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revision 860, Wed Aug 17 05:50:50 2005 UTC revision 1877, Tue Jun 5 17:06:34 2007 UTC
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1    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
4              SuiteSparse
5            * [r4426] src/Makefile: add ./UFconfig to the include path for
6              compilation
7            * [r4427] src/cs.c, src/cs.h: update to CSparse version 2.2.0
8            * [r4428] inst/doc/UFsparse/* src/AMD/* src/CHOLMOD/*
9              src/COLAMD/* src/UFconfig/UFconfig.h: Update to version 3.0.0 of
10              SuiteSparse
11    
12    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
15            * R/sparseMatrix.R (prSpMatrix): now gives a message about
16            suppressed column names.
17    
18    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
19    
20            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
21              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
22              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
23              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
24              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
25              Remove warnings after change to const char* CHAR
26    
27    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
28    
29            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
30              type of M_cholmod_ssmult
31    
32    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
33    
34            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
35              src/init.c: Yet another cholmod export - cholmod_ssmult
36    
37    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * NAMESPACE: exported drop0(), since
40            * man/drop0.Rd: I have seen several cases, I really wanted to use
41            it, so our users may want too.
42    
43    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * man/colSums.Rd: separately document colSums() etc, since these
46            have the extra argument 'sparseResult'.
47    
48    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
51            * man/spMatrix.Rd: docu., including examples
52    
53            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
54            in order to make colMeans() etc fast *and* correct.
55            * R/sparseVector.R (replSPvec): "[<-" functionality for
56            sparseVectors; tested in
57            * tests/simple.R:
58    
59    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
62            (very) sparse Matrices; output similar to Matlab's print().
63    
64    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
67            0-based, indices (Jose Quesada <quesada@gmail.com>).
68    
69    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
70    
71            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
72    
73    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (sparsapply): new utility, much faster than
76            tapply1() for large sparse matrices.
77    
78    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Matrix.R (dim<-): reshape now via sparseVector.
81    
82            * R/sparseVector.R: methods and function for
83            * R/AllClass.R: new "sparseVector" class and daughters.
84            * NAMESPACE: export new classes
85    
86    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): 0.99875-1
89            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
90    
91    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
94            indexing
95            * tests/indexing.R: test set for that.
96    
97    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
100            entries.
101            * tests/indexing.R(out): add regression test for it
102    
103    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
106            name for "!" method definitions.
107    
108    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Tsparse.R (intI): new utility, used for "[" :
111                    Cleanup up there, and fixes for duplicated indices - more TODO!
112    
113            * tests/indexing.R(out): more tests
114    
115    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
118            code that is now part of the R Lapack library.
119    
120            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
121            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
122    
123    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
126    
127    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
130            up with extraneous names '0'...'<n-1>'
131    
132    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dgTMatrix.R (mat2dgT): care about NAs
135    
136    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/kronecker.R: triangularity preserving methods
139    
140    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/kronecker.R: new file collecting kronecker() methods in one
143                    place.  Goal: become much faster!
144    
145    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
148            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
149            can be much faster.
150    
151            * tests/matprod.R: add regression tests for these (upper & lower).
152    
153    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R (diff): method for our Matrices.
156    
157            * R/sparseMatrix.R (isDiagonal): check dim()!
158    
159    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (dim<-): new method for "reshape()" built on a
162            proposal from Tamas Papp.
163    
164    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
167    
168            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
169            rather define and export  cBind() and rBind() only.
170            --> useRs *must* change code that used to have cbind()/rbind() !!
171    
172            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
173            * R/bind.Rout.save: ditto
174    
175    2007-02-16  Douglas Bates  <bates@r-project.org>
176    
177            * DESCRIPTION (Date, Version): 0.9975-11 with new date
178            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
179            const modifier on declaration of the array 'valid'
180    
181    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
182    
183            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
184    
185    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
188    
189            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
190            * tests/simple.R: test the above and some of these coercions:
191    
192            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
193                    be careful to avoid infinite recursion, using new coercions in
194            * R/ngCMatrix.R and nsC... and ntC...
195            * R/lsparseMatrix.R: ditto
196    
197            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
198    
199            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
200            * R/Rsparse.R: reactivate .Call()s
201    
202            * tests/Class+Meth.R: a bit more on actual classes
203    
204    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
207    
208    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.9975-10 to upload
211    
212            * tests/Class+Meth.R (tstMatrixClass): require coercions to
213            specific classes less unconditionally.
214    
215            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
216    
217            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
218    
219            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
220            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
221            R_to_CMatrix segfaults on one platform.
222            Eliminate most coercion method to *specific* classes, and replace
223            with virtual classes coercions.
224    
225    
226    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
227    
228            * src/init.c: export the CHM...._validate() placeholders, since
229            they *are* called.
230    
231            * tests/Class+Meth.R (classCanCoerce): and starting to test
232            all as(<from>, <to>)
233    
234    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
237            * tests/indexing.R: tested now
238            * tests/indexing.Rout.save: updated
239    
240            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
241            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
242            appropriate.
243    
244            * NAMESPACE: export a trivial
245            * R/Matrix.R: drop() Matrix-method
246    
247            * R/AllClass.R: moved all prototypes to virtual super classes.
248    
249            * R/Rsparse.R: many more coercions to have less exceptions in
250            * tests/Class+Meth.R:
251    
252            * R/Ops.R (Compare): tweak for case with NA
253            * tests/simpl.R: hence another 'FIXME' eliminated
254    
255    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
258            objects.
259    
260            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
261              and more of "!", "&", "|", all, any; coercions
262    
263            * R/Rsparse.R: many coercions (which enable quite a few other
264            methods), thanks to enhancements in
265            * src/dgCMatrix.c (R_to_CMatrix): new, and
266            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
267            symmetric & triangular and ..RMatrix objects.
268    
269            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
270            renamed file from src/dsTMatrix.c;
271            now dealing with symmetric and triangular Tsparse coercions, both
272            to dense and general.
273    
274    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
277    
278            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
279            where sensible when the <numeric> is of length > 1.
280    
281    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/Matrix.R ([<-): for M[] <- value: fix length
284    
285    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
288            * R/ndenseMatrix.R: new coercions n* -> l*
289    
290    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
293    
294            * R/Ops.R ("Logic"): and other "Ops", many updates
295    
296    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * src/Mutils.h (SET_DimNames): new utility
299    
300            * R/Auxiliaries.R (nnzero): improved and now exported via
301    
302            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
303    
304    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/diagMatrix.R (!): fix typo.
307    
308    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (as_Csparse): and quite a few others:
311                    allow to pass class definition --> speedup
312            * R/sparseMatrix.R: apply the above
313    
314            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
315    
316            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
317            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
318            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
319    
320            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
321    
322            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
323            and use it for "sparse*" as well, since it's faster than the
324            as_Csparse(.) way.
325    
326    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
329    
330    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
333            as method for   M[ ij ] <- v
334            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
335    
336            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
337            FALSE answer
338    
339            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
340            * tests/indexing.R: test it, and some of the above
341    
342    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Auxiliaries.R (is_duplicatedT): new utility
345    
346    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * src/init.c (R_init_Matrix): export cholmod_scale
349    
350    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
353            base::as.matrix to (x, ...)
354    
355    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
358            file; start using "Logic", hence
359    
360            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
361            * NAMESPACE: import and export "Logic"
362    
363    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
366            only needed previously to R version 2.5.0.
367    
368    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
371    
372            * R/Tsparse.R (replTmat): fix subassignment of triangular
373            * R/Csparse.R (replCmat): ditto
374            * tests/indexing.R: more tests, incl the above fix
375    
376    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Auxiliaries.R (drop0): extend for non CSparse
379            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
380    
381            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
382                    use uplo correctly (!); other places: use uplo_P() macro
383    
384            * R/Csparse.R (replCmat): call diagU2N() when needed
385            * R/Tsparse.R (replTmat): ditto
386    
387            * src/dtCMatrix.c (tCMatrix_validate): new
388            * src/dtTMatrix.c (tTMatrix_validate): new, used in
389            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
390    
391            * R/diagMatrix.R (replDiag): to use in [<-
392    
393    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
396                    also more general diagU2N().
397    
398    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
401            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
402    
403    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * tests/bind.R: a few more cases
406            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
407    
408            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
409            * R/ddenseMatrix.R (cbind2/rbind2)
410            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
411            * tests/indexing.R
412            * tests/indexing.Rout.save: updated
413    
414    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
417            * tests/indexing.R
418    
419    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
422            align with proper position of "0", i.e., right for integers.
423            argument 'align' by default is "fancy".
424    
425    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
428            * R/Csparse.R: and fix "Compare" for more cases.
429            * tests/Class+Meth.R: test some of these (m == m, m != m)
430    
431    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/lsparseMatrix.R: all() and any() methods
434            * R/ldenseMatrix.R:      ditto
435            * NAMESPACE, R/Matrix.R: ditto
436    
437            * man/all-methods.Rd: document them minimally
438    
439            * tests/simple.R: add a few examples for these
440    
441    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Tsparse.R ([): fix long standing typo in symmetric case
444            * man/dsCMatrix-class.Rd: add example exhibiting the above case
445    
446    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
449            to LL before converting to a sparse matrix. (The LDL form can be
450            converted to a sparse matrix but it is implicitly a unit
451            triangular matrix and a diagonal matrix overwritten on the diagonal.)
452    
453    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
456    
457    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
458    
459            * DESCRIPTION (Version): updated -> release 0.9975-7
460            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
461    
462    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
465    
466    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
467    
468            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
469            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
470            is exactly singular.
471    
472    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * DESCRIPTION (Date): updated -> release 0.9975-6
475    
476    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
479            now returns symmetric.
480    
481            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
482    
483            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
484            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
485    
486            * R/Auxiliaries.R (.type.kind): added
487    
488    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
491            running src/CSparse_install.sh
492    
493            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
494    
495    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
498            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
499    
500            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
501    
502            * tests/Class+Meth.R (tstMatrixClass): now assure
503            the (important in method programming) property :
504    
505                    ###>>  Every "Matrix" is either
506                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
507    
508                    (where "*" stands for "Matrix")
509    
510            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
511    
512            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
513            * tests/validObj.R: checks for "comparison"
514    
515            * R/sparseMatrix.R ([): improved indexing for sparse;
516                    trying to keep <symmetric>[ n, n] symmmetric
517    
518            * tests/indexing.R: indexing for logical sparse now ok
519    
520    
521    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * src/Tsparse.c: use xTsparse_validate() , and hence remove
524    
525            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
526    
527    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
530    
531            * tests/simple.R: validObject() checking the above.
532    
533            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
534            replacing both dgCMatrix_validate and lgCM*.
535    
536            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
537            fix dimnames setting in other places.
538            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
539    
540    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
543    
544            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
545            symmetry test, via
546            * R/Auxiliaries.R (.as.dgC.0.factors):
547    
548    2006-11-01  Douglas Bates  <bates@r-project.org>
549    
550            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
551            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
552            <CsparseMatrix>) added
553    
554    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * tests/matprod.R: add a variation of Harri's example
557    
558            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
559            recursive infinitely.
560    
561            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
562    
563            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
564    
565    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
568            matrix if possible; test m+m == 2*m; now test dgRMatrix.
569            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
570            satisfy the above test.
571    
572    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
575    
576            * R/dgCMatrix.R: solve(a, b="missing") based on
577            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
578            RHS = NULL.
579    
580            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
581            add more (needed) [t]crossprod() methods.
582    
583            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
584    
585            * R/Auxiliaries.R (as_CspClass): cleanup
586            (drop0): internal utility for "Csparse_drop(*, 0)"
587            (.bail.out.2): encourage active feedback
588    
589    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/dMatrix.R(Compare): new(), then slots [no validity check]
592    
593            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
594            non-valid or 'sorted' case).
595    
596            * R/dsparseMatrix.R: add "chol" method.
597            * R/ddenseMatrix.R: ditto
598    
599            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
600            * NAMESPACE (Ops)
601            * R/diagMatrix.R (diag2T): simple utility used "higher level"
602            coercion; deprecating direct lower level coercions.
603    
604            * R/*.R (seq): use seq_len() and seq_along() where possible.
605    
606    
607    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * DESCRIPTION (Version): 0.9975-5 ready for release
610    
611    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
614    
615    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/AllClass.R (corMatrix): add 'validity' check;
618                    comment out unused "LDL" class definition
619            * NAMESPACE: mention, but do not export "LDL" class
620            * R/corMatrix.R: new (simple), needed for R-devel with
621            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
622              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
623    
624    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
627            use Rprintf and R's error handling.
628    
629    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
632            * tests/matprod.R: add tests for the bug fixed.
633    
634    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
637            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
638    
639    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
642    
643    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * DESCRIPTION (Version): 0.9975-3
646    
647            * R/diagMatrix.R (bdiag): new function constructing block diagonal
648            (sparse) matrices.
649            * man/bdiag.Rd: docu + examples
650    
651            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
652    
653            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
654            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
655    
656            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
657            that result is sparse or diagonal (and not dense).
658    
659            * man/Subassign-methods.Rd: fix examples
660    
661            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
662            should always return a sparse (and not sometimes a diagonal) matrix.
663    
664    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
667    
668    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * DESCRIPTION (Version): 0.9975-2
671    
672            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
673    
674    2006-10-02  Douglas Bates  <bates@R-project.org>
675    
676            * tests/dg_Matrix.R: Simplify test taking into account new code.
677    
678    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
681    
682            * R/lsTMatrix.R: new files w/ missing methods
683            * R/nsTMatrix.R:  "  'for completeness'
684    
685            * tests/Class+Meth.R: a bit less 'not.ok.classes'
686    
687            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
688    
689    
690    2006-09-28  Douglas Bates  <bates@R-project.org>
691    
692            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
693            included.
694    
695            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
696            Export C-callable functions used in Zt_create in lme4.
697    
698    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): 0.9975-1
701    
702            * tests/simple.R: less checks fail; using NA, found that our
703                    kronecker() is not base-compatible with NA's.
704    
705            * R/dMatrix.R: "Compare" method now implemented for all cases
706    
707            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
708    
709            * man/dtpMatrix-class.Rd: mention length of 'x' slot
710    
711            * src/dtpMatrix.c (dtpMatrix_validate): fix check
712            * src/dspMatrix.c (dspMatrix_validate): ditto
713    
714            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
715              including coercion to [nl]tTMatrix.
716    
717            * R/diagMatrix.R (show): print a header line as for other classes.
718    
719    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/Makefile.win (SUBDIRS): fix typo
722    
723    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
726    
727    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
730            symmetric and y missing in R code using %*% (cholmod_aat doesn't
731            accept a symmetric matrix).
732            * tests/group-methods.R: Uncomment test of crossprod applied to
733            lsCMatrix objects.
734    
735    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/AllClass.R (symmetricMatrix): add validity method (available
738            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
739    
740            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
741    
742            * tests/indexing.Rout.save:
743            * tests/indexing.R: additions, mainly for 'lsparse'
744    
745            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
746            case.
747    
748            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
749    
750    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
753                    as 'N' (1-letter - Ok?)
754    
755            * tests/group-methods.R: add test for logical + NAs
756    
757            * R/dMatrix.R ("Compare"): fix to work with NA's
758    
759            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
760    
761            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
762                    which is implemented.
763    
764    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * src/chm_common.c: coerce logical <-> double instead of
767            typecasting;  needed for "l" matrix handling in cholmod.
768    
769            * tests/other-pkgs.R (graph): small extension in "graph" checks.
770    
771            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
772            (Tsp2grNEL): other fixes needed
773    
774    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
777                    Matrices, since "lMatrix", also "lsparseM" can have NA
778            * R/ndenseMatrix.R, etc: new source files
779            * man/nsparseMatrix-classes.Rd, etc: new help files
780            * tests/: adaptions
781            * src/chm_common.c (chm_dense_to_SEXP): and others:
782                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
783            * src/Csparse.c, etc: ditto
784    
785    2006-09-11  Douglas Bates  <bates@R-project.org>
786    
787            * src/Mutils.[ch],init.c inst/include/*.h: Move the
788            alloc_d**Matrix functions to the lme4 package.
789    
790    2006-09-09  Douglas Bates  <bates@R-project.org>
791    
792            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
793            fixed
794    
795    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/lMatrix.R: new
798    
799            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
800    
801            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
802            * man/tcrossprod.Rd: ditto
803    
804    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
805    
806            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
807            for exported functions
808            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
809            Remove partitioning algorithms for sparse matrix reordering.  The
810            copyright on the Metis code was problematic and the methods were
811            rarely used.
812            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
813            operations are now done entirely in CHOLMOD code.
814    
815    2006-09-06  Douglas Bates  <bates@R-project.org>
816    
817            * src/Mutils.h: Remove functions that are no longer used.
818    
819    2006-09-04  Douglas Bates  <bates@R-project.org>
820    
821            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
822            * src/DEPS.mkf: update
823    
824    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * created branches/Matrix-for-R-2.3.x;  on trunk: do
827            * DESCRIPTION (Version): 0.9975-0
828            (Depends): R (>= 2.4.0)
829    
830    2006-09-01  Douglas Bates  <bates@R-project.org>
831    
832            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
833    
834    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
837            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
838    
839            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
840    
841    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
844            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
845            * R/dsparseMatrix.R: ditto
846            * R/Csparse.R: ditto
847    
848    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/dMatrix.R (Compare): improve availability of "<", etc
851            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
852    
853    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
856            of a 0-index which was used as 1-index (..hmm)
857    
858            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
859    
860            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
861            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
862            (.is.diagonal): ditto
863    
864            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
865    
866            * R/Matrix.R (Matrix): also work for NA data
867    
868    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
871            in all cases.
872    
873    2006-08-27  Douglas Bates  <bates@R-project.org>
874    
875            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
876            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
877    
878    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
881            subclasses of "ddenseMatrix"
882            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
883            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
884            instead of half dozen specialized ones.
885    
886    2006-08-25  Douglas Bates  <bates@R-project.org>
887    
888            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
889            <tillard@cirad.fr> - ordering standard errors to match effects.
890    
891    2006-08-24  Douglas Bates  <bates@R-project.org>
892    
893            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
894            on R_ldl.
895            * R/lCholCMatrix.R,
896            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
897            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
898            * many files in ./R and ./src: Use more general version of
899            dup_mMatrix_as_dgeMatrix to simplify method definitions.
900            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
901            dtpMatrix, dspMatrix and dppMatrix conversions.
902    
903    
904    2006-08-23  Douglas Bates  <bates@R-project.org>
905    
906            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
907            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
908            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
909            dgeMatrix_crossprod (may need to do this in other places).
910            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
911            generic and method for dsCMatrix.  Use CHOLMOD for chol().
912    
913    2006-08-22  Douglas Bates  <bates@R-project.org>
914    
915            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
916            types of classed Matrices, matrices or numeric or logical vectors.
917            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
918            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
919            to Mutils.h (as an inline) and change name to Matrix_check_class;
920            fixes in as_cholmod_factor and chm_factor_to_SEXP.
921            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
922            dsCMatrix_matrix_solve.  Comment out vestigial functions.
923            * src/Csparse.c: use diag_P and uplo_P macros.
924    
925    2006-08-21  Douglas Bates  <bates@R-project.org>
926    
927            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
928            valgrind.
929            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
930            inverses.
931            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
932            -Wall warnings.
933            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
934            Use dup_mMatrix_as_dgeMatrix.
935    
936    2006-08-20  Douglas Bates  <bates@R-project.org>
937    
938            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
939            * tests/sparseQR.R: Added
940            * man/sparseQR-class.Rd: Document methods for qr.* generics
941            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
942    
943    2006-08-19  Douglas Bates  <bates@R-project.org>
944    
945            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
946            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
947            and qr.fitted.
948            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
949            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
950    
951    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
954            the base version has no "..." argument.
955    
956            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
957    
958            * R/Matrix.R: define and
959            * NAMESPACE: export as.numeric() and as.logical() methods.
960                    Let's hope these do not badly slow down something...
961            Finally export the zapsmall() method.
962    
963    2006-08-17  Douglas Bates  <bates@R-project.org>
964    
965            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
966            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
967            * src/dtCMatrix.c :Remove code that is no longer used
968            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
969    
970    2006-08-14  Douglas Bates  <bates@R-project.org>
971    
972            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
973            Csparse_to_logical and Csparse_symmetric_to_general.
974            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
975            coercion methods between CsparseMatrix and TsparseMatrix.
976    
977    2006-08-14  Douglas Bates  <bates@R-project.org>
978    
979            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
980            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
981            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
982            possible.
983    
984    2006-08-12  Douglas Bates  <bates@R-project.org>
985    
986            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
987              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
988              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
989              generalize conversions between TsparseMatrix, CsparseMatrix,
990              denseMatrix and matrix.  Preserve triangularity property and
991              propagate Dimnames in the easy cases.
992    
993    2006-08-10  Douglas Bates  <bates@R-project.org>
994    
995            * src/lmer.c: adjust checks in glmer_init for S4SXP
996            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
997            before S4SXP but for the wrong reasons.
998    
999    2006-08-08  Douglas Bates  <bates@R-project.org>
1000    
1001            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1002            Later modified to return the upper triangle only.
1003            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1004    
1005    2006-08-07  Douglas Bates  <bates@R-project.org>
1006    
1007            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1008            R-level conversion to a sparse symmetric class.
1009            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1010            Remove conversion to sparse symmetric classes (now done in C code).
1011    
1012    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1015            * man/band.Rd:  adapt the \dontshow{} unit test.
1016    
1017    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * DESCRIPTION (Version): 0.995-14  for CRAN
1020    
1021            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1022    
1023            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1024            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1025    
1026            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1027            * R/Tsparse.R (tril, triu, band): methods
1028            * R/dgRMatrix.R (tril, ...):    ditto
1029            * man/band.Rd:                  ditto
1030    
1031    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1034                    to be up-to-date automatically.
1035    
1036    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1039    
1040            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1041            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1042            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1043            such that the S4 objects are always created by the current version
1044            of R and 'Matrix' class definitions.
1045    
1046    2006-08-01  Douglas Bates  <bates@R-project.org>
1047    
1048            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1049            inst/external/test3comp.rda: Added warnings for convergence on
1050            boundary and test cases.
1051    
1052            * src/lmer.c (mer_postVar): Modified to return the variances that
1053            are marginal to the fixed effects, not conditional on them (which
1054            is what the bVar slot contents represent).
1055    
1056    2006-07-31  Douglas Bates  <bates@R-project.org>
1057    
1058            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1059            function which calls the C function mer_hat_trace2.
1060    
1061            * man/ranef.Rd: Include description of "postVar" argument and
1062            producing a caterpillar plot.
1063    
1064    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * NAMESPACE:    change  "correlation" to "corMatrix"
1067            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1068            * R/dpoMatrix.R: ditto
1069            * R/lmer.R:      ditto
1070    
1071    2006-07-28  Douglas Bates  <bates@R-project.org>
1072    
1073            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1074            RZXinv slot's contents into a separate internal function that can
1075            be used in mer_hat_trace.
1076    
1077    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1078    
1079            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1080            via new smart
1081            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1082            utility functions.
1083    
1084    
1085    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1088            matrices when appropriate; band() even symmetric ones.
1089            (replCmat): extend to potentially all "CsparseMatrix"
1090            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1091            allow subassignment for special sparse matrices.
1092    
1093            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1094    
1095            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1096            argument; in glmer_*(): print only if(verbose).
1097    
1098            speed-optimize a few places by moving REAL(.) out of loops.
1099    
1100            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1101    
1102    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1105                    since that wrongly triggers also for M[ logi , ]
1106    
1107            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1108            a symmetric matrix that results in a non-symmetric one.
1109            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1110    
1111            * R/dMatrix.R: make round(M) work as round(M, 0)
1112    
1113            * R/dgTMatrix.R (image): coordinate system and axis now use
1114            1-based indices, not 0-based ones.
1115    
1116            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1117            * tests/indexing.R: test it.
1118    
1119            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1120            * man/isSymmetric-methods.Rd: and document it.
1121    
1122            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1123            * man/SparseM-conv.Rd: docu them
1124    
1125            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1126                    for 'SparseM' conversions
1127    
1128    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1129    
1130            * R/Matrix.R (head): added head() and tail() methods.
1131    
1132    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * DESCRIPTION (Version): 0.995-12 released to CRAN
1135    
1136    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * tests/simple.R: add check for correct dsT -> dgT coercion;
1139                    add check for correct printing of symmetric sparse matrices.
1140    
1141            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1142            for sparse symmetric matrices.
1143    
1144            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1145            diagonal twice.
1146    
1147    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1148    
1149            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1150            being applied to the x slot (detected by Brian Ripley).
1151    
1152    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1153    
1154            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1155    
1156            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1157    
1158    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * src/lgCMatrix.c (lgCMatrix_diag): new function
1161            * R/lgCMatrix.R (diag): for new method
1162    
1163            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1164                 ==> construction of illegal "*gTMatrix" via new() should
1165                 now be much less easy:
1166            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1167    
1168            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1169                    directly.
1170            * man/Matrix.Rd: documents it.
1171    
1172    2006-07-06  Douglas Bates  <bates@R-project.org>
1173    
1174            * src/pedigree.c (pedigree_inbreeding): Correction in
1175            initialization.  This function is not currently being used and is
1176            not fully tested.
1177    
1178            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1179            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1180            objects.  Modified validity check on pedigree objects to account
1181            for nonparallel patterns of missingness of parents.
1182    
1183            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1184            class.
1185    
1186    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * R/pMatrix.R: coercion pMatrix -> Tsparse
1189    
1190    2006-06-12  Douglas Bates  <bates@R-project.org>
1191    
1192            * DESCRIPTION (Version): 0.995-11 released to CRAN
1193    
1194            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1195            the output from mcmcsamp.
1196    
1197    2006-06-10  Douglas Bates  <bates@R-project.org>
1198    
1199            * R/lmer.R (simulestimate): added C code for calculating the trace
1200            of the hat matrix.
1201    
1202    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1205            classes.
1206            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1207    
1208    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * R/dgTMatrix.R (colSums): etc. All four of
1211            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1212            all "Matrices".
1213    
1214    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1215    
1216            * R/lmer.R (panel.ci): Add a reference line at zero and a
1217            background grid to the qqmath plot of ranef.lmer.
1218    
1219    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1220    
1221            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1222            grouping factors to be specified in the formula as (1|foo/bar).
1223    
1224    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1225    
1226            * R/lmer.R (findbars and others): Change check of is.numeric to
1227            !is.language to resolve the bug reported by Jacob Wegelin.
1228    
1229            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1230            code to evaluate inbreeding coefficients without calculating T,
1231            based on code in Sargolzaei and Iwaisaki's paper.
1232    
1233    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1234    
1235            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1236            generic and mer methods for isNested and denomDF. This denomDF was
1237            an attempt to emulate that in lme but I don't think that makes
1238            sense.  Use the trace of the hat matrix instead.
1239    
1240    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1243            the C code depending on a slot structure that's no longer valid.
1244            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1245    
1246    
1247    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1248    
1249            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1250            of lowerTriMatrix generic and methods to tril (also upper to triu)
1251            and added a general band extractor.
1252    
1253    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1254    
1255            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1256            allowable range with NAs. Added a corresponding check in the
1257            validity check for the pedigree class.
1258    
1259            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1260            crossprod methods now inherits from symmetricMatrix.
1261    
1262    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1263    
1264            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1265            generics lowerTriMatrix and upperTriMatrix along with methods for
1266            the Csparse virtual class.  Also added a C function Csparse_band
1267            that implements these methods by calling cholmod_band.
1268    
1269    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1272            erased when it was NULL.  This led to invalid subselections!
1273    
1274    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1275    
1276            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1277            in method for "t" so as not to lose the unit diagonal property.
1278    
1279    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1280    
1281            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1282            and methods.  This is now an option to the ranef method for the
1283            mer class.
1284    
1285            * src/cs_utils.c: Ensure that the nz component is -1 for a
1286            compressed column-oriented matrix.  Minor formatting cleanup.
1287    
1288            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1289            objects.
1290    
1291    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1294            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1295    
1296    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1297    
1298            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1299            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1300    
1301            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1302            for the dtCMatrix class.
1303    
1304    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1305    
1306            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1307            and methods for it.
1308    
1309    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1310    
1311            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1312            arguments, such that M %*% 1:6 now works
1313            * Tests/matprod.R: test the above
1314    
1315    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1316    
1317            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1318            the ranef.lmer class.
1319    
1320            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1321            methods to extract the posterior variances from the bVar slot.
1322    
1323    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1324    
1325            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1326            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1327    
1328            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1329            * tests/simple: (extended)
1330    
1331            * R/sparseMatrix.R (isTriangular): now using much improved
1332            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1333    
1334    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1335    
1336            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1337            (problem report from Franklin Parlamis).  This should be done
1338            generally.
1339    
1340    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1341    
1342            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1343            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1344            update the plot methods.
1345    
1346    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1347    
1348            * R/lmer.R (resid and ranef methods):  Added methods for the
1349            "residuals" and "resid" generic but only for linear mixed model
1350            fits.  Changed the ranef method to return a list of data frames so
1351            that the plot methods now work.
1352    
1353    2006-03-16  Douglas Bates  <bates@bates2>
1354    
1355            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1356            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1357    
1358            * DESCRIPTION (Date): New release
1359    
1360    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1361    
1362            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1363    
1364            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1365            * man/KNex.Rd: and other help files
1366            * tests/*.R: several ones needed adaption
1367            * inst/doc/Comparisons.Rnw: ditto
1368    
1369    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1370    
1371            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1372    
1373            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1374    
1375    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1376    
1377            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1378    
1379            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1380    
1381    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1382    
1383            * R/dMatrix.R: enable things like  M [ M < 10 ]
1384            * R/dgeMatrix.R: implement it
1385    
1386    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1387    
1388            * R/AllClass.R: define "summary.mer" and "*.lmer"
1389            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1390            * R/lmer.R (show): now works with summary()
1391    
1392    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1393    
1394            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1395            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1396                    support the above
1397    
1398    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1399    
1400            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1401            Use glmFit$prior.weights for weights in a glmm.
1402            Allow an option usePQL = FALSE to skip the PQL steps for the
1403            Laplace method (and, in time, the AGQ method).
1404    
1405            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1406            into a separate function internal_mer_Xfactor to be able to call
1407            it from internal_bhat.
1408    
1409    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1410    
1411            * tests/Class+Meth.R (tstMatrixClass): function for much better
1412            testing; now again of all actual classes.
1413    
1414            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1415                    use macros and define make_d_matrix_* and make_i_matrix_*
1416                    where _i_ is for the ldense routines:
1417    
1418            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1419            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1420    
1421            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1422    
1423    
1424    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1425    
1426            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1427                    many different kinds of matrices.
1428            * R/*.R: quite a few new methods were needed for R CMD check with
1429                    new Matrix().  Very good for users playing around.
1430    
1431    
1432    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1433    
1434            * src/dgeMatrix.c (dMatrix_validate): new
1435            * src/Mutils.c (dense_nonpacked_validate): new
1436    
1437            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1438    
1439    
1440    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1441    
1442            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1443    
1444    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1445    
1446            * DESCRIPTION (Version): 0.99-6 released to CRAN
1447    
1448            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1449            segfault in cases with multiple non-nested grouping factors.
1450    
1451    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1452    
1453            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1454                    (Depends): also on 'utils'
1455    
1456            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1457            * R/diagMatrix.R (Diagonal): constructor and methods for
1458            diagonal matrices
1459    
1460            * R/ltTMatrix.R: new "minimal methods"
1461    
1462    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1463    
1464            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1465            all methods (and help files).
1466    
1467    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1468    
1469            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1470                    for case (dimn.  op  no_dimn.)
1471    
1472    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1473    
1474            * DESCRIPTION (Version): 0.99-2  released to CRAN
1475    
1476    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1477    
1478            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1479            by Julian Faraway.
1480    
1481    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1482    
1483            * R/Auxiliaries.R (try_as): new utility
1484            * R/sparseMatrix.R: use try_as() in coercion to original class
1485    
1486    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1487    
1488            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1489    
1490    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1491    
1492            * R/Auxiliaries.R (dimNamesCheck): added
1493    
1494            * R/Matrix.R (as.array), (as.vector): new
1495    
1496    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1497    
1498            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1499                    default.
1500            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1501                    "pMatrix" now contains "sparseMatrix"
1502    
1503    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1504    
1505            * tests/Class+Meth.R: new tests; t(t(m)) == m
1506    
1507            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1508    
1509            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1510            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1511    
1512            * R/dspMatrix.R: typo in "t" method
1513    
1514    2005-09-18  Douglas Bates  <bates@wisc.edu>
1515    
1516            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1517            * R/Tsparse.R: instead of R/gTMatrix.R
1518            * R/Csparse.R: new
1519            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1520            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1521            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1522                            via cholmod
1523    
1524    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/Auxiliaries.R (non0ind): new function using new C code
1527            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1528    
1529    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1530    
1531            * src/chm_common.h: header file required by all C sources that
1532            call CHOLMOD functions.  It defines a cholmod_common structure
1533            called 'c' whose address is passed as the last argument to
1534            (virtually) every CHOLMOD function.
1535    
1536            * src/Pattern.c: Simple example of the use of CHOLMOD.
1537    
1538            * src/init.c: initialize and finalize the cholmod_common structure.
1539    
1540            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1541            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1542    
1543    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * inst/test-tools.R: new file collecting the utility functions used
1546                    in ./tests/*.R
1547    
1548            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1549            * R/Matrix.R (cbind2): methods for NULL and missing
1550    
1551    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1552    
1553            * R/AllClass.R: new "index" class for "[" and "[<-":
1554                    First cut at "symmetricMatrix" and "triangularMatrix"
1555            * R/gTMatrix.R (.ind.prep): new function;
1556                    Logical and character indexing now work too.
1557            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1558            * tests/indexing.R: new, including *.Rout.save
1559            * tests/dgTMatrix.R: new
1560    
1561    2005-08-29  Douglas Bates  <bates@wisc.edu>
1562    
1563            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1564            indicator pos not being updated.  Also enforced upper triangular
1565            for symmetric case.  Need to coerce edges component of elements of
1566            edge list - grr! (Why don't they define their classes cleanly?)
1567    
1568    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * R/Matrix.R:  added first "[<-" methods; not yet functional
1571            * R/denseMatrix.R: ditto
1572            * man/Subassign-methods.Rd: new help file for these
1573    
1574    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1575    
1576            * DESCRIPTION (Version): 0.98-6
1577    
1578            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1579            matrices.
1580    
1581    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1582    
1583            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1584                    as( <logical>, "matrix")
1585    
1586            * R/pMatrix.R: coercion to "lgTMatrix"
1587    
1588            * R/gTMatrix.R: new virtual class to define "[" methods for.
1589            * man/gTMatrix-class.Rd:
1590            * General slight re-organization of where "[" methods are defined.
1591              more to come.
1592    
1593    2005-08-18  Douglas Bates  <bates@wisc.edu>
1594    
1595            * DESCRIPTION (Version): 0.98-5  released to CRAN
1596    
1597            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1598            * .....
1599    
1600    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1601    
1602            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1603            or glmer objects.
1604    
1605  2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1606    
1607          * DESCRIPTION (Version): 0.98-4 : upload to CRAN          * DESCRIPTION (Version): 0.98-4 : upload to CRAN

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