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revision 1472, Fri Sep 1 15:31:04 2006 UTC revision 1654, Fri Oct 27 16:58:15 2006 UTC
# Line 5  Line 5 
5    
6  ## Need to consider NAs ;  "== 0" even works for logical & complex:  ## Need to consider NAs ;  "== 0" even works for logical & complex:
7  is0  <- function(x) !is.na(x) & x == 0  is0  <- function(x) !is.na(x) & x == 0
8    isN0 <- function(x)  is.na(x) | x != 0
9  all0 <- function(x) !any(is.na(x)) && all(x == 0)  all0 <- function(x) !any(is.na(x)) && all(x == 0)
10    
11    allTrue  <- function(x) !any(is.na(x)) && all(x)
12    allFalse <- function(x) !any(is.na(x)) && !any(x)
13    
14    
15  ## For %*% (M = Matrix; v = vector (double or integer {complex maybe?}):  ## For %*% (M = Matrix; v = vector (double or integer {complex maybe?}):
16  .M.v <- function(x, y) callGeneric(x, as.matrix(y))  .M.v <- function(x, y) callGeneric(x, as.matrix(y))
17  .v.M <- function(x, y) callGeneric(rbind(x), y)  .v.M <- function(x, y) callGeneric(rbind(x), y)
# Line 17  Line 22 
22      function(x) !identical(list(NULL,NULL), x@Dimnames)      function(x) !identical(list(NULL,NULL), x@Dimnames)
23    
24  .bail.out.1 <- function(fun, cl) {  .bail.out.1 <- function(fun, cl) {
25      stop(gettextf('not-yet-implemented method for %s(<%s>)', fun, cl),      stop(gettextf('not-yet-implemented method for %s(<%s>).\n ->>  Ask the package authors to implement the missing feature.', fun, cl),
26           call. = FALSE)           call. = FALSE)
27  }  }
28  .bail.out.2 <- function(fun, cl1, cl2) {  .bail.out.2 <- function(fun, cl1, cl2) {
29      stop(gettextf('not-yet-implemented method for %s(<%s>, <%s>)',      stop(gettextf('not-yet-implemented method for %s(<%s>, <%s>).\n ->>  Ask the package authors to implement the missing feature.',
30                    fun, cl1, cl2), call. = FALSE)                    fun, cl1, cl2), call. = FALSE)
31  }  }
32    
33    ## This should be done in C and be exported by 'methods':  [FIXME - ask JMC ]
34    copyClass <- function(x, newCl, sNames =
35                          intersect(slotNames(newCl), slotNames(x))) {
36        r <- new(newCl)
37        for(n in sNames)
38            slot(r, n) <- slot(x, n)
39        r
40    }
41    
42  ## chol() via "dpoMatrix"  ## chol() via "dpoMatrix"
43  cholMat <- function(x, pivot, LINPACK) {  cholMat <- function(x, pivot, ...) {
44      px <- as(x, "dpoMatrix")      px <- as(x, "dpoMatrix")
45      if (isTRUE(validObject(px, test=TRUE))) chol(px)      if (isTRUE(validObject(px, test=TRUE))) chol(px)
46      else stop("'x' is not positive definite -- chol() undefined.")      else stop("'x' is not positive definite -- chol() undefined.")
# Line 107  Line 121 
121      x      x
122  }  }
123    
124    ### TODO:  write in C and port to base (or 'utils') R
125    indTri <- function(n, upper = TRUE) {
126        ## == which(upper.tri(diag(n)) or
127        ##    which(lower.tri(diag(n)) -- but much more efficiently for largish 'n'
128        stopifnot(length(n) == 1, n == (n. <- as.integer(n)), (n <- n.) >= 0)
129        if(n <= 2)
130            return(if(n == 2) as.integer(if(upper) n+1 else n) else integer(0))
131        ## First, compute the 'diff(.)'  fast.  Use integers
132        one <- 1:1 ; two <- 2:2
133        n1 <- n - one
134        n2 <- n1 - one
135        r <- rep.int(one, n*n1/two - one)
136        r[cumsum(if(upper) 1:n2 else c(n1, if(n >= 4) n2:two))] <- if(upper) n:3 else 3:n
137        ## now have "dliu" difference; revert to "liu":
138        cumsum(c(if(upper) n+one else two, r))
139    }
140    
141    
142  prTriang <- function(x, digits = getOption("digits"),  prTriang <- function(x, digits = getOption("digits"),
143                       maxp = getOption("max.print"),                       maxp = getOption("max.print"),
144                       justify = "none", right = TRUE)                       justify = "none", right = TRUE)
# Line 152  Line 184 
184      invisible(x)# as print() S3 methods do      invisible(x)# as print() S3 methods do
185  }  }
186    
187    nonFALSE <- function(x) {
188        ## typically used for lMatrices:  (TRUE,NA,FALSE) |-> (TRUE,FALSE)
189        if(any(ix <- is.na(x))) x[ix] <- TRUE
190        x
191    }
192    
193    nz.NA <- function(x, na.value) {
194        ## Non-Zeros of x
195        ## na.value: TRUE: NA's give TRUE, they are not 0
196        ##             NA: NA's are not known ==> result := NA
197        ##          FALSE: NA's give FALSE, could be 0
198        stopifnot(is.logical(na.value) && length(na.value) == 1)
199        if(is.na(na.value)) x != 0
200        else  if(na.value)  isN0(x)
201        else                x != 0 & !is.na(x)
202    }
203    
204    ## Number of non-zeros :
205    ## FIXME? -- make this into a generic function (?)
206    nnzero <- function(x, na.counted = NA) {
207        ## na.counted: TRUE: NA's are counted, they are not 0
208        ##               NA: NA's are not known (0 or not) ==>  result := NA
209        ##            FALSE: NA's are omitted before counting
210        cl <- class(x)
211        if(!extends(cl, "Matrix"))
212            sum(nz.NA(x, na.counted))
213        else if(extends(cl, "sparseMatrix"))
214            ## NOTA BENE: The number of *structural* non-zeros {could have other '0'}!
215           switch(.sp.class(cl),
216                   "CsparseMatrix" = length(x@i),
217                   "TsparseMatrix" = length(x@i),
218                   "RsparseMatrix" = length(x@j))
219        else ## denseMatrix
220            sum(nz.NA(as_geClass(x, cl)@x, na.counted))
221    }
222    
223  ## For sparseness handling  ## For sparseness handling
224  ## return a 2-column (i,j) matrix of  ## return a 2-column (i,j) matrix of
225  ## 0-based indices of non-zero entries  :  ## 0-based indices of non-zero entries  :
226  non0ind <- function(x) {  non0ind <- function(x) {
227    
228      if(is.numeric(x))      if(is.numeric(x))
229          return(if((n <- length(x))) (0:(n-1))[x != 0] else integer(0))          return(if((n <- length(x))) (0:(n-1))[isN0(x)] else integer(0))
230      ## else      ## else
231      stopifnot(is(x, "sparseMatrix"))      stopifnot(is(x, "sparseMatrix"))
232      non0.i <- function(M) {      non0.i <- function(M) {
233          if(is(M, "TsparseMatrix"))          if(is(M, "TsparseMatrix"))
234              return(unique(cbind(M@i,M@j)))              return(unique(cbind(M@i,M@j)))
235          if(is(M, "pMatrix"))          if(is(M, "pMatrix"))
236              return(cbind(seq(length=nrow(M)), M@perm) - 1:1)              return(cbind(seq_len(nrow(M)), M@perm) - 1:1)
237          ## else:          ## else:
238          isC <- any("i" == slotNames(M)) # is Csparse (not Rsparse)          isC <- any("i" == slotNames(M)) # is Csparse (not Rsparse)
239          .Call(compressed_non_0_ij, M, isC)          .Call(compressed_non_0_ij, M, isC)
# Line 178  Line 246 
246      }      }
247      else if(is(x, "triangularMatrix")) { # check for "U" diag      else if(is(x, "triangularMatrix")) { # check for "U" diag
248          if(x@diag == "U") {          if(x@diag == "U") {
249              i <- seq(length = dim(x)[1]) - 1:1              i <- seq_len(dim(x)[1]) - 1:1
250              rbind(non0.i(x), cbind(i,i))              rbind(non0.i(x), cbind(i,i))
251          } else non0.i(x)          } else non0.i(x)
252      }      }
# Line 238  Line 306 
306             "lgTMatrix" = as(as(x, "lgCMatrix"), "lgTMatrix"),             "lgTMatrix" = as(as(x, "lgCMatrix"), "lgTMatrix"),
307             "lsTMatrix" = as(as(x, "lsCMatrix"), "lsTMatrix"),             "lsTMatrix" = as(as(x, "lsCMatrix"), "lsTMatrix"),
308             "ltTMatrix" = as(as(x, "ltCMatrix"), "ltTMatrix"),             "ltTMatrix" = as(as(x, "ltCMatrix"), "ltTMatrix"),
309               ## do we need this for "logical" ones, there's no sum() there!
310               "ngTMatrix" = as(as(x, "ngCMatrix"), "ngTMatrix"),
311               "nsTMatrix" = as(as(x, "nsCMatrix"), "nsTMatrix"),
312               "ntTMatrix" = as(as(x, "ntCMatrix"), "ntTMatrix"),
313             ## otherwise:             ## otherwise:
314             stop("not yet implemented for class ", class.x))             stop("not yet implemented for class ", class.x))
315  }  }
# Line 247  Line 319 
319  ## would be slightly more efficient than as( <dgC> , "dgTMatrix")  ## would be slightly more efficient than as( <dgC> , "dgTMatrix")
320  ## but really efficient would be to use only one .Call(.) for uniq(.) !  ## but really efficient would be to use only one .Call(.) for uniq(.) !
321    
322    drop0 <- function(x, clx = c(class(x))) {
323        ## FIXME: Csparse_drop should do this (not losing symm./triang.):
324        ## Careful: 'Csparse_drop' also drops triangularity,...
325        ## .Call(Csparse_drop, as_CspClass(x, clx), 0)
326        as_CspClass(.Call(Csparse_drop, as_CspClass(x, clx), 0.),
327                    clx)
328    }
329    
330  uniq <- function(x) {  uniq <- function(x) {
331      if(is(x, "TsparseMatrix")) uniqTsparse(x) else x      if(is(x, "TsparseMatrix")) uniqTsparse(x) else
332      ## else:  not 'Tsparse', i.e. "uniquely" represented in any case      if(is(x, "sparseMatrix")) drop0(x) else x
333  }  }
334    
335  asTuniq <- function(x) {  asTuniq <- function(x) {
# Line 317  Line 397 
397      ## FIXME: treat 'factors' smartly {not for triangular!}      ## FIXME: treat 'factors' smartly {not for triangular!}
398  }  }
399    
400    ## -> ./ndenseMatrix.R :
401    n2d_Matrix <- function(from) {
402        stopifnot(is(from, "nMatrix"))
403        fixupDense(new(sub("^n", "d", class(from)),
404                       x = as.double(from@x),
405                       Dim = from@Dim, Dimnames = from@Dimnames),
406                   from)
407        ## FIXME: treat 'factors' smartly {not for triangular!}
408    }
409    n2l_spMatrix <- function(from) {
410        stopifnot(is(from, "nMatrix"))
411        new(sub("^n", "l", class(from)),
412            ##x = as.double(from@x),
413            Dim = from@Dim, Dimnames = from@Dimnames)
414    }
415    
416  if(FALSE)# unused  if(FALSE)# unused
417  l2d_meth <- function(x) {  l2d_meth <- function(x) {
418      cl <- class(x)      cl <- class(x)
419      as(callGeneric(as(x, sub("^l", "d", cl))), cl)      as(callGeneric(as(x, sub("^l", "d", cl))), cl)
420  }  }
421    
422  ## return "d" or "l" or "z"  ## return "d" or "l" or "n" or "z"
423  .M.kind <- function(x, clx = class(x)) {  .M.kind <- function(x, clx = class(x)) {
424      if(is.matrix(x)) { ## 'old style matrix'      if(is.matrix(x)) { ## 'old style matrix'
425          if     (is.numeric(x)) "d"          if     (is.numeric(x)) "d"
426          else if(is.logical(x)) "l"          else if(is.logical(x)) "l" ## FIXME ? "n" if no NA ??
427          else if(is.complex(x)) "z"          else if(is.complex(x)) "z"
428          else stop("not yet implemented for matrix w/ typeof ", typeof(x))          else stop("not yet implemented for matrix w/ typeof ", typeof(x))
429      }      }
430      else if(extends(clx, "dMatrix")) "d"      else if(extends(clx, "dMatrix")) "d"
431        else if(extends(clx, "nMatrix")) "n"
432      else if(extends(clx, "lMatrix")) "l"      else if(extends(clx, "lMatrix")) "l"
433      else if(extends(clx, "zMatrix")) "z"      else if(extends(clx, "zMatrix")) "z"
434        else if(extends(clx, "pMatrix")) "n" # permutation -> pattern
435      else stop(" not yet be implemented for ", clx)      else stop(" not yet be implemented for ", clx)
436  }  }
437    
# Line 362  Line 460 
460  geClass <- function(x) {  geClass <- function(x) {
461      if     (is(x, "dMatrix")) "dgeMatrix"      if     (is(x, "dMatrix")) "dgeMatrix"
462      else if(is(x, "lMatrix")) "lgeMatrix"      else if(is(x, "lMatrix")) "lgeMatrix"
463        else if(is(x, "nMatrix")) "ngeMatrix"
464      else if(is(x, "zMatrix")) "zgeMatrix"      else if(is(x, "zMatrix")) "zgeMatrix"
465      else stop("general Matrix class not yet implemented for ",      else stop("general Matrix class not yet implemented for ",
466                class(x))                class(x))
# Line 382  Line 481 
481      as(x, paste(.M.kind(x), .dense.prefixes[.M.shape(x)], "Matrix", sep=''))      as(x, paste(.M.kind(x), .dense.prefixes[.M.shape(x)], "Matrix", sep=''))
482  }  }
483    
484    .sp.class <- function(x) { ## find and return the "sparseness class"
485        if(!is.character(x)) x <- class(x)
486        for(cl in paste(c("C","T","R"), "sparseMatrix", sep=''))
487            if(extends(x, cl))
488                return(cl)
489        ## else (should rarely happen)
490        as.character(NA)
491    }
492    
493  as_Csparse <- function(x) {  as_Csparse <- function(x) {
494      as(x, paste(.M.kind(x), .sparse.prefixes[.M.shape(x)], "CMatrix", sep=''))      as(x, paste(.M.kind(x), .sparse.prefixes[.M.shape(x)], "CMatrix", sep=''))
495  }  }
# Line 405  Line 513 
513  }  }
514    
515  as_CspClass <- function(x, cl) {  as_CspClass <- function(x, cl) {
516      if ((extends(cl, "diagonalMatrix")  && isDiagonal(x)) ||      if (## diagonal is *not* sparse:
517            ##(extends(cl, "diagonalMatrix") && isDiagonal(x)) ||
518          (extends(cl, "symmetricMatrix") &&  isSymmetric(x)) ||          (extends(cl, "symmetricMatrix") &&  isSymmetric(x)) ||
519          (extends(cl, "triangularMatrix")&& isTriangular(x)))          (extends(cl, "triangularMatrix")&& isTriangular(x)))
520          as(x, cl)          as(x, cl)
521        else if(is(x, "CsparseMatrix")) x
522      else as(x, paste(.M.kind(x), "gCMatrix", sep=''))      else as(x, paste(.M.kind(x), "gCMatrix", sep=''))
523  }  }
524    
# Line 513  Line 623 
623  }  }
624    
625    
626    ## FIXME? -- this should also work for "ltT", "ntT", ... :
627  diagU2N <- function(x)  diagU2N <- function(x)
628  {  {
629      ## Purpose: Transform a *unit diagonal* triangular matrix      ## Purpose: Transform a *unit diagonal* sparse triangular matrix
630      ##  into one with explicit diagonal entries '1'      ##  into one with explicit diagonal entries '1'
631      xT <- as(x, "dgTMatrix")      xT <- as(x, "dgTMatrix")
632      ## leave it as  T* - the caller can always coerce to C* if needed:      ## leave it as  T* - the caller can always coerce to C* if needed:

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