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

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pkg/R/diagMatrix.R revision 1655, Mon Oct 30 17:16:27 2006 UTC pkg/Matrix/R/diagMatrix.R revision 2608, Tue Aug 10 08:23:48 2010 UTC
# Line 16  Line 16 
16      if(missing(x)) ## unit diagonal matrix      if(missing(x)) ## unit diagonal matrix
17          new("ddiMatrix", Dim = c(n,n), diag = "U")          new("ddiMatrix", Dim = c(n,n), diag = "U")
18      else {      else {
19          stopifnot(length(x) == n)          lx <- length(x)
20            stopifnot(lx == 1 || lx == n) # but keep 'x' short for now
21          if(is.logical(x))          if(is.logical(x))
22              cl <- "ldiMatrix"              cl <- "ldiMatrix"
23          else if(is.numeric(x)) {          else if(is.numeric(x)) {
# Line 26  Line 27 
27          else if(is.complex(x)) {          else if(is.complex(x)) {
28              cl <- "zdiMatrix"  # will not yet work              cl <- "zdiMatrix"  # will not yet work
29          } else stop("'x' has invalid data type")          } else stop("'x' has invalid data type")
30          new(cl, Dim = c(n,n), diag = "N", x = x)          new(cl, Dim = c(n,n), diag = "N",
31                x = if(lx == 1) rep.int(x,n) else x)
32      }      }
33  }  }
34    
35    .sparseDiagonal <- function(n, x = rep.int(1,m), uplo = "U",
36                                shape = if(missing(cols)) "t" else "g",
37                                kind, cols = if(n) 0:(n - 1L) else integer(0))
38    {
39        stopifnot(n == (n. <- as.integer(n)), (n <- n.) >= 0)
40        if(!missing(cols))
41            stopifnot(0 <= (cols <- as.integer(cols)), cols < n)
42        m <- length(cols)
43        if(missing(kind))
44            kind <-
45                if(is.double(x)) "d"
46                else if(is.logical(x)) "l"
47                else { ## for now
48                    storage.mode(x) <- "double"
49                    "d"
50                }
51        else stopifnot(any(kind == c("d","l","n")))
52        if(kind != "n") {
53            if((lx <- length(x)) == 1) x <- rep.int(x, m)
54            else if(lx != m) stop("length(x) must be either 1 or #{cols}")
55        }
56        stopifnot(is.character(shape), nchar(shape) == 1,
57                  any(shape == c("t","s","g"))) # triangular / symmetric / general
58        if(kind == "n") {
59            if(shape == "g")
60                new("ngCMatrix", Dim = c(n,m), i = cols, p = 0:m)
61            else new(paste0("n", shape, "CMatrix"), Dim = c(n,m), uplo = uplo,
62                     i = cols, p = 0:m)
63        }
64        ## kind != "n" -- have x slot :
65        else if(shape == "g")
66            new(paste0(kind, "gCMatrix"), Dim = c(n,m),
67                x = x, i = cols, p = 0:m)
68        else new(paste0(kind, shape, "CMatrix"), Dim = c(n,m), uplo = uplo,
69                 x = x, i = cols, p = 0:m)
70    }
71    
72    ## Pkg 'spdep' had (relatively slow) versions of this as_dsCMatrix_I()
73    .symDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
74        .sparseDiagonal(n, x, uplo, shape = "s")
75    
76    # instead of   diagU2N(as(Diagonal(n), "CsparseMatrix")), diag = "N" in any case:
77    .trDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
78        .sparseDiagonal(n, x, uplo, shape = "t")
79    
80    
81  ### This is modified from a post of Bert Gunter to R-help on  1 Sep 2005.  ### This is modified from a post of Bert Gunter to R-help on  1 Sep 2005.
82  ### Bert's code built on a post by Andy Liaw who most probably was influenced  ### Bert's code built on a post by Andy Liaw who most probably was influenced
83  ### by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002  ### by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002
84  ### who posted his bdiag() function written in December 1995.  ### who posted his bdiag() function written in December 1995.
85    if(FALSE)##--- no longer used:
86  bdiag <- function(...) {  .bdiag <- function(lst) {
87      if(nargs() == 0) return(new("dgCMatrix"))      ### block-diagonal matrix [a dgTMatrix] from list of matrices
88      ## else :      stopifnot(is.list(lst), length(lst) >= 1)
89      mlist <- if (nargs() == 1) as.list(...) else list(...)      dims <- sapply(lst, dim, USE.NAMES=FALSE)
     dims <- sapply(mlist, dim)  
90      ## make sure we had all matrices:      ## make sure we had all matrices:
91      if(!(is.matrix(dims) && nrow(dims) == 2))      if(!(is.matrix(dims) && nrow(dims) == 2))
92          stop("some arguments are not matrices")          stop("some arguments are not matrices")
93      csdim <- rbind(rep.int(0:0, 2),      csdim <- rbind(rep.int(0L, 2),
94                     apply(sapply(mlist, dim), 1, cumsum))                     apply(dims, 1, cumsum))
95      ret <- new("dgTMatrix", Dim = as.integer(csdim[nrow(csdim),]))      r <- new("dgTMatrix")
96        r@Dim <- as.integer(csdim[nrow(csdim),])
97      add1 <- matrix(1:0, 2,2)      add1 <- matrix(1:0, 2,2)
98      for(i in seq_along(mlist)) {      for(i in seq_along(lst)) {
99          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])
100          if(is.null(dim(indx))) ## non-square matrix          if(is.null(dim(indx))) ## non-square matrix
101              ret[indx[[1]],indx[[2]]] <- mlist[[i]]              r[indx[[1]],indx[[2]]] <- lst[[i]]
102          else ## square matrix          else ## square matrix
103              ret[indx[,1],indx[,2]] <- mlist[[i]]              r[indx[,1], indx[,2]] <- lst[[i]]
104        }
105        r
106    }
107    ## expand(<mer>) needed something like bdiag() for lower-triangular
108    ## (Tsparse) Matrices; hence Doug Bates provided a much more efficient
109    ##  implementation for those; now extended and generalized:
110    .bdiag <- function(lst) {
111        ## block-diagonal matrix [a dgTMatrix] from list of matrices
112        stopifnot(is.list(lst), (nl <- length(lst)) >= 1)
113    
114        Tlst <- lapply(lapply(lst, Matrix:::as_Csp2), # includes "diagU2N"
115                       as, "TsparseMatrix")
116        if(nl == 1) return(Tlst[[1]])
117        ## else
118        i_off <- c(0L, cumsum(sapply(Tlst, nrow)))
119        j_off <- c(0L, cumsum(sapply(Tlst, ncol)))
120    
121        clss <- sapply(Tlst, class)
122        knds <- substr(clss, 2, 2)
123        sym  <- knds == "s" # symmetric ones
124        tri  <- knds == "t" # triangular ones
125        use.n <- any(is.n <- substr(clss,1,1) == "n")
126        if(use.n && !(use.n <- all(is.n)))
127            Tlst[is.n] <- lapply(Tlst[is.n], as, "lMatrix")
128        if(all(sym)) { ## result should be *symmetric*
129            uplos <- sapply(Tlst, slot, "uplo") ## either "U" or "L"
130            tLU <- table(uplos)# of length 1 or 2 ..
131            if(length(tLU) == 1) { ## all "U" or all "L"
132                useU <- uplos[1] == "U"
133            } else { ## length(tLU) == 2, counting "L" and "U"
134                useU <- diff(tLU) >= 0
135                if(useU && (hasL <- tLU[1] > 0))
136                    Tlst[hasL] <- lapply(Tlst[hasL], t)
137                else if(!useU && (hasU <- tLU[2] > 0))
138                    Tlst[hasU] <- lapply(Tlst[hasU], t)
139            }
140            if(use.n) { ## return nsparseMatrix :
141                r <- new("nsTMatrix")
142            } else {
143                r <- new("dsTMatrix")
144                r@x <- unlist(lapply(Tlst, slot, "x"))
145            }
146            r@uplo <- if(useU) "U" else "L"
147        }
148        else if(all(tri) && { ULs <- sapply(Tlst, slot, "uplo")##  "U" or "L"
149                              all(ULs[1L] == ULs[-1L]) } ## all upper or all lower
150           ){ ## *triangular* result
151    
152            if(use.n) { ## return nsparseMatrix :
153                r <- new("ntTMatrix")
154            } else {
155                r <- new("dtTMatrix")
156                r@x <- unlist(lapply(Tlst, slot, "x"))
157            }
158            r@uplo <- ULs[1L]
159        }
160        else {
161            if(any(sym))
162                Tlst[sym] <- lapply(Tlst[sym], as, "generalMatrix")
163            if(use.n) { ## return nsparseMatrix :
164                r <- new("ngTMatrix")
165            } else {
166                r <- new("dgTMatrix")
167                r@x <- unlist(lapply(Tlst, slot, "x"))
168            }
169      }      }
170      ## slightly debatable if we really should return Csparse.. :      r@Dim <- c(i_off[nl+1], j_off[nl + 1])
171      as(ret, "CsparseMatrix")      r@i <- unlist(lapply(1:nl, function(k) Tlst[[k]]@i + i_off[k]))
172        r@j <- unlist(lapply(1:nl, function(k) Tlst[[k]]@j + j_off[k]))
173        r
174  }  }
175    
176  diag2T <- function(from) {  bdiag <- function(...) {
177      i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1:1      if((nA <- nargs()) == 0) return(new("dgCMatrix"))
178      new(paste(.M.kind(from), "tTMatrix", sep=''),      if(nA == 1 && !is.list(...))
179            return(as(..., "CsparseMatrix"))
180        alis <- if(nA == 1 && is.list(..1)) ..1 else list(...)
181        if(length(alis) == 1)
182            return(as(alis[[1]], "CsparseMatrix"))
183    
184        ## else : two or more arguments
185        as(.bdiag(alis), "CsparseMatrix")
186    }
187    
188    
189    .diag2tT <- function(from, uplo = "U", kind = .M.kind(from)) {
190        ## to triangular Tsparse
191        i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L
192        new(paste(kind, "tTMatrix", sep=''),
193          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
194            uplo = uplo,
195          x = from@x, # <- ok for diag = "U" and "N" (!)          x = from@x, # <- ok for diag = "U" and "N" (!)
196          i = i, j = i)          i = i, j = i)
197  }  }
198    
199  setAs("diagonalMatrix", "triangularMatrix", diag2T)  .diag2sT <- function(from, uplo = "U", kind = .M.kind(from)) {
200  setAs("diagonalMatrix", "sparseMatrix", diag2T)      ## to symmetric Tsparse
201  ## is better than this:      n <- from@Dim[1]
202  ## setAs("diagonalMatrix", "sparseMatrix",      i <- seq_len(n) - 1L
203  ##       function(from)      new(paste(kind, "sTMatrix", sep=''),
204  ##        as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))          Dim = from@Dim, Dimnames = from@Dimnames,
205  setAs("diagonalMatrix", "CsparseMatrix",          i = i, j = i, uplo = uplo,
206        function(from) as(diag2T(from), "CsparseMatrix"))          x = if(from@diag == "N") from@x else ## "U"-diag
207            rep.int(switch(kind,
208                           "d" = 1.,
209                           "l" =,
210                           "n" = TRUE,
211                           ## otherwise
212                           stop("'", kind,"' kind not yet implemented")), n))
213    }
214    
215    ## diagonal -> triangular,  upper / lower depending on "partner":
216    diag2tT.u <- function(d, x, kind = .M.kind(d))
217        .diag2tT(d, uplo = if(is(x,"triangularMatrix")) x@uplo else "U", kind)
218    
219    ## diagonal -> sparse {triangular OR symmetric} (upper / lower) depending on "partner":
220    diag2Tsmart <- function(d, x, kind = .M.kind(d)) {
221        clx <- getClassDef(class(x))
222        if(extends(clx, "symmetricMatrix"))
223            .diag2sT(d, uplo = x@uplo, kind)
224        else
225            .diag2tT(d, uplo = if(extends(clx,"triangularMatrix")) x@uplo else "U", kind)
226    }
227    
228    
229  setAs("diagonalMatrix", "matrix",  ## In order to evade method dispatch ambiguity warnings,
230    ## and because we can save a .M.kind() call, we use this explicit
231    ## "hack"  instead of signature  x = "diagonalMatrix" :
232    ##
233    ## ddi*:
234    diag2tT <- function(from) .diag2tT(from, "U", "d")
235    setAs("ddiMatrix", "triangularMatrix", diag2tT)
236    ##_no_longer_ setAs("ddiMatrix", "sparseMatrix", diag2tT)
237    ## needed too (otherwise <dense> -> Tsparse is taken):
238    setAs("ddiMatrix", "TsparseMatrix", diag2tT)
239    setAs("ddiMatrix", "dsparseMatrix", diag2tT)
240    setAs("ddiMatrix", "CsparseMatrix",
241          function(from) as(.diag2tT(from, "U", "d"), "CsparseMatrix"))
242    setAs("ddiMatrix", "symmetricMatrix",
243          function(from) .diag2sT(from, "U", "d"))
244    ##
245    ## ldi*:
246    diag2tT <- function(from) .diag2tT(from, "U", "l")
247    setAs("ldiMatrix", "triangularMatrix", diag2tT)
248    ##_no_longer_ setAs("ldiMatrix", "sparseMatrix", diag2tT)
249    ## needed too (otherwise <dense> -> Tsparse is taken):
250    setAs("ldiMatrix", "TsparseMatrix", diag2tT)
251    setAs("ldiMatrix", "lsparseMatrix", diag2tT)
252    setAs("ldiMatrix", "CsparseMatrix",
253          function(from) as(.diag2tT(from, "U", "l"), "CsparseMatrix"))
254    setAs("ldiMatrix", "symmetricMatrix",
255          function(from) .diag2sT(from, "U", "l"))
256    
257    
258    setAs("diagonalMatrix", "nMatrix",
259        function(from) {        function(from) {
260            n <- from@Dim[1]            n <- from@Dim[1]
261            diag(x = if(from@diag == "U") { if(is.numeric(from@x)) 1. else TRUE            i <- if(from@diag == "U") integer(0) else which(isN0(from@x)) - 1L
262                                       } else from@x,            new("ntTMatrix", i = i, j = i, diag = from@diag,
263                 nrow = n, ncol = n)                Dim = from@Dim, Dimnames = from@Dimnames)
264        })        })
265    
266  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:  setAs("diagonalMatrix", "nsparseMatrix", function(from) as(from, "nMatrix"))
       function(from) as(from, paste(.M.kind(from), "gCMatrix", sep='')))  
   
 .diag.x <- function(m) {  
     if(m@diag == "U")  
         rep.int(if(is.numeric(m@x)) 1. else TRUE,  
                 m@Dim[1])  
     else m@x  
 }  
267    
268  .diag.2N <- function(m) {  ## Cheap fast substitute for diag() which *does* preserve the mode of x :
269      if(m@diag == "U") m@diag <- "N"  mkDiag <- function(x, n) {
270      m      y <- matrix(as0(mod=mode(x)), n,n)
271        if (n > 0) y[1L + 0:(n - 1L) * (n + 1L)] <- x
272        y
273  }  }
274    
275  ## given the above, the following  4  coercions should be all unneeded;  setAs("diagonalMatrix", "matrix",
 ## we prefer triangular to general:  
 setAs("ddiMatrix", "dgTMatrix",  
276        function(from) {        function(from) {
277            .Deprecated("as(, \"sparseMatrix\")")            ## want "ldiMatrix" -> <logical> "matrix" :
278            n <- from@Dim[1]            mkDiag(if(from@diag == "U") as1(from@x) else from@x,
279            i <- seq_len(n) - 1:1                   n = from@Dim[1])
280            new("dgTMatrix", i = i, j = i, x = .diag.x(from),        })
               Dim = c(n,n), Dimnames = from@Dimnames) })  
281    
282  setAs("ddiMatrix", "dgCMatrix",  setMethod("as.vector", signature(x = "diagonalMatrix", mode="missing"),
283        function(from) as(as(from, "sparseMatrix"), "dgCMatrix"))            function(x, mode) {
284                  n <- x@Dim[1]
285                  mod.x <- mode(x@x)
286                  r <- vector(mod.x, length = n^2)
287                  if(n)
288                      r[1 + 0:(n - 1) * (n + 1)] <-
289                          if(x@diag == "U") as1(mod=mod.x) else x@x
290                  r
291              })
292    
293  setAs("ldiMatrix", "lgTMatrix",  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
294        function(from) {        function(from) as(as(from, "CsparseMatrix"), "generalMatrix"))
295            .Deprecated("as(, \"sparseMatrix\")")  
296            n <- from@Dim[1]  setAs("diagonalMatrix", "denseMatrix",
297            if(from@diag == "U") { # unit-diagonal        function(from) as(as(from, "CsparseMatrix"), "denseMatrix"))
               x <- rep.int(TRUE, n)  
               i <- seq_len(n) - 1:1  
           } else { # "normal"  
               nz <- nz.NA(from@x, na. = TRUE)  
               x <- from@x[nz]  
               i <- which(nz) - 1:1  
           }  
           new("lgTMatrix", i = i, j = i, x = x,  
               Dim = c(n,n), Dimnames = from@Dimnames) })  
298    
299  setAs("ldiMatrix", "lgCMatrix",  .diag.x <- function(m) if(m@diag == "U") rep.int(as1(m@x), m@Dim[1]) else m@x
       function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))  
300    
301    .diag.2N <- function(m) {
302        if(m@diag == "U") m@diag <- "N"
303        m
304    }
305    
 if(FALSE) # now have faster  "ddense" -> "dge"  
306  setAs("ddiMatrix", "dgeMatrix",  setAs("ddiMatrix", "dgeMatrix",
307        function(from) as(as(from, "matrix"), "dgeMatrix"))        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
308    setAs("ddiMatrix", "ddenseMatrix",
309          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
310    setAs("ldiMatrix", "ldenseMatrix",
311          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
312    
313    
314  setAs("matrix", "diagonalMatrix",  setAs("matrix", "diagonalMatrix",
315        function(from) {        function(from) {
316            d <- dim(from)            d <- dim(from)
317            if(d[1] != (n <- d[2])) stop("non-square matrix")            if(d[1] != (n <- d[2])) stop("non-square matrix")
318            if(any(from[row(from) != col(from)] != 0))            if(any(from[row(from) != col(from)] != 0))
319                stop("has non-zero off-diagonal entries")                stop("matrix with non-zero off-diagonals cannot be coerced to diagonalMatrix")
320            x <- diag(from)            x <- diag(from)
321            if(is.logical(x)) {            if(is.logical(x)) {
322                cl <- "ldiMatrix"                cl <- "ldiMatrix"
323                uni <- all(x)                uni <- allTrue(x) ## uni := {is it unit-diagonal ?}
324            } else {            } else {
325                cl <- "ddiMatrix"                cl <- "ddiMatrix"
326                uni <- all(x == 1)                uni <- allTrue(x == 1)
327                storage.mode(x) <- "double"                storage.mode(x) <- "double"
328            } ## TODO: complex            } ## TODO: complex
329            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 163  Line 340 
340            x <- diag(from)            x <- diag(from)
341            if(is.logical(x)) {            if(is.logical(x)) {
342                cl <- "ldiMatrix"                cl <- "ldiMatrix"
343                uni <- all(x)                uni <- allTrue(x)
344            } else {            } else {
345                cl <- "ddiMatrix"                cl <- "ddiMatrix"
346                uni <- all(x == 1)                uni <- allTrue(x == 1)
347                storage.mode(x) <- "double"                storage.mode(x) <- "double"
348            }            } ## TODO: complex
349            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
350                x = if(uni) x[FALSE] else x)                x = if(uni) x[FALSE] else x)
351        })        })
352    
353    
354    setMethod("diag", signature(x = "diagonalMatrix"),
355              function(x = 1, nrow, ncol) .diag.x(x))
356    
357    subDiag <- function(x, i, j, ..., drop) {
358        x <- as(x, "CsparseMatrix") ## << was "TsparseMatrix" (Csparse is faster now)
359        x <- if(missing(i))
360            x[, j, drop=drop]
361        else if(missing(j))
362            if(nargs() == 4) x[i, , drop=drop] else x[i, drop=drop]
363        else
364            x[i,j, drop=drop]
365        if(isS4(x) && isDiagonal(x)) as(x, "diagonalMatrix") else x
366    }
367    
368    setMethod("[", signature(x = "diagonalMatrix", i = "index",
369                             j = "index", drop = "logical"), subDiag)
370    setMethod("[", signature(x = "diagonalMatrix", i = "index",
371                             j = "missing", drop = "logical"),
372              function(x, i, j, ..., drop) {
373                  na <- nargs()
374                  Matrix.msg("diag[i,m,l] : nargs()=", na, .M.level = 2)
375                  if(na == 4)
376                       subDiag(x, i=i, , drop=drop)
377                  else subDiag(x, i=i,   drop=drop)
378              })
379    setMethod("[", signature(x = "diagonalMatrix", i = "missing",
380                             j = "index", drop = "logical"),
381              function(x, i, j, ..., drop) subDiag(x, j=j, drop=drop))
382    
383  ## When you assign to a diagonalMatrix, the result should be  ## When you assign to a diagonalMatrix, the result should be
384  ## diagonal or sparse  ## diagonal or sparse ---
385    ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch
386    ## Only(?) current bug:  x[i] <- value  is wrong when  i is *vector*
387    replDiag <- function(x, i, j, ..., value) {
388        x <- as(x, "TsparseMatrix")
389        if(missing(i))
390            x[, j] <- value
391        else if(missing(j)) { ##  x[i , ] <- v  *OR*   x[i] <- v
392            na <- nargs()
393    ##         message("diagnosing replDiag() -- nargs()= ", na)
394            if(na == 4)
395                x[i, ] <- value
396            else if(na == 3)
397                x[i] <- value
398            else stop("Internal bug: nargs()=",na,"; please report")
399        } else
400            x[i,j] <- value
401        if(isDiagonal(x)) as(x, "diagonalMatrix") else x
402    }
403    
404    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
405                                    j = "index", value = "replValue"), replDiag)
406    
407    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
408                                    j = "missing", value = "replValue"),
409                     function(x,i,j, ..., value) {
410                         ## message("before replDiag() -- nargs()= ", nargs())
411                         if(nargs() == 3)
412                             replDiag(x, i=i, value=value)
413                         else ## nargs() == 4 :
414                             replDiag(x, i=i, , value=value)
415                     })
416    
417  setReplaceMethod("[", signature(x = "diagonalMatrix",  setReplaceMethod("[", signature(x = "diagonalMatrix",
418                                  i = "ANY", j = "ANY", value = "ANY"),                                  i = "matrix", # 2-col.matrix
419                   function(x, i, j, value) {                                  j = "missing", value = "replValue"),
420                       r <- callGeneric(x = as(x,"sparseMatrix"),                   function(x,i,j, ..., value) {
421                                        i=i, j=j, value=value)                       if(ncol(i) == 2) {
422                       if(isDiagonal(r)) as(r, "diagonalMatrix") else r                           if(all((ii <- i[,1]) == i[,2])) { # replace in diagonal only
423                                 if(x@diag == "U") {
424                                     one <- as1(x@x)
425                                     if(any(value != one | is.na(value))) {
426                                         x@diag <- "N"
427                                         x@x <- rep.int(one, x@Dim[1])
428                                     }
429                                 }
430                                 x@x[ii] <- value
431                                 x
432                             } else { ## no longer diagonal, but remain sparse:
433                                 x <- as(x, "TsparseMatrix")
434                                 x[i] <- value
435                                 x
436                             }
437                         }
438                         else { # behave as "base R": use as if vector
439                             x <- as(x, "matrix")
440                             x[i] <- value
441                             Matrix(x)
442                         }
443                   })                   })
444    
445    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
446                                    j = "index", value = "replValue"),
447                     function(x,i,j, ..., value) replDiag(x, j=j, value=value))
448    
449    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
450                                    value = "sparseMatrix"),
451                     function (x, i, j, ..., value)
452                     callGeneric(x=x, , j=j, value = as(value, "sparseVector")))
453    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
454                                    value = "sparseMatrix"),
455                     function (x, i, j, ..., value)
456                     callGeneric(x=x, i=i, , value = as(value, "sparseVector")))
457    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
458                                    value = "sparseMatrix"),
459                     function (x, i, j, ..., value)
460                     callGeneric(x=x, i=i, j=j, value = as(value, "sparseVector")))
461    
462    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
463                                    value = "sparseVector"),
464                     replDiag)
465    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
466                                    value = "sparseVector"),
467                     replDiag)
468    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
469                                    value = "sparseVector"),
470                     replDiag)
471    
472    
473  setMethod("t", signature(x = "diagonalMatrix"),  setMethod("t", signature(x = "diagonalMatrix"),
474            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })
# Line 192  Line 478 
478  setMethod("isTriangular", signature(object = "diagonalMatrix"),  setMethod("isTriangular", signature(object = "diagonalMatrix"),
479            function(object) TRUE)            function(object) TRUE)
480  setMethod("isSymmetric", signature(object = "diagonalMatrix"),  setMethod("isSymmetric", signature(object = "diagonalMatrix"),
481            function(object) TRUE)            function(object, ...) TRUE)
482    
483  setMethod("chol", signature(x = "ddiMatrix"),# pivot = "ANY"  setMethod("symmpart", signature(x = "diagonalMatrix"), function(x) x)
484            function(x, pivot) {  setMethod("skewpart", signature(x = "diagonalMatrix"), setZero)
485                if(any(x@x < 0)) stop("chol() is undefined for diagonal matrix with negative entries")  
486    setMethod("chol", signature(x = "ddiMatrix"),
487              function(x, pivot, ...) {
488                  if(x@diag == "U") return(x)
489                  ## else
490                  if(any(x@x < 0))
491                      stop("chol() is undefined for diagonal matrix with negative entries")
492                x@x <- sqrt(x@x)                x@x <- sqrt(x@x)
493                x                x
494            })            })
495  ## chol(L) is L for logical diagonal:  ## chol(L) is L for logical diagonal:
496  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot) x)  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot, ...) x)
   
497    
498  setMethod("diag", signature(x = "diagonalMatrix"),  setMethod("determinant", signature(x = "diagonalMatrix", logarithm = "logical"),
499            function(x = 1, nrow, ncol = n) {            function(x, logarithm, ...) mkDet(.diag.x(x), logarithm))
              if(x@diag == "U")  
                  rep.int(if(is.logical(x@x)) TRUE else 1, x@Dim[1])  
              else x@x  
           })  
500    
501  setMethod("!", "ldiMatrix", function(e1) {  setMethod("norm", signature(x = "diagonalMatrix", type = "character"),
502      if(e1@diag == "N")            function(x, type, ...) {
503          e1@x <- !e1@x                if((n <- x@Dim[1]) == 0) return(0) # as for "sparseMatrix"
504      else { ## "U"                type <- toupper(substr(type[1], 1, 1))
505          e1@diag <- "N"                isU <- (x@diag == "U") # unit-diagonal
506          e1@x <- rep.int(FALSE, e1@Dim[1])                if(type == "F") sqrt(if(isU) n else sum(x@x^2))
507                  else { ## norm == "I","1","O","M" :
508                      if(isU) 1 else max(abs(x@x))
509      }      }
     x  
510  })  })
511    
512    
513    
514  ## Basic Matrix Multiplication {many more to add}  ## Basic Matrix Multiplication {many more to add}
515  ##       ---------------------  ##       ---------------------
516  ## Note that "ldi" logical are treated as numeric  ## Note that "ldi" logical are treated as numeric
517  diagdiagprod <- function(x, y) {  diagdiagprod <- function(x, y) {
518      if(any(dim(x) != dim(y))) stop("non-matching dimensions")      n <- dimCheck(x,y)[1]
519      if(x@diag != "U") {      if(x@diag != "U") {
520          if(y@diag != "U") {          if(y@diag != "U") {
521              nx <- x@x * y@x              nx <- x@x * y@x
# Line 253  Line 543 
543    
544    
545  diagmatprod <- function(x, y) {  diagmatprod <- function(x, y) {
546        ## x is diagonalMatrix
547      dx <- dim(x)      dx <- dim(x)
548      dy <- dim(y)      dy <- dim(y)
549      if(dx[2] != dy[1]) stop("non-matching dimensions")      if(dx[2] != dy[1]) stop("non-matching dimensions")
550      n <- dx[1]      n <- dx[1]
551      as(if(x@diag == "U") y else x@x * y, "Matrix")      as(if(x@diag == "U") y else x@x * y, "Matrix")
552  }  }
   
553  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),
554            diagmatprod)            diagmatprod)
555    ## sneaky .. :
556  formals(diagmatprod) <- alist(x=, y=NULL)  formals(diagmatprod) <- alist(x=, y=NULL)
557  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),
558            diagmatprod)            diagmatprod)
 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "matrix"),  
           diagmatprod)  
559    
560  diagdgeprod <- function(x, y) {  diagGeprod <- function(x, y) {
561      dx <- dim(x)      dx <- dim(x)
562      dy <- dim(y)      dy <- dim(y)
563      if(dx[2] != dy[1]) stop("non-matching dimensions")      if(dx[2] != dy[1]) stop("non-matching dimensions")
# Line 276  Line 565 
565          y@x <- x@x * y@x          y@x <- x@x * y@x
566      y      y
567  }  }
568  setMethod("%*%", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("%*%", signature(x= "diagonalMatrix", y= "dgeMatrix"), diagGeprod)
569            diagdgeprod, valueClass = "dgeMatrix")  setMethod("%*%", signature(x= "diagonalMatrix", y= "lgeMatrix"), diagGeprod)
570  formals(diagdgeprod) <- alist(x=, y=NULL)  formals(diagGeprod) <- alist(x=, y=NULL)
571  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),
572            diagdgeprod, valueClass = "dgeMatrix")            diagGeprod, valueClass = "dgeMatrix")
573    setMethod("crossprod", signature(x = "diagonalMatrix", y = "lgeMatrix"),
574              diagGeprod)
575    
576  setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"),  matdiagprod <- function(x, y) {
           function(x, y) {  
577                dx <- dim(x)                dx <- dim(x)
578                dy <- dim(y)                dy <- dim(y)
579                if(dx[2] != dy[1]) stop("non-matching dimensions")                if(dx[2] != dy[1]) stop("non-matching dimensions")
580                as(if(y@diag == "U") x else x * rep(y@x, each = dx[1]), "Matrix")      Matrix(if(y@diag == "U") x else x * rep(y@x, each = dx[1]))
581            })  }
582    setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"),
583              matdiagprod)
584    formals(matdiagprod) <- alist(x=, y=NULL)
585    setMethod("tcrossprod", signature(x = "matrix", y = "diagonalMatrix"),
586              matdiagprod)
587    
588  setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),  gediagprod <- function(x, y) {
           function(x, y) {  
589                dx <- dim(x)                dx <- dim(x)
590                dy <- dim(y)                dy <- dim(y)
591                if(dx[2] != dy[1]) stop("non-matching dimensions")                if(dx[2] != dy[1]) stop("non-matching dimensions")
592                if(y@diag == "N")                if(y@diag == "N")
593                    x@x <- x@x * rep(y@x, each = dx[1])                    x@x <- x@x * rep(y@x, each = dx[1])
594                x                x
595            })  }
596    setMethod("%*%", signature(x= "dgeMatrix", y= "diagonalMatrix"), gediagprod)
597    setMethod("%*%", signature(x= "lgeMatrix", y= "diagonalMatrix"), gediagprod)
598    formals(gediagprod) <- alist(x=, y=NULL)
599    setMethod("tcrossprod", signature(x = "dgeMatrix", y = "diagonalMatrix"),
600              gediagprod)
601    setMethod("tcrossprod", signature(x = "lgeMatrix", y = "diagonalMatrix"),
602              gediagprod)
603    
604  ## crossprod {more of these}  ## crossprod {more of these}
605    
606  ## tcrossprod --- all are not yet there: do the dense ones here:  ## tcrossprod --- all are not yet there: do the dense ones here:
607    
608    setMethod("%*%", signature(x = "diagonalMatrix", y = "denseMatrix"),
609              function(x, y) if(x@diag == "U") y else x %*% as(y, "generalMatrix"))
610    setMethod("%*%", signature(x = "denseMatrix", y = "diagonalMatrix"),
611              function(x, y) if(y@diag == "U") x else as(x, "generalMatrix") %*% y)
612    
613    
614  ## FIXME:  ## FIXME:
615  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),
616  ##        function(x, y = NULL) {  ##        function(x, y = NULL) {
617  ##           })  ##           })
618    
619  ## setMethod("tcrossprod", signature(x = "denseMatrix", y = "diagonalMatrix"),  Cspdiagprod <- function(x, y) {
620  ##        function(x, y = NULL) {      dx <- dim(x <- .Call(Csparse_diagU2N, x))
621  ##           })      dy <- dim(y)
622        if(dx[2] != dy[1]) stop("non-matching dimensions")
623        ind <- rep.int(seq_len(dx[2]), x@p[-1] - x@p[-dx[2]-1L])
624        if(y@diag == "N")
625            x@x <- x@x * y@x[ind]
626        if(is(x, "compMatrix") && length(xf <- x@factors)) {
627            ## instead of dropping all factors, be smart about some
628            ## TODO ......
629            x@factors <- list()
630        }
631        x
632    }
633    
634    diagCspprod <- function(x, y) {
635        dx <- dim(x)
636        dy <- dim(y <- .Call(Csparse_diagU2N, y))
637        if(dx[2] != dy[1]) stop("non-matching dimensions")
638        if(x@diag == "N")
639            y@x <- y@x * x@x[y@i + 1L]
640        if(is(y, "compMatrix") && length(yf <- y@factors)) {
641            ## instead of dropping all factors, be smart about some
642            ## TODO
643            keep <- character()
644            if(iLU <- names(yf) == "LU") {
645                ## TODO keep <- "LU"
646            }
647            y@factors <- yf[keep]
648        }
649        y
650    }
651    
652    setMethod("crossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
653              function(x, y = NULL) diagCspprod(x, y))
654    
655    setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
656              function(x, y = NULL) diagCspprod(x, as(y, "CsparseMatrix")))
657    
658    ## Prefer calling diagCspprod to Cspdiagprod if going to transpose anyway
659    ##  x'y == (y'x)'
660    setMethod("crossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
661              function(x, y = NULL) t(diagCspprod(y, x)))
662    
663    setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
664              function(x, y = NULL) t(diagCspprod(y, as(x, "Csparsematrix"))))
665    
666    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
667              function(x, y = NULL) diagCspprod(x, t(y)))
668    
669    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
670              function(x, y = NULL) diagCspprod(x, t(as(y, "CsparseMatrix"))))
671    
672    setMethod("tcrossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
673              function(x, y = NULL) Cspdiagprod(x, y))
674    
675    setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
676              function(x, y = NULL) Cspdiagprod(as(x, "CsparseMatrix"), y))
677    
678    setMethod("%*%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
679              function(x, y) diagCspprod(x, y))
680    
681    setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
682              function(x, y) diagCspprod(as(x, "CsparseMatrix"), y))
683    
684    setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),
685              function(x, y) Cspdiagprod(as(x, "CsparseMatrix"), y))
686    
687    setMethod("%*%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
688              function(x, y) Cspdiagprod(x, y))
689    
690    ## TODO: Write tests in ./tests/ which ensure that many "ops" with diagonal*
691    ##       do indeed work by going through sparse (and *not* ddense)!
692    
693    setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),
694              function(a, b, ...) {
695                  a@x <- 1/ a@x
696                  a@Dimnames <- a@Dimnames[2:1]
697                  a
698              })
699    
700    solveDiag <- function(a, b, ...) {
701        if((n <- a@Dim[1]) != nrow(b))
702            stop("incompatible matrix dimensions")
703        ## trivially invert a 'in place' and multiply:
704        a@x <- 1/ a@x
705        a@Dimnames <- a@Dimnames[2:1]
706        a %*% b
707    }
708    setMethod("solve", signature(a = "diagonalMatrix", b = "matrix"),
709              solveDiag)
710    setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),
711              solveDiag)
712    
713    ## Schur()  ---> ./eigen.R
714    
715    
 ### ---------------- diagonal  o  sparse  -----------------------------  
716    
717    ###---------------- <Ops> (<Arith>, <Logic>, <Compare> ) ----------------------
718    
719  ## Use function for several signatures, in order to evade  ## Use function for several signatures, in order to evade
720  ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)  ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)
721  diagOdiag <- function(e1,e2) { # result should also be diagonal  diagOdiag <- function(e1,e2) {
722        ## result should also be diagonal _ if possible _
723      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
724        ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
725        r00 <- callGeneric(if(is.numeric(e1@x)) 0 else FALSE,
726                           if(is.numeric(e2@x)) 0 else FALSE)
727        if(is0(r00)) { ##  r00 == 0 or FALSE --- result *is* diagonal
728      if(is.numeric(r)) {      if(is.numeric(r)) {
729          if(is.numeric(e2@x)) {          if(is.numeric(e2@x)) {
730              e2@x <- r; return(.diag.2N(e2)) }              e2@x <- r; return(.diag.2N(e2)) }
# Line 334  Line 738 
738      e1@x <- r      e1@x <- r
739      .diag.2N(e1)      .diag.2N(e1)
740  }  }
741        else { ## result not diagonal, but at least symmetric:
742            ## e.g., m == m
743            isNum <- (is.numeric(r) || is.numeric(r00))
744            isLog <- (is.logical(r) || is.logical(r00))
745            Matrix.msg("exploding <diag> o <diag> into dense matrix", .M.level = 2)
746            d <- e1@Dim
747            n <- d[1]
748            stopifnot(length(r) == n)
749            xx <- as.vector(matrix(rbind(r, matrix(r00,n,n)), n,n))
750            newcl <-
751                paste(if(isNum) "d" else if(isLog) {
752                    if(!any(is.na(r)) && !any(is.na(r00))) "n" else "l"
753                } else stop("not yet implemented .. please report")
754                      ,
755                      "syMatrix", sep='')
756    
757            new(newcl, Dim = e1@Dim, Dimnames = e1@Dimnames, x = xx)
758        }
759    }
760    
761    ### This would be *the* way, but we get tons of "ambiguous method dispatch"
762    ## we use this hack instead of signature  x = "diagonalMatrix" :
763    diCls <- names(getClass("diagonalMatrix")@subclasses)
764    if(FALSE) {
765  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
766            diagOdiag)            diagOdiag)
767  ## These two are just for method disambiguation:  } else { ## These are just for method disambiguation:
768  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "diagonalMatrix"),      for(c1 in diCls)
769            diagOdiag)          for(c2 in diCls)
770  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ddiMatrix"),              setMethod("Ops", signature(e1 = c1, e2 = c2), diagOdiag)
771            diagOdiag)  }
772    
773    ## diagonal  o  triangular  |-->  triangular
774    ## diagonal  o  symmetric   |-->  symmetric
775    ##    {also when other is sparse: do these "here" --
776    ##     before conversion to sparse, since that loses "diagonality"}
777    
778  ## For almost everything else, diag* shall be treated "as sparse" :  ## For almost everything else, diag* shall be treated "as sparse" :
779  ## These are cheap implementations via coercion  ## These are cheap implementations via coercion
780    
781  ## for disambiguation  ## For disambiguation --- define this for "sparseMatrix" , then for "ANY";
782  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "sparseMatrix"),  ## and because we can save an .M.kind() call, we use this explicit
783            function(e1,e2) callGeneric(as(e1, "sparseMatrix"), e2))  ## "hack" for all diagonalMatrix *subclasses* instead of just "diagonalMatrix" :
784  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "diagonalMatrix"),  ##
785            function(e1,e2) callGeneric(e1, as(e2, "sparseMatrix")))  ## ddi*:
786  ## in general:  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "sparseMatrix"),
787  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ANY"),            function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
788            function(e1,e2) callGeneric(as(e1,"sparseMatrix"), e2))  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ddiMatrix"),
789  setMethod("Ops", signature(e1 = "ANY", e2 = "diagonalMatrix"),            function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
790            function(e1,e2) callGeneric(e1, as(e2,"sparseMatrix")))  ## ldi*
791    setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "sparseMatrix"),
792              function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
793    setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ldiMatrix"),
794              function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
795    
796    ## Ops:  Arith  --> numeric : "dMatrix"
797    ##       Compare --> logical
798    ##       Logic   --> logical: "lMatrix"
799    
800    ##  other = "numeric" : stay diagonal if possible
801    ## ddi*: Arith: result numeric, potentially ddiMatrix
802    setMethod("Arith", signature(e1 = "ddiMatrix", e2 = "numeric"),
803              function(e1,e2) {
804                  n <- e1@Dim[1]; nsq <- n^2
805                  f0 <- callGeneric(0, e2)
806                  if(all(is0(f0))) { # remain diagonal
807                      L1 <- (le <- length(e2)) == 1L
808                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
809                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
810                          e1@diag <- "N"
811                          if(L1) r <- rep.int(r, n)
812                      } else
813                          r <- callGeneric(e1@x, e2)
814                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
815                      return(e1)
816                  }
817                  callGeneric(diag2tT.u(e1,e2, "d"), e2)
818              })
819    
820    setMethod("Arith", signature(e1 = "numeric", e2 = "ddiMatrix"),
821              function(e1,e2) {
822                  n <- e2@Dim[1]; nsq <- n^2
823                  f0 <- callGeneric(e1, 0)
824                  if(all(is0(f0))) { # remain diagonal
825                      L1 <- (le <- length(e1)) == 1L
826                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
827                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
828                          e2@diag <- "N"
829                          if(L1) r <- rep.int(r, n)
830                      } else
831                          r <- callGeneric(e1, e2@x)
832                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
833                      return(e2)
834                  }
835                  callGeneric(e1, diag2tT.u(e2,e1, "d"))
836              })
837    
838    ## ldi* Arith --> result numeric, potentially ddiMatrix
839    setMethod("Arith", signature(e1 = "ldiMatrix", e2 = "numeric"),
840              function(e1,e2) {
841                  n <- e1@Dim[1]; nsq <- n^2
842                  f0 <- callGeneric(0, e2)
843                  if(all(is0(f0))) { # remain diagonal
844                      L1 <- (le <- length(e2)) == 1L
845                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
846                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
847                          e1@diag <- "N"
848                          if(L1) r <- rep.int(r, n)
849                      } else
850                          r <- callGeneric(e1@x, e2)
851                      e1 <- copyClass(e1, "ddiMatrix", c("diag", "Dim", "Dimnames"))
852                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
853                      return(e1)
854                  }
855                  callGeneric(diag2tT.u(e1,e2, "d"), e2)
856              })
857    
858  ## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()  setMethod("Arith", signature(e1 = "numeric", e2 = "ldiMatrix"),
859              function(e1,e2) {
860                  n <- e2@Dim[1]; nsq <- n^2
861                  f0 <- callGeneric(e1, 0)
862                  if(all(is0(f0))) { # remain diagonal
863                      L1 <- (le <- length(e1)) == 1L
864                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
865                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
866                          e2@diag <- "N"
867                          if(L1) r <- rep.int(r, n)
868                      } else
869                          r <- callGeneric(e1, e2@x)
870                      e2 <- copyClass(e2, "ddiMatrix", c("diag", "Dim", "Dimnames"))
871                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
872                      return(e2)
873                  }
874                  callGeneric(e1, diag2tT.u(e2,e1, "d"))
875              })
876    
877  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),  ## ddi*: for "Ops" without Arith --> result logical, potentially ldi
878            function(x, y) as(x, "sparseMatrix") %*% y)  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "numeric"),
879              function(e1,e2) {
880                  n <- e1@Dim[1]; nsq <- n^2
881                  f0 <- callGeneric(0, e2)
882                  if(all(is0(f0))) { # remain diagonal
883                      L1 <- (le <- length(e2)) == 1L
884                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
885                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
886                          e1@diag <- "N"
887                          if(L1) r <- rep.int(r, n)
888                      } else
889                          r <- callGeneric(e1@x, e2)
890                      e1 <- copyClass(e1, "ldiMatrix", c("diag", "Dim", "Dimnames"))
891                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
892                      return(e1)
893                  }
894                  callGeneric(diag2tT.u(e1,e2, "l"), e2)
895              })
896    
897  setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("Ops", signature(e1 = "numeric", e2 = "ddiMatrix"),
898            function(x, y) x %*% as(y, "sparseMatrix"))            function(e1,e2) {
899                  n <- e2@Dim[1]; nsq <- n^2
900                  f0 <- callGeneric(e1, 0)
901                  if(all(is0(f0))) { # remain diagonal
902                      L1 <- (le <- length(e1)) == 1L
903                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
904                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
905                          e2@diag <- "N"
906                          if(L1) r <- rep.int(r, n)
907                      } else
908                          r <- callGeneric(e1, e2@x)
909                      e2 <- copyClass(e2, "ldiMatrix", c("diag", "Dim", "Dimnames"))
910                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
911                      return(e2)
912                  }
913                  callGeneric(e1, diag2tT.u(e2,e1, "l"))
914              })
915    
916  setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  ## ldi*: for "Ops" without Arith --> result logical, potentially ldi
917            function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })  setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "numeric"),
918              function(e1,e2) {
919                  n <- e1@Dim[1]; nsq <- n^2
920                  f0 <- callGeneric(FALSE, e2)
921                  if(all(is0(f0))) { # remain diagonal
922                      L1 <- (le <- length(e2)) == 1L
923                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
924                      if(e1@diag == "U" && any((r <- callGeneric(TRUE, e2)) != 1)) {
925                          e1@diag <- "N"
926                          if(L1) r <- rep.int(r, n)
927                      } else
928                          r <- callGeneric(e1@x, e2)
929                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
930                      return(e1)
931                  }
932                  callGeneric(diag2tT.u(e1,e2, "l"), e2)
933              })
934    
935  setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("Ops", signature(e1 = "numeric", e2 = "ldiMatrix"),
936            function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })            function(e1,e2) {
937                  n <- e2@Dim[1]; nsq <- n^2
938                  f0 <- callGeneric(e1, FALSE)
939                  if(all(is0(f0))) { # remain diagonal
940                      L1 <- (le <- length(e1)) == 1L
941                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
942                      if(e2@diag == "U" && any((r <- callGeneric(e1, TRUE)) != 1)) {
943                          e2@diag <- "N"
944                          if(L1) r <- rep.int(r, n)
945                      } else
946                          r <- callGeneric(e1, e2@x)
947                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
948                      return(e2)
949                  }
950                  callGeneric(e1, diag2tT.u(e2,e1, "l"))
951              })
952    
 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  
           function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })  
953    
 setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  
           function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })  
954    
955    ## Not {"sparseMatrix", "numeric} :  {"denseMatrix", "matrix", ... }
956    for(other in c("ANY", "Matrix", "dMatrix")) {
957        ## ddi*:
958        setMethod("Ops", signature(e1 = "ddiMatrix", e2 = other),
959                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
960        setMethod("Ops", signature(e1 = other, e2 = "ddiMatrix"),
961                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
962        ## ldi*:
963        setMethod("Ops", signature(e1 = "ldiMatrix", e2 = other),
964                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
965        setMethod("Ops", signature(e1 = other, e2 = "ldiMatrix"),
966                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
967    }
968    
969    ## Direct subclasses of "denseMatrix": currently ddenseMatrix, ldense... :
970    if(FALSE)## too general, would contain  denseModelMatrix:
971    dense.subCl <- local({ dM.scl <- getClass("denseMatrix")@subclasses
972                           names(dM.scl)[sapply(dM.scl, slot, "distance") == 1] })
973    dense.subCl <- paste(c("d","l","n"), "denseMatrix", sep="")
974    for(DI in diCls) {
975        for(c2 in c(dense.subCl, "Matrix")) {
976            for(Fun in c("*", "^", "&")) {
977                setMethod(Fun, signature(e1 = DI, e2 = c2),
978                          function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
979                setMethod(Fun, signature(e1 = c2, e2 = DI),
980                          function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
981            }
982            ## NB: This arguably implicitly uses  0/0 :== 0  to keep diagonality
983            for(Fun in c("%%", "%/%", "/")) {
984                setMethod(Fun, signature(e1 = DI, e2 = c2),
985                          function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
986            }
987        }
988    }
989    
990    
991    ### "Summary" : "max"   "min"   "range" "prod"  "sum"   "any"   "all"
992    ### ----------   the last 4: separately here
993    for(cl in diCls) {
994    setMethod("any", cl,
995              function (x, ..., na.rm) {
996                  if(any(x@Dim == 0)) FALSE
997                  else if(x@diag == "U") TRUE else any(x@x, ..., na.rm = na.rm)
998              })
999    setMethod("all",  cl, function (x, ..., na.rm) {
1000        n <- x@Dim[1]
1001        if(n >= 2) FALSE
1002        else if(n == 0 || x@diag == "U") TRUE
1003        else all(x@x, ..., na.rm = na.rm)
1004    })
1005    setMethod("prod", cl, function (x, ..., na.rm) {
1006        n <- x@Dim[1]
1007        if(n >= 2) 0
1008        else if(n == 0 || x@diag == "U") 1
1009        else ## n == 1, diag = "N" :
1010            prod(x@x, ..., na.rm = na.rm)
1011    })
1012    
1013    setMethod("sum", cl,
1014              function(x, ..., na.rm) {
1015                  r <- sum(x@x, ..., na.rm = na.rm)# double or integer, correctly
1016                  if(x@diag == "U" && !is.na(r)) r + x@Dim[1] else r
1017              })
1018    }
1019    
1020    ## The remaining ones are  max, min, range :
1021    
1022    setMethod("Summary", "ddiMatrix",
1023              function(x, ..., na.rm) {
1024                  if(any(x@Dim == 0)) callGeneric(numeric(0), ..., na.rm=na.rm)
1025                  else if(x@diag == "U")
1026                      callGeneric(x@x, 0, 1, ..., na.rm=na.rm)
1027                  else callGeneric(x@x, 0, ..., na.rm=na.rm)
1028              })
1029    setMethod("Summary", "ldiMatrix",
1030              function(x, ..., na.rm) {
1031                  if(any(x@Dim == 0)) callGeneric(logical(0), ..., na.rm=na.rm)
1032                  else if(x@diag == "U")
1033                      callGeneric(x@x, FALSE, TRUE, ..., na.rm=na.rm)
1034                  else callGeneric(x@x, FALSE, ..., na.rm=na.rm)
1035              })
1036    
1037    
1038    
# Line 393  Line 1047 
1047      invisible(x)      invisible(x)
1048  }  }
1049    
1050    ## somewhat consistent with "print" for sparseMatrix :
1051    setMethod("print", signature(x = "diagonalMatrix"), prDiag)
1052    
1053  setMethod("show", signature(object = "diagonalMatrix"),  setMethod("show", signature(object = "diagonalMatrix"),
1054            function(object) {            function(object) {
1055                d <- dim(object)                d <- dim(object)
1056                cl <- class(object)                cl <- class(object)
1057                cat(sprintf('%d x %d diagonal matrix of class "%s"\n',                cat(sprintf('%d x %d diagonal matrix of class "%s"',
1058                            d[1], d[2], cl))                            d[1], d[2], cl))
1059                  if(d[1] < 50) {
1060                      cat("\n")
1061                prDiag(object)                prDiag(object)
1062                  } else {
1063                      cat(", with diagonal entries\n")
1064                      show(diag(object))
1065                      invisible(object)
1066                  }
1067            })            })

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