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[matrix] Diff of /pkg/R/Auxiliaries.R
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Diff of /pkg/R/Auxiliaries.R

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revision 1332, Thu Jul 27 13:42:18 2006 UTC revision 1654, Fri Oct 27 16:58:15 2006 UTC
# Line 1  Line 1 
1  #### "Namespace private" Auxiliaries  such as method functions  #### "Namespace private" Auxiliaries  such as method functions
2  #### (called from more than one place --> need to be defined early)  #### (called from more than one place --> need to be defined early)
3    
4    .isR_24 <- (paste(R.version$major, R.version$minor, sep=".") >= "2.4")
5    
6    ## Need to consider NAs ;  "== 0" even works for logical & complex:
7    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)
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 11  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 89  Line 109 
109  isPacked <- function(x)  isPacked <- function(x)
110  {  {
111      ## Is 'x' a packed (dense) matrix ?      ## Is 'x' a packed (dense) matrix ?
112      is(x,"Matrix") && !is.null(x@x) && length(x@x) < prod(dim(x))      is(x, "denseMatrix") &&
113        any("x" == slotNames(x)) && length(x@x) < prod(dim(x))
114  }  }
115    
116  emptyColnames <- function(x)  emptyColnames <- function(x)
# Line 100  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"),
144                       justify = "none", right = TRUE)                       justify = "none", right = TRUE)
145  {  {
146      ## modeled along stats:::print.dist      ## modeled along stats:::print.dist
     diag <- TRUE  
147      upper <- x@uplo == "U"      upper <- x@uplo == "U"
148    
149      m <- as(x, "matrix")      m <- as(x, "matrix")
# Line 113  Line 152 
152          cf[row(cf) > col(cf)] <- "."          cf[row(cf) > col(cf)] <- "."
153      else      else
154          cf[row(cf) < col(cf)] <- "."          cf[row(cf) < col(cf)] <- "."
155      print(cf, quote = FALSE, right = right)      if(.isR_24)
156             print(cf, quote = FALSE, right = right, max = maxp)
157        else print(cf, quote = FALSE, right = right)
158      invisible(x)      invisible(x)
159  }  }
160    
161  prMatrix <- function(x, digits = getOption("digits")) {  prMatrix <- function(x, digits = getOption("digits"),
162                         maxp = getOption("max.print")) {
163      d <- dim(x)      d <- dim(x)
164      cl <- class(x)      cl <- class(x)
165      cat(sprintf('%d x %d Matrix of class "%s"\n', d[1], d[2], cl))      cat(sprintf('%d x %d Matrix of class "%s"\n', d[1], d[2], cl))
     maxp <- getOption("max.print")  
166      if(prod(d) <= maxp) {      if(prod(d) <= maxp) {
167          if(is(x, "triangularMatrix"))          if(is(x, "triangularMatrix"))
168              prTriang(x, digits = digits)              prTriang(x, digits = digits, maxp = maxp)
169          else          else {
170              print(as(x, "matrix"), digits = digits)              if(.isR_24)
171                     print(as(x, "matrix"), digits = digits, max = maxp)
172                else print(as(x, "matrix"), digits = digits)
173            }
174      }      }
175      else { ## d[1] > maxp / d[2] >= nr :      else { ## d[1] > maxp / d[2] >= nr :
176          m <- as(x, "matrix")          m <- as(x, "matrix")
# Line 140  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
225    ## 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"))
     ## return a 2-column (i,j) matrix of  
     ## 0-based indices of non-zero entries  :  
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 163  Line 244 
244          notdiag <- ij[,1] != ij[,2]# but not the diagonals again          notdiag <- ij[,1] != ij[,2]# but not the diagonals again
245          rbind(ij, ij[notdiag, 2:1])          rbind(ij, ij[notdiag, 2:1])
246      }      }
247        else if(is(x, "triangularMatrix")) { # check for "U" diag
248            if(x@diag == "U") {
249                i <- seq_len(dim(x)[1]) - 1:1
250                rbind(non0.i(x), cbind(i,i))
251            } else non0.i(x)
252        }
253      else      else
254          non0.i(x)          non0.i(x)
255  }  }
# Line 219  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 ", clx))             stop("not yet implemented for class ", class.x))
315  }  }
316    
317  ## Note: maybe, using  ## Note: maybe, using
# Line 228  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) {
336        if(is(x, "TsparseMatrix")) uniqTsparse(x) else as(x,"TsparseMatrix")
337  }  }
338    
339  if(FALSE) ## try an "efficient" version  if(FALSE) ## try an "efficient" version
# Line 294  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 339  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 349  Line 471 
471                       "s" = "sy",                       "s" = "sy",
472                       "g" = "ge")                       "g" = "ge")
473    
474  .Csparse.prefix <- function(ch) {  .sparse.prefixes <- c("d" = "t", ## map diagonal to triangular
475      switch(ch,                        "t" = "t",
476             "d" =, "t" = "tC",                        "s" = "s",
477             "s" = "sC",                        "g" = "g")
            "g" = "gC",  
            stop("invalid Matrix shape: ", ch))  
 }  
478    
479  ## Used, e.g. after subsetting: Try to use specific class -- if feasible :  ## Used, e.g. after subsetting: Try to use specific class -- if feasible :
480  as_dense <- function(x) {  as_dense <- function(x) {
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), .Csparse.prefix(.M.shape(x)), "Matrix", sep=''))      as(x, paste(.M.kind(x), .sparse.prefixes[.M.shape(x)], "CMatrix", sep=''))
495    }
496    as_Rsparse <- function(x) {
497        as(x, paste(.M.kind(x), .sparse.prefixes[.M.shape(x)], "RMatrix", sep=''))
498    }
499    as_Tsparse <- function(x) {
500        as(x, paste(.M.kind(x), .sparse.prefixes[.M.shape(x)], "TMatrix", sep=''))
501  }  }
502    
503  as_geClass <- function(x, cl) {  as_geClass <- function(x, cl) {
504      if     (extends(cl, "diagonalMatrix")  && isDiagonal(x))      if     (extends(cl, "diagonalMatrix")  && isDiagonal(x))
505          as(x, cl)          as(x, cl)
506      else if(extends(cl, "symmetricMatrix") &&  isSymmetric(x))      else if(extends(cl, "symmetricMatrix") &&  isSymmetric(x)) {
507            kind <- .M.kind(x)
508          as(x, class2(cl, kind, do.sub= kind != "d"))          as(x, class2(cl, kind, do.sub= kind != "d"))
509      else if(extends(cl, "triangularMatrix") && isTriangular(x))      } else if(extends(cl, "triangularMatrix") && isTriangular(x))
510          as(x, cl)          as(x, cl)
511      else      else
512          as(x, paste(.M.kind(x), "geMatrix", sep=''))          as(x, paste(.M.kind(x), "geMatrix", sep=''))
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 416  Line 553 
553      ## else slower test      ## else slower test
554      if(!is.matrix(object))      if(!is.matrix(object))
555          object <- as(object,"matrix")          object <- as(object,"matrix")
     ## == 0 even works for logical & complex:  
556      if(is.na(upper)) {      if(is.na(upper)) {
557          if(all(object[lower.tri(object)] == 0))          if(all0(object[lower.tri(object)]))
558              structure(TRUE, kind = "U")              structure(TRUE, kind = "U")
559          else if(all(object[upper.tri(object)] == 0))          else if(all0(object[upper.tri(object)]))
560              structure(TRUE, kind = "L")              structure(TRUE, kind = "L")
561          else FALSE          else FALSE
562      } else if(upper)      } else if(upper)
563          all(object[lower.tri(object)] == 0)          all0(object[lower.tri(object)])
564      else ## upper is FALSE      else ## upper is FALSE
565          all(object[upper.tri(object)] == 0)          all0(object[upper.tri(object)])
566  }  }
567    
568  ## For Csparse matrices  ## For Csparse matrices
# Line 462  Line 598 
598  }  }
599    
600  .is.diagonal <- function(object) {  .is.diagonal <- function(object) {
601        ## "matrix" or "denseMatrix" (but not "diagonalMatrix")
602      d <- dim(object)      d <- dim(object)
603      if(d[1] != (n <- d[2])) FALSE      if(d[1] != (n <- d[2])) FALSE
604      else all(object[rep(c(FALSE, rep.int(TRUE,n)), length = n^2)] == 0)      else if(is.matrix(object))
605            ## requires that "vector-indexing" works for 'object' :
606            all0(object[rep(c(FALSE, rep.int(TRUE,n)), length = n^2)])
607        else ## "denseMatrix" -- packed or unpacked
608            if(is(object, "generalMatrix")) # "dge", "lge", ...
609                all0(object@x[rep(c(FALSE, rep.int(TRUE,n)), length = n^2)])
610            else { ## "dense" but not {diag, general}, i.e. triangular or symmetric:
611                ## -> has 'uplo'  differentiate between packed and unpacked
612    
613    ### .......... FIXME ...............
614    
615                packed <- isPacked(object)
616                if(object@uplo == "U") {
617                } else { ## uplo == "L"
618                }
619    
620    ### very cheap workaround
621                all0(as.matrix(object)[rep(c(FALSE, rep.int(TRUE,n)), length = n^2)])
622  }  }
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:
# Line 477  Line 634 
634          Dimnames = x@Dimnames, uplo = x@uplo, diag = "N")          Dimnames = x@Dimnames, uplo = x@uplo, diag = "N")
635  }  }
636    
637    ## FIXME: this should probably be dropped / replaced by as_Csparse
638  .as.dgC.Fun <- function(x, na.rm = FALSE, dims = 1) {  .as.dgC.Fun <- function(x, na.rm = FALSE, dims = 1) {
639      x <- as(x, "dgCMatrix")      x <- as(x, "dgCMatrix")
640      callGeneric()      callGeneric()
641  }  }
642    
643  .as.dgT.Fun <- function(x, na.rm = FALSE, dims = 1) {  .as.dgT.Fun <- function(x, na.rm = FALSE, dims = 1) {
644        ## used e.g. inside colSums() etc methods
645      x <- as(x, "dgTMatrix")      x <- as(x, "dgTMatrix")
646      callGeneric()      callGeneric()
647  }  }

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