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

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revision 1805, Tue Mar 27 16:46:03 2007 UTC revision 2493, Mon Nov 2 11:55:05 2009 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,n), uplo = "U", shape = "t") {
36        stopifnot(n == (n. <- as.integer(n)), (n <- n.) >= 0)
37        if((lx <- length(x)) == 1) x <- rep.int(x, n)
38        else if(lx != n) stop("length(x) must be 1 or n")
39        stopifnot(is.character(shape), nchar(shape) == 1,
40                  any(shape == c("t","s","g"))) # triangular / symmetric / general
41        kind <-
42            if(is.double(x)) "d"
43            else if(is.logical(x)) "l"
44            else { ## for now
45                storage.mode(x) <- "double"
46                "d"
47            }
48        ii <- if(n) 0:(n - 1L) else integer(0)
49        if(shape == "g")
50            new(paste0(kind, "gCMatrix"), Dim = c(n,n),
51                x = x, i = ii, p = 0:n)
52        else new(paste0(kind, shape, "CMatrix"), Dim = c(n,n), uplo = uplo,
53                 x = x, i = ii, p = 0:n)
54    }
55    
56    ## Pkg 'spdep' had (relatively slow) versions of this as_dsCMatrix_I()
57    .symDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
58        .sparseDiagonal(n, x, uplo, shape = "s")
59    
60    ## instead of   diagU2N(as(Diagonal(n), "CsparseMatrix")), diag = "N" in any case:
61    .trDiagonal <- function(n, x = rep.int(1,n), uplo = "U")
62        .sparseDiagonal(n, x, uplo, shape = "t")
63    
64    
65  ### 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.
66  ### 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
67  ### 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
68  ### who posted his bdiag() function written in December 1995.  ### who posted his bdiag() function written in December 1995.
69    if(FALSE)##--- no longer used:
70  bdiag <- function(...) {  .bdiag <- function(lst) {
71      if(nargs() == 0) return(new("dgCMatrix"))      ### block-diagonal matrix [a dgTMatrix] from list of matrices
72      ## else :      stopifnot(is.list(lst), length(lst) >= 1)
73      mlist <- if (nargs() == 1) as.list(...) else list(...)      dims <- sapply(lst, dim, USE.NAMES=FALSE)
     dims <- sapply(mlist, dim)  
74      ## make sure we had all matrices:      ## make sure we had all matrices:
75      if(!(is.matrix(dims) && nrow(dims) == 2))      if(!(is.matrix(dims) && nrow(dims) == 2))
76          stop("some arguments are not matrices")          stop("some arguments are not matrices")
77      csdim <- rbind(rep.int(0:0, 2),      csdim <- rbind(rep.int(0L, 2),
78                     apply(sapply(mlist, dim), 1, cumsum))                     apply(dims, 1, cumsum))
79      ret <- new("dgTMatrix", Dim = as.integer(csdim[nrow(csdim),]))      r <- new("dgTMatrix")
80        r@Dim <- as.integer(csdim[nrow(csdim),])
81      add1 <- matrix(1:0, 2,2)      add1 <- matrix(1:0, 2,2)
82      for(i in seq_along(mlist)) {      for(i in seq_along(lst)) {
83          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])
84          if(is.null(dim(indx))) ## non-square matrix          if(is.null(dim(indx))) ## non-square matrix
85              ret[indx[[1]],indx[[2]]] <- mlist[[i]]              r[indx[[1]],indx[[2]]] <- lst[[i]]
86          else ## square matrix          else ## square matrix
87              ret[indx[,1],indx[,2]] <- mlist[[i]]              r[indx[,1], indx[,2]] <- lst[[i]]
88        }
89        r
90    }
91    ## expand(<mer>) needed something like bdiag() for lower-triangular
92    ## (Tsparse) Matrices; hence Doug Bates provided a much more efficient
93    ##  implementation for those; now extended and generalized:
94    .bdiag <- function(lst) {
95        ## block-diagonal matrix [a dgTMatrix] from list of matrices
96        stopifnot(is.list(lst), (nl <- length(lst)) >= 1)
97    
98        Tlst <- lapply(lapply(lst, Matrix:::as_Csp2), # includes "diagU2N"
99                       as, "TsparseMatrix")
100        if(nl == 1) return(Tlst[[1]])
101        ## else
102        i_off <- c(0L, cumsum(sapply(Tlst, nrow)))
103        j_off <- c(0L, cumsum(sapply(Tlst, ncol)))
104    
105        clss <- sapply(Tlst, class)
106        knds <- substr(clss, 2, 2)
107        sym  <- knds == "s" # symmetric ones
108        tri  <- knds == "t" # triangular ones
109        use.n <- any(is.n <- substr(clss,1,1) == "n")
110        if(use.n && !(use.n <- all(is.n)))
111            Tlst[is.n] <- lapply(Tlst[is.n], as, "lMatrix")
112        if(all(sym)) { ## result should be *symmetric*
113            uplos <- sapply(Tlst, slot, "uplo") ## either "U" or "L"
114            tLU <- table(uplos)# of length 1 or 2 ..
115            if(length(tLU) == 1) { ## all "U" or all "L"
116                useU <- uplos[1] == "U"
117            } else { ## length(tLU) == 2, counting "L" and "U"
118                useU <- diff(tLU) >= 0
119                if(useU && (hasL <- tLU[1] > 0))
120                    Tlst[hasL] <- lapply(Tlst[hasL], t)
121                else if(!useU && (hasU <- tLU[2] > 0))
122                    Tlst[hasU] <- lapply(Tlst[hasU], t)
123            }
124            if(use.n) { ## return nsparseMatrix :
125                r <- new("nsTMatrix")
126            } else {
127                r <- new("dsTMatrix")
128                r@x <- unlist(lapply(Tlst, slot, "x"))
129      }      }
130      ## slightly debatable if we really should return Csparse.. :          r@uplo <- if(useU) "U" else "L"
     as(ret, "CsparseMatrix")  
131  }  }
132        else if(all(tri) && { ULs <- sapply(Tlst, slot, "uplo")##  "U" or "L"
133                              all(ULs[1L] == ULs[-1L]) } ## all upper or all lower
134           ){ ## *triangular* result
135    
136  diag2T <- function(from) {          if(use.n) { ## return nsparseMatrix :
137      i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1:1              r <- new("ntTMatrix")
138      new(paste(.M.kind(from), "tTMatrix", sep=''),          } else {
139                r <- new("dtTMatrix")
140                r@x <- unlist(lapply(Tlst, slot, "x"))
141            }
142            r@uplo <- ULs[1L]
143        }
144        else {
145            if(any(sym))
146                Tlst[sym] <- lapply(Tlst[sym], as, "generalMatrix")
147            if(use.n) { ## return nsparseMatrix :
148                r <- new("ngTMatrix")
149            } else {
150                r <- new("dgTMatrix")
151                r@x <- unlist(lapply(Tlst, slot, "x"))
152            }
153        }
154        r@Dim <- c(i_off[nl+1], j_off[nl + 1])
155        r@i <- unlist(lapply(1:nl, function(k) Tlst[[k]]@i + i_off[k]))
156        r@j <- unlist(lapply(1:nl, function(k) Tlst[[k]]@j + j_off[k]))
157        r
158    }
159    
160    bdiag <- function(...) {
161        if((nA <- nargs()) == 0) return(new("dgCMatrix"))
162        if(nA == 1 && !is.list(...))
163            return(as(..., "CsparseMatrix"))
164        alis <- if(nA == 1 && is.list(..1)) ..1 else list(...)
165        if(length(alis) == 1)
166            return(as(alis[[1]], "CsparseMatrix"))
167    
168        ## else : two or more arguments
169        as(.bdiag(alis), "CsparseMatrix")
170    }
171    
172    
173    .diag2tT <- function(from, uplo = "U", kind = .M.kind(from)) {
174        ## to triangular Tsparse
175        i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1L
176        new(paste(kind, "tTMatrix", sep=''),
177          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,          diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
178            uplo = uplo,
179          x = from@x, # <- ok for diag = "U" and "N" (!)          x = from@x, # <- ok for diag = "U" and "N" (!)
180          i = i, j = i)          i = i, j = i)
181  }  }
182    
183  setAs("diagonalMatrix", "triangularMatrix", diag2T)  .diag2sT <- function(from, uplo = "U", kind = .M.kind(from)) {
184  setAs("diagonalMatrix", "sparseMatrix", diag2T)      ## to symmetric Tsparse
185        n <- from@Dim[1]
186        i <- seq_len(n) - 1L
187        new(paste(kind, "sTMatrix", sep=''),
188            Dim = from@Dim, Dimnames = from@Dimnames,
189            i = i, j = i, uplo = uplo,
190            x = if(from@diag == "N") from@x else ## "U"-diag
191            rep.int(switch(kind,
192                           "d" = 1.,
193                           "l" =,
194                           "n" = TRUE,
195                           ## otherwise
196                           stop("'", kind,"' kind not yet implemented")), n))
197    }
198    
199    ## diagonal -> triangular,  upper / lower depending on "partner":
200    diag2tT.u <- function(d, x, kind = .M.kind(d))
201        .diag2tT(d, uplo = if(is(x,"triangularMatrix")) x@uplo else "U", kind)
202    
203    ## diagonal -> sparse {triangular OR symmetric} (upper / lower) depending on "partner":
204    diag2Tsmart <- function(d, x, kind = .M.kind(d)) {
205        clx <- getClassDef(class(x))
206        if(extends(clx, "symmetricMatrix"))
207            .diag2sT(d, uplo = x@uplo, kind)
208        else
209            .diag2tT(d, uplo = if(extends(clx,"triangularMatrix")) x@uplo else "U", kind)
210    }
211    
212    
213    ## In order to evade method dispatch ambiguity warnings,
214    ## and because we can save a .M.kind() call, we use this explicit
215    ## "hack"  instead of signature  x = "diagonalMatrix" :
216    ##
217    ## ddi*:
218    diag2tT <- function(from) .diag2tT(from, "U", "d")
219    setAs("ddiMatrix", "triangularMatrix", diag2tT)
220    ##_no_longer_ setAs("ddiMatrix", "sparseMatrix", diag2tT)
221    ## needed too (otherwise <dense> -> Tsparse is taken):
222    setAs("ddiMatrix", "TsparseMatrix", diag2tT)
223    setAs("ddiMatrix", "dsparseMatrix", diag2tT)
224    setAs("ddiMatrix", "CsparseMatrix",
225          function(from) as(.diag2tT(from, "U", "d"), "CsparseMatrix"))
226    setAs("ddiMatrix", "symmetricMatrix",
227          function(from) .diag2sT(from, "U", "d"))
228    ##
229    ## ldi*:
230    diag2tT <- function(from) .diag2tT(from, "U", "l")
231    setAs("ldiMatrix", "triangularMatrix", diag2tT)
232    ##_no_longer_ setAs("ldiMatrix", "sparseMatrix", diag2tT)
233  ## needed too (otherwise <dense> -> Tsparse is taken):  ## needed too (otherwise <dense> -> Tsparse is taken):
234  setAs("diagonalMatrix", "TsparseMatrix", diag2T)  setAs("ldiMatrix", "TsparseMatrix", diag2tT)
235  ## is better than this:  setAs("ldiMatrix", "lsparseMatrix", diag2tT)
236  ## setAs("diagonalMatrix", "sparseMatrix",  setAs("ldiMatrix", "CsparseMatrix",
237  ##       function(from)        function(from) as(.diag2tT(from, "U", "l"), "CsparseMatrix"))
238  ##        as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))  setAs("ldiMatrix", "symmetricMatrix",
239  setAs("diagonalMatrix", "CsparseMatrix",        function(from) .diag2sT(from, "U", "l"))
       function(from) as(diag2T(from), "CsparseMatrix"))  
240    
241  setAs("diagonalMatrix", "matrix",  
242    setAs("diagonalMatrix", "nMatrix",
243        function(from) {        function(from) {
244            n <- from@Dim[1]            n <- from@Dim[1]
245            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
246                                       } else from@x,            new("ntTMatrix", i = i, j = i, diag = from@diag,
247                 nrow = n, ncol = n)                Dim = from@Dim, Dimnames = from@Dimnames)
248        })        })
249    
250  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:  setAs("diagonalMatrix", "nsparseMatrix", function(from) as(from, "nMatrix"))
       function(from) as(from, paste(.M.kind(from), "gCMatrix", sep='')))  
251    
252  .diag.x <- function(m) {  ## Cheap fast substitute for diag() which *does* preserve the mode of x :
253      if(m@diag == "U")  mkDiag <- function(x, n) {
254          rep.int(if(is.numeric(m@x)) 1. else TRUE,      y <- matrix(as0(mod=mode(x)), n,n)
255                  m@Dim[1])      if (n > 0) y[1L + 0:(n - 1L) * (n + 1L)] <- x
256      else m@x      y
 }  
   
 .diag.2N <- function(m) {  
     if(m@diag == "U") m@diag <- "N"  
     m  
257  }  }
258    
259  ## given the above, the following  4  coercions should be all unneeded;  setAs("diagonalMatrix", "matrix",
 ## we prefer triangular to general:  
 setAs("ddiMatrix", "dgTMatrix",  
260        function(from) {        function(from) {
261            .Deprecated("as(, \"sparseMatrix\")")            ## want "ldiMatrix" -> <logical> "matrix" :
262            n <- from@Dim[1]            mkDiag(if(from@diag == "U") as1(from@x) else from@x,
263            i <- seq_len(n) - 1:1                   n = from@Dim[1])
264            new("dgTMatrix", i = i, j = i, x = .diag.x(from),        })
               Dim = c(n,n), Dimnames = from@Dimnames) })  
265    
266  setAs("ddiMatrix", "dgCMatrix",  setMethod("as.vector", signature(x = "diagonalMatrix", mode="missing"),
267        function(from) as(as(from, "sparseMatrix"), "dgCMatrix"))            function(x, mode) {
268                  n <- x@Dim[1]
269                  mod.x <- mode(x@x)
270                  r <- vector(mod.x, length = n^2)
271                  if(n)
272                      r[1 + 0:(n - 1) * (n + 1)] <-
273                          if(x@diag == "U") as1(mod=mod.x) else x@x
274                  r
275              })
276    
277  setAs("ldiMatrix", "lgTMatrix",  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
278        function(from) {        function(from) as(as(from, "CsparseMatrix"), "generalMatrix"))
           .Deprecated("as(, \"sparseMatrix\")")  
           n <- from@Dim[1]  
           if(from@diag == "U") { # unit-diagonal  
               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) })  
279    
280  setAs("ldiMatrix", "lgCMatrix",  setAs("diagonalMatrix", "denseMatrix",
281        function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))        function(from) as(as(from, "CsparseMatrix"), "denseMatrix"))
282    
283    .diag.x <- function(m) if(m@diag == "U") rep.int(as1(m@x), m@Dim[1]) else m@x
284    
285    .diag.2N <- function(m) {
286        if(m@diag == "U") m@diag <- "N"
287        m
288    }
289    
 if(FALSE) # now have faster  "ddense" -> "dge"  
290  setAs("ddiMatrix", "dgeMatrix",  setAs("ddiMatrix", "dgeMatrix",
291        function(from) as(as(from, "matrix"), "dgeMatrix"))        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
292    setAs("ddiMatrix", "ddenseMatrix",
293          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
294    setAs("ldiMatrix", "ldenseMatrix",
295          function(from) as(as(from, "triangularMatrix"),"denseMatrix"))
296    
297    
298  setAs("matrix", "diagonalMatrix",  setAs("matrix", "diagonalMatrix",
299        function(from) {        function(from) {
300            d <- dim(from)            d <- dim(from)
301            if(d[1] != (n <- d[2])) stop("non-square matrix")            if(d[1] != (n <- d[2])) stop("non-square matrix")
302            if(any(from[row(from) != col(from)] != 0))            if(any(from[row(from) != col(from)] != 0))
303                stop("has non-zero off-diagonal entries")                stop("matrix with non-zero off-diagonals cannot be coerced to diagonalMatrix")
304            x <- diag(from)            x <- diag(from)
305            if(is.logical(x)) {            if(is.logical(x)) {
306                cl <- "ldiMatrix"                cl <- "ldiMatrix"
307                uni <- all(x)                uni <- allTrue(x) ## uni := {is it unit-diagonal ?}
308            } else {            } else {
309                cl <- "ddiMatrix"                cl <- "ddiMatrix"
310                uni <- all(x == 1)                uni <- allTrue(x == 1)
311                storage.mode(x) <- "double"                storage.mode(x) <- "double"
312            } ## TODO: complex            } ## TODO: complex
313            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 165  Line 324 
324            x <- diag(from)            x <- diag(from)
325            if(is.logical(x)) {            if(is.logical(x)) {
326                cl <- "ldiMatrix"                cl <- "ldiMatrix"
327                uni <- all(x)                uni <- allTrue(x)
328            } else {            } else {
329                cl <- "ddiMatrix"                cl <- "ddiMatrix"
330                uni <- all(x == 1)                uni <- allTrue(x == 1)
331                storage.mode(x) <- "double"                storage.mode(x) <- "double"
332            }            } ## TODO: complex
333            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
334                x = if(uni) x[FALSE] else x)                x = if(uni) x[FALSE] else x)
335        })        })
336    
337    
338  setMethod("diag", signature(x = "diagonalMatrix"),  setMethod("diag", signature(x = "diagonalMatrix"),
339            function(x = 1, nrow, ncol = n) .diag.x(x))            function(x = 1, nrow, ncol) .diag.x(x))
   
340    
341  subDiag <- function(x, i, j, drop) {  subDiag <- function(x, i, j, ..., drop) {
342      x <- as(x, "sparseMatrix")      x <- as(x, "TsparseMatrix")
343      x <- if(missing(i))      x <- if(missing(i))
344          x[, j, drop=drop]          x[, j, drop=drop]
345      else if(missing(j))      else if(missing(j))
346          x[i, , drop=drop]          if(nargs() == 4) x[i, , drop=drop] else x[i, drop=drop]
347      else      else
348          x[i,j, drop=drop]          x[i,j, drop=drop]
349      if(isDiagonal(x)) as(x, "diagonalMatrix") else x      if(isS4(x) && isDiagonal(x)) as(x, "diagonalMatrix") else x
350  }  }
351    
352  setMethod("[", signature(x = "diagonalMatrix", i = "index",  setMethod("[", signature(x = "diagonalMatrix", i = "index",
353                           j = "index", drop = "logical"), subDiag)                           j = "index", drop = "logical"), subDiag)
354  setMethod("[", signature(x = "diagonalMatrix", i = "index",  setMethod("[", signature(x = "diagonalMatrix", i = "index",
355                          j = "missing", drop = "logical"),                          j = "missing", drop = "logical"),
356            function(x, i, drop) subDiag(x, i=i, drop=drop))            function(x, i, j, ..., drop) {
357                  na <- nargs()
358                  Matrix.msg("diag[i,m,l] : nargs()=", na, .M.level = 2)
359                  if(na == 4)
360                       subDiag(x, i=i, , drop=drop)
361                  else subDiag(x, i=i,   drop=drop)
362              })
363  setMethod("[", signature(x = "diagonalMatrix", i = "missing",  setMethod("[", signature(x = "diagonalMatrix", i = "missing",
364                           j = "index", drop = "logical"),                           j = "index", drop = "logical"),
365            function(x, j, drop) subDiag(x, j=j, drop=drop))            function(x, i, j, ..., drop) subDiag(x, j=j, drop=drop))
366    
367  ## When you assign to a diagonalMatrix, the result should be  ## When you assign to a diagonalMatrix, the result should be
368  ## diagonal or sparse ---  ## diagonal or sparse ---
369  ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch  ## FIXME: this now fails because the "denseMatrix" methods come first in dispatch
370  replDiag <- function(x, i, j, value) {  ## Only(?) current bug:  x[i] <- value  is wrong when  i is *vector*
371      x <- as(x, "sparseMatrix")  replDiag <- function(x, i, j, ..., value) {
372        x <- as(x, "TsparseMatrix")
373      if(missing(i))      if(missing(i))
374          x[, j] <- value          x[, j] <- value
375      else if(missing(j))      else if(missing(j)) { ##  x[i , ] <- v  *OR*   x[i] <- v
376            na <- nargs()
377    ##         message("diagnosing replDiag() -- nargs()= ", na)
378            if(na == 4)
379          x[i, ] <- value          x[i, ] <- value
380      else          else if(na == 3)
381                x[i] <- value
382            else stop("Internal bug: nargs()=",na,"; please report")
383        } else
384          x[i,j] <- value          x[i,j] <- value
385      if(isDiagonal(x)) as(x, "diagonalMatrix") else x      if(isDiagonal(x)) as(x, "diagonalMatrix") else x
386  }  }
387    
388  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
389                                  j = "index", value = "replValue"), replDiag)                                  j = "index", value = "replValue"), replDiag)
390    
391  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index",
392                                  j = "missing", value = "replValue"),                                  j = "missing", value = "replValue"),
393                   function(x, i, value) replDiag(x, i=i, value=value))                   function(x,i,j, ..., value) {
394                         ## message("before replDiag() -- nargs()= ", nargs())
395                         if(nargs() == 3)
396                             replDiag(x, i=i, value=value)
397                         else ## nargs() == 4 :
398                             replDiag(x, i=i, , value=value)
399                     })
400    
401    setReplaceMethod("[", signature(x = "diagonalMatrix",
402                                    i = "matrix", # 2-col.matrix
403                                    j = "missing", value = "replValue"),
404                     function(x,i,j, ..., value) {
405                         if(ncol(i) == 2) {
406                             if(all((ii <- i[,1]) == i[,2])) { # replace in diagonal only
407                                 if(x@diag == "U") {
408                                     one <- as1(x@x)
409                                     if(any(value != one | is.na(value))) {
410                                         x@diag <- "N"
411                                         x@x <- rep.int(one, x@Dim[1])
412                                     }
413                                 }
414                                 x@x[ii] <- value
415                                 x
416                             } else { ## no longer diagonal, but remain sparse:
417                                 x <- as(x, "TsparseMatrix")
418                                 x[i] <- value
419                                 x
420                             }
421                         }
422                         else { # behave as "base R": use as if vector
423                             x <- as(x, "matrix")
424                             x[i] <- value
425                             Matrix(x)
426                         }
427                     })
428    
429  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",  setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing",
430                                  j = "index", value = "replValue"),                                  j = "index", value = "replValue"),
431                   function(x, j, value) replDiag(x, j=j, value=value))                   function(x,i,j, ..., value) replDiag(x, j=j, value=value))
432    
433    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
434                                    value = "sparseMatrix"),
435                     function (x, i, j, ..., value)
436                     callGeneric(x=x, , j=j, value = as(value, "sparseVector")))
437    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
438                                    value = "sparseMatrix"),
439                     function (x, i, j, ..., value)
440                     callGeneric(x=x, i=i, , value = as(value, "sparseVector")))
441    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
442                                    value = "sparseMatrix"),
443                     function (x, i, j, ..., value)
444                     callGeneric(x=x, i=i, j=j, value = as(value, "sparseVector")))
445    
446    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "missing", j = "index",
447                                    value = "sparseVector"),
448                     replDiag)
449    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "missing",
450                                    value = "sparseVector"),
451                     replDiag)
452    setReplaceMethod("[", signature(x = "diagonalMatrix", i = "index", j = "index",
453                                    value = "sparseVector"),
454                     replDiag)
455    
456    
457  setMethod("t", signature(x = "diagonalMatrix"),  setMethod("t", signature(x = "diagonalMatrix"),
# Line 232  Line 462 
462  setMethod("isTriangular", signature(object = "diagonalMatrix"),  setMethod("isTriangular", signature(object = "diagonalMatrix"),
463            function(object) TRUE)            function(object) TRUE)
464  setMethod("isSymmetric", signature(object = "diagonalMatrix"),  setMethod("isSymmetric", signature(object = "diagonalMatrix"),
465            function(object) TRUE)            function(object, ...) TRUE)
466    
467  setMethod("chol", signature(x = "ddiMatrix"),# pivot = "ANY"  setMethod("symmpart", signature(x = "diagonalMatrix"), function(x) x)
468            function(x, pivot) {  setMethod("skewpart", signature(x = "diagonalMatrix"), setZero)
469                if(any(x@x < 0)) stop("chol() is undefined for diagonal matrix with negative entries")  
470    setMethod("chol", signature(x = "ddiMatrix"),
471              function(x, pivot, ...) {
472                  if(x@diag == "U") return(x)
473                  ## else
474                  if(any(x@x < 0))
475                      stop("chol() is undefined for diagonal matrix with negative entries")
476                x@x <- sqrt(x@x)                x@x <- sqrt(x@x)
477                x                x
478            })            })
479  ## chol(L) is L for logical diagonal:  ## chol(L) is L for logical diagonal:
480  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot) x)  setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot, ...) x)
481    
482  setMethod("!", "ldiMatrix", function(e1) {  setMethod("determinant", signature(x = "diagonalMatrix", logarithm = "logical"),
483      if(e1@diag == "N")            function(x, logarithm, ...) mkDet(.diag.x(x), logarithm))
484          e1@x <- !e1@x  
485      else { ## "U"  setMethod("norm", signature(x = "diagonalMatrix", type = "character"),
486          e1@diag <- "N"            function(x, type, ...) {
487          e1@x <- rep.int(FALSE, e1@Dim[1])                if((n <- x@Dim[1]) == 0) return(0) # as for "sparseMatrix"
488                  type <- toupper(substr(type[1], 1, 1))
489                  isU <- (x@diag == "U") # unit-diagonal
490                  if(type == "F") sqrt(if(isU) n else sum(x@x^2))
491                  else { ## norm == "I","1","O","M" :
492                      if(isU) 1 else max(abs(x@x))
493      }      }
     e1  
494  })  })
495    
496    
497    
498  ## Basic Matrix Multiplication {many more to add}  ## Basic Matrix Multiplication {many more to add}
499  ##       ---------------------  ##       ---------------------
500  ## Note that "ldi" logical are treated as numeric  ## Note that "ldi" logical are treated as numeric
501  diagdiagprod <- function(x, y) {  diagdiagprod <- function(x, y) {
502      if(any(dim(x) != dim(y))) stop("non-matching dimensions")      n <- dimCheck(x,y)[1]
503      if(x@diag != "U") {      if(x@diag != "U") {
504          if(y@diag != "U") {          if(y@diag != "U") {
505              nx <- x@x * y@x              nx <- x@x * y@x
# Line 285  Line 527 
527    
528    
529  diagmatprod <- function(x, y) {  diagmatprod <- function(x, y) {
530        ## x is diagonalMatrix
531      dx <- dim(x)      dx <- dim(x)
532      dy <- dim(y)      dy <- dim(y)
533      if(dx[2] != dy[1]) stop("non-matching dimensions")      if(dx[2] != dy[1]) stop("non-matching dimensions")
534      n <- dx[1]      n <- dx[1]
535      as(if(x@diag == "U") y else x@x * y, "Matrix")      as(if(x@diag == "U") y else x@x * y, "Matrix")
536  }  }
   
537  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "matrix"),
538            diagmatprod)            diagmatprod)
539    ## sneaky .. :
540  formals(diagmatprod) <- alist(x=, y=NULL)  formals(diagmatprod) <- alist(x=, y=NULL)
541  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),
542            diagmatprod)            diagmatprod)
 setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "matrix"),  
           diagmatprod)  
543    
544  diagdgeprod <- function(x, y) {  diagGeprod <- function(x, y) {
545      dx <- dim(x)      dx <- dim(x)
546      dy <- dim(y)      dy <- dim(y)
547      if(dx[2] != dy[1]) stop("non-matching dimensions")      if(dx[2] != dy[1]) stop("non-matching dimensions")
# Line 308  Line 549 
549          y@x <- x@x * y@x          y@x <- x@x * y@x
550      y      y
551  }  }
552  setMethod("%*%", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("%*%", signature(x= "diagonalMatrix", y= "dgeMatrix"), diagGeprod)
553            diagdgeprod, valueClass = "dgeMatrix")  setMethod("%*%", signature(x= "diagonalMatrix", y= "lgeMatrix"), diagGeprod)
554  formals(diagdgeprod) <- alist(x=, y=NULL)  formals(diagGeprod) <- alist(x=, y=NULL)
555  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "dgeMatrix"),
556            diagdgeprod, valueClass = "dgeMatrix")            diagGeprod, valueClass = "dgeMatrix")
557    setMethod("crossprod", signature(x = "diagonalMatrix", y = "lgeMatrix"),
558              diagGeprod)
559    
560  setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"),  matdiagprod <- function(x, y) {
           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")
564                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]))
565            })  }
566    setMethod("%*%", signature(x = "matrix", y = "diagonalMatrix"),
567              matdiagprod)
568    formals(matdiagprod) <- alist(x=, y=NULL)
569    setMethod("tcrossprod", signature(x = "matrix", y = "diagonalMatrix"),
570              matdiagprod)
571    
572  setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),  gediagprod <- function(x, y) {
           function(x, y) {  
573                dx <- dim(x)                dx <- dim(x)
574                dy <- dim(y)                dy <- dim(y)
575                if(dx[2] != dy[1]) stop("non-matching dimensions")                if(dx[2] != dy[1]) stop("non-matching dimensions")
576                if(y@diag == "N")                if(y@diag == "N")
577                    x@x <- x@x * rep(y@x, each = dx[1])                    x@x <- x@x * rep(y@x, each = dx[1])
578                x                x
579            })  }
580    setMethod("%*%", signature(x= "dgeMatrix", y= "diagonalMatrix"), gediagprod)
581    setMethod("%*%", signature(x= "lgeMatrix", y= "diagonalMatrix"), gediagprod)
582    formals(gediagprod) <- alist(x=, y=NULL)
583    setMethod("tcrossprod", signature(x = "dgeMatrix", y = "diagonalMatrix"),
584              gediagprod)
585    setMethod("tcrossprod", signature(x = "lgeMatrix", y = "diagonalMatrix"),
586              gediagprod)
587    
588  ## crossprod {more of these}  ## crossprod {more of these}
589    
590  ## tcrossprod --- all are not yet there: do the dense ones here:  ## tcrossprod --- all are not yet there: do the dense ones here:
591    
592    setMethod("%*%", signature(x = "diagonalMatrix", y = "denseMatrix"),
593              function(x, y) if(x@diag == "U") y else x %*% as(y, "generalMatrix"))
594    setMethod("%*%", signature(x = "denseMatrix", y = "diagonalMatrix"),
595              function(x, y) if(y@diag == "U") x else as(x, "generalMatrix") %*% y)
596    
597    
598  ## FIXME:  ## FIXME:
599  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),  ## setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "denseMatrix"),
600  ##        function(x, y = NULL) {  ##        function(x, y = NULL) {
601  ##           })  ##           })
602    
603  ## setMethod("tcrossprod", signature(x = "denseMatrix", y = "diagonalMatrix"),  Cspdiagprod <- function(x, y) {
604  ##        function(x, y = NULL) {      dx <- dim(x <- .Call(Csparse_diagU2N, x))
605  ##           })      dy <- dim(y)
606        if(dx[2] != dy[1]) stop("non-matching dimensions")
607        ind <- rep.int(seq_len(dx[2]), x@p[-1] - x@p[-dx[2]-1L])
608        if(y@diag == "N")
609            x@x <- x@x * y@x[ind]
610        x
611    }
612    
613    diagCspprod <- function(x, y) {
614        dx <- dim(x)
615        dy <- dim(y <- .Call(Csparse_diagU2N, y))
616        if(dx[2] != dy[1]) stop("non-matching dimensions")
617        if(x@diag == "N")
618            y@x <- y@x * x@x[y@i + 1L]
619        y
620    }
621    
622    setMethod("crossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
623              function(x, y = NULL) diagCspprod(x, y))
624    
625  setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
626            function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })            function(x, y = NULL) diagCspprod(x, as(y, "CsparseMatrix")))
627    
628    ## Prefer calling diagCspprod to Cspdiagprod if going to transpose anyway
629    ##  x'y == (y'x)'
630    setMethod("crossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
631              function(x, y = NULL) t(diagCspprod(y, x)))
632    
633  setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("crossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
634            function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })            function(x, y = NULL) t(diagCspprod(y, as(x, "Csparsematrix"))))
635    
636    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
637              function(x, y = NULL) diagCspprod(x, t(y)))
638    
639  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "sparseMatrix"),
640            function(x, y = NULL) { x <- as(x, "sparseMatrix"); callGeneric() })            function(x, y = NULL) diagCspprod(x, t(as(y, "CsparseMatrix"))))
641    
642    setMethod("tcrossprod", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
643              function(x, y = NULL) Cspdiagprod(x, y))
644    
645  setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("tcrossprod", signature(x = "sparseMatrix", y = "diagonalMatrix"),
646            function(x, y = NULL) { y <- as(y, "sparseMatrix"); callGeneric() })            function(x, y = NULL) Cspdiagprod(as(x, "CsparseMatrix"), y))
647    
648    setMethod("%*%", signature(x = "diagonalMatrix", y = "CsparseMatrix"),
649              function(x, y) diagCspprod(x, y))
650    
 ## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()  
651  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
652            function(x, y) as(x, "sparseMatrix") %*% y)            function(x, y) diagCspprod(as(x, "CsparseMatrix"), y))
 ## 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)!  
653    
654  setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),  setMethod("%*%", signature(x = "sparseMatrix", y = "diagonalMatrix"),
655            function(x, y) x %*% as(y, "sparseMatrix"))            function(x, y) Cspdiagprod(as(x, "CsparseMatrix"), y))
656    
657    setMethod("%*%", signature(x = "CsparseMatrix", y = "diagonalMatrix"),
658              function(x, y) Cspdiagprod(x, y))
659    
660    ## TODO: Write tests in ./tests/ which ensure that many "ops" with diagonal*
661    ##       do indeed work by going through sparse (and *not* ddense)!
662    
663  setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),  setMethod("solve", signature(a = "diagonalMatrix", b = "missing"),
664            function(a, b, ...) {            function(a, b, ...) {
# Line 396  Line 680 
680  setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),  setMethod("solve", signature(a = "diagonalMatrix", b = "Matrix"),
681            solveDiag)            solveDiag)
682    
683    ## Schur()  ---> ./eigen.R
684    
685    
686    
687  ### ---------------- diagonal  o  sparse  -----------------------------  ###---------------- <Ops> (<Arith>, <Logic>, <Compare> ) ----------------------
   
688    
689  ## Use function for several signatures, in order to evade  ## Use function for several signatures, in order to evade
690  ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)  ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)
691  diagOdiag <- function(e1,e2) { # result should also be diagonal  diagOdiag <- function(e1,e2) {
692        ## result should also be diagonal _ if possible _
693      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"      r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
694        ## Check what happens with non-diagonals, i.e. (0 o 0), (FALSE o 0), ...:
695        r00 <- callGeneric(if(is.numeric(e1@x)) 0 else FALSE,
696                           if(is.numeric(e2@x)) 0 else FALSE)
697        if(is0(r00)) { ##  r00 == 0 or FALSE --- result *is* diagonal
698      if(is.numeric(r)) {      if(is.numeric(r)) {
699          if(is.numeric(e2@x)) {          if(is.numeric(e2@x)) {
700              e2@x <- r; return(.diag.2N(e2)) }              e2@x <- r; return(.diag.2N(e2)) }
# Line 419  Line 708 
708      e1@x <- r      e1@x <- r
709      .diag.2N(e1)      .diag.2N(e1)
710  }  }
711        else { ## result not diagonal, but at least symmetric:
712            isNum <- (is.numeric(r) || is.numeric(r00))
713            isLog <- (is.logical(r) || is.logical(r00))
714    
715            Matrix.msg("exploding   <diag>  o  <diag>  into dense matrix")
716            d <- e1@Dim
717            n <- d[1]
718            stopifnot(length(r) == n)
719            xx <- as.vector(matrix(rbind(r, matrix(r00,n,n)), n,n))
720            newcl <-
721                paste(if(isNum) "d" else if(isLog) {
722                    if(!any(is.na(r)) && !any(is.na(r00))) "n" else "l"
723                } else stop("not yet implemented .. please report")
724                      ,
725                      "syMatrix", sep='')
726    
727            new(newcl, Dim = e1@Dim, Dimnames = e1@Dimnames, x = xx)
728        }
729    }
730    
731    ### This would be *the* way, but we get tons of "ambiguous method dispatch"
732    ## we use this hack instead of signature  x = "diagonalMatrix" :
733    diCls <- names(getClass("diagonalMatrix")@subclasses)
734    if(FALSE) {
735  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
736            diagOdiag)            diagOdiag)
737  ## These two are just for method disambiguation:  } else { ## These are just for method disambiguation:
738  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "diagonalMatrix"),      for(c1 in diCls)
739            diagOdiag)          for(c2 in diCls)
740  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ddiMatrix"),              setMethod("Ops", signature(e1 = c1, e2 = c2), diagOdiag)
741            diagOdiag)  }
742    
743    ## diagonal  o  triangular  |-->  triangular
744    ## diagonal  o  symmetric   |-->  symmetric
745    ##    {also when other is sparse: do these "here" --
746    ##     before conversion to sparse, since that loses "diagonality"}
747    
748  ## For almost everything else, diag* shall be treated "as sparse" :  ## For almost everything else, diag* shall be treated "as sparse" :
749  ## These are cheap implementations via coercion  ## These are cheap implementations via coercion
750    
751  ## for disambiguation  ## For disambiguation --- define this for "sparseMatrix" , then for "ANY";
752  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "sparseMatrix"),  ## and because we can save an .M.kind() call, we use this explicit
753            function(e1,e2) callGeneric(as(e1, "sparseMatrix"), e2))  ## "hack" for all diagonalMatrix *subclasses* instead of just "diagonalMatrix" :
754  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "diagonalMatrix"),  ##
755            function(e1,e2) callGeneric(e1, as(e2, "sparseMatrix")))  ## ddi*:
756  ## in general:  setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "sparseMatrix"),
757  setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ANY"),            function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
758            function(e1,e2) callGeneric(as(e1,"sparseMatrix"), e2))  setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ddiMatrix"),
759  setMethod("Ops", signature(e1 = "ANY", e2 = "diagonalMatrix"),            function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
760            function(e1,e2) callGeneric(e1, as(e2,"sparseMatrix")))  ## ldi*
761    setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "sparseMatrix"),
762              function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
763    setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "ldiMatrix"),
764              function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
765    
766    ## Ops:  Arith  --> numeric : "dMatrix"
767    ##       Compare --> logical
768    ##       Logic   --> logical: "lMatrix"
769    
770    ##  other = "numeric" : stay diagonal if possible
771    ## ddi*: Arith: result numeric, potentially ddiMatrix
772    setMethod("Arith", signature(e1 = "ddiMatrix", e2 = "numeric"),
773              function(e1,e2) {
774                  n <- e1@Dim[1]; nsq <- n^2
775                  f0 <- callGeneric(0, e2)
776                  if(all(is0(f0))) { # remain diagonal
777                      L1 <- (le <- length(e2)) == 1L
778                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
779                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
780                          e1@diag <- "N"
781                          if(L1) r <- rep.int(r, n)
782                      } else
783                          r <- callGeneric(e1@x, e2)
784                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
785                      return(e1)
786                  }
787                  callGeneric(diag2tT.u(e1,e2, "d"), e2)
788              })
789    
790    setMethod("Arith", signature(e1 = "numeric", e2 = "ddiMatrix"),
791              function(e1,e2) {
792                  n <- e2@Dim[1]; nsq <- n^2
793                  f0 <- callGeneric(e1, 0)
794                  if(all(is0(f0))) { # remain diagonal
795                      L1 <- (le <- length(e1)) == 1L
796                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
797                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
798                          e2@diag <- "N"
799                          if(L1) r <- rep.int(r, n)
800                      } else
801                          r <- callGeneric(e1, e2@x)
802                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
803                      return(e2)
804                  }
805                  callGeneric(e1, diag2tT.u(e2,e1, "d"))
806              })
807    
808    ## ldi* Arith --> result numeric, potentially ddiMatrix
809    setMethod("Arith", signature(e1 = "ldiMatrix", e2 = "numeric"),
810              function(e1,e2) {
811                  n <- e1@Dim[1]; nsq <- n^2
812                  f0 <- callGeneric(0, e2)
813                  if(all(is0(f0))) { # remain diagonal
814                      L1 <- (le <- length(e2)) == 1L
815                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
816                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
817                          e1@diag <- "N"
818                          if(L1) r <- rep.int(r, n)
819                      } else
820                          r <- callGeneric(e1@x, e2)
821                      e1 <- copyClass(e1, "ddiMatrix", c("diag", "Dim", "Dimnames"))
822                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
823                      return(e1)
824                  }
825                  callGeneric(diag2tT.u(e1,e2, "d"), e2)
826              })
827    
828    setMethod("Arith", signature(e1 = "numeric", e2 = "ldiMatrix"),
829              function(e1,e2) {
830                  n <- e2@Dim[1]; nsq <- n^2
831                  f0 <- callGeneric(e1, 0)
832                  if(all(is0(f0))) { # remain diagonal
833                      L1 <- (le <- length(e1)) == 1L
834                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
835                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
836                          e2@diag <- "N"
837                          if(L1) r <- rep.int(r, n)
838                      } else
839                          r <- callGeneric(e1, e2@x)
840                      e2 <- copyClass(e2, "ddiMatrix", c("diag", "Dim", "Dimnames"))
841                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
842                      return(e2)
843                  }
844                  callGeneric(e1, diag2tT.u(e2,e1, "d"))
845              })
846    
847    ## ddi*: for "Ops" without Arith --> result logical, potentially ldi
848    setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "numeric"),
849              function(e1,e2) {
850                  n <- e1@Dim[1]; nsq <- n^2
851                  f0 <- callGeneric(0, e2)
852                  if(all(is0(f0))) { # remain diagonal
853                      L1 <- (le <- length(e2)) == 1L
854                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
855                      if(e1@diag == "U" && any((r <- callGeneric(1, e2)) != 1)) {
856                          e1@diag <- "N"
857                          if(L1) r <- rep.int(r, n)
858                      } else
859                          r <- callGeneric(e1@x, e2)
860                      e1 <- copyClass(e1, "ldiMatrix", c("diag", "Dim", "Dimnames"))
861                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
862                      return(e1)
863                  }
864                  callGeneric(diag2tT.u(e1,e2, "l"), e2)
865              })
866    
867    setMethod("Ops", signature(e1 = "numeric", e2 = "ddiMatrix"),
868              function(e1,e2) {
869                  n <- e2@Dim[1]; nsq <- n^2
870                  f0 <- callGeneric(e1, 0)
871                  if(all(is0(f0))) { # remain diagonal
872                      L1 <- (le <- length(e1)) == 1L
873                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
874                      if(e2@diag == "U" && any((r <- callGeneric(e1, 1)) != 1)) {
875                          e2@diag <- "N"
876                          if(L1) r <- rep.int(r, n)
877                      } else
878                          r <- callGeneric(e1, e2@x)
879                      e2 <- copyClass(e2, "ldiMatrix", c("diag", "Dim", "Dimnames"))
880                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
881                      return(e2)
882                  }
883                  callGeneric(e1, diag2tT.u(e2,e1, "l"))
884              })
885    
886    ## ldi*: for "Ops" without Arith --> result logical, potentially ldi
887    setMethod("Ops", signature(e1 = "ldiMatrix", e2 = "numeric"),
888              function(e1,e2) {
889                  n <- e1@Dim[1]; nsq <- n^2
890                  f0 <- callGeneric(FALSE, e2)
891                  if(all(is0(f0))) { # remain diagonal
892                      L1 <- (le <- length(e2)) == 1L
893                      if(!L1 && le != nsq) e2 <- rep(e2, length.out = nsq)
894                      if(e1@diag == "U" && any((r <- callGeneric(TRUE, e2)) != 1)) {
895                          e1@diag <- "N"
896                          if(L1) r <- rep.int(r, n)
897                      } else
898                          r <- callGeneric(e1@x, e2)
899                      e1@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
900                      return(e1)
901                  }
902                  callGeneric(diag2tT.u(e1,e2, "l"), e2)
903              })
904    
905    setMethod("Ops", signature(e1 = "numeric", e2 = "ldiMatrix"),
906              function(e1,e2) {
907                  n <- e2@Dim[1]; nsq <- n^2
908                  f0 <- callGeneric(e1, FALSE)
909                  if(all(is0(f0))) { # remain diagonal
910                      L1 <- (le <- length(e1)) == 1L
911                      if(!L1 && le != nsq) e1 <- rep(e1, length.out = nsq)
912                      if(e2@diag == "U" && any((r <- callGeneric(e1, TRUE)) != 1)) {
913                          e2@diag <- "N"
914                          if(L1) r <- rep.int(r, n)
915                      } else
916                          r <- callGeneric(e1, e2@x)
917                      e2@x <- if(L1) r else r[1L + (n+1L)*(0:(n-1L))]
918                      return(e2)
919                  }
920                  callGeneric(e1, diag2tT.u(e2,e1, "l"))
921              })
922    
923    
924    
925    ## Not {"sparseMatrix", "numeric} :  {"denseMatrix", "matrix", ... }
926    for(other in c("ANY", "Matrix", "dMatrix")) {
927        ## ddi*:
928        setMethod("Ops", signature(e1 = "ddiMatrix", e2 = other),
929                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "d"), e2))
930        setMethod("Ops", signature(e1 = other, e2 = "ddiMatrix"),
931                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "d")))
932        ## ldi*:
933        setMethod("Ops", signature(e1 = "ldiMatrix", e2 = other),
934                  function(e1,e2) callGeneric(diag2Tsmart(e1,e2, "l"), e2))
935        setMethod("Ops", signature(e1 = other, e2 = "ldiMatrix"),
936                  function(e1,e2) callGeneric(e1, diag2Tsmart(e2,e1, "l")))
937    }
938    
939    ## Direct subclasses of "denseMatrix": currently ddenseMatrix, ldense... :
940    dense.subCl <- local({ dM.scl <- getClass("denseMatrix")@subclasses
941                           names(dM.scl)[sapply(dM.scl, slot, "distance") == 1] })
942    for(DI in diCls) {
943        for(c2 in c(dense.subCl, "Matrix")) {
944            for(Fun in c("*", "^", "&")) {
945                setMethod(Fun, signature(e1 = DI, e2 = c2),
946                          function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
947                setMethod(Fun, signature(e1 = c2, e2 = DI),
948                          function(e1,e2) callGeneric(Diagonal(x = diag(e1)), e2))
949            }
950            ## NB: This arguably implicitly uses  0/0 :== 0  to keep diagonality
951            for(Fun in c("%%", "%/%", "/")) {
952                setMethod(Fun, signature(e1 = DI, e2 = c2),
953                          function(e1,e2) callGeneric(e1, Diagonal(x = diag(e2))))
954            }
955        }
956    }
957    
958    
959    ### "Summary" : "max"   "min"   "range" "prod"  "sum"   "any"   "all"
960    ### ----------   the last 4: separately here
961    for(cl in diCls) {
962    setMethod("any", cl,
963              function (x, ..., na.rm) {
964                  if(any(x@Dim == 0)) FALSE
965                  else if(x@diag == "U") TRUE else any(x@x, ..., na.rm = na.rm)
966              })
967    setMethod("all",  cl, function (x, ..., na.rm) {
968        n <- x@Dim[1]
969        if(n >= 2) FALSE
970        else if(n == 0 || x@diag == "U") TRUE
971        else all(x@x, ..., na.rm = na.rm)
972    })
973    setMethod("prod", cl, function (x, ..., na.rm) {
974        n <- x@Dim[1]
975        if(n >= 2) 0
976        else if(n == 0 || x@diag == "U") 1
977        else ## n == 1, diag = "N" :
978            prod(x@x, ..., na.rm = na.rm)
979    })
980    
981    setMethod("sum", cl,
982              function(x, ..., na.rm) {
983                  r <- sum(x@x, ..., na.rm = na.rm)# double or integer, correctly
984                  if(x@diag == "U" && !is.na(r)) r + x@Dim[1] else r
985              })
986    }
987    
988    ## The remaining ones are  max, min, range :
989    
990    setMethod("Summary", "ddiMatrix",
991              function(x, ..., na.rm) {
992                  if(any(x@Dim == 0)) callGeneric(numeric(0), ..., na.rm=na.rm)
993                  else if(x@diag == "U")
994                      callGeneric(x@x, 0, 1, ..., na.rm=na.rm)
995                  else callGeneric(x@x, 0, ..., na.rm=na.rm)
996              })
997    setMethod("Summary", "ldiMatrix",
998              function(x, ..., na.rm) {
999                  if(any(x@Dim == 0)) callGeneric(logical(0), ..., na.rm=na.rm)
1000                  else if(x@diag == "U")
1001                      callGeneric(x@x, FALSE, TRUE, ..., na.rm=na.rm)
1002                  else callGeneric(x@x, FALSE, ..., na.rm=na.rm)
1003              })
1004    
1005    
1006    
# Line 455  Line 1015 
1015      invisible(x)      invisible(x)
1016  }  }
1017    
1018    ## somewhat consistent with "print" for sparseMatrix :
1019    setMethod("print", signature(x = "diagonalMatrix"), prDiag)
1020    
1021  setMethod("show", signature(object = "diagonalMatrix"),  setMethod("show", signature(object = "diagonalMatrix"),
1022            function(object) {            function(object) {
1023                d <- dim(object)                d <- dim(object)
1024                cl <- class(object)                cl <- class(object)
1025                cat(sprintf('%d x %d diagonal matrix of class "%s"\n',                cat(sprintf('%d x %d diagonal matrix of class "%s"',
1026                            d[1], d[2], cl))                            d[1], d[2], cl))
1027                  if(d[1] < 50) {
1028                      cat("\n")
1029                prDiag(object)                prDiag(object)
1030                  } else {
1031                      cat(", with diagonal entries\n")
1032                      show(diag(object))
1033                      invisible(object)
1034                  }
1035            })            })

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