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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1725, Wed Jan 17 08:01:10 2007 UTC
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1    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (!): fix typo.
4    
5    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (as_Csparse): and quite a few others:
8                    allow to pass class definition --> speedup
9            * R/sparseMatrix.R: apply the above
10    
11            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
12    
13            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
14            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
15            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
16    
17            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
18    
19            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
20            and use it for "sparse*" as well, since it's faster than the
21            as_Csparse(.) way.
22    
23    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
26    
27    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
30            as method for   M[ ij ] <- v
31            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
32    
33            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
34            FALSE answer
35    
36            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
37            * tests/indexing.R: test it, and some of the above
38    
39    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (is_duplicatedT): new utility
42    
43    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * src/init.c (R_init_Matrix): export cholmod_scale
46    
47    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
50            base::as.matrix to (x, ...)
51    
52    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
55            file; start using "Logic", hence
56    
57            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
58            * NAMESPACE: import and export "Logic"
59    
60    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
63            only needed previously to R version 2.5.0.
64    
65    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
68    
69            * R/Tsparse.R (replTmat): fix subassignment of triangular
70            * R/Csparse.R (replCmat): ditto
71            * tests/indexing.R: more tests, incl the above fix
72    
73    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (drop0): extend for non CSparse
76            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
77    
78            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
79                    use uplo correctly (!); other places: use uplo_P() macro
80    
81            * R/Csparse.R (replCmat): call diagU2N() when needed
82            * R/Tsparse.R (replTmat): ditto
83    
84            * src/dtCMatrix.c (tCMatrix_validate): new
85            * src/dtTMatrix.c (tTMatrix_validate): new, used in
86            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
87    
88            * R/diagMatrix.R (replDiag): to use in [<-
89    
90    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
93                    also more general diagU2N().
94    
95    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
98            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
99    
100    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/bind.R: a few more cases
103            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
104    
105            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
106            * R/ddenseMatrix.R (cbind2/rbind2)
107            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
108            * tests/indexing.R
109            * tests/indexing.Rout.save: updated
110    
111    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
114            * tests/indexing.R
115    
116    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
119            align with proper position of "0", i.e., right for integers.
120            argument 'align' by default is "fancy".
121    
122    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
125            * R/Csparse.R: and fix "Compare" for more cases.
126            * tests/Class+Meth.R: test some of these (m == m, m != m)
127    
128    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/lsparseMatrix.R: all() and any() methods
131            * R/ldenseMatrix.R:      ditto
132            * NAMESPACE, R/Matrix.R: ditto
133    
134            * man/all-methods.Rd: document them minimally
135    
136            * tests/simple.R: add a few examples for these
137    
138    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R ([): fix long standing typo in symmetric case
141            * man/dsCMatrix-class.Rd: add example exhibiting the above case
142    
143    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
146            to LL before converting to a sparse matrix. (The LDL form can be
147            converted to a sparse matrix but it is implicitly a unit
148            triangular matrix and a diagonal matrix overwritten on the diagonal.)
149    
150    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
153    
154    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * DESCRIPTION (Version): updated -> release 0.9975-7
157            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
158    
159    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
162    
163    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
166            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
167            is exactly singular.
168    
169    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Date): updated -> release 0.9975-6
172    
173    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
176            now returns symmetric.
177    
178            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
179    
180            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
181            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
182    
183            * R/Auxiliaries.R (.type.kind): added
184    
185    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
188            running src/CSparse_install.sh
189    
190            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
191    
192    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
195            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
196    
197            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
198    
199            * tests/Class+Meth.R (tstMatrixClass): now assure
200            the (important in method programming) property :
201    
202                    ###>>  Every "Matrix" is either
203                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
204    
205                    (where "*" stands for "Matrix")
206    
207            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
208    
209            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
210            * tests/validObj.R: checks for "comparison"
211    
212            * R/sparseMatrix.R ([): improved indexing for sparse;
213                    trying to keep <symmetric>[ n, n] symmmetric
214    
215            * tests/indexing.R: indexing for logical sparse now ok
216    
217    
218    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/Tsparse.c: use xTsparse_validate() , and hence remove
221    
222            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
223    
224    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
227    
228            * tests/simple.R: validObject() checking the above.
229    
230            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
231            replacing both dgCMatrix_validate and lgCM*.
232    
233            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
234            fix dimnames setting in other places.
235            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
236    
237    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
240    
241            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
242            symmetry test, via
243            * R/Auxiliaries.R (.as.dgC.0.factors):
244    
245    2006-11-01  Douglas Bates  <bates@r-project.org>
246    
247            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
248            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
249            <CsparseMatrix>) added
250    
251    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * tests/matprod.R: add a variation of Harri's example
254    
255            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
256            recursive infinitely.
257    
258            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
259    
260            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
261    
262    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
265            matrix if possible; test m+m == 2*m; now test dgRMatrix.
266            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
267            satisfy the above test.
268    
269    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
272    
273            * R/dgCMatrix.R: solve(a, b="missing") based on
274            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
275            RHS = NULL.
276    
277            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
278            add more (needed) [t]crossprod() methods.
279    
280            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
281    
282            * R/Auxiliaries.R (as_CspClass): cleanup
283            (drop0): internal utility for "Csparse_drop(*, 0)"
284            (.bail.out.2): encourage active feedback
285    
286    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dMatrix.R(Compare): new(), then slots [no validity check]
289    
290            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
291            non-valid or 'sorted' case).
292    
293            * R/dsparseMatrix.R: add "chol" method.
294            * R/ddenseMatrix.R: ditto
295    
296            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
297            * NAMESPACE (Ops)
298            * R/diagMatrix.R (diag2T): simple utility used "higher level"
299            coercion; deprecating direct lower level coercions.
300    
301            * R/*.R (seq): use seq_len() and seq_along() where possible.
302    
303    
304    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * DESCRIPTION (Version): 0.9975-5 ready for release
307    
308    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
309    
310            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
311    
312    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/AllClass.R (corMatrix): add 'validity' check;
315                    comment out unused "LDL" class definition
316            * NAMESPACE: mention, but do not export "LDL" class
317            * R/corMatrix.R: new (simple), needed for R-devel with
318            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
319              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
320    
321    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
322    
323            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
324            use Rprintf and R's error handling.
325    
326    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
329            * tests/matprod.R: add tests for the bug fixed.
330    
331    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
332    
333            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
334            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
335    
336    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
339    
340    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.9975-3
343    
344            * R/diagMatrix.R (bdiag): new function constructing block diagonal
345            (sparse) matrices.
346            * man/bdiag.Rd: docu + examples
347    
348            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
349    
350            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
351            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
352    
353            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
354            that result is sparse or diagonal (and not dense).
355    
356            * man/Subassign-methods.Rd: fix examples
357    
358            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
359            should always return a sparse (and not sometimes a diagonal) matrix.
360    
361    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
364    
365    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * DESCRIPTION (Version): 0.9975-2
368    
369            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
370    
371    2006-10-02  Douglas Bates  <bates@R-project.org>
372    
373            * tests/dg_Matrix.R: Simplify test taking into account new code.
374    
375    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
378    
379            * R/lsTMatrix.R: new files w/ missing methods
380            * R/nsTMatrix.R:  "  'for completeness'
381    
382            * tests/Class+Meth.R: a bit less 'not.ok.classes'
383    
384            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
385    
386    
387    2006-09-28  Douglas Bates  <bates@R-project.org>
388    
389            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
390            included.
391    
392            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
393            Export C-callable functions used in Zt_create in lme4.
394    
395    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * DESCRIPTION (Version): 0.9975-1
398    
399            * tests/simple.R: less checks fail; using NA, found that our
400                    kronecker() is not base-compatible with NA's.
401    
402            * R/dMatrix.R: "Compare" method now implemented for all cases
403    
404            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
405    
406            * man/dtpMatrix-class.Rd: mention length of 'x' slot
407    
408            * src/dtpMatrix.c (dtpMatrix_validate): fix check
409            * src/dspMatrix.c (dspMatrix_validate): ditto
410    
411            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
412              including coercion to [nl]tTMatrix.
413    
414            * R/diagMatrix.R (show): print a header line as for other classes.
415    
416    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * src/Makefile.win (SUBDIRS): fix typo
419    
420    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
423    
424    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
425    
426            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
427            symmetric and y missing in R code using %*% (cholmod_aat doesn't
428            accept a symmetric matrix).
429            * tests/group-methods.R: Uncomment test of crossprod applied to
430            lsCMatrix objects.
431    
432    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/AllClass.R (symmetricMatrix): add validity method (available
435            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
436    
437            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
438    
439            * tests/indexing.Rout.save:
440            * tests/indexing.R: additions, mainly for 'lsparse'
441    
442            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
443            case.
444    
445            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
446    
447    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
450                    as 'N' (1-letter - Ok?)
451    
452            * tests/group-methods.R: add test for logical + NAs
453    
454            * R/dMatrix.R ("Compare"): fix to work with NA's
455    
456            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
457    
458            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
459                    which is implemented.
460    
461    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/chm_common.c: coerce logical <-> double instead of
464            typecasting;  needed for "l" matrix handling in cholmod.
465    
466            * tests/other-pkgs.R (graph): small extension in "graph" checks.
467    
468            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
469            (Tsp2grNEL): other fixes needed
470    
471    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
474                    Matrices, since "lMatrix", also "lsparseM" can have NA
475            * R/ndenseMatrix.R, etc: new source files
476            * man/nsparseMatrix-classes.Rd, etc: new help files
477            * tests/: adaptions
478            * src/chm_common.c (chm_dense_to_SEXP): and others:
479                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
480            * src/Csparse.c, etc: ditto
481    
482    2006-09-11  Douglas Bates  <bates@R-project.org>
483    
484            * src/Mutils.[ch],init.c inst/include/*.h: Move the
485            alloc_d**Matrix functions to the lme4 package.
486    
487    2006-09-09  Douglas Bates  <bates@R-project.org>
488    
489            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
490            fixed
491    
492    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/lMatrix.R: new
495    
496            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
497    
498            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
499            * man/tcrossprod.Rd: ditto
500    
501    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
504            for exported functions
505            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
506            Remove partitioning algorithms for sparse matrix reordering.  The
507            copyright on the Metis code was problematic and the methods were
508            rarely used.
509            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
510            operations are now done entirely in CHOLMOD code.
511    
512    2006-09-06  Douglas Bates  <bates@R-project.org>
513    
514            * src/Mutils.h: Remove functions that are no longer used.
515    
516    2006-09-04  Douglas Bates  <bates@R-project.org>
517    
518            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
519            * src/DEPS.mkf: update
520    
521    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * created branches/Matrix-for-R-2.3.x;  on trunk: do
524            * DESCRIPTION (Version): 0.9975-0
525            (Depends): R (>= 2.4.0)
526    
527    2006-09-01  Douglas Bates  <bates@R-project.org>
528    
529            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
530    
531    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
534            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
535    
536            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
537    
538    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
541            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
542            * R/dsparseMatrix.R: ditto
543            * R/Csparse.R: ditto
544    
545    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/dMatrix.R (Compare): improve availability of "<", etc
548            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
549    
550    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
553            of a 0-index which was used as 1-index (..hmm)
554    
555            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
556    
557            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
558            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
559            (.is.diagonal): ditto
560    
561            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
562    
563            * R/Matrix.R (Matrix): also work for NA data
564    
565    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
568            in all cases.
569    
570    2006-08-27  Douglas Bates  <bates@R-project.org>
571    
572            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
573            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
574    
575    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
578            subclasses of "ddenseMatrix"
579            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
580            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
581            instead of half dozen specialized ones.
582    
583    2006-08-25  Douglas Bates  <bates@R-project.org>
584    
585            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
586            <tillard@cirad.fr> - ordering standard errors to match effects.
587    
588    2006-08-24  Douglas Bates  <bates@R-project.org>
589    
590            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
591            on R_ldl.
592            * R/lCholCMatrix.R,
593            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
594            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
595            * many files in ./R and ./src: Use more general version of
596            dup_mMatrix_as_dgeMatrix to simplify method definitions.
597            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
598            dtpMatrix, dspMatrix and dppMatrix conversions.
599    
600    
601    2006-08-23  Douglas Bates  <bates@R-project.org>
602    
603            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
604            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
605            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
606            dgeMatrix_crossprod (may need to do this in other places).
607            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
608            generic and method for dsCMatrix.  Use CHOLMOD for chol().
609    
610    2006-08-22  Douglas Bates  <bates@R-project.org>
611    
612            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
613            types of classed Matrices, matrices or numeric or logical vectors.
614            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
615            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
616            to Mutils.h (as an inline) and change name to Matrix_check_class;
617            fixes in as_cholmod_factor and chm_factor_to_SEXP.
618            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
619            dsCMatrix_matrix_solve.  Comment out vestigial functions.
620            * src/Csparse.c: use diag_P and uplo_P macros.
621    
622    2006-08-21  Douglas Bates  <bates@R-project.org>
623    
624            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
625            valgrind.
626            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
627            inverses.
628            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
629            -Wall warnings.
630            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
631            Use dup_mMatrix_as_dgeMatrix.
632    
633    2006-08-20  Douglas Bates  <bates@R-project.org>
634    
635            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
636            * tests/sparseQR.R: Added
637            * man/sparseQR-class.Rd: Document methods for qr.* generics
638            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
639    
640    2006-08-19  Douglas Bates  <bates@R-project.org>
641    
642            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
643            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
644            and qr.fitted.
645            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
646            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
647    
648    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
651            the base version has no "..." argument.
652    
653            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
654    
655            * R/Matrix.R: define and
656            * NAMESPACE: export as.numeric() and as.logical() methods.
657                    Let's hope these do not badly slow down something...
658            Finally export the zapsmall() method.
659    
660    2006-08-17  Douglas Bates  <bates@R-project.org>
661    
662            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
663            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
664            * src/dtCMatrix.c :Remove code that is no longer used
665            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
666    
667    2006-08-14  Douglas Bates  <bates@R-project.org>
668    
669            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
670            Csparse_to_logical and Csparse_symmetric_to_general.
671            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
672            coercion methods between CsparseMatrix and TsparseMatrix.
673    
674    2006-08-14  Douglas Bates  <bates@R-project.org>
675    
676            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
677            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
678            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
679            possible.
680    
681    2006-08-12  Douglas Bates  <bates@R-project.org>
682    
683            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
684              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
685              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
686              generalize conversions between TsparseMatrix, CsparseMatrix,
687              denseMatrix and matrix.  Preserve triangularity property and
688              propagate Dimnames in the easy cases.
689    
690    2006-08-10  Douglas Bates  <bates@R-project.org>
691    
692            * src/lmer.c: adjust checks in glmer_init for S4SXP
693            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
694            before S4SXP but for the wrong reasons.
695    
696    2006-08-08  Douglas Bates  <bates@R-project.org>
697    
698            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
699            Later modified to return the upper triangle only.
700            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
701    
702    2006-08-07  Douglas Bates  <bates@R-project.org>
703    
704            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
705            R-level conversion to a sparse symmetric class.
706            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
707            Remove conversion to sparse symmetric classes (now done in C code).
708    
709    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
712            * man/band.Rd:  adapt the \dontshow{} unit test.
713    
714    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * DESCRIPTION (Version): 0.995-14  for CRAN
717    
718            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
719    
720            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
721            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
722    
723            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
724            * R/Tsparse.R (tril, triu, band): methods
725            * R/dgRMatrix.R (tril, ...):    ditto
726            * man/band.Rd:                  ditto
727    
728    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/Matrix.R (head, tail): directly use utils:::head.matrix
731                    to be up-to-date automatically.
732    
733    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
736    
737            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
738            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
739            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
740            such that the S4 objects are always created by the current version
741            of R and 'Matrix' class definitions.
742    
743    2006-08-01  Douglas Bates  <bates@R-project.org>
744    
745            * R/lmer.R (LMEoptimize method), tests/lmer.R,
746            inst/external/test3comp.rda: Added warnings for convergence on
747            boundary and test cases.
748    
749            * src/lmer.c (mer_postVar): Modified to return the variances that
750            are marginal to the fixed effects, not conditional on them (which
751            is what the bVar slot contents represent).
752    
753    2006-07-31  Douglas Bates  <bates@R-project.org>
754    
755            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
756            function which calls the C function mer_hat_trace2.
757    
758            * man/ranef.Rd: Include description of "postVar" argument and
759            producing a caterpillar plot.
760    
761    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * NAMESPACE:    change  "correlation" to "corMatrix"
764            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
765            * R/dpoMatrix.R: ditto
766            * R/lmer.R:      ditto
767    
768    2006-07-28  Douglas Bates  <bates@R-project.org>
769    
770            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
771            RZXinv slot's contents into a separate internal function that can
772            be used in mer_hat_trace.
773    
774    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
777            via new smart
778            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
779            utility functions.
780    
781    
782    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/Csparse.R (tril, triu, band): do return *triangular* classed
785            matrices when appropriate; band() even symmetric ones.
786            (replCmat): extend to potentially all "CsparseMatrix"
787            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
788            allow subassignment for special sparse matrices.
789    
790            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
791    
792            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
793            argument; in glmer_*(): print only if(verbose).
794    
795            speed-optimize a few places by moving REAL(.) out of loops.
796    
797            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
798    
799    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
802                    since that wrongly triggers also for M[ logi , ]
803    
804            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
805            a symmetric matrix that results in a non-symmetric one.
806            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
807    
808            * R/dMatrix.R: make round(M) work as round(M, 0)
809    
810            * R/dgTMatrix.R (image): coordinate system and axis now use
811            1-based indices, not 0-based ones.
812    
813            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
814            * tests/indexing.R: test it.
815    
816            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
817            * man/isSymmetric-methods.Rd: and document it.
818    
819            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
820            * man/SparseM-conv.Rd: docu them
821    
822            * tests/other-pkgs.R: renamed from tests/graph.R and add example
823                    for 'SparseM' conversions
824    
825    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
826    
827            * R/Matrix.R (head): added head() and tail() methods.
828    
829    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * DESCRIPTION (Version): 0.995-12 released to CRAN
832    
833    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * tests/simple.R: add check for correct dsT -> dgT coercion;
836                    add check for correct printing of symmetric sparse matrices.
837    
838            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
839            for sparse symmetric matrices.
840    
841            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
842            diagonal twice.
843    
844    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
845    
846            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
847            being applied to the x slot (detected by Brian Ripley).
848    
849    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
852    
853            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
854    
855    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * src/lgCMatrix.c (lgCMatrix_diag): new function
858            * R/lgCMatrix.R (diag): for new method
859    
860            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
861                 ==> construction of illegal "*gTMatrix" via new() should
862                 now be much less easy:
863            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
864    
865            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
866                    directly.
867            * man/Matrix.Rd: documents it.
868    
869    2006-07-06  Douglas Bates  <bates@R-project.org>
870    
871            * src/pedigree.c (pedigree_inbreeding): Correction in
872            initialization.  This function is not currently being used and is
873            not fully tested.
874    
875            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
876            Introduced the glmer class.  Added code for mcmcmsamp on glmer
877            objects.  Modified validity check on pedigree objects to account
878            for nonparallel patterns of missingness of parents.
879    
880            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
881            class.
882    
883    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/pMatrix.R: coercion pMatrix -> Tsparse
886    
887    2006-06-12  Douglas Bates  <bates@R-project.org>
888    
889            * DESCRIPTION (Version): 0.995-11 released to CRAN
890    
891            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
892            the output from mcmcsamp.
893    
894    2006-06-10  Douglas Bates  <bates@R-project.org>
895    
896            * R/lmer.R (simulestimate): added C code for calculating the trace
897            of the hat matrix.
898    
899    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
902            classes.
903            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
904    
905    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/dgTMatrix.R (colSums): etc. All four of
908            colSums(), rowSums(), colMeans(), rowMeans() now should work for
909            all "Matrices".
910    
911  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
912    
913          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 938 
938    
939          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
940          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
941          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
942    
943    
944  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 1061 
1061          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1062          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1063          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1064          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1065    
1066  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
# Line 355  Line 1265 
1265  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1266    
1267          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1268          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1269          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1270    
1271  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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