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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1724, Sat Jan 13 21:06:51 2007 UTC
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1    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
4            as method for   M[ ij ] <- v
5            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
6    
7            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
8            FALSE answer
9    
10            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
11            * tests/indexing.R: test it, and some of the above
12    
13    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Auxiliaries.R (is_duplicatedT): new utility
16    
17    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * src/init.c (R_init_Matrix): export cholmod_scale
20    
21    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
24            base::as.matrix to (x, ...)
25    
26    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
29            file; start using "Logic", hence
30    
31            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
32            * NAMESPACE: import and export "Logic"
33    
34    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
37            only needed previously to R version 2.5.0.
38    
39    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
42    
43            * R/Tsparse.R (replTmat): fix subassignment of triangular
44            * R/Csparse.R (replCmat): ditto
45            * tests/indexing.R: more tests, incl the above fix
46    
47    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Auxiliaries.R (drop0): extend for non CSparse
50            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
51    
52            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
53                    use uplo correctly (!); other places: use uplo_P() macro
54    
55            * R/Csparse.R (replCmat): call diagU2N() when needed
56            * R/Tsparse.R (replTmat): ditto
57    
58            * src/dtCMatrix.c (tCMatrix_validate): new
59            * src/dtTMatrix.c (tTMatrix_validate): new, used in
60            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
61    
62            * R/diagMatrix.R (replDiag): to use in [<-
63    
64    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
67                    also more general diagU2N().
68    
69    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
72            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
73    
74    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * tests/bind.R: a few more cases
77            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
78    
79            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
80            * R/ddenseMatrix.R (cbind2/rbind2)
81            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
82            * tests/indexing.R
83            * tests/indexing.Rout.save: updated
84    
85    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
88            * tests/indexing.R
89    
90    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
93            align with proper position of "0", i.e., right for integers.
94            argument 'align' by default is "fancy".
95    
96    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
99            * R/Csparse.R: and fix "Compare" for more cases.
100            * tests/Class+Meth.R: test some of these (m == m, m != m)
101    
102    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/lsparseMatrix.R: all() and any() methods
105            * R/ldenseMatrix.R:      ditto
106            * NAMESPACE, R/Matrix.R: ditto
107    
108            * man/all-methods.Rd: document them minimally
109    
110            * tests/simple.R: add a few examples for these
111    
112    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Tsparse.R ([): fix long standing typo in symmetric case
115            * man/dsCMatrix-class.Rd: add example exhibiting the above case
116    
117    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
120            to LL before converting to a sparse matrix. (The LDL form can be
121            converted to a sparse matrix but it is implicitly a unit
122            triangular matrix and a diagonal matrix overwritten on the diagonal.)
123    
124    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
125    
126            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
127    
128    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
129    
130            * DESCRIPTION (Version): updated -> release 0.9975-7
131            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
132    
133    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
136    
137    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
140            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
141            is exactly singular.
142    
143    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * DESCRIPTION (Date): updated -> release 0.9975-6
146    
147    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
150            now returns symmetric.
151    
152            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
153    
154            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
155            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
156    
157            * R/Auxiliaries.R (.type.kind): added
158    
159    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
162            running src/CSparse_install.sh
163    
164            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
165    
166    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
169            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
170    
171            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
172    
173            * tests/Class+Meth.R (tstMatrixClass): now assure
174            the (important in method programming) property :
175    
176                    ###>>  Every "Matrix" is either
177                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
178    
179                    (where "*" stands for "Matrix")
180    
181            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
182    
183            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
184            * tests/validObj.R: checks for "comparison"
185    
186            * R/sparseMatrix.R ([): improved indexing for sparse;
187                    trying to keep <symmetric>[ n, n] symmmetric
188    
189            * tests/indexing.R: indexing for logical sparse now ok
190    
191    
192    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * src/Tsparse.c: use xTsparse_validate() , and hence remove
195    
196            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
197    
198    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
201    
202            * tests/simple.R: validObject() checking the above.
203    
204            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
205            replacing both dgCMatrix_validate and lgCM*.
206    
207            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
208            fix dimnames setting in other places.
209            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
210    
211    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
214    
215            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
216            symmetry test, via
217            * R/Auxiliaries.R (.as.dgC.0.factors):
218    
219    2006-11-01  Douglas Bates  <bates@r-project.org>
220    
221            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
222            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
223            <CsparseMatrix>) added
224    
225    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * tests/matprod.R: add a variation of Harri's example
228    
229            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
230            recursive infinitely.
231    
232            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
233    
234            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
235    
236    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
239            matrix if possible; test m+m == 2*m; now test dgRMatrix.
240            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
241            satisfy the above test.
242    
243    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
246    
247            * R/dgCMatrix.R: solve(a, b="missing") based on
248            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
249            RHS = NULL.
250    
251            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
252            add more (needed) [t]crossprod() methods.
253    
254            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
255    
256            * R/Auxiliaries.R (as_CspClass): cleanup
257            (drop0): internal utility for "Csparse_drop(*, 0)"
258            (.bail.out.2): encourage active feedback
259    
260    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dMatrix.R(Compare): new(), then slots [no validity check]
263    
264            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
265            non-valid or 'sorted' case).
266    
267            * R/dsparseMatrix.R: add "chol" method.
268            * R/ddenseMatrix.R: ditto
269    
270            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
271            * NAMESPACE (Ops)
272            * R/diagMatrix.R (diag2T): simple utility used "higher level"
273            coercion; deprecating direct lower level coercions.
274    
275            * R/*.R (seq): use seq_len() and seq_along() where possible.
276    
277    
278    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Version): 0.9975-5 ready for release
281    
282    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
285    
286    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/AllClass.R (corMatrix): add 'validity' check;
289                    comment out unused "LDL" class definition
290            * NAMESPACE: mention, but do not export "LDL" class
291            * R/corMatrix.R: new (simple), needed for R-devel with
292            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
293              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
294    
295    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
298            use Rprintf and R's error handling.
299    
300    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
303            * tests/matprod.R: add tests for the bug fixed.
304    
305    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
308            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
309    
310    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
313    
314    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * DESCRIPTION (Version): 0.9975-3
317    
318            * R/diagMatrix.R (bdiag): new function constructing block diagonal
319            (sparse) matrices.
320            * man/bdiag.Rd: docu + examples
321    
322            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
323    
324            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
325            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
326    
327            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
328            that result is sparse or diagonal (and not dense).
329    
330            * man/Subassign-methods.Rd: fix examples
331    
332            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
333            should always return a sparse (and not sometimes a diagonal) matrix.
334    
335    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
338    
339    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * DESCRIPTION (Version): 0.9975-2
342    
343            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
344    
345    2006-10-02  Douglas Bates  <bates@R-project.org>
346    
347            * tests/dg_Matrix.R: Simplify test taking into account new code.
348    
349    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
352    
353            * R/lsTMatrix.R: new files w/ missing methods
354            * R/nsTMatrix.R:  "  'for completeness'
355    
356            * tests/Class+Meth.R: a bit less 'not.ok.classes'
357    
358            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
359    
360    
361    2006-09-28  Douglas Bates  <bates@R-project.org>
362    
363            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
364            included.
365    
366            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
367            Export C-callable functions used in Zt_create in lme4.
368    
369    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version): 0.9975-1
372    
373            * tests/simple.R: less checks fail; using NA, found that our
374                    kronecker() is not base-compatible with NA's.
375    
376            * R/dMatrix.R: "Compare" method now implemented for all cases
377    
378            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
379    
380            * man/dtpMatrix-class.Rd: mention length of 'x' slot
381    
382            * src/dtpMatrix.c (dtpMatrix_validate): fix check
383            * src/dspMatrix.c (dspMatrix_validate): ditto
384    
385            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
386              including coercion to [nl]tTMatrix.
387    
388            * R/diagMatrix.R (show): print a header line as for other classes.
389    
390    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * src/Makefile.win (SUBDIRS): fix typo
393    
394    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
397    
398    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
401            symmetric and y missing in R code using %*% (cholmod_aat doesn't
402            accept a symmetric matrix).
403            * tests/group-methods.R: Uncomment test of crossprod applied to
404            lsCMatrix objects.
405    
406    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/AllClass.R (symmetricMatrix): add validity method (available
409            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
410    
411            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
412    
413            * tests/indexing.Rout.save:
414            * tests/indexing.R: additions, mainly for 'lsparse'
415    
416            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
417            case.
418    
419            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
420    
421    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
424                    as 'N' (1-letter - Ok?)
425    
426            * tests/group-methods.R: add test for logical + NAs
427    
428            * R/dMatrix.R ("Compare"): fix to work with NA's
429    
430            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
431    
432            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
433                    which is implemented.
434    
435    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * src/chm_common.c: coerce logical <-> double instead of
438            typecasting;  needed for "l" matrix handling in cholmod.
439    
440            * tests/other-pkgs.R (graph): small extension in "graph" checks.
441    
442            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
443            (Tsp2grNEL): other fixes needed
444    
445    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
448                    Matrices, since "lMatrix", also "lsparseM" can have NA
449            * R/ndenseMatrix.R, etc: new source files
450            * man/nsparseMatrix-classes.Rd, etc: new help files
451            * tests/: adaptions
452            * src/chm_common.c (chm_dense_to_SEXP): and others:
453                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
454            * src/Csparse.c, etc: ditto
455    
456    2006-09-11  Douglas Bates  <bates@R-project.org>
457    
458            * src/Mutils.[ch],init.c inst/include/*.h: Move the
459            alloc_d**Matrix functions to the lme4 package.
460    
461    2006-09-09  Douglas Bates  <bates@R-project.org>
462    
463            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
464            fixed
465    
466    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/lMatrix.R: new
469    
470            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
471    
472            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
473            * man/tcrossprod.Rd: ditto
474    
475    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
476    
477            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
478            for exported functions
479            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
480            Remove partitioning algorithms for sparse matrix reordering.  The
481            copyright on the Metis code was problematic and the methods were
482            rarely used.
483            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
484            operations are now done entirely in CHOLMOD code.
485    
486    2006-09-06  Douglas Bates  <bates@R-project.org>
487    
488            * src/Mutils.h: Remove functions that are no longer used.
489    
490    2006-09-04  Douglas Bates  <bates@R-project.org>
491    
492            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
493            * src/DEPS.mkf: update
494    
495    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * created branches/Matrix-for-R-2.3.x;  on trunk: do
498            * DESCRIPTION (Version): 0.9975-0
499            (Depends): R (>= 2.4.0)
500    
501    2006-09-01  Douglas Bates  <bates@R-project.org>
502    
503            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
504    
505    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
508            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
509    
510            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
511    
512    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
515            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
516            * R/dsparseMatrix.R: ditto
517            * R/Csparse.R: ditto
518    
519    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dMatrix.R (Compare): improve availability of "<", etc
522            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
523    
524    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
527            of a 0-index which was used as 1-index (..hmm)
528    
529            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
530    
531            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
532            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
533            (.is.diagonal): ditto
534    
535            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
536    
537            * R/Matrix.R (Matrix): also work for NA data
538    
539    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
542            in all cases.
543    
544    2006-08-27  Douglas Bates  <bates@R-project.org>
545    
546            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
547            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
548    
549    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
552            subclasses of "ddenseMatrix"
553            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
554            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
555            instead of half dozen specialized ones.
556    
557    2006-08-25  Douglas Bates  <bates@R-project.org>
558    
559            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
560            <tillard@cirad.fr> - ordering standard errors to match effects.
561    
562    2006-08-24  Douglas Bates  <bates@R-project.org>
563    
564            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
565            on R_ldl.
566            * R/lCholCMatrix.R,
567            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
568            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
569            * many files in ./R and ./src: Use more general version of
570            dup_mMatrix_as_dgeMatrix to simplify method definitions.
571            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
572            dtpMatrix, dspMatrix and dppMatrix conversions.
573    
574    
575    2006-08-23  Douglas Bates  <bates@R-project.org>
576    
577            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
578            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
579            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
580            dgeMatrix_crossprod (may need to do this in other places).
581            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
582            generic and method for dsCMatrix.  Use CHOLMOD for chol().
583    
584    2006-08-22  Douglas Bates  <bates@R-project.org>
585    
586            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
587            types of classed Matrices, matrices or numeric or logical vectors.
588            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
589            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
590            to Mutils.h (as an inline) and change name to Matrix_check_class;
591            fixes in as_cholmod_factor and chm_factor_to_SEXP.
592            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
593            dsCMatrix_matrix_solve.  Comment out vestigial functions.
594            * src/Csparse.c: use diag_P and uplo_P macros.
595    
596    2006-08-21  Douglas Bates  <bates@R-project.org>
597    
598            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
599            valgrind.
600            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
601            inverses.
602            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
603            -Wall warnings.
604            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
605            Use dup_mMatrix_as_dgeMatrix.
606    
607    2006-08-20  Douglas Bates  <bates@R-project.org>
608    
609            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
610            * tests/sparseQR.R: Added
611            * man/sparseQR-class.Rd: Document methods for qr.* generics
612            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
613    
614    2006-08-19  Douglas Bates  <bates@R-project.org>
615    
616            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
617            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
618            and qr.fitted.
619            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
620            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
621    
622    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
625            the base version has no "..." argument.
626    
627            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
628    
629            * R/Matrix.R: define and
630            * NAMESPACE: export as.numeric() and as.logical() methods.
631                    Let's hope these do not badly slow down something...
632            Finally export the zapsmall() method.
633    
634    2006-08-17  Douglas Bates  <bates@R-project.org>
635    
636            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
637            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
638            * src/dtCMatrix.c :Remove code that is no longer used
639            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
640    
641    2006-08-14  Douglas Bates  <bates@R-project.org>
642    
643            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
644            Csparse_to_logical and Csparse_symmetric_to_general.
645            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
646            coercion methods between CsparseMatrix and TsparseMatrix.
647    
648    2006-08-14  Douglas Bates  <bates@R-project.org>
649    
650            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
651            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
652            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
653            possible.
654    
655  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
656    
657          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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