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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 1290, Thu Jun 8 09:30:21 2006 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
# Line 1  Line 1 
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2    
3    
4    ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5    
6    setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7    setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8    
9  ## ## probably not needed eventually:  ## ## probably not needed eventually:
10  ## setAs(from = "ddenseMatrix", to = "matrix",  ## setAs(from = "ddenseMatrix", to = "matrix",
11  ##       function(from) {  ##       function(from) {
# Line 12  Line 18 
18  ## for 'Matrix' objects, as.array() should be equivalent:  ## for 'Matrix' objects, as.array() should be equivalent:
19  setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))  setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
20    
21    ## head and tail apply to all Matrix objects for which subscripting is allowed:
22    ## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23        setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24        setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25    ## } else { # R 2.4.0 and newer
26    ##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27    ##     setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28    ## }
29    
30  ## slow "fall back" method {subclasses should have faster ones}:  ## slow "fall back" method {subclasses should have faster ones}:
31  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
32            function(x) as.vector(as(x, "matrix")))            function(x) as.vector(as(x, "matrix")))
33    
34    ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
35    setMethod("as.numeric", signature(x = "Matrix"),
36              function(x, ...) as.numeric(as.vector(x)))
37    setMethod("as.logical", signature(x = "Matrix"),
38              function(x, ...) as.logical(as.vector(x)))
39    
40    
41  ## Note that isSymmetric is *not* exported  ## Note that isSymmetric is *not* exported
42  ## but that "base" has an isSymmetric() S3-generic since R 2.3.0  ## but that "base" has an isSymmetric() S3-generic since R 2.3.0
# Line 77  Line 98 
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)                sparse = NULL, forceCheck = FALSE)
102  {  {
103      sparseDefault <- function(m)      sparseDefault <- function(m)
104          prod(dim(m)) > 2*sum(as(m, "matrix") != 0)          prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
# Line 86  Line 107 
107      if(is.null(sparse) && (i.M || is(data, "matrix")))      if(is.null(sparse) && (i.M || is(data, "matrix")))
108          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
109    
110      if (i.M) {      doDN <- TRUE
111        if (i.M && !forceCheck) {
112          sM <- is(data,"sparseMatrix")          sM <- is(data,"sparseMatrix")
113          if((sparse && sM) || (!sparse && !sM))          if((sparse && sM) || (!sparse && !sM))
114              return(data)              return(data)
# Line 97  Line 119 
119              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
120          else if (missing(ncol))          else if (missing(ncol))
121              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
122            if(length(data) == 1 && data == 0 && !identical(sparse,FALSE)) {
123                if(is.null(sparse)) sparse <- TRUE
124                ## will be sparse: do NOT construct full matrix!
125                data <- new(if(is.numeric(data)) "dgTMatrix" else
126                            if(is.logical(data)) "lgTMatrix" else
127                            stop("invalid 'data'"),
128                            Dim = as.integer(c(nrow,ncol)),
129                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
130                            else dimnames)
131            } else { ## normal case
132          data <- .Internal(matrix(data, nrow, ncol, byrow))          data <- .Internal(matrix(data, nrow, ncol, byrow))
133          if(is.null(sparse))          if(is.null(sparse))
134              sparse <- sparseDefault(data)              sparse <- sparseDefault(data)
135          dimnames(data) <- dimnames          dimnames(data) <- dimnames
136      } else if (!is.null(dimnames))          }
137          dimnames(data) <- dimnames          doDN <- FALSE
138        }
139      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
140        if (doDN && !is.null(dimnames))
141            dimnames(data) <- dimnames
142    
143      ## check for symmetric / triangular / diagonal :      ## check for symmetric / triangular / diagonal :
144      isSym <- isSymmetric(data)      isSym <- isSymmetric(data)
# Line 163  Line 197 
197    
198  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
199            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
   
200  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
201            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
202    
203    ## The as.matrix() promotion seems illogical to MM,
204    ## but is according to help(tcrossprod, package = "base") :
205    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
206              function(x, y = NULL) callGeneric(x, as.matrix(y)))
207    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
208              function(x, y = NULL)  callGeneric(as.matrix(x), y))
209    
210  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
211            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
# Line 180  Line 220 
220            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
221  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
222            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
223    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
224              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
225    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
226              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
227    
228    ## cheap fallbacks
229    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
230              function(x, y = NULL) t(x) %*% y)
231    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
232              function(x, y = NULL) x %*% t(y))
233    
234  ## There are special sparse methods; this is a "fall back":  ## There are special sparse methods; this is a "fall back":
235  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
# Line 192  Line 242 
242                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
243    
244    
245    setMethod("diag", signature(x = "Matrix"),
246              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
247  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
248            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
249    
# Line 254  Line 306 
306                           drop = "ANY"),                           drop = "ANY"),
307            function (x, i, j, drop) {            function (x, i, j, drop) {
308                as(x, geClass(x))@x[as.vector(i)]                as(x, geClass(x))@x[as.vector(i)]
309                                          # -> error when lengths don't match                ## -> error when lengths don't match
310            })            })
311    
312    ## FIXME: The following is good for    M [ <logical>   ]
313    ##        *BUT* it also triggers for   M [ <logical> , ] where it is *WRONG*
314    ##       using nargs() does not help: it gives '3' for both cases
315    if(FALSE)
316  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
317                           drop = "ANY"),                           drop = "ANY"),
318            function (x, i, j, drop) as(x, geClass(x))@x[i])            function (x, i, j, drop) {
319                  ## DEBUG
320                  cat("[(Matrix,i,..): nargs=", nargs(),"\n")
321                  as(x, geClass(x))@x[i] })
322    
323    
324  ## "FIXME:"  ## "FIXME:"

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