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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 1551, Tue Sep 12 16:39:13 2006 UTC revision 1665, Fri Nov 3 23:18:07 2006 UTC
# Line 6  Line 6 
6  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8    
9    ## Most of these work; this is a last resort:
10  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
11        function(from) .bail.out.2("coerce", class(from), class(to)))        function(from) .bail.out.2("coerce", class(from), class(to)))
12    setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
13    
14  ## ## probably not needed eventually:  ## ## probably not needed eventually:
15  ## setAs(from = "ddenseMatrix", to = "matrix",  ## setAs(from = "ddenseMatrix", to = "matrix",
# Line 77  Line 79 
79      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
80                sparse = NULL, forceCheck = FALSE)                sparse = NULL, forceCheck = FALSE)
81  {  {
82      sparseDefault <- function(m)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
         prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)  
83    
84      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
85      if(is.null(sparse) && (i.M || is(data, "matrix")))  
86        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
87          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
88    
89      doDN <- TRUE      doDN <- TRUE
# Line 96  Line 98 
98              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
99          else if (missing(ncol))          else if (missing(ncol))
100              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
101          if(length(data) == 1 && !is.na(data) && data == 0 &&          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
102             !identical(sparse, FALSE)) {              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
103                if(is.null(sparse)) sparse1 <- sparse <- TRUE
             if(is.null(sparse)) sparse <- TRUE  
104              ## will be sparse: do NOT construct full matrix!              ## will be sparse: do NOT construct full matrix!
105              data <- new(if(is.numeric(data)) "dgTMatrix" else              data <- new(if(is.numeric(data)) "dgTMatrix" else
106                          if(is.logical(data)) "lgTMatrix" else                          if(is.logical(data)) "lgTMatrix" else
# Line 127  Line 128 
128      if(isDiag)      if(isDiag)
129          isDiag <- isDiagonal(data)          isDiag <- isDiagonal(data)
130    
 ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R  
   
131      ## Find proper matrix class 'cl'      ## Find proper matrix class 'cl'
132      cl <-      cl <-
133          if(isDiag)          if(isDiag && !isTRUE(sparse1))
134              "diagonalMatrix" # -> will automatically check for type              "diagonalMatrix" # -> will automatically check for type
135          else {          else {
136              ## consider it's type              ## consider it's type
# Line 172  Line 171 
171            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
172    
173  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
174            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
175    
176  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
177            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
# Line 186  Line 185 
185  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
186            function(x, y = NULL)  callGeneric(as.matrix(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
187    
188    ## maybe not optimal
189    setMethod("solve", signature(a = "Matrix", b = "missing"),
190              function(a, b, ...) solve(a, Diagonal(nrow(a))))
191    
192  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
193            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
194    ## when no sub-class method is found, bail out
195    setMethod("solve", signature(a = "Matrix", b = "matrix"),
196              function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
197    
198  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
199  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 221  Line 227 
227                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
228    
229    
230    ## FIXME: All of these should never be called
231    setMethod("chol", signature(x = "Matrix"),
232              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
233    setMethod("determinant", signature(x = "Matrix"),
234              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
235    
236  setMethod("diag", signature(x = "Matrix"),  setMethod("diag", signature(x = "Matrix"),
237            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
238  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
# Line 235  Line 247 
247                0-e1                0-e1
248            })            })
249    
250  ## bail-outs:  ## old-style matrices are made into new ones
251  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),  setMethod("Ops", signature(e1 = "Matrix", e2 = "matrix"),
252              function(e1, e2) callGeneric(e1, Matrix(e2)))
253    ##          callGeneric(e1, Matrix(e2, sparse=is(e1,"sparseMatrix"))))
254    setMethod("Ops", signature(e1 = "matrix", e2 = "Matrix"),
255              function(e1, e2) callGeneric(Matrix(e1), e2))
256    
257    ## bail-outs -- on highest possible level, hence "Ops", not "Compare"/"Arith" :
258    setMethod("Ops", signature(e1 = "Matrix", e2 = "Matrix"),
259            function(e1, e2) {            function(e1, e2) {
260                d <- dimCheck(e1,e2)                d <- dimCheck(e1,e2)
261                .bail.out.2(.Generic, class(e1), class(e2))                .bail.out.2(.Generic, class(e1), class(e2))
262            })            })
263  setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),  setMethod("Ops", signature(e1 = "Matrix", e2 = "ANY"),
264            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
265  setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),  setMethod("Ops", signature(e1 = "ANY", e2 = "Matrix"),
266            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
267    
268    
# Line 314  Line 333 
333  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
334                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
335            function (x, value) {            function (x, value) {
336                  ## Fails for 'nMatrix' ... FIXME : make sure have method there
337                x@x <- value                x@x <- value
338                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
339                x                x
340            })            })
341    
342  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
343                                    value = "Matrix"),
344                     function (x, i, j, value)
345                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
346    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
347                                    value = "matrix"),
348                     function (x, i, j, value)
349                     callGeneric(x=x, i=i, j=j, value = c(value)))
350    
351  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## (ANY,ANY,ANY) is used when no `real method' is implemented :
352  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
353                                  value = "ANY"),                                  value = "ANY"),
354            function (x, i, j, value) {            function (x, i, j, value) {
355                if(!is.atomic(value))                if(!is.atomic(value))
356                    stop("RHS 'value' must match matrix class ", class(x))                    stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
357                                   class(value),class(x)))
358                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
359            })            })
360    

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