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Diff of /pkg/R/Matrix.R

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revision 956, Fri Sep 30 17:28:00 2005 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
43  setMethod("isSymmetric", signature(object = "symmetricMatrix"),  setMethod("isSymmetric", signature(object = "symmetricMatrix"),
44            function(object) TRUE)            function(object,tol) TRUE)
45  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
46            ## FIXME: 'TRUE' if *diagonal*, i.e. return(isDiagonal(object))            ## TRUE iff diagonal:
47            function(object) FALSE)            function(object,tol) isDiagonal(object))
48  setMethod("isDiagonal", signature(object = "sparseMatrix"),  
49            function(object) {  if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
50                gT <- as(object, "TsparseMatrix")      ## need a "matrix" method as in R 2.3 and later
51                all(gT@i == gT@j)      setMethod("isSymmetric", signature(object = "matrix"),
52                  function(object, tol = 100*.Machine$double.eps, ...)
53              {
54                  ## pretest: is it square?
55                  d <- dim(object)
56                  if(d[1] != d[2]) return(FALSE)
57                  ## for `broken' all.equal in R <= 2.2.x:
58                  dn <- dimnames(object)
59                  if(!identical(dn[1], dn[2])) return(FALSE)
60                  test <-
61                      if(is.complex(object))
62                          all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
63                      else              # numeric, character, ..
64                          all.equal(object, t(object), tol = tol, ...)
65                  isTRUE(test)
66            })            })
67    
68    
69    setMethod("isTriangular", signature(object = "triangularMatrix"),
70              function(object, ...) TRUE)
71    
72    setMethod("isTriangular", signature(object = "matrix"), isTriMat)
73    
74    setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
75    
76    
77    
78  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
79            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
80  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
# Line 52  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 61  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 72  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      }      }
137            doDN <- FALSE
138        }
139      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
140      ## FIXME: consider it's type (logical,....)      if (doDN && !is.null(dimnames))
141      ## ctype <- substr(class(data), 1,1) # "d", "l", ...          dimnames(data) <- dimnames
142      ## FIXME(2): check for symmetric / triangular / ...  
143      if(sparse)      ## check for symmetric / triangular / diagonal :
144          as(data, "dgCMatrix")      isSym <- isSymmetric(data)
145      else      if((isTri <- !isSym))
146          as(data, "dgeMatrix")          isTri <- isTriangular(data)
147        isDiag <- isSym # cannot be diagonal if it isn't symmetric
148        if(isDiag)
149            isDiag <- isDiagonal(data)
150    
151    ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
152    
153        ## Find proper matrix class 'cl'
154        cl <-
155            if(isDiag)
156                "diagonalMatrix" # -> will automatically check for type
157            else {
158                ## consider it's type
159                ctype <-
160                    if(is(data,"Matrix")) class(data)
161                    else {
162                        if("complex" == (ctype <- typeof(data)))
163                            "z" else ctype
164                    }
165                ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
166                if(ctype == "z")
167                    stop("complex matrices not yet implemented in Matrix package")
168                if(ctype == "i") {
169                    warning("integer matrices not yet implemented in 'Matrix'; ",
170                            "using 'double' ones'")
171                    ctype <- "d"
172                }
173                paste(ctype,
174                      if(sparse) {
175                          if(isSym) "sCMatrix" else
176                          if(isTri) "tCMatrix" else "gCMatrix"
177                      } else { ## dense
178                          if(isSym) "syMatrix" else
179                          if(isTri) "trMatrix" else "geMatrix"
180                      }, sep="")
181            }
182    
183        ## Now coerce and return
184        as(data, cl)
185  }  }
186    
187  ## Methods for operations where one argument is numeric  ## Methods for operations where one argument is numeric
# Line 101  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 118  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 130  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 167  Line 281 
281  setMethod("[", signature(x = "Matrix",  setMethod("[", signature(x = "Matrix",
282                           i = "missing", j = "missing", drop = "ANY"),                           i = "missing", j = "missing", drop = "ANY"),
283            function (x, i, j, drop) x)            function (x, i, j, drop) x)
284    
285  ## missing 'drop' --> 'drop = TRUE'  ## missing 'drop' --> 'drop = TRUE'
286  ##                     -----------  ##                     -----------
287  ## select rows  ## select rows
# Line 186  Line 301 
301            function(x,i,j, drop)            function(x,i,j, drop)
302            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
303    
304    ##  "logical *vector* indexing, such as  M [ M >= 10 ] :
305    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
306                             drop = "ANY"),
307              function (x, i, j, drop) {
308                  as(x, geClass(x))@x[as.vector(i)]
309                  ## -> 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",
317                             drop = "ANY"),
318              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:"
325  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?
326  ##  and                A[ LL ]  where LL is a logical *vector*  ##  and                A[ LL ]  where LL is a logical *vector*
# Line 196  Line 331 
331    
332  ## x[] <- value :  ## x[] <- value :
333  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
334                                  value = "index"),##  double/logical/...                                  value = "ANY"),## double/logical/...
335            function (x, value) { x@x <- value ; validObject(x); x })            function (x, value) {
336                  x@x <- value
337                  validObject(x)# check if type and lengths above match
338                  x
339              })
340    
341  ## Otherwise (value is not "index"): bail out  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
342    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
343  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
344                                  value = "ANY"),                                  value = "ANY"),
345            function (x, i, j, value)            function (x, i, j, value) {
346                   if(!is(value,"index"))                if(!is.atomic(value))
347                   stop("RHS 'value' must be of class \"index\"")                    stop("RHS 'value' must match matrix class ", class(x))
348                   else stop("not-yet-implemented 'Matrix[<-' method"))                else stop("not-yet-implemented 'Matrix[<-' method")
349              })
   
   
 ## NOTE: the following only works for R 2.2.x (and later) ---  
 ## ----  *and* 'Matrix' must have been *installed* by R >= 2.2.x  
350    
 if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {  
351    
352      ## The trivial methods :      ## The trivial methods :
353      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
# Line 244  Line 379 
379                    colCheck(x,y)                    colCheck(x,y)
380                    t(cbind2(t(x), t(y)))                    t(cbind2(t(x), t(y)))
381                })                })
   
 }## R-2.2.x and newer  

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