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

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revision 1673, Mon Nov 6 20:54:26 2006 UTC revision 1825, Thu Apr 12 13:21:51 2007 UTC
# Line 3  Line 3 
3    
4  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5    
6  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))  setAs("Matrix", "sparseMatrix", function(from) as(from, "CsparseMatrix"))
7    setAs("Matrix", "CsparseMatrix", function(from) as_Csparse(from))
8  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
9    
10    ## Maybe TODO:
11    ## setAs("Matrix", "nMatrix", function(from) ....)
12    
13  ## Most of these work; this is a last resort:  ## Most of these work; this is a last resort:
14  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
15        function(from) .bail.out.2("coerce", class(from), class(to)))        function(from) .bail.out.2("coerce", class(from), class(to)))
# Line 27  Line 31 
31  setMethod("head", signature(x = "Matrix"), utils::head.matrix)  setMethod("head", signature(x = "Matrix"), utils::head.matrix)
32  setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)  setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
33    
34    setMethod("drop", signature(x = "Matrix"),
35              function(x) if(all(dim(x) != 1)) x else drop(as(x, "matrix")))
36    
37  ## slow "fall back" method {subclasses should have faster ones}:  ## slow "fall back" method {subclasses should have faster ones}:
38  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
39            function(x) as.vector(as(x, "matrix")))            function(x) as.vector(as(x, "matrix")))
# Line 56  Line 63 
63    
64  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
65            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
66    
67    setMethod("length", "Matrix", function(x) prod(dim(x)))
68    
69  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
70    
71    
72  ## not exported but used more than once for "dimnames<-" method :  ## not exported but used more than once for "dimnames<-" method :
73  ## -- or do only once for all "Matrix" classes ??  ## -- or do only once for all "Matrix" classes ??
74  dimnamesGets <- function (x, value) {  dimnamesGets <- function (x, value) {
# Line 75  Line 87 
87  setMethod("unname", signature("Matrix", force="missing"),  setMethod("unname", signature("Matrix", force="missing"),
88            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
89    
90    setMethod("all", signature(x = "Matrix"),
91              function(x, ..., na.rm) { x <- as(x, "lMatrix"); callGeneric()})
92    setMethod("any", signature(x = "Matrix"),
93              function(x, ..., na.rm) { x <- as(x, "lMatrix"); callGeneric()})
94    
95    setMethod("!", "Matrix", function(e1) !as(e1, "lMatrix"))
96    
97    
98    
99  Matrix <-  Matrix <-
100      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
101                sparse = NULL, forceCheck = FALSE)                sparse = NULL, forceCheck = FALSE)
# Line 88  Line 109 
109    
110      doDN <- TRUE      doDN <- TRUE
111      if (i.M) {      if (i.M) {
112            if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
113                warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
114          sM <- is(data,"sparseMatrix")          sM <- is(data,"sparseMatrix")
115          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
116              return(data)              return(data)
# Line 101  Line 124 
124          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
125              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
126              if(is.null(sparse)) sparse1 <- sparse <- TRUE              if(is.null(sparse)) sparse1 <- sparse <- TRUE
127                i.M <- sM <- TRUE
128              ## will be sparse: do NOT construct full matrix!              ## will be sparse: do NOT construct full matrix!
129              data <- new(if(is.numeric(data)) "dgTMatrix" else              data <- new(if(is.numeric(data)) "dgTMatrix" else
130                          if(is.logical(data)) "lgTMatrix" else                          if(is.logical(data)) "lgTMatrix" else
# Line 115  Line 139 
139              dimnames(data) <- dimnames              dimnames(data) <- dimnames
140          }          }
141          doDN <- FALSE          doDN <- FALSE
142      }      } else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
143            warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
144    
145      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
146      if (doDN && !is.null(dimnames))      if (doDN && !is.null(dimnames))
147          dimnames(data) <- dimnames          dimnames(data) <- dimnames
# Line 158  Line 184 
184                    }, sep="")                    }, sep="")
185          }          }
186    
187      ## Now coerce and return      ## Can we coerce and be done?
188        if(!canCoerce(data,cl)) { ## try to coerce ``via'' virtual classes
189            if(sparse && !sM)
190                data <- as(data, "sparseMatrix")
191            else if(!sparse && !is(data, "denseMatrix"))
192                data <- as(data, "denseMatrix")
193            if(isTri && !is(data, "triangularMatrix"))
194                data <- as(data, "triangularMatrix")
195            else if(isSym && !is(data, "symmetricMatrix"))
196                data <- as(data, "symmetricMatrix")
197        }
198        ## now coerce in any case .. maybe producing sensible error message:
199      as(data, cl)      as(data, cl)
200  }  }
201    
# Line 194  Line 231 
231  ## when no sub-class method is found, bail out  ## when no sub-class method is found, bail out
232  setMethod("solve", signature(a = "Matrix", b = "matrix"),  setMethod("solve", signature(a = "Matrix", b = "matrix"),
233            function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))            function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
234    setMethod("solve", signature(a = "Matrix", b = "Matrix"),
235              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
236    
237  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
238  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 220  Line 259 
259  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
260                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
261            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
262                  if(is(X, "sparseMatrix"))
263                      warning("using slow kronecker() method")
264                X <- as(X, "matrix") ; Matrix(callGeneric()) })                X <- as(X, "matrix") ; Matrix(callGeneric()) })
265    
266  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
267                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
268            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
269                  if(is(Y, "sparseMatrix"))
270                      warning("using slow kronecker() method")
271                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
272    
273    
# Line 238  Line 282 
282  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
283            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
284    
285  ## Group Methods  setMethod("dim<-", signature(x = "Matrix", value = "ANY"),
286  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, value) {
287  ## "fallback":                if(!is.numeric(value) || length(value) != 2)
288  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),                    stop("dim(.) value must be numeric of length 2")
289            function(e1) {                if(prod(dim(x)) != prod(value <- as.integer(value)))
290                warning("inefficient method used for \"- e1\"")                    stop("dimensions don't match the number of cells")
291                0-e1                clx <- class(x)
292                  if(substring(clx,2) == "geMatrix") {
293                      x@Dim <- value
294                      if(length(x@factors) > 0)
295                          x@factors <- list()
296                      x
297                  } else if(extends(clx, "denseMatrix")) {
298                      x <- as_geSimpl2(x, clx)
299                      dim(x) <- value
300                  } else { ## FIXME: this is very inefficient for large sparse x
301                      Matrix(as.vector(x), value[1], value[2])
302                  }
303            })            })
304    
305  ## old-style matrices are made into new ones  ## MM: More or less "Cut & paste" from
306  setMethod("Ops", signature(e1 = "Matrix", e2 = "matrix"),  ## --- diff.default() from  R/src/library/base/R/diff.R :
307            function(e1, e2) callGeneric(e1, Matrix(e2)))  setMethod("diff", signature(x = "Matrix"),
308  ##          callGeneric(e1, Matrix(e2, sparse=is(e1,"sparseMatrix"))))            function(x, lag = 1, differences = 1, ...) {
309  setMethod("Ops", signature(e1 = "matrix", e2 = "Matrix"),                if (length(lag) > 1 || length(differences) > 1 ||
310            function(e1, e2) callGeneric(Matrix(e1), e2))                    lag < 1 || differences < 1)
311                      stop("'lag' and 'differences' must be integers >= 1")
312  ## bail-outs -- on highest possible level, hence "Ops", not "Compare"/"Arith" :                xlen <- nrow(x)
313  setMethod("Ops", signature(e1 = "Matrix", e2 = "Matrix"),                if (lag * differences >= xlen)
314            function(e1, e2) {                    return(x[,FALSE][0])  # empty of proper mode
315                d <- dimCheck(e1,e2)  
316                .bail.out.2(.Generic, class(e1), class(e2))                i1 <- -1:-lag
317                  for (i in 1:differences)
318                      x <- x[i1, , drop = FALSE] -
319                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
320                  x
321            })            })
 setMethod("Ops", signature(e1 = "Matrix", e2 = "ANY"),  
           function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  
 setMethod("Ops", signature(e1 = "ANY", e2 = "Matrix"),  
           function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  
322    
323    
324    ## Group Methods
325    
326    ##-> see ./Ops.R
327    
328  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
329  ###  ###
# Line 285  Line 343 
343  ## select rows  ## select rows
344  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
345                           drop = "missing"),                           drop = "missing"),
346            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, drop) {
347                  if(nargs() == 1) { ## e.g. M[0] , M[TRUE],  M[1:2]
348                      if(any(i)) as.vector(x)[i] else as.vector(x[1,1])[FALSE]
349                  } else callGeneric(x, i=i, drop= TRUE)})
350    
351  ## select columns  ## select columns
352  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
353                           drop = "missing"),                           drop = "missing"),
# Line 313  Line 375 
375          stop("not-yet-implemented 'Matrix' subsetting") ## FIXME          stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
376    
377      } else stop("nargs() = ", nA,      } else stop("nargs() = ", nA,
378                  " should never happen; please report.")                  ".  Extraneous illegal arguments inside '[ .. ]' ?")
379  }  }
380  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
381                           drop = "ANY"),                           drop = "ANY"),
# Line 343  Line 405 
405          ## potentially inefficient -- FIXME --          ## potentially inefficient -- FIXME --
406          unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))          unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
407    
408      } else stop("nargs() = ", nA, " should never happen; please report.")      } else stop("nargs() = ", nA,
409                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
410  }  }
411  setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"  setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
412            .M.sub.i.2col)            .M.sub.i.2col)
# Line 356  Line 419 
419                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
420            function (x, value) {            function (x, value) {
421                ## Fails for 'nMatrix' ... FIXME : make sure have method there                ## Fails for 'nMatrix' ... FIXME : make sure have method there
422                x@x <- value                x@x <- rep(value, length = length(x@x))
423                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
424                x                x
425            })            })
426    
427  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
428    ## ----------------   The cheap general method --- FIXME: provide special ones
429  .M.repl.i.2col <- function (x, i, j, value)  .M.repl.i.2col <- function (x, i, j, value)
430  {  {
431      nA <- nargs()      nA <- nargs()
# Line 369  Line 433 
433          if(!is.integer(nc <- ncol(i)))          if(!is.integer(nc <- ncol(i)))
434              stop("'i' has no integer column number",              stop("'i' has no integer column number",
435                   " should never happen; please report")                   " should never happen; please report")
436            else if(!is.numeric(i) || nc != 2)
437                stop("such indexing must be by logical or 2-column numeric matrix")
438          if(is.logical(i)) {          if(is.logical(i)) {
439                message(".M.repl.i.2col(): drop 'matrix' case ...")
440              i <- c(i) # drop "matrix"              i <- c(i) # drop "matrix"
441              return( callNextMethod() )              return( callNextMethod() )
442          } else if(!is.numeric(i) || nc != 2)          }
443              stop("such indexing must be by logical or 2-column numeric matrix")          if(!is.integer(i)) storage.mode(i) <- "integer"
444            if(any(i < 0))
445                stop("negative values are not allowed in a matrix subscript")
446            if(any(is.na(i)))
447                stop("NAs are not allowed in subscripted assignments")
448            if(any(i0 <- (i == 0))) # remove them
449                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
450            ## now have integer i >= 1
451          m <- nrow(i)          m <- nrow(i)
452          mod.x <- .type.kind[.M.kind(x)]          ## mod.x <- .type.kind[.M.kind(x)]
453          if(length(value) > 0 && m %% length(value) != 0)          if(length(value) > 0 && m %% length(value) != 0)
454              warning("number of items to replace is not a multiple of replacement length")              warning("number of items to replace is not a multiple of replacement length")
455          ## recycle:          ## recycle:
# Line 385  Line 459 
459          ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)          ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
460          for(k in seq_len(m))          for(k in seq_len(m))
461              x[i1[k], i2[k]] <- value[k]              x[i1[k], i2[k]] <- value[k]
         x  
462    
463      } else stop("nargs() = ", nA, " should never happen; please report.")          x
464        } else stop("nargs() = ", nA,
465                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
466  }  }
467    
468  setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
469                                  value = "replValue"),                                  value = "replValue"),
470            .M.repl.i.2col)            .M.repl.i.2col)
# Line 396  Line 472 
472    
473  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
474                                  value = "Matrix"),                                  value = "Matrix"),
475                     function (x, i, j, value) {
476    ### *TEMPORARY* diagnostic output:
477    ##                  cat("<Matrix1>[i,j] <- <Matrix1>:\n<Matrix1> = x :")
478    ##                  str(x)
479    ##                  cat("<Matrix2> = value :")
480    ##                  str(value)
481    ##                  cat("i :"); if(!missing(i)) str(i) else cat("<missing>\n")
482    ##                  cat("j :"); if(!missing(j)) str(j) else cat("<missing>\n")
483    
484                         callGeneric(x=x, i=i, j=j, value = as.vector(value))
485                     })
486    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
487                                    value = "Matrix"),
488                   function (x, i, j, value)                   function (x, i, j, value)
489                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))
490    
491  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
492                                  value = "matrix"),                                  value = "matrix"),
493                   function (x, i, j, value)                   function (x, i, j, value)
# Line 412  Line 502 
502                                 class(value),class(x)))                                 class(value),class(x)))
503                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
504            })            })
   
   
 ## The trivial methods :  
 setMethod("cbind2", signature(x = "Matrix", y = "NULL"),  
           function(x, y) x)  
 setMethod("cbind2", signature(x = "Matrix", y = "missing"),  
           function(x, y) x)  
 setMethod("cbind2", signature(x = "NULL", y="Matrix"),  
           function(x, y) x)  
   
 setMethod("rbind2", signature(x = "Matrix", y = "NULL"),  
           function(x, y) x)  
 setMethod("rbind2", signature(x = "Matrix", y = "missing"),  
           function(x, y) x)  
 setMethod("rbind2", signature(x = "NULL", y="Matrix"),  
           function(x, y) x)  
   
 ## Makes sure one gets x decent error message for the unimplemented cases:  
 setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),  
           function(x, y) {  
               rowCheck(x,y)  
               stop(gettextf("cbind2() method for (%s,%s) not-yet defined",  
                             class(x), class(y)))  
           })  
   
 ## Use a working fall back {particularly useful for sparse}:  
 ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones  
 setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),  
           function(x, y) {  
               colCheck(x,y)  
               t(cbind2(t(x), t(y)))  
           })  

Legend:
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  Added in v.1825

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