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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 2175, Wed Apr 23 11:23:50 2008 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, mode) as.vector(as(x, "matrix"), mode))
40    
41  ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:  ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
42  setMethod("as.numeric", signature(x = "Matrix"),  setMethod("as.numeric", signature(x = "Matrix"),
# Line 37  Line 44 
44  setMethod("as.logical", signature(x = "Matrix"),  setMethod("as.logical", signature(x = "Matrix"),
45            function(x, ...) as.logical(as.vector(x)))            function(x, ...) as.logical(as.vector(x)))
46    
47    setMethod("mean", signature(x = "Matrix"),
48              function(x, trim = 0, ...) ## TODO: provide 'sparseMatrix method
49              if(is0(trim)) sum(x, ...) / length(x)
50              else mean(as.numeric(x), ...))
51    
52    setMethod("cov2cor", signature(V = "Matrix"),
53              function(V) { ## was as(cov2cor(as(V, "matrix")), "dpoMatrix"))
54                  r <- V
55                  p <- (d <- dim(V))[1]
56                  if(p != d[2]) stop("'V' is not a square matrix")
57                  Is <- sqrt(1/diag(V)) # diag( 1/sigma_i )
58                  if(any(!is.finite(Is)))
59                      warning("diag(.) had 0 or NA entries; non-finite result is doubtful")
60                  Is <- Diagonal(x = Is)
61                  r <- Is %*% V %*% Is
62                  r[cbind(1L:p,1L:p)] <- 1 # exact in diagonal
63                  as(forceSymmetric(r), "dpoMatrix")
64              })
65    
66  ## "base" has an isSymmetric() S3-generic since R 2.3.0  ## "base" has an isSymmetric() S3-generic since R 2.3.0
67  setMethod("isSymmetric", signature(object = "symmetricMatrix"),  setMethod("isSymmetric", signature(object = "symmetricMatrix"),
68            function(object,tol) TRUE)            function(object, ...) TRUE)
69  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
70            ## TRUE iff diagonal:            ## TRUE iff diagonal:
71            function(object,tol) isDiagonal(object))            function(object, ...) isDiagonal(object))
   
 setMethod("isTriangular", signature(object = "triangularMatrix"),  
           function(object, ...) TRUE)  
72    
73  setMethod("isTriangular", signature(object = "matrix"), isTriMat)  setMethod("isTriangular", signature(object = "matrix"), isTriMat)
74    
75  setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)  setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
76    
77    ## The "catch all" methods -- far from optimal:
78    setMethod("symmpart", signature(x = "Matrix"),
79              function(x) as((x + t(x))/2, "symmetricMatrix"))
80    setMethod("skewpart", signature(x = "Matrix"),
81              function(x) (x - t(x))/2)
82    
83    ## FIXME: do this (similarly as for "ddense.." in C
84    setMethod("symmpart", signature(x = "matrix"), function(x) (x + t(x))/2)
85    setMethod("skewpart", signature(x = "matrix"), function(x) (x - t(x))/2)
86    
87    
88    
89    
90  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
91            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
92    
93    setMethod("length", "Matrix", function(x) prod(dim(x)))
94    
95  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
96    
97    
98  ## not exported but used more than once for "dimnames<-" method :  ## not exported but used more than once for "dimnames<-" method :
99  ## -- or do only once for all "Matrix" classes ??  ## -- or do only once for all "Matrix" classes ??
100  dimnamesGets <- function (x, value) {  dimnamesGets <- function (x, value) {
# Line 75  Line 113 
113  setMethod("unname", signature("Matrix", force="missing"),  setMethod("unname", signature("Matrix", force="missing"),
114            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
115    
116  Matrix <-  setMethod("all", signature(x = "Matrix"),
117      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,            function(x, ..., na.rm)
118                sparse = NULL, forceCheck = FALSE)            callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
119    
120    setMethod("any", signature(x = "Matrix"),
121              function(x, ..., na.rm)
122              callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
123    
124    ## NOTE:  "&" and "|"  are now in group "Logic" c "Ops" --> ./Ops.R
125    ##        "!" is in ./not.R
126    
127    
128    Matrix <- function (data = NA, nrow = 1, ncol = 1, byrow = FALSE,
129                        dimnames = NULL, sparse = NULL, forceCheck = FALSE)
130  {  {
131      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
132    
133      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
134        if(!i.M && inherits(data, "table")) # special treatment
135            class(data) <- "matrix" # "matrix" first for S4 dispatch
136      if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))      if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
137          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
138        sM <- FALSE
139      doDN <- TRUE      doDN <- TRUE
140      if (i.M) {      if (i.M) {
141            if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
142                warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
143          sM <- is(data,"sparseMatrix")          sM <- is(data,"sparseMatrix")
144          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
145              return(data)              return(data)
# Line 101  Line 153 
153          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
154              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
155              if(is.null(sparse)) sparse1 <- sparse <- TRUE              if(is.null(sparse)) sparse1 <- sparse <- TRUE
156                i.M <- sM <- TRUE
157                isSym <- nrow == ncol
158              ## will be sparse: do NOT construct full matrix!              ## will be sparse: do NOT construct full matrix!
159              data <- new(if(is.numeric(data)) "dgTMatrix" else              data <- new(paste(if(is.numeric(data)) "d" else
160                          if(is.logical(data)) "lgTMatrix" else                                if(is.logical(data)) "l" else
161                          stop("invalid 'data'"),                          stop("invalid 'data'"),
162                                  if(isSym) "s" else "g", "CMatrix", sep=''),
163                            p = rep.int(0L, ncol+1L),
164                          Dim = as.integer(c(nrow,ncol)),                          Dim = as.integer(c(nrow,ncol)),
165                          Dimnames = if(is.null(dimnames)) list(NULL,NULL)                          Dimnames = if(is.null(dimnames)) list(NULL,NULL)
166                          else dimnames)                          else dimnames)
167          } else { ## normal case          } else { ## normal case - using .Internal() to avoid more copying
168                if(getRversion() >= "2.7.0")
169                    data <- .Internal(matrix(data, nrow, ncol, byrow, dimnames))
170                else {
171              data <- .Internal(matrix(data, nrow, ncol, byrow))              data <- .Internal(matrix(data, nrow, ncol, byrow))
172                    dimnames(data) <- dimnames
173                }
174              if(is.null(sparse))              if(is.null(sparse))
175                  sparse <- sparseDefault(data)                  sparse <- sparseDefault(data)
             dimnames(data) <- dimnames  
176          }          }
177          doDN <- FALSE          doDN <- FALSE
178      }      } else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
179            warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
180    
181      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
182      if (doDN && !is.null(dimnames))      if (doDN && !is.null(dimnames))
183          dimnames(data) <- dimnames          dimnames(data) <- dimnames
# Line 126  Line 188 
188          isTri <- isTriangular(data)          isTri <- isTriangular(data)
189      isDiag <- isSym # cannot be diagonal if it isn't symmetric      isDiag <- isSym # cannot be diagonal if it isn't symmetric
190      if(isDiag)      if(isDiag)
191          isDiag <- isDiagonal(data)          isDiag <- !isTRUE(sparse1) && isDiagonal(data)
192    
193      ## Find proper matrix class 'cl'      ## try to coerce ``via'' virtual classes
194      cl <-      if(isDiag) { ## diagonal is preferred to sparse !
195          if(isDiag && !isTRUE(sparse1))          data <- as(data, "diagonalMatrix")
196              "diagonalMatrix" # -> will automatically check for type          isSym <- FALSE
197          else {      } else if(sparse && !sM)
198              ## consider it's type          data <- as(data, "sparseMatrix")
199              ctype <-      else if(!sparse) {
200                  if(is(data,"Matrix")) class(data)          if(i.M) { ## data is 'Matrix'
201                  else {              if(!is(data, "denseMatrix"))
202                      if("complex" == (ctype <- typeof(data)))                  data <- as(data, "denseMatrix")
203                          "z" else ctype          } else { ## data is "matrix" (and result "dense" -> go via "general"
204                  }              ctype <- typeof(data)
205              ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"              if (ctype == "complex")
             if(ctype == "z")  
206                  stop("complex matrices not yet implemented in Matrix package")                  stop("complex matrices not yet implemented in Matrix package")
207              if(ctype == "i") {              if (ctype == "integer") ## integer Matrices not yet implemented
208                  warning("integer matrices not yet implemented in 'Matrix'; ",                  storage.mode(data) <- "double"
209                          "using 'double' ones'")              data <- new(paste(.M.kind(data), "geMatrix", sep=''),
210                  ctype <- "d"                          Dim = dim(data),
211              }                          Dimnames = .M.DN(data),
212              paste(ctype,                          x = c(data))
213                    if(sparse) {          }
                       if(isSym) "sCMatrix" else  
                       if(isTri) "tCMatrix" else "gCMatrix"  
                   } else { ## dense  
                       if(isSym) "syMatrix" else  
                       if(isTri) "trMatrix" else "geMatrix"  
                   }, sep="")  
214          }          }
215    
216      ## Now coerce and return      if(isTri && !is(data, "triangularMatrix")) {
217      as(data, cl)          data <- if(attr(isTri,"kind") == "L") tril(data) else triu(data)
218                                            #was as(data, "triangularMatrix")
219        } else if(isSym && !is(data, "symmetricMatrix"))
220            data <- forceSymmetric(data) #was as(data, "symmetricMatrix")
221    
222        data
223  }  }
224    
225  ## Methods for operations where one argument is numeric  ## Methods for operations where one argument is numeric
# Line 169  Line 229 
229    
230  setMethod("%*%", signature(x = "Matrix", y = "numeric"),  setMethod("%*%", signature(x = "Matrix", y = "numeric"),
231            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
   
232  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
233            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
234    
235    setMethod("%*%", signature(x = "Matrix", y = "matrix"),
236              function(x, y) callGeneric(x, Matrix(y)))
237    setMethod("%*%", signature(x = "matrix", y = "Matrix"),
238              function(x, y) callGeneric(Matrix(x), y))
239    
240    
241  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
242            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
243  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
244            function(x, y = NULL)  callGeneric(as.matrix(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
245    
246    setMethod("crossprod", signature(x = "Matrix", y = "matrix"),
247              function(x, y = NULL) callGeneric(x, Matrix(y)))
248    setMethod("crossprod", signature(x = "matrix", y = "Matrix"),
249              function(x, y = NULL) callGeneric(Matrix(x), y))
250    
251  ## The as.matrix() promotion seems illogical to MM,  ## The as.matrix() promotion seems illogical to MM,
252  ## but is according to help(tcrossprod, package = "base") :  ## but is according to help(tcrossprod, package = "base") :
253  setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),  setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
254            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
255  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
256            function(x, y = NULL)  callGeneric(as.matrix(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
257    setMethod("tcrossprod", signature(x = "Matrix", y = "matrix"),
258              function(x, y = NULL) callGeneric(x, Matrix(y)))
259    setMethod("tcrossprod", signature(x = "matrix", y = "Matrix"),
260              function(x, y = NULL) callGeneric(Matrix(x), y))
261    
262  ## maybe not optimal  ## maybe not 100% optimal, but elegant:
263  setMethod("solve", signature(a = "Matrix", b = "missing"),  setMethod("solve", signature(a = "Matrix", b = "missing"),
264            function(a, b, ...) solve(a, Diagonal(nrow(a))))            function(a, b, ...) solve(a, Diagonal(nrow(a))))
265    
266  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
267            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, Matrix(b)))
 ## when no sub-class method is found, bail out  
268  setMethod("solve", signature(a = "Matrix", b = "matrix"),  setMethod("solve", signature(a = "Matrix", b = "matrix"),
269            function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))            function(a, b, ...) callGeneric(a, Matrix(b)))
270    setMethod("solve", signature(a = "matrix", b = "Matrix"),
271              function(a, b, ...) callGeneric(Matrix(a), b))
272    
273    ## when no sub-class method is found, bail out
274    setMethod("solve", signature(a = "Matrix", b = "Matrix"),
275              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
276    
277  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
278  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 220  Line 299 
299  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
300                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
301            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
302                  if(is(X, "sparseMatrix"))
303                      warning("using slow kronecker() method")
304                X <- as(X, "matrix") ; Matrix(callGeneric()) })                X <- as(X, "matrix") ; Matrix(callGeneric()) })
305    
306  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
307                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
308            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
309                  if(is(Y, "sparseMatrix"))
310                      warning("using slow kronecker() method")
311                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
312    
313    
314    setMethod("determinant", signature(x = "Matrix", logarithm = "missing"),
315              function(x, logarithm, ...)
316              determinant(x, logarithm = TRUE, ...))
317    
318    if(FALSE) { ## This is desired "in theory" - but gives
319        ## "The following object(s) are masked from package:base :   det
320    ## base::det() calls [base::]determinant();
321    ## our det() should call our determinant() :
322    det <- base::det
323    environment(det) <- environment()## == as.environment("Matrix")
324    }
325    
326  ## FIXME: All of these should never be called  ## FIXME: All of these should never be called
327  setMethod("chol", signature(x = "Matrix"),  setMethod("chol", signature(x = "Matrix"),
328            function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))            function(x, pivot, ...) .bail.out.1(.Generic, class(x)))
329  setMethod("determinant", signature(x = "Matrix"),  setMethod("determinant", signature(x = "Matrix", logarithm = "logical"),
330            function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))            function(x, logarithm, ...) .bail.out.1(.Generic, class(x)))
331    
332  setMethod("diag", signature(x = "Matrix"),  setMethod("diag", signature(x = "Matrix"),
333            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
334  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
335            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
336    
337  ## Group Methods  setMethod("norm", signature(x = "Matrix", type = "character"),
338  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, type, ...) .bail.out.1(.Generic, class(x)))
339  ## "fallback":  setMethod("rcond", signature(x = "Matrix", norm = "character"),
340  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),            function(x, norm, ...) .bail.out.1(.Generic, class(x)))
341            function(e1) {  
342                warning("inefficient method used for \"- e1\"")  
343                0-e1  ## for all :
344    setMethod("norm", signature(x = "ANY", type = "missing"),
345              function(x, type, ...) norm(x, type = "O", ...))
346    setMethod("rcond", signature(x = "ANY", norm = "missing"),
347              function(x, norm, ...) rcond(x, norm = "O", ...))
348    
349    
350    
351    
352    
353    ## MM: More or less "Cut & paste" from
354    ## --- diff.default() from  R/src/library/base/R/diff.R :
355    setMethod("diff", signature(x = "Matrix"),
356              function(x, lag = 1, differences = 1, ...) {
357                  if (length(lag) > 1 || length(differences) > 1 ||
358                      lag < 1 || differences < 1)
359                      stop("'lag' and 'differences' must be integers >= 1")
360                  xlen <- nrow(x)
361                  if (lag * differences >= xlen)
362                      return(x[,FALSE][0])  # empty of proper mode
363    
364                  i1 <- -1:-lag
365                  for (i in 1:differences)
366                      x <- x[i1, , drop = FALSE] -
367                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
368                  x
369            })            })
370    
371  ## old-style matrices are made into new ones  setMethod("image", "Matrix",
372  setMethod("Ops", signature(e1 = "Matrix", e2 = "matrix"),            function(x, ...) { # coercing to sparse is not inefficient,
373            function(e1, e2) callGeneric(e1, Matrix(e2)))                ##               since we need 'i' and 'j' for levelplot()
374  ##          callGeneric(e1, Matrix(e2, sparse=is(e1,"sparseMatrix"))))                x <- as(as(x, "sparseMatrix"), "dMatrix")
375  setMethod("Ops", signature(e1 = "matrix", e2 = "Matrix"),                callGeneric()
           function(e1, e2) callGeneric(Matrix(e1), e2))  
   
 ## bail-outs -- on highest possible level, hence "Ops", not "Compare"/"Arith" :  
 setMethod("Ops", signature(e1 = "Matrix", e2 = "Matrix"),  
           function(e1, e2) {  
               d <- dimCheck(e1,e2)  
               .bail.out.2(.Generic, class(e1), class(e2))  
376            })            })
 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)))  
377    
378    
379    ## Group Methods
380    
381    ## For all  non-dMatrix objects, and note that  "all" and "any" have their own
382    setMethod("Summary", signature(x = "Matrix", na.rm = "ANY"),
383              function(x, ..., na.rm)
384              callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
385    
386    Summary.l <- function(x, ..., na.rm) { ## must be method directly
387        r <- callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm)
388        if(!is.infinite(r) && .Generic %in% c("max", "min", "range", "sum"))
389            as.integer(r) else r
390    }
391    setMethod("Summary", signature(x = "lMatrix", na.rm = "ANY"), Summary.l)
392    setMethod("Summary", signature(x = "nMatrix", na.rm = "ANY"), Summary.l)
393    setMethod("Summary", signature(x = "pMatrix", na.rm = "ANY"), Summary.l)
394    
395    ## Further, see ./Ops.R
396    ##                ~~~~~
397    
398    
399  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
400  ###  ###
# Line 278  Line 407 
407  ## "x[]":  ## "x[]":
408  setMethod("[", signature(x = "Matrix",  setMethod("[", signature(x = "Matrix",
409                           i = "missing", j = "missing", drop = "ANY"),                           i = "missing", j = "missing", drop = "ANY"),
410            function (x, i, j, drop) x)            function (x, i, j, ..., drop) x)
411    
412  ## missing 'drop' --> 'drop = TRUE'  ## missing 'drop' --> 'drop = TRUE'
413  ##                     -----------  ##                     -----------
414  ## select rows  ## select rows __ or __ vector indexing:
415  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
416                           drop = "missing"),                           drop = "missing"),
417            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, ..., drop) {
418                  if(nargs() == 2) { ## e.g. M[0] , M[TRUE],  M[1:2]
419                      if(any(as.logical(i)) || prod(dim(x)) == 0)
420                          ## FIXME: for *large sparse*, use sparseVector !
421                          as.vector(x)[i]
422                      else ## save memory (for large sparse M):
423                          as.vector(x[1,1])[FALSE]
424                  } else {
425                      callGeneric(x, i=i, , drop=TRUE)
426                      ##                  ^^
427                  }
428              })
429    
430  ## select columns  ## select columns
431  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
432                           drop = "missing"),                           drop = "missing"),
433            function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))            function(x,i,j, ..., drop) callGeneric(x, j=j, drop= TRUE))
434  setMethod("[", signature(x = "Matrix", i = "index", j = "index",  setMethod("[", signature(x = "Matrix", i = "index", j = "index",
435                           drop = "missing"),                           drop = "missing"),
436            function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))            function(x,i,j, ..., drop) callGeneric(x, i=i, j=j, drop= TRUE))
437    
438  ## bail out if any of (i,j,drop) is "non-sense"  ## bail out if any of (i,j,drop) is "non-sense"
439  setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),  setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
440            function(x,i,j, drop)            function(x,i,j, ..., drop)
441            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
442    
443  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
444  ## The following is *both* for    M [ <logical>   ]  ## The following is *both* for    M [ <logical>   ]
445  ##                 and also for   M [ <logical> , ]  ##                 and also for   M [ <logical> , ]
446  .M.sub.i.logical <- function (x, i, j, drop)  .M.sub.i.logical <- function (x, i, j, ..., drop)
447  {  {
448      nA <- nargs()      nA <- nargs()
449      if(nA == 2) { ##  M [ M >= 7 ]      if(nA == 2) { ##  M [ M >= 7 ]
450          ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient          ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
451          as(x, geClass(x))@x[as.vector(i)]          if(is(x, "sparseMatrix"))
452                message("<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient")
453            toC <- geClass(x)
454            if(canCoerce(x, toC)) as(x, toC)@x[as.vector(i)]
455            else as(as(as(x, "generalMatrix"), "denseMatrix"), toC)@x[as.vector(i)]
456          ## -> error when lengths don't match          ## -> error when lengths don't match
457      } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]      } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
458          stop("not-yet-implemented 'Matrix' subsetting") ## FIXME          stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
459    
460      } else stop("nargs() = ", nA,      } else stop("nargs() = ", nA,
461                  " should never happen; please report.")                  ".  Extraneous illegal arguments inside '[ .. ]' (i.logical)?")
462  }  }
463  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
464                           drop = "ANY"),                           drop = "ANY"),
# Line 323  Line 468 
468            .M.sub.i.logical)            .M.sub.i.logical)
469    
470    
471  ## A[ ij ]  where ij is (i,j) 2-column matrix :  subset.ij <- function(x, ij) {
472  .M.sub.i.2col <- function (x, i, j, drop)      m <- nrow(ij)
473        if(m > 3) {
474            cld <- getClassDef(class(x))
475            sym.x <- extends(cld, "symmetricMatrix")
476            if(sym.x) {
477                W <- if(x@uplo == "U") # stored only [i,j] with i <= j
478                    ij[,1] > ij[,2] else ij[,1] < ij[,2]
479                if(any(W))
480                    ij[W,] <- ij[W, 2:1]
481            }
482            if(extends(cld, "sparseMatrix")) {
483                ## do something smarter:
484                nr <- nrow(x)
485                if(!extends(cld, "CsparseMatrix")) {
486                    x <- as(x, "CsparseMatrix") # simpler; our standard
487                    cld <- getClassDef(class(x))
488                }
489                tri.x <- extends(cld, "triangularMatrix")
490                if(tri.x) {
491                    ## need these for the 'x' slot in any case
492                    if (x@diag == "U") x <- .Call(Csparse_diagU2N, x)
493                    ## slightly more efficient than non0.i() or non0ind():
494                    ij.x <- .Call(compressed_non_0_ij, x, isC=TRUE)
495                } else { ## symmetric / general : for symmetric, only "existing"b
496                    ij.x <- non0.i(x, cld)
497                }
498    
499                mi <- match(encodeInd(ij.x,   nr),
500                            encodeInd(ij -1L, nr), nomatch=0)
501                mmi <- mi != 0
502                ## Result:
503                ans <- vector(mode = .type.kind[.M.kindC(cld)], length = m)
504                ## those that are *not* zero:
505                ans[mi[mmi]] <-
506                    if(extends(cld, "nsparseMatrix")) TRUE else x@x[mmi]
507                ans
508    
509            } else { ## non-sparse : dense
510                ##---- NEVER happens:  'denseMatrix' has its own setMethod(.) !
511                message("m[ <ij-matrix> ]: inefficiently indexing single elements")
512                i1 <- ij[,1]
513                i2 <- ij[,2]
514                ## very inefficient for large m
515                unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
516            }
517        } else { # 1 <= m <= 3
518            i1 <- ij[,1]
519            i2 <- ij[,2]
520            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
521        }
522    }
523    
524    ## A[ ij ]  where ij is (i,j) 2-column matrix -- but also when that is logical mat!
525    .M.sub.i.2col <- function (x, i, j, ..., drop)
526  {  {
527      nA <- nargs()      nA <- nargs()
528      if(nA == 2) { ##  M [ cbind(ii,jj) ]      if(nA == 2) { ##  M [ cbind(ii,jj) ] or M [ <logical matrix> ]
529          if(!is.integer(nc <- ncol(i)))          if(!is.integer(nc <- ncol(i)))
530              stop("'i' has no integer column number",              stop(".M.sub.i.2col(): 'i' has no integer column number;\n",
531                   " should never happen; please report")                   " should never happen; please report")
532          if(is.logical(i))          if(is.logical(i))
533              return(.M.sub.i.logical(x,i,j,drop))              return(.M.sub.i.logical(x, i=i)) # call with 2 args!
534          else if(!is.numeric(i) || nc != 2)          else if(!is.numeric(i) || nc != 2)
535              stop("such indexing must be by logical or 2-column numeric matrix")              stop("such indexing must be by logical or 2-column numeric matrix")
536          m <- nrow(i)          m <- nrow(i)
537          if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))          if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
538          ## else          ## else
539          i1 <- i[,1]          subset.ij(x, i)
         i2 <- i[,2]  
         ## potentially inefficient -- FIXME --  
         unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))  
540    
541      } else stop("nargs() = ", nA, " should never happen; please report.")      } else stop("nargs() = ", nA,
542                    ".  Extraneous illegal arguments inside '[ .. ]' (i.2col)?")
543  }  }
544  setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"  setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
545            .M.sub.i.2col)            .M.sub.i.2col)
# Line 356  Line 552 
552                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
553            function (x, value) {            function (x, value) {
554                ## Fails for 'nMatrix' ... FIXME : make sure have method there                ## Fails for 'nMatrix' ... FIXME : make sure have method there
555                x@x <- value                x@x <- rep(value, length = length(x@x))
556                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
557                x                x
558            })            })
559    
560  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
561  .M.repl.i.2col <- function (x, i, j, value)  ## ----------------
562    ## The cheap general method --- FIXME: provide special ones; done for Tsparse..
563    ## NOTE:  need '...' below such that setMethod() does
564    ##        not use .local() such that nargs() will work correctly:
565    .M.repl.i.2col <- function (x, i, j, ..., value)
566  {  {
567      nA <- nargs()      nA <- nargs()
568      if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value      if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value  or M [ Lmat ] <- value
569          if(!is.integer(nc <- ncol(i)))          if(!is.integer(nc <- ncol(i)))
570              stop("'i' has no integer column number",              stop(".M.repl.i.2col(): 'i' has no integer column number;\n",
571                   " should never happen; please report")                   " should never happen; please report")
572          if(is.logical(i)) {          else if(!is.numeric(i) || nc != 2)
             i <- c(i) # drop "matrix"  
             return( callNextMethod() )  
         } else if(!is.numeric(i) || nc != 2)  
573              stop("such indexing must be by logical or 2-column numeric matrix")              stop("such indexing must be by logical or 2-column numeric matrix")
574            if(is.logical(i)) {
575                message(".M.repl.i.2col(): drop 'matrix' case ...")
576                ## c(i) : drop "matrix" to logical vector
577                return( callGeneric(x, i=c(i), value=value) )
578            }
579            if(!is.integer(i)) storage.mode(i) <- "integer"
580            if(any(i < 0))
581                stop("negative values are not allowed in a matrix subscript")
582            if(any(is.na(i)))
583                stop("NAs are not allowed in subscripted assignments")
584            if(any(i0 <- (i == 0))) # remove them
585                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
586            ## now have integer i >= 1
587          m <- nrow(i)          m <- nrow(i)
588          mod.x <- .type.kind[.M.kind(x)]          ## mod.x <- .type.kind[.M.kind(x)]
589          if(length(value) > 0 && m %% length(value) != 0)          if(length(value) > 0 && m %% length(value) != 0)
590              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")
591          ## recycle:          ## recycle:
592          value <- rep(value, length = m)          value <- rep(value, length = m)
593          i1 <- i[,1]          i1 <- i[,1]
594          i2 <- i[,2]          i2 <- i[,2]
595            if(m > 2)
596                message("m[ <ij-matrix> ] <- v: inefficiently treating single elements")
597          ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)          ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
598          for(k in seq_len(m))          for(k in seq_len(m))
599              x[i1[k], i2[k]] <- value[k]              x[i1[k], i2[k]] <- value[k]
         x  
600    
601      } else stop("nargs() = ", nA, " should never happen; please report.")          x
602        } else stop("nargs() = ", nA,
603                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
604  }  }
605    
606  setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
607                                  value = "replValue"),                                  value = "replValue"),
608            .M.repl.i.2col)            .M.repl.i.2col)
609    
610    
611    setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
612                                    value = "Matrix"),
613                     function (x, i, j, ..., value)
614                     callGeneric(x=x, , j=j, value = as.vector(value)))
615    
616    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
617                                    value = "Matrix"),
618                     function (x, i, j, ..., value)
619                     callGeneric(x=x, i=i, , value = as.vector(value)))
620    
621  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
622                                  value = "Matrix"),                                  value = "Matrix"),
623                   function (x, i, j, value)                   function (x, i, j, ..., value)
624                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))
625    
626    setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
627                                    value = "matrix"),
628                     function (x, i, j, ..., value)
629                     callGeneric(x=x, , j=j, value = c(value)))
630    
631    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
632                                    value = "matrix"),
633                     function (x, i, j, ..., value)
634                     callGeneric(x=x, i=i, , value = c(value)))
635    
636  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
637                                  value = "matrix"),                                  value = "matrix"),
638                   function (x, i, j, value)                   function (x, i, j, value)
# Line 412  Line 647 
647                                 class(value),class(x)))                                 class(value),class(x)))
648                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
649            })            })
   
   
 ## 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:
Removed from v.1673  
changed lines
  Added in v.2175

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