                      r <- new(paste0(.M.kindC(getClassDef(class(x))),"tTMatrix"))# of all "0"
460                      r@Dim <- x@Dim
461                      r@Dimnames <- x@Dimnames
462                      r
463                  } else { ## typically non-sense: assigning to full sparseMatrix
464                      x[TRUE] <- value
465                      x
466                  }
467              })
468    
469    
470    setReplaceMethod("[", signature(x = "diagonalMatrix",
471                                    i = "matrix", # 2-col.matrix
472                                  j = "missing", value = "replValue"),                                  j = "missing", value = "replValue"),
473                   function(x, i, value) {                   function(x,i,j, ..., value) {
474                       if(ncol(i) == 2) {                       if(ncol(i) == 2) {
475                           if(all((ii <- i[,1]) == i[,2])) { # replace in diagonal only                           if(all((ii <- i[,1]) == i[,2])) { # replace in diagonal only
476                                 if(x@diag == "U") {
477                                     one <- as1(x@x)
478                                     if(any(value != one | is.na(value))) {
479                                         x@diag <- "N"
480                                         x@x <- rep.int(one, x@Dim[1])
481                                     } else return(x)
482                                 }
483                               x@x[ii] <- value                               x@x[ii] <- value
484                               x                               x
485                           } else { ## no longer diagonal, but remain sparse:                           } else { ## no longer diagonal, but remain sparse:
486                               x <- as(x, "sparseMatrix")                               x <- as(x, "TsparseMatrix")
487                               x[i] <- value                               x[i] <- value
488                               x                               x
489                           }                           }
# Line 249  Line 495 
495                       }                       }
496                   })                   })
497    
498  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",  
499                                  j = "index", value = "replValue"),  ## value = "sparseMatrix":
500                   function(x, j, value) replDiag(x, j=j, value=value))  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
501                                    value = "sparseMatrix"),
502                     function (x, i, j, ..., value)
503                     callGeneric(x=x, , j=j, value = as(value, "sparseVector")))
504    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
505                                    value = "sparseMatrix"),
506                     function (x, i, j, ..., value)
507                     callGeneric(x=x, i=i, , value = as(value, "sparseVector")))
508    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
509                                    value = "sparseMatrix"),
510                     function (x, i, j, ..., value)
511                     callGeneric(x=x, i=i, j=j, value = as(value, "sparseVector")))
512    
513    ## value = "sparseVector":
514    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
515                                    value = "sparseVector"),
516                     replDiag)
517    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
518                                    value = "sparseVector"),
519                     replDiag)
520    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
521                                    value = "sparseVector"),
522                     replDiag)
523    
524    
525  setMethod("t", signature(x = "diagonalMatrix"),  setMethod("t", signature(x = "diagonalMatrix"),
526            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })
527    
528  setMethod("isDiagonal", signature(object = "diagonalMatrix"),  setMethod("isDiagonal",   "diagonalMatrix", function(object) TRUE)
529            function(object) TRUE)  setMethod("isTriangular", "diagonalMatrix", function(object, upper=NA, ...) TRUE)
530  setMethod("isTriangular", signature(object = "diagonalMatrix"),  setMethod("isSymmetric",  "diagonalMatrix", function(object, ...) TRUE)
531            function(object) TRUE)  
532  setMethod("isSymmetric", signature(object = "diagonalMatrix"),  setMethod("symmpart", signature(x = "diagonalMatrix"), function(x) x)
533            function(object) TRUE)  setMethod("skewpart", signature(x = "diagonalMatrix"), function(x) .setZero(x))
534    
535  setMethod("chol", signature(x = "ddiMatrix"),# pivot = "ANY"  setMethod("chol", signature(x = "ddiMatrix"),
536            function(x, pivot) {            function(x, pivot, ...) {
537                if(any(x@x < 0)) stop("chol() is undefined for diagonal matrix with negative entries")                if(x@diag == "U") return(x)
538                  ## else
539                  if(any(x@x < 0))
540                      stop("chol() is undefined for diagonal matrix with negative entries")
541                x@x <- sqrt(x@x)                x@x <- sqrt(x@x)
542                x                x
543            })            })
544  ## chol(L) is L for logical diagonal:  ## chol(L) is L for logical diagonal:
545  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot) x)  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot, ...) x)
546    
547    setMethod("determinant", signature(x = "diagonalMatrix", logarithm = "logical"),
548              function(x, logarithm, ...) mkDet(.diag.x(x), logarithm))
549    
550    setMethod("norm", signature(x = "diagonalMatrix", type = "character"),
551              function(x, type, ...) {
552                  if((n <- x@Dim[1]) == 0) return(0) # as for "sparseMatrix"
553                  type <- toupper(substr(type[1], 1, 1))
554                  isU <- (x@diag == "U") # unit-diagonal
555                  if(type == "F") sqrt(if(isU) n else sum(x@x^2))
556                  else { ## norm == "I","1","O","M" :
557                      if(isU) 1 else max(abs(x@x))
558                  }
559              })
560    
561    
562    
563  ## Basic Matrix Multiplication {many more to add}  ## Basic Matrix Multiplication {many more to add}
564  ##       ---------------------  ##       ---------------------
565  ## Note that "ldi" logical are treated as numeric  ## Note that "ldi" logical are treated as numeric
566  diagdiagprod <- function(x, y) {  diagdiagprod <- function(x, y) {
567      if(any(dim(x) != dim(y))) stop("non-matching dimensions")      dimCheck(x,y)
568      if(x@diag != "U") {      if(x@diag != "U") {
569          if(y@diag != "U") {          if(y@diag != "U") {
570              nx <- x@x * y@x              nx <- x@x * y@x
# Line 290  Line 577 
577      return(y)      return(y)
578  }  }
579    
580    ##' Boolean Algebra/Arithmetic Product of Diagonal Matrices
581    ##'  %&%
582    diagdiagprodBool <- function(x, y) {
583        dimCheck(x,y)
584        if(x@diag != "U") {
585            if(!is.logical(x@x)) x <- as(x, "lMatrix")
586            if(y@diag != "U") {
587                nx <- x@x & y@x
588                x@x <- as.logical(nx)
589            }
590            x
591        } else { ## x is unit diagonal: return y
592            if(!is.logical(y@x)) y <- as(y, "lMatrix")
593            y
594        }
595    }
596    
597  setMethod("%*%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
598            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
599    
600  formals(diagdiagprod) <- alist(x=, y=x)  setMethod("%&%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
601              diagdiagprodBool, valueClass = "ldiMatrix")# do *not* have "ndiMatrix" !
602    
603    formals(diagdiagprod) <- alist(x=, y=NULL, ...=)
604    ##                                  -----  ---  matching the [t]crossprod generic
605  setMethod("crossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
606            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
607  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
608            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
609    
610    ##' crossprod(x) := x'x
611    diagprod <- function(x, y=NULL, ...) {
612        if(x@diag != "U") {
613            nx <- x@x * x@x
614            if(is.numeric(nx) && !is.numeric(x@x))
615                x <- as(x, "dMatrix")
616            x@x <- as.numeric(nx)
617        }
618        x
619    }
620  setMethod("crossprod", signature(x = "diagonalMatrix", y = "missing"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "missing"),
621            diagdiagprod, valueClass = "ddiMatrix")            diagprod, valueClass = "ddiMatrix")
622  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "missing"),  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "missing"),
623            diagdiagprod, valueClass = "ddiMatrix")            diagprod, valueClass = "ddiMatrix")
624    
625    
626    ## analogous to matdiagprod() below:
627  diagmatprod <- function(x, y) {  diagmatprod <- function(x, y) {
628      dx <- dim(x)      ## x is diagonalMatrix
629      dy <- dim(y)      if(x@Dim[2] != nrow(y)) stop("non-matching dimensions")
630      if(dx[2] != dy[1]) stop("non-matching dimensions")      Matrix(if(x@diag == "U") y else x@x * y)
     n <- dx[1]  
     as(if(x@diag == "U") y else x@x * y, "Matrix")  
631  }  }
   
632  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),
633            diagmatprod)            diagmatprod)
 formals(diagmatprod) <- alist(x=, y=NULL)  
 setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),  
           diagmatprod)  
 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "matrix"),  
           diagmatprod)  
634    
635  diagdgeprod <- function(x, y) {  formals(diagmatprod) <- alist(x=, y=NULL, ...=)
636      dx <- dim(x)  setMethod("crossprod",  signature(x = "diagonalMatrix", y = "matrix"), diagmatprod)
637      dy <- dim(y)  
638      if(dx[2] != dy[1]) stop("non-matching dimensions")  diagGeprod <- function(x, y) {
639        if(x@Dim[2] != y@Dim[1]) stop("non-matching dimensions")
640      if(x@diag != "U")      if(x@diag != "U")
641          y@x <- x@x * y@x          y@x <- x@x * y@x
642      y      y
643  }  }
644  setMethod("%*%", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("%*%", signature(x= "diagonalMatrix", y= "dgeMatrix"), diagGeprod)
645            diagdgeprod, valueClass = "dgeMatrix")  setMethod("%*%", signature(x= "diagonalMatrix", y= "lgeMatrix"), diagGeprod)
646  formals(diagdgeprod) <- alist(x=, y=NULL)  formals(diagGeprod) <- alist(x=, y=NULL, ...=)
647  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),
648            diagdgeprod, valueClass = "dgeMatrix")            diagGeprod, valueClass = "dgeMatrix")
649    setMethod("crossprod", signature(x = "diagonalMatrix", y = "lgeMatrix"),
650              diagGeprod)
651    
652    diagGeprodBool <- function(x, y) {
653        if(x@Dim[2] != y@Dim[1]) stop("non-matching dimensions")
654        if(!is.logical(y@x)) y <- as(y, "lMatrix")
655        if(x@diag != "U")
656            y@x <- x@x & y@x
657        y
658    }
659    setMethod("%&%", signature(x= "diagonalMatrix", y= "geMatrix"), diagGeprodBool)
660    
661  setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"),  
662            function(x, y) {  ## analogous to diagmatprod() above:
663    matdiagprod <- function(x, y) {
664                dx <- dim(x)                dx <- dim(x)
665                dy <- dim(y)      if(dx[2] != y@Dim[1]) stop("non-matching dimensions")
666                if(dx[2] != dy[1]) stop("non-matching dimensions")      Matrix(if(y@diag == "U") x else x * rep(y@x, each = dx[1]))
667                as(if(y@diag == "U") x else x * rep(y@x, each = dx[1]), "Matrix")  }
668    setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"), matdiagprod)
669    formals(matdiagprod) <- alist(x=, y=NULL, ...=)
670    setMethod("tcrossprod",signature(x = "matrix", y = "diagonalMatrix"), matdiagprod)
671    setMethod("crossprod", signature(x = "matrix", y = "diagonalMatrix"),
672              function(x, y=NULL, ...) {
673                  dx <- dim(x)
674                  if(dx[1] != y@Dim[1]) stop("non-matching dimensions")
675                  Matrix(t(rep.int(y@x, dx[2]) * x))
676            })            })
677    
678  setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),  gediagprod <- function(x, y) {
           function(x, y) {  
679                dx <- dim(x)                dx <- dim(x)
680                dy <- dim(y)      if(dx[2] != y@Dim[1]) stop("non-matching dimensions")
               if(dx[2] != dy[1]) stop("non-matching dimensions")  
681                if(y@diag == "N")                if(y@diag == "N")
682                    x@x <- x@x * rep(y@x, each = dx[1])                    x@x <- x@x * rep(y@x, each = dx[1])
683                x                x
684            })  }
685    setMethod("%*%", signature(x= "dgeMatrix", y= "diagonalMatrix"), gediagprod)
686    setMethod("%*%", signature(x= "lgeMatrix", y= "diagonalMatrix"), gediagprod)
687    formals(gediagprod) <- alist(x=, y=NULL, ...=)
688    setMethod("tcrossprod", signature(x = "dgeMatrix", y = "diagonalMatrix"),
689              gediagprod)
690    setMethod("tcrossprod", signature(x = "lgeMatrix", y = "diagonalMatrix"),
691              gediagprod)
692    
693    gediagprodBool <- function(x, y) {
694        dx <- dim(x)
695        if(dx[2] != y@Dim[1]) stop("non-matching dimensions")
696        if(!is.logical(x@x)) x <- as(x, "lMatrix")
697        if(y@diag == "N")
698            x@x <- x@x & rep(y@x, each = dx[1])
699        x
700    }
701    setMethod("%&%", signature(x= "geMatrix", y= "diagonalMatrix"), gediagprodBool)
702    
703  ## crossprod {more of these}  ## crossprod {more of these}
704    
705  ## tcrossprod --- all are not yet there: do the dense ones here:  ## tcrossprod --- all are not yet there: do the dense ones here:
706    
707    setMethod("%*%", signature(x = "diagonalMatrix", y = "denseMatrix"),
708              function(x, y) if(x@diag == "U") y else x %*% as(y, "generalMatrix"))
709    setMethod("%*%", signature(x = "denseMatrix", y = "diagonalMatrix"),
710              function(x, y) if(y@diag == "U") x else as(x, "generalMatrix") %*% y)
711    
712    
713  ## FIXME:  ## FIXME:
714  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),
715  ##        function(x, y = NULL) {  ##        function(x, y = NULL) {
716  ##           })  ##           })
717    
718  ## setMethod("tcrossprod", signature(x = "denseMatrix", y = "diagonalMatrix"),  ##' @param x CsparseMatrix
719  ##        function(x, y = NULL) {  ##' @param y diagonalMatrix
720  ##           })  ##' @return x %*% y
721    Cspdiagprod <- function(x, y, boolArith = NA) {
722        if((m <- ncol(x)) != y@Dim[1]) stop("non-matching dimensions")
723        if(y@diag == "N") { ## otherwise: y == Diagonal(n) : multiplication is identity
724            x <- .Call(Csparse_diagU2N, x)
725            cx <- getClass(class(x))
726            if(!all(y@x[1L] == y@x[-1L]) && extends(cx, "symmetricMatrix"))
727                x <- as(x, "generalMatrix")
728            ind <- rep.int(seq_len(m), x@p[-1] - x@p[-m-1L])
729            if(isTRUE(boolArith)) {
730                if(extends(cx, "nMatrix")) x <- as(x, "lMatrix") # so, has y@x
731                x@x <- x@x & y@x[x@i + 1L]
732                if(!extends(cx, "diagonalMatrix")) x <- as(drop0(x), "nMatrix")
733            } else {
734                if(!extends(cx, "dMatrix")) x <- as(x, "dMatrix") # <- FIXME if we have zMatrix
735                x@x <- x@x * y@x[ind]
736            }
737            if(.hasSlot(x, "factors") && length(x@factors)) {# drop cashed ones
738                ## instead of dropping all factors, be smart about some
739                ## TODO ......
740                x@factors <- list()
741            }
742        }
743        x
744    }
745    
746    ##' @param x diagonalMatrix
747    ##' @param y CsparseMatrix
748    ##' @return x %*% y
749    diagCspprod <- function(x, y, boolArith = FALSE) {
750        if(x@Dim[2] != y@Dim[1]) stop("non-matching dimensions")
751        if(x@diag == "N") {
752            y <- .Call(Csparse_diagU2N, y)
753            cy <- getClass(class(y))
754            if(!all(x@x[1L] == x@x[-1L]) && extends(cy, "symmetricMatrix"))
755                y <- as(y, "generalMatrix")
756            if(isTRUE(boolArith)) {
757                if(extends(cy, "nMatrix")) y <- as(y, "lMatrix") # so, has y@x
758                y@x <- y@x & x@x[y@i + 1L]
759                if(!extends(cy, "diagonalMatrix")) y <- as(drop0(y), "nMatrix")
760            } else {
761                if(!extends(cy, "dMatrix")) y <- as(y, "dMatrix") # <- FIXME if we have zMatrix
762                y@x <- y@x * x@x[y@i + 1L]
763            }
764            if(.hasSlot(y, "factors") && length(y@factors)) {
765         ## if(.hasSlot(y, "factors") && length(yf <- y@factors)) { ## -- TODO? --
766                ## instead of dropping all factors, be smart about some
767                ## keep <- character()
768                ## if(any(names(yf) == "LU")) { ## <- not easy: y = P'LUQ,  x y = xP'LUQ => LU ???
769                ##     keep <- "LU"
770                ## }
771                ## y@factors <- yf[keep]
772                y@factors <- list()
773            }
774        }
775        y
776    }
777    
778    ## + 'boolArith' argument  { ==> .local() is used in any case; keep formals simple :}
779    setMethod("crossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
780              function(x, y, boolArith=NA) diagCspprod(x, y, boolArith=boolArith))
781    
782  setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
783            function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })            function(x, y, boolArith=NA)
784                  diagCspprod(x, as(y, "CsparseMatrix"), boolArith=boolArith))
785    
786    ## Prefer calling diagCspprod to Cspdiagprod if going to transpose anyway
787    ##  x'y == (y'x)'
788    setMethod("crossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
789              function(x, y, boolArith=NA) t(diagCspprod(y, x, boolArith=boolArith)))
790    
791  setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
792            function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })            function(x, y, boolArith=NA) t(diagCspprod(y, as(x, "Csparsematrix"), boolArith=boolArith)))
793    
794    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
795              function(x, y, boolArith=NA) diagCspprod(x, t(y), boolArith=boolArith))
796    
797  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
798            function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })            function(x, y, boolArith=NA) diagCspprod(x, t(as(y, "CsparseMatrix")), boolArith=boolArith))
799    
800    setMethod("tcrossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
801              function(x, y, boolArith=NA) Cspdiagprod(x, y, boolArith=boolArith))
802    
803  setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
804            function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })            function(x, y, boolArith=NA) Cspdiagprod(as(x, "CsparseMatrix"), y, boolArith=boolArith))
805    
806    setMethod("%*%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
807              function(x, y) diagCspprod(x, y, boolArith=NA))
808    setMethod("%&%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
809              function(x, y) diagCspprod(x, y, boolArith=TRUE))
810    
811    ## instead of "sparseMatrix", use: [RT]sparse.. ("closer" in method dispatch)
812    for(cl in c("TsparseMatrix", "RsparseMatrix")) {
813    
 ## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()  
814  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
815            function(x, y) as(x, "sparseMatrix") %*% y)            function(x, y) diagCspprod(as(x, "CsparseMatrix"), y, boolArith=NA))
 ## NB: The previous is *not* triggering for  "ddi" o "dgC" (= distance 3)  
 ##     since there's a "ddense" o "Csparse" at dist. 2 => triggers first.  
 ## ==> do this:  
 setMethod("%*%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),  
           function(x, y) as(x, "CsparseMatrix") %*% y)  
 setMethod("%*%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),  
           function(x, y) x %*% as(y, "CsparseMatrix"))  
 ## NB: this is *not* needed for Tsparse & Rsparse  
 ## TODO: Write tests in ./tests/ which ensure that many "ops" with diagonal*  
 ##       do indeed work by going through sparse (and *not* ddense)!  
816    
817  setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),
818            function(x, y) x %*% as(y, "sparseMatrix"))            function(x, y) Cspdiagprod(as(x, "CsparseMatrix"), y, boolArith=NA))
819    
820    setMethod("%&%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
821              function(x, y) diagCspprod(as(x, "CsparseMatrix"), y, boolArith=TRUE))
822    
823    setMethod("%&%", signature(x = "sparseMatrix", y = "diagonalMatrix"),
824              function(x, y) Cspdiagprod(as(x, "CsparseMatrix"), y, boolArith=TRUE))
825    
826    }
827    
828    setMethod("%*%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
829              function(x, y) Cspdiagprod(x, y, boolArith=NA))
830    setMethod("%&%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
831              function(x, y) Cspdiagprod(x, y, boolArith=TRUE))
832    
833    ## TODO: Write tests in ./tests/ which ensure that many "ops" with diagonal*
834    ##       do indeed work by going through sparse (and *not* ddense)!
835    
836  setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),  setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),
837            function(a, b, ...) {            function(a, b, ...) {
# Line 404  Line 841 
841            })            })
842    
843  solveDiag <- function(a, b, ...) {  solveDiag <- function(a, b, ...) {
844      if((n <- a@Dim[1]) != nrow(b))      if(a@Dim[1] != nrow(b))
845          stop("incompatible matrix dimensions")          stop("incompatible matrix dimensions")
846      ## trivially invert a 'in place' and multiply:      ## trivially invert a 'in place' and multiply:
847      a@x <- 1/ a@x      a@x <- 1/ a@x
# Line 416  Line 853 
853  setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),  setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),
854            solveDiag)            solveDiag)
855    
856    ## Schur()  ---> ./eigen.R
857    
858    
859    
860  ### ---------------- diagonal  o  sparse  -----------------------------  ###---------------- <Ops> (<Arith>, <Logic>, <Compare> ) ----------------------
   
861    
862  ## Use function for several signatures, in order to evade  ## Use function for several signatures, in order to evade
863  ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)  diagOdiag <- function(e1,e2) {
864  diagOdiag <- function(e1,e2) { # result should also be diagonal      ## result should also be diagonal _ if possible _
865      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
866      if(is.numeric(r)) {      ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
867        r00 <- callGeneric(if(is.numeric(e1@x)) 0 else FALSE,
868                           if(is.numeric(e2@x)) 0 else FALSE)
869        if(is0(r00)) { ##  r00 == 0 or FALSE --- result *is* diagonal
870            if(is.numeric(r)) { # "double" *or* "integer"
871          if(is.numeric(e2@x)) {          if(is.numeric(e2@x)) {
872              e2@x <- r; return(.diag.2N(e2)) }              e2@x <- r; return(.diag.2N(e2)) }
873          if(!is.numeric(e1@x))          if(!is.numeric(e1@x))
874              ## e.g. e1, e2 are logical;              ## e.g. e1, e2 are logical;
875              e1 <- as(e1, "dMatrix")              e1 <- as(e1, "dMatrix")
876                if(!is.double(r)) r <- as.double(r)
877      }      }
878      else if(is.logical(r))      else if(is.logical(r))
879          e1 <- as(e1, "lMatrix")          e1 <- as(e1, "lMatrix")
880      else stop("intermediate 'r' is of type", typeof(r))          else stop(gettextf("intermediate 'r' is of type %s",
881                               typeof(r)), domain=NA)
882      e1@x <- r      e1@x <- r
883      .diag.2N(e1)      .diag.2N(e1)
884  }  }
885        else { ## result not diagonal, but at least symmetric:
886            ## e.g., m == m
887            isNum <- (is.numeric(r) || is.numeric(r00))
888            isLog <- (is.logical(r) || is.logical(r00))
889            Matrix.msg("exploding <diag> o <diag> into dense matrix", .M.level = 2)
890            d <- e1@Dim
891            n <- d[1]
892            stopifnot(length(r) == n)
893            if(isNum && !is.double(r)) r <- as.double(r)
894            xx <- as.vector(matrix(rbind(r, matrix(r00,n,n)), n,n))
895            newcl <-
896                paste0(if(isNum) "d" else if(isLog) {
897                    if(!any(is.na(r)) && !any(is.na(r00))) "n" else "l"
898                } else stop("not yet implemented .. please report"), "syMatrix")
899    
900            new(newcl, Dim = e1@Dim, Dimnames = e1@Dimnames, x = xx)
901        }
902    }
903    
904    ### This would be *the* way, but we get tons of "ambiguous method dispatch"
905    ## we use this hack instead of signature  x = "diagonalMatrix" :
906    diCls <- names(getClass("diagonalMatrix")@subclasses)
907    if(FALSE) {
908  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
909            diagOdiag)            diagOdiag)
910  ## These two are just for method disambiguation:  } else { ## These are just for method disambiguation:
911  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "diagonalMatrix"),      for(c1 in diCls)
912            diagOdiag)          for(c2 in diCls)
913  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ddiMatrix"),              setMethod("Ops", signature(e1 = c1, e2 = c2), diagOdiag)
914            diagOdiag)  }
915    
916  ## FIXME:    diagonal  o  triangular  |-->  triangular  ## diagonal  o  triangular  |-->  triangular
917  ## -----     diagonal  o  symmetric   |-->  symmetric  ## diagonal  o  symmetric   |-->  symmetric
918  ##    {also when other is sparse: do these "here" --  ##    {also when other is sparse: do these "here" --
919  ##     before conversion to sparse, since that loses "diagonality"}  ##     before conversion to sparse, since that loses "diagonality"}
920    diagOtri <- function(e1,e2) {
921        ## result must be triangular
922        r <- callGeneric(d1 <- .diag.x(e1), diag(e2)) # error if not "compatible"
923        ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
924        e1.0 <- if(is.numeric(d1)) 0 else FALSE
925        r00 <- callGeneric(e1.0, if(.n2 <- is.numeric(e2[0])) 0 else FALSE)
926        if(is0(r00)) { ##  r00 == 0 or FALSE --- result *is* triangular
927            diag(e2) <- r
928            ## check what happens "in the triangle"
929            e2.2 <- if(.n2) 2 else TRUE
930            if(!callGeneric(e1.0, e2.2) == e2.2) { # values "in triangle" can change:
931                n <- dim(e2)[1L]
932                it <- indTri(n, upper = (e2@uplo == "U"))
933                e2[it] <- callGeneric(e1.0, e2[it])
934            }
935            e2
936        }
937        else { ## result not triangular ---> general
938            rr <- as(e2, "generalMatrix")
939            diag(rr) <- r
940            rr
941        }
942    }
943    
944    
945    setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "triangularMatrix"),
946              diagOtri)
947    ## For the reverse,  Ops == "Arith" | "Compare" | "Logic"
948    ##   'Arith'  :=  '"+"', '"-"', '"*"', '"^"', '"%%"', '"%/%"', '"/"'
949    setMethod("Arith", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
950              function(e1,e2)
951          { ## this must only trigger for *dense* e1
952              switch(.Generic,
953                     "+" = .Call(dtrMatrix_addDiag, as(e1,"dtrMatrix"),   .diag.x(e2)),
954                     "-" = .Call(dtrMatrix_addDiag, as(e1,"dtrMatrix"), - .diag.x(e2)),
955                     "*" = {
956                         n <- e2@Dim[1L]
957                         d2 <- if(e2@diag == "U") { # unit-diagonal
958                             d <- rep.int(as1(e2@x), n)
959                             e2@x <- d
960                             e2@diag <- "N"
961                             d
962                         } else e2@x
963                         e2@x <- diag(e1) * d2
964                         e2
965                     },
966                     "^" = { ## will be dense ( as  <ANY> ^ 0 == 1 ):
967                         e1 ^ as(e2, "denseMatrix")
968                     },
969                     ## otherwise:
970                     callGeneric(e1, diag2Tsmart(e2,e1)))
971    })
972    
973    ## Compare --> 'swap' (e.g.   e1 < e2   <==>  e2 > e1 ):
974    setMethod("Compare", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
975              .Cmp.swap)
976    ## '&' and "|'  are commutative:
977    setMethod("Logic", signature(e1 = "triangularMatrix", e2 = "diagonalMatrix"),
978              function(e1,e2) callGeneric(e2, e1))
979    
980  ## For almost everything else, diag* shall be treated "as sparse" :  ## For almost everything else, diag* shall be treated "as sparse" :
981  ## These are cheap implementations via coercion  ## These are cheap implementations via coercion
982    
983  ## for disambiguation  ## For disambiguation --- define this for "sparseMatrix" , then for "ANY";
984  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "sparseMatrix"),  ## and because we can save an .M.kind() call, we use this explicit
985            function(e1,e2) callGeneric(as(e1, "sparseMatrix"), e2))  ## "hack" for all diagonalMatrix *subclasses* instead of just "diagonalMatrix" :
986  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "diagonalMatrix"),  ##
987            function(e1,e2) callGeneric(e1, as(e2, "sparseMatrix")))  ## ddi*:
988  ## in general:  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "sparseMatrix"),
989  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ANY"),            function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
990            function(e1,e2) callGeneric(as(e1,"sparseMatrix"), e2))  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ddiMatrix"),
991  setMethod("Ops", signature(e1 = "ANY", e2 = "diagonalMatrix"),            function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
992            function(e1,e2) callGeneric(e1, as(e2,"sparseMatrix")))  ## ldi*
993    setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "sparseMatrix"),
994              function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
995    setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ldiMatrix"),
996              function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
997    
998    ## Ops:  Arith  --> numeric : "dMatrix"
999    ##       Compare --> logical
1000    ##       Logic   --> logical: "lMatrix"
1001    
1002    ## Other = "numeric" : stay diagonal if possible
1003    ## ddi*: Arith: result numeric, potentially ddiMatrix
1004    for(arg2 in c("numeric","logical"))
1005    setMethod("Arith", signature(e1 = "ddiMatrix", e2 = arg2),
1006              function(e1,e2) {
1007                  n <- e1@Dim[1]
1008                  f0 <- callGeneric(0, e2)
1009                  if(all0(f0)) { # remain diagonal
1010                      L1 <- (le <- length(e2)) == 1L
1011                      if(e1@diag == "U") {
1012                          if(any((r <- callGeneric(1, e2)) != 1)) {
1013                              e1@diag <- "N"
1014                              e1@x[seq_len(n)] <- r # possibly recycling r
1015                          } ## else: result = e1  (is "U" diag)
1016                      } else {
1017                          r <- callGeneric(e1@x, e2)
1018                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1019                          e1@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1020                      }
1021                      e1
1022                  } else
1023                      callGeneric(diag2tT.u(e1,e2, "d"), e2)
1024              })
1025    
1026    for(arg1 in c("numeric","logical"))
1027    setMethod("Arith", signature(e1 = arg1, e2 = "ddiMatrix"),
1028              function(e1,e2) {
1029                  n <- e2@Dim[1]
1030                  f0 <- callGeneric(e1, 0)
1031                  if(all0(f0)) { # remain diagonal
1032                      L1 <- (le <- length(e1)) == 1L
1033                      if(e2@diag == "U") {
1034                          if(any((r <- callGeneric(e1, 1)) != 1)) {
1035                              e2@diag <- "N"
1036                              e2@x[seq_len(n)] <- r # possibly recycling r
1037                          } ## else: result = e2  (is "U" diag)
1038                      } else {
1039                          r <- callGeneric(e1, e2@x)
1040                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1041                          e2@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1042                      }
1043                      e2
1044                  } else
1045                      callGeneric(e1, diag2tT.u(e2,e1, "d"))
1046              })
1047    
1048    ## ldi* Arith --> result numeric, potentially ddiMatrix
1049    for(arg2 in c("numeric","logical"))
1050    setMethod("Arith", signature(e1 = "ldiMatrix", e2 = arg2),
1051              function(e1,e2) {
1052                  n <- e1@Dim[1]
1053                  f0 <- callGeneric(0, e2)
1054                  if(all0(f0)) { # remain diagonal
1055                      L1 <- (le <- length(e2)) == 1L
1056                      E <- copyClass(e1, "ddiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
1057                      ## storage.mode(E@x) <- "double"
1058                      if(e1@diag == "U") {
1059                          if(any((r <- callGeneric(1, e2)) != 1)) {
1060                              E@diag <- "N"
1061                              E@x[seq_len(n)] <- r # possibly recycling r
1062                          } ## else: result = E  (is "U" diag)
1063                      } else {
1064                          r <- callGeneric(e1@x, e2)
1065                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1066                          E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1067                      }
1068                      E
1069                  } else
1070                      callGeneric(diag2tT.u(e1,e2, "l"), e2)
1071              })
1072    
1073    for(arg1 in c("numeric","logical"))
1074    setMethod("Arith", signature(e1 = arg1, e2 = "ldiMatrix"),
1075              function(e1,e2) {
1076                  n <- e2@Dim[1]
1077                  f0 <- callGeneric(e1, 0)
1078                  if(all0(f0)) { # remain diagonal
1079                      L1 <- (le <- length(e1)) == 1L
1080                      E <- copyClass(e2, "ddiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
1081                      ## storage.mode(E@x) <- "double"
1082                      if(e2@diag == "U") {
1083                          if(any((r <- callGeneric(e1, 1)) != 1)) {
1084                              E@diag <- "N"
1085                              E@x[seq_len(n)] <- r # possibly recycling r
1086                          } ## else: result = E  (is "U" diag)
1087                      } else {
1088                          r <- callGeneric(e1, e2@x)
1089                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1090                          E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1091                      }
1092                      E
1093                  } else
1094                      callGeneric(e1, diag2tT.u(e2,e1, "l"))
1095              })
1096    
1097    ## ddi*: for "Ops" without "Arith": <Compare> or <Logic> --> result logical, potentially ldi
1098    ##
1099    ## Note that  ("numeric", "ddiMatrix")  is simply swapped, e.g.,
1100    if(FALSE) {
1101        selectMethod("<", c("numeric","lMatrix"))# Compare
1102        selectMethod("&", c("numeric","lMatrix"))# Logic
1103    } ## so we don't need to define a method here :
1104    
1105    for(arg2 in c("numeric","logical"))
1106    setMethod("Ops", signature(e1 = "ddiMatrix", e2 = arg2),
1107              function(e1,e2) {
1108                  n <- e1@Dim[1]
1109                  f0 <- callGeneric(0, e2)
1110                  if(all0(f0)) { # remain diagonal
1111                      L1 <- (le <- length(e2)) == 1L
1112                      E <- copyClass(e1, "ldiMatrix", c("diag", "Dim", "Dimnames"), check=FALSE)
1113                      ## storage.mode(E@x) <- "logical"
1114                      if(e1@diag == "U") {
1115                          if(any((r <- callGeneric(1, e2)) != 1)) {
1116                              E@diag <- "N"
1117                              E@x[seq_len(n)] <- r # possibly recycling r
1118                          } ## else: result = E  (is "U" diag)
1119                      } else {
1120                          r <- callGeneric(e1@x, e2)
1121                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1122                          E@x[seq_len(n)] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1123                      }
1124                      E
1125                  } else
1126                      callGeneric(diag2tT.u(e1,e2, "d"), e2)
1127              })
1128    
1129    ## ldi*: for "Ops" without "Arith": <Compare> or <Logic> --> result logical, potentially ldi
1130    for(arg2 in c("numeric","logical"))
1131    setMethod("Ops", signature(e1 = "ldiMatrix", e2 = arg2),
1132              function(e1,e2) {
1133                  n <- e1@Dim[1]
1134                  f0 <- callGeneric(FALSE, e2)
1135                  if(all0(f0)) { # remain diagonal
1136                      L1 <- (le <- length(e2)) == 1L
1137    
1138                      if(e1@diag == "U") {
1139                          if(any((r <- callGeneric(TRUE, e2)) != 1)) {
1140                              e1@diag <- "N"
1141                              e1@x[seq_len(n)] <- r # possibly recycling r
1142                          } ## else: result = e1  (is "U" diag)
1143                      } else {
1144                          r <- callGeneric(e1@x, e2)
1145                          ## "future fixme": if we have idiMatrix, and r is 'integer', use idiMatrix
1146                          e1@x[] <- if(L1) r else r[1L + ((n+1)*(0:(n-1L))) %% le]
1147                      }
1148                      e1
1149                  } else
1150                      callGeneric(diag2tT.u(e1,e2, "l"), e2)
1151              })
1152    
1153    
1154    ## Not {"sparseMatrix", "numeric} :  {"denseMatrix", "matrix", ... }
1155    for(other in c("ANY", "Matrix", "dMatrix")) {
1156        ## ddi*:
1157        setMethod("Ops", signature(e1 = "ddiMatrix", e2 = other),
1158                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
1159        setMethod("Ops", signature(e1 = other, e2 = "ddiMatrix"),
1160                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
1161        ## ldi*:
1162        setMethod("Ops", signature(e1 = "ldiMatrix", e2 = other),
1163                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
1164        setMethod("Ops", signature(e1 = other, e2 = "ldiMatrix"),
1165                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
1166    }
1167    
1168    ## Direct subclasses of "denseMatrix": currently ddenseMatrix, ldense... :
1169    if(FALSE) # now also contains "geMatrix"
1170    dense.subCl <- local({ dM.scl <- getClass("denseMatrix")@subclasses
1171                           names(dM.scl)[vapply(dM.scl, slot, 0, "distance") == 1] })
1172    dense.subCl <- paste0(c("d","l","n"), "denseMatrix")
1173    for(DI in diCls) {
1174        dMeth <- if(extends(DI, "dMatrix"))
1175            function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2)
1176        else # "lMatrix", the only other kind for now
1177            function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2)
1178        for(c2 in c(dense.subCl, "Matrix")) {
1179            for(Fun in c("*", "&")) {
1180                setMethod(Fun, signature(e1 = DI, e2 = c2),
1181                          function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
1182                setMethod(Fun, signature(e1 = c2, e2 = DI),
1183                          function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
1184            }
1185            setMethod("^", signature(e1 = c2, e2 = DI),
1186                      function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
1187            for(Fun in c("%%", "%/%", "/")) ## 0 <op> 0 |--> NaN  for these.
1188                setMethod(Fun, signature(e1 = DI, e2 = c2), dMeth)
1189        }
1190    }
1191    
1192    ## Group methods "Math", "Math2" in                     --> ./Math.R
1193    
1194    ### "Summary" : "max"   "min"   "range" "prod"  "sum"   "any"   "all"
1195    ### ----------   the last 4: separately here
1196    for(cl in diCls) {
1197    setMethod("any", cl,
1198              function (x, ..., na.rm) {
1199                  if(any(x@Dim == 0)) FALSE
1200                  else if(x@diag == "U") TRUE else any(x@x, ..., na.rm = na.rm)
1201              })
1202    setMethod("all",  cl, function (x, ..., na.rm) {
1203        n <- x@Dim[1]
1204        if(n >= 2) FALSE
1205        else if(n == 0 || x@diag == "U") TRUE
1206        else all(x@x, ..., na.rm = na.rm)
1207    })
1208    setMethod("prod", cl, function (x, ..., na.rm) {
1209        n <- x@Dim[1]
1210        if(n >= 2) 0
1211        else if(n == 0 || x@diag == "U") 1
1212        else ## n == 1, diag = "N" :
1213            prod(x@x, ..., na.rm = na.rm)
1214    })
1215    
1216    setMethod("sum", cl,
1217              function(x, ..., na.rm) {
1218                  r <- sum(x@x, ..., na.rm = na.rm)# double or integer, correctly
1219                  if(x@diag == "U" && !is.na(r)) r + x@Dim[1] else r
1220              })
1221    }
1222    
1223    ## The remaining ones are  max, min, range :
1224    
1225    setMethod("Summary", "ddiMatrix",
1226              function(x, ..., na.rm) {
1227                  if(any(x@Dim == 0)) callGeneric(numeric(0), ..., na.rm=na.rm)
1228                  else if(x@diag == "U")
1229                      callGeneric(x@x, 0, 1, ..., na.rm=na.rm)
1230                  else callGeneric(x@x, 0, ..., na.rm=na.rm)
1231              })
1232    setMethod("Summary", "ldiMatrix",
1233              function(x, ..., na.rm) {
1234                  if(any(x@Dim == 0)) callGeneric(logical(0), ..., na.rm=na.rm)
1235                  else if(x@diag == "U")
1236                      callGeneric(x@x, FALSE, TRUE, ..., na.rm=na.rm)
1237                  else callGeneric(x@x, FALSE, ..., na.rm=na.rm)
1238              })
1239    
1240    
1241    
# Line 480  Line 1250 
1250      invisible(x)      invisible(x)
1251  }  }
1252    
1253    ## somewhat consistent with "print" for sparseMatrix :
1254    setMethod("print", signature(x = "diagonalMatrix"), prDiag)
1255    
1256  setMethod("show", signature(object = "diagonalMatrix"),  setMethod("show", signature(object = "diagonalMatrix"),
1257            function(object) {            function(object) {
1258                d <- dim(object)                d <- dim(object)
1259                cl <- class(object)                cl <- class(object)
1260                cat(sprintf('%d x %d diagonal matrix of class "%s"\n',                cat(sprintf('%d x %d diagonal matrix of class "%s"',
1261                            d[1], d[2], cl))                            d[1], d[2], cl))
1262                  if(d[1] < 50) {
1263                      cat("\n")
1264                prDiag(object)                prDiag(object)
1265                  } else {
1266                      cat(", with diagonal entries\n")
1267                      show(diag(object))
1268                      invisible(object)
1269                  }
1270            })            })
1271    
1272    rm(arg1, arg2, other, DI, Fun, cl, c1, c2,
1273       dense.subCl, diCls)# not used elsewhere
1274    
1275    setMethod("summary", signature(object = "diagonalMatrix"),
1276              function(object, ...) {
1277                  d <- dim(object)
1278                  r <- summary(object@x, ...)
1279                  attr(r, "header") <-
1280                      sprintf('%d x %d diagonal Matrix of class "%s"',
1281                              d[1], d[2], class(object))
1282                  ## use ole' S3 technology for such a simple case
1283                  class(r) <- c("diagSummary", class(r))
1284                  r
1285              })
1286    
1287    print.diagSummary <- function (x, ...) {
1288        cat(attr(x, "header"),"\n")
1289        class(x) <- class(x)[-1]
1290        print(x, ...)
1291        invisible(x)
1292    }

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