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Diff of /pkg/R/diagMatrix.R

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revision 1331, Sat Jul 22 17:59:53 2006 UTC revision 1655, Mon Oct 30 17:16:27 2006 UTC
# Line 1  Line 1 
1    #### All methods for "diagonalMatrix" and its subclasses,
2    ####  currently "ddiMatrix", "ldiMatrix"
3    
4  ## Purpose: Constructor of diagonal matrices -- ~= diag() ,  ## Purpose: Constructor of diagonal matrices -- ~= diag() ,
5  ##          but *not* diag() extractor!  ##          but *not* diag() extractor!
6  Diagonal <- function(n, x = NULL)  Diagonal <- function(n, x = NULL)
# Line 10  Line 13 
13          n <- as.integer(n)          n <- as.integer(n)
14      }      }
15    
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)          stopifnot(length(x) == n)
20          if(is.logical(x))          if(is.logical(x))
21              cl <- "ldiMatrix"              cl <- "ldiMatrix"
22          else {          else if(is.numeric(x)) {
23              cl <- "ddiMatrix"              cl <- "ddiMatrix"
24              x <- as.numeric(x)              x <- as.numeric(x)
25          }          }
26            else if(is.complex(x)) {
27                cl <- "zdiMatrix"  # will not yet work
28            } else stop("'x' has invalid data type")
29          new(cl, Dim = c(n,n), diag = "N", x = x)          new(cl, Dim = c(n,n), diag = "N", x = x)
30      }      }
31  }  }
32    
33  setAs("diagonalMatrix", "triangularMatrix",  ### This is modified from a post of Bert Gunter to R-help on  1 Sep 2005.
34        function(from) {  ### Bert's code built on a post by Andy Liaw who most probably was influenced
35            n <- from@Dim[1]  ### by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002
36            i <- seq(length = n)  ### who posted his bdiag() function written in December 1995.
37            x <- from@x  
38            new(if(is.numeric(x)) "dtTMatrix" else "ltTMatrix",  bdiag <- function(...) {
39        if(nargs() == 0) return(new("dgCMatrix"))
40        ## else :
41        mlist <- if (nargs() == 1) as.list(...) else list(...)
42        dims <- sapply(mlist, dim)
43        ## make sure we had all matrices:
44        if(!(is.matrix(dims) && nrow(dims) == 2))
45            stop("some arguments are not matrices")
46        csdim <- rbind(rep.int(0:0, 2),
47                       apply(sapply(mlist, dim), 1, cumsum))
48        ret <- new("dgTMatrix", Dim = as.integer(csdim[nrow(csdim),]))
49        add1 <- matrix(1:0, 2,2)
50        for(i in seq_along(mlist)) {
51            indx <- apply(csdim[i:(i+1),] + add1, 2, function(n) n[1]:n[2])
52            if(is.null(dim(indx))) ## non-square matrix
53                ret[indx[[1]],indx[[2]]] <- mlist[[i]]
54            else ## square matrix
55                ret[indx[,1],indx[,2]] <- mlist[[i]]
56        }
57        ## slightly debatable if we really should return Csparse.. :
58        as(ret, "CsparseMatrix")
59    }
60    
61    diag2T <- function(from) {
62        i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1:1
63        new(paste(.M.kind(from), "tTMatrix", sep=''),
64                diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,                diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
65                x = x, i = i, j = i)          x = from@x, # <- ok for diag = "U" and "N" (!)
66            })          i = i, j = i)
67    }
68    
69    setAs("diagonalMatrix", "triangularMatrix", diag2T)
70    setAs("diagonalMatrix", "sparseMatrix", diag2T)
71    ## is better than this:
72    ## setAs("diagonalMatrix", "sparseMatrix",
73    ##       function(from)
74    ##        as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))
75    setAs("diagonalMatrix", "CsparseMatrix",
76          function(from) as(diag2T(from), "CsparseMatrix"))
77    
78  setAs("diagonalMatrix", "matrix",  setAs("diagonalMatrix", "matrix",
79        function(from) {        function(from) {
# Line 42  Line 83 
83                 nrow = n, ncol = n)                 nrow = n, ncol = n)
84        })        })
85    
86  setAs("diagonalMatrix", "generalMatrix",  setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
87        function(from) {        function(from) as(from, paste(.M.kind(from), "gCMatrix", sep='')))
           x <- as(from, "matrix")  
           as(x,  
              if(is.logical(x)) "lgeMatrix"  
 ## Not yet:  
 ##              else if(is.complex(x)) "zgeMatrix"  
 ##              else if(is.integer(x)) "igeMatrix"  
              else "dgeMatrix")  
       })  
88    
89    .diag.x <- function(m) {
90        if(m@diag == "U")
91            rep.int(if(is.numeric(m@x)) 1. else TRUE,
92                    m@Dim[1])
93        else m@x
94    }
95    
96    .diag.2N <- function(m) {
97        if(m@diag == "U") m@diag <- "N"
98        m
99    }
100    
101    ## given the above, the following  4  coercions should be all unneeded;
102    ## we prefer triangular to general:
103  setAs("ddiMatrix", "dgTMatrix",  setAs("ddiMatrix", "dgTMatrix",
104        function(from) {        function(from) {
105              .Deprecated("as(, \"sparseMatrix\")")
106            n <- from@Dim[1]            n <- from@Dim[1]
107            i <- seq(length = n) - 1:1            i <- seq_len(n) - 1:1
108            new("dgTMatrix", i = i, j = i,            new("dgTMatrix", i = i, j = i, x = .diag.x(from),
               x = if(from@diag == "U") rep(1,n) else from@x,  
109                Dim = c(n,n), Dimnames = from@Dimnames) })                Dim = c(n,n), Dimnames = from@Dimnames) })
110    
111  setAs("ddiMatrix", "dgCMatrix",  setAs("ddiMatrix", "dgCMatrix",
112        function(from) as(as(from, "dgTMatrix"), "dgCMatrix"))        function(from) as(as(from, "sparseMatrix"), "dgCMatrix"))
113    
114  setAs("ldiMatrix", "lgTMatrix",  setAs("ldiMatrix", "lgTMatrix",
115        function(from) {        function(from) {
116              .Deprecated("as(, \"sparseMatrix\")")
117            n <- from@Dim[1]            n <- from@Dim[1]
118            i <- (if(from@diag == "U") seq(length = n) else which(from@x)) - 1:1            if(from@diag == "U") { # unit-diagonal
119            new("lgTMatrix", i = i, j = i,                x <- rep.int(TRUE, n)
120                  i <- seq_len(n) - 1:1
121              } else { # "normal"
122                  nz <- nz.NA(from@x, na. = TRUE)
123                  x <- from@x[nz]
124                  i <- which(nz) - 1:1
125              }
126              new("lgTMatrix", i = i, j = i, x = x,
127                Dim = c(n,n), Dimnames = from@Dimnames) })                Dim = c(n,n), Dimnames = from@Dimnames) })
128    
129  setAs("ldiMatrix", "lgCMatrix",  setAs("ldiMatrix", "lgCMatrix",
130        function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))        function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))
131    
 setAs("diagonalMatrix", "sparseMatrix",  
       function(from)  
           as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))  
132    
133    if(FALSE) # now have faster  "ddense" -> "dge"
134  setAs("ddiMatrix", "dgeMatrix",  setAs("ddiMatrix", "dgeMatrix",
135        function(from) as(as(from, "matrix"), "dgeMatrix"))        function(from) as(as(from, "matrix"), "dgeMatrix"))
136    
# Line 95  Line 148 
148                cl <- "ddiMatrix"                cl <- "ddiMatrix"
149                uni <- all(x == 1)                uni <- all(x == 1)
150                storage.mode(x) <- "double"                storage.mode(x) <- "double"
151            }            } ## TODO: complex
152            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",            new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
153                x = if(uni) x[FALSE] else x)                x = if(uni) x[FALSE] else x)
154        })        })
# Line 120  Line 173 
173                x = if(uni) x[FALSE] else x)                x = if(uni) x[FALSE] else x)
174        })        })
175    
176    ## When you assign to a diagonalMatrix, the result should be
177    ## diagonal or sparse
178    setReplaceMethod("[", signature(x = "diagonalMatrix",
179                                    i = "ANY", j = "ANY", value = "ANY"),
180                     function(x, i, j, value) {
181                         r <- callGeneric(x = as(x,"sparseMatrix"),
182                                          i=i, j=j, value=value)
183                         if(isDiagonal(r)) as(r, "diagonalMatrix") else r
184                     })
185    
186    
187  setMethod("t", signature(x = "diagonalMatrix"),  setMethod("t", signature(x = "diagonalMatrix"),
188            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })            function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })
189    
# Line 130  Line 194 
194  setMethod("isSymmetric", signature(object = "diagonalMatrix"),  setMethod("isSymmetric", signature(object = "diagonalMatrix"),
195            function(object) TRUE)            function(object) TRUE)
196    
197    setMethod("chol", signature(x = "ddiMatrix"),# pivot = "ANY"
198              function(x, pivot) {
199                  if(any(x@x < 0)) stop("chol() is undefined for diagonal matrix with negative entries")
200                  x@x <- sqrt(x@x)
201                  x
202              })
203    ## chol(L) is L for logical diagonal:
204    setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot) x)
205    
206    
207  setMethod("diag", signature(x = "diagonalMatrix"),  setMethod("diag", signature(x = "diagonalMatrix"),
208            function(x = 1, nrow, ncol = n) {            function(x = 1, nrow, ncol = n) {
209               if(x@diag == "U")               if(x@diag == "U")
# Line 148  Line 222 
222  })  })
223    
224  ## Basic Matrix Multiplication {many more to add}  ## Basic Matrix Multiplication {many more to add}
225    ##       ---------------------
226  ## FIXME: extend this for 'ldi', i.e. do "diagonalMatrix"  ## Note that "ldi" logical are treated as numeric
227  diagdiagprod <- function(x, y) {  diagdiagprod <- function(x, y) {
228      if(any(dim(x) != dim(y))) stop("non-matching dimensions")      if(any(dim(x) != dim(y))) stop("non-matching dimensions")
229      if(x@diag != "U") {      if(x@diag != "U") {
230          if(y@diag != "U") x@x <- x@x * y@x          if(y@diag != "U") {
231                nx <- x@x * y@x
232                if(is.numeric(nx) && !is.numeric(x@x))
233                    x <- as(x, "dMatrix")
234                x@x <- as.numeric(nx)
235            }
236          return(x)          return(x)
237      } else ## x is unit diagonal      } else ## x is unit diagonal
238      return(y)      return(y)
239  }  }
240    
241  setMethod("%*%", signature(x = "ddiMatrix", y = "ddiMatrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
242            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
243    
244  formals(diagdiagprod) <- alist(x=, y=NULL)  formals(diagdiagprod) <- alist(x=, y=x)
245  setMethod("crossprod", signature(x = "ddiMatrix", y = "ddiMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
246              diagdiagprod, valueClass = "ddiMatrix")
247    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
248            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
249  setMethod("tcrossprod", signature(x = "ddiMatrix", y = "ddiMatrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "missing"),
250              diagdiagprod, valueClass = "ddiMatrix")
251    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "missing"),
252            diagdiagprod, valueClass = "ddiMatrix")            diagdiagprod, valueClass = "ddiMatrix")
253    
254    
# Line 182  Line 265 
265  formals(diagmatprod) <- alist(x=, y=NULL)  formals(diagmatprod) <- alist(x=, y=NULL)
266  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),  setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),
267            diagmatprod)            diagmatprod)
268    setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "matrix"),
269              diagmatprod)
270    
271  diagdgeprod <- function(x, y) {  diagdgeprod <- function(x, y) {
272      dx <- dim(x)      dx <- dim(x)
# Line 202  Line 287 
287                dx <- dim(x)                dx <- dim(x)
288                dy <- dim(y)                dy <- dim(y)
289                if(dx[2] != dy[1]) stop("non-matching dimensions")                if(dx[2] != dy[1]) stop("non-matching dimensions")
290                as(if(y@diag == "U") x else x * rep.int(y@x, dx[1]), "Matrix")                as(if(y@diag == "U") x else x * rep(y@x, each = dx[1]), "Matrix")
291            })            })
292    
293  setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),  setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),
# Line 211  Line 296 
296                dy <- dim(y)                dy <- dim(y)
297                if(dx[2] != dy[1]) stop("non-matching dimensions")                if(dx[2] != dy[1]) stop("non-matching dimensions")
298                if(y@diag == "N")                if(y@diag == "N")
299                    x@x <- x@x * rep.int(y@x, dx[1])                    x@x <- x@x * rep(y@x, each = dx[1])
300                x                x
301            })            })
302    
# Line 231  Line 316 
316    
317  ### ---------------- diagonal  o   sparse  -----------------------------  ### ---------------- diagonal  o   sparse  -----------------------------
318    
319    
320    ## Use function for several signatures, in order to evade
321    ## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)
322    diagOdiag <- function(e1,e2) { # result should also be diagonal
323        r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
324        if(is.numeric(r)) {
325            if(is.numeric(e2@x)) {
326                e2@x <- r; return(.diag.2N(e2)) }
327            if(!is.numeric(e1@x))
328                ## e.g. e1, e2 are logical;
329                e1 <- as(e1, "dMatrix")
330        }
331        else if(is.logical(r))
332            e1 <- as(e1, "lMatrix")
333        else stop("intermediate 'r' is of type", typeof(r))
334        e1@x <- r
335        .diag.2N(e1)
336    }
337    
338    setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
339              diagOdiag)
340    ## These two are just for method disambiguation:
341    setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "diagonalMatrix"),
342              diagOdiag)
343    setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ddiMatrix"),
344              diagOdiag)
345    
346    ## For almost everything else, diag* shall be treated "as sparse" :
347  ## These are cheap implementations via coercion  ## These are cheap implementations via coercion
348    
349    ## for disambiguation
350    setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "sparseMatrix"),
351              function(e1,e2) callGeneric(as(e1, "sparseMatrix"), e2))
352    setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "diagonalMatrix"),
353              function(e1,e2) callGeneric(e1, as(e2, "sparseMatrix")))
354    ## in general:
355    setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ANY"),
356              function(e1,e2) callGeneric(as(e1,"sparseMatrix"), e2))
357    setMethod("Ops", signature(e1 = "ANY", e2 = "diagonalMatrix"),
358              function(e1,e2) callGeneric(e1, as(e2,"sparseMatrix")))
359    
360    
361    
362  ## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()  ## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()
363    
364  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),  setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
# Line 268  Line 394 
394  }  }
395    
396  setMethod("show", signature(object = "diagonalMatrix"),  setMethod("show", signature(object = "diagonalMatrix"),
397            function(object) prDiag(object))            function(object) {
398                  d <- dim(object)
399                  cl <- class(object)
400                  cat(sprintf('%d x %d diagonal matrix of class "%s"\n',
401                              d[1], d[2], cl))
402                  prDiag(object)
403              })

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