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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 2041, Tue Aug 7 11:09:11 2007 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
4            must copy its *expanded* x slot before LAPACK call.
5    
6            * tests/matprod.R: test the last days' changes.
7    
8    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
9    
10            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
11              as well as in sources
12    
13    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
16                    ("Matrix", "matrix") which is needed in some cases.
17            Ditto for solve().
18    
19            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
20            infinite recursion in dispatch for some cases.
21    
22    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
23    
24            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
25              so pointers match
26    
27    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * DESCRIPTION (Date): set ready for release -- 0.999375-1
30    
31    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
32    
33            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
34              src/chm_common.c, src/chm_common.h: Change API for
35              numeric_as_chm_dense and N_AS_CHM_DN
36    
37    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
40            * tests/matprod.R: regr.test for it
41    
42    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
45            * tests/group-methods.R: and regression-test it
46    
47    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
48    
49            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
50              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
51              triplet_to_sparse, documentation, use typedefs
52    
53    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * man/dpoMatrix-class.Rd: added 'corMatrix' example
56    
57            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
58            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
59            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
60    
61            * R/lsparseMatrix.R: bug fix in "all" method
62            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
63    
64            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
65            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
66                    + matrix |-> nMatrix coercion
67            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
68            * man/pMatrix-class.Rd: ditto
69    
70            * R/Matrix.R (Summary): method for non-dMatrix
71    
72            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
73            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
74                    test all Summary methods.
75    
76    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
79    
80    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
83    
84            * R/pMatrix.R (t?crossprod): methods for pMatrix
85    
86    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
89    
90    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
93              trying to fix a subtle bug - which has been somewhere else.
94    
95    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
96    
97            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
98              solve the bug
99    
100    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/dgCMatrix.c (compressed_to_TMatrix):
103    
104    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * src/Csparse.c (Rsparse_validate): new, to have some validity
107            checking for RsparseMatrix
108            * src/dgCMatrix.c (xRMatrix_validate): ditto
109            * src/dtCMatrix.c (tRMatrix_validate): ditto
110    
111    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
112    
113            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
114              lgRMatrix
115            * [r4568] DESCRIPTION: Prepare for bug-fix release
116            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
117              for declaration of cholmod_symmetry
118    
119    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
122            release.
123    
124    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
125    
126            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
127              functions - no longer used
128            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
129              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
130              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
131              Alloca
132    
133    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
134    
135            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
136              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
137              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
138              src/t_gCMatrix_colSums.c: more R_CheckStack()s
139    
140    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
141    
142            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
143              the required amount of memory then call M_numeric_as_chm_dense.
144            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
145              (like Calloc but calling alloca)
146    
147    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
150            and extended with more sophisticated 'col.names' option.
151            * NAMESPACE: export  printSparseMatrix()
152            * man/printSpMatrix.Rd: document, incl. examples
153    
154    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
155    
156            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
157              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
158              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
159    
160    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * DESCRIPTION (Version): 0.99875-4
163    
164            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
165            some dimnames perservation.
166    
167            * R/dsTMatrix.R (t-method): keep dimnames
168            * R/dtTMatrix.R:  ditto
169    
170            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
171            and ncol(.) < 10
172    
173            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
174            from Mutils.h
175    
176            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
177            e.g. in as(<ngCMatrix>, "matrix")
178    
179    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
180    
181            * [r4529] .: Create a branch for the API changes from the 0.99875
182              series to the 0.999375 series
183            * [r4530] DESCRIPTION, inst/include/Matrix.h,
184              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
185              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
186              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
187              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
188              as_cholmod_x functions
189    
190    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
191    
192            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
193              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
194              to Comparisons
195    
196    >>>>>>> .merge-right.r4561
197    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.99875-3 ready to be released.
200    
201            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
202    
203            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
204            that should also work in a future version of R.
205    
206    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
209    
210            * R/sparseVector.R: more *sparseVector coercions, notably for
211            non - double ones.
212    
213    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
216              notably the new ones building on the new .Call(.)s:
217    
218            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
219            all 4 of [dlin]gCMatrix_colSums().
220    
221    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
224            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
225              result
226    
227    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/kronecker.R: fix typo (could lead to inf.recursion)
230            * test/simple.R: testing that
231    
232            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
233            method as well (which can have arguments, show() can't).
234    
235    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
236    
237            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
238              added dgCMatrix_colSums for [col,row][Sums,Means]
239    
240    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
241    
242            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
243              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
244              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
245            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
246              class
247            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
248              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
249              row names to store the levels - duh!  Added an example.
250    
251    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/Csparse.c (Csparse_validate): check for *repeated* entries
254            thanks to example from Christian Buchta; with a test here:
255            * tests/simple.R:
256    
257    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
260            of colSums(*, sparseResult = TRUE)
261    
262    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
265            'na.rm = FALSE' as "everywhere" else in R.
266    
267    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
268    
269            * [r4421] src/CSparse_install.sh: Modify for new organization of
270              CSparse package
271            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
272              SuiteSparse
273            * [r4426] src/Makefile: add ./UFconfig to the include path for
274              compilation
275            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
276            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
277              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
278    
279    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
282            * R/sparseMatrix.R (prSpMatrix): now gives a message about
283            suppressed column names.
284    
285    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
286    
287            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
288              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
289              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
290              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
291              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
292              Remove warnings after change to const char* CHAR
293    
294    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
295    
296            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
297              type of M_cholmod_ssmult
298    
299    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
300    
301            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
302              src/init.c: Yet another cholmod export - cholmod_ssmult
303    
304    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * NAMESPACE: exported drop0(), since
307            * man/drop0.Rd: I have seen several cases, I really wanted to use
308            it, so our users may want too.
309    
310    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * man/colSums.Rd: separately document colSums() etc, since these
313            have the extra argument 'sparseResult'.
314    
315    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
318            * man/spMatrix.Rd: docu., including examples
319    
320            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
321            in order to make colMeans() etc fast *and* correct.
322            * R/sparseVector.R (replSPvec): "[<-" functionality for
323            sparseVectors; tested in
324            * tests/simple.R:
325    
326    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
329            (very) sparse Matrices; output similar to Matlab's print().
330    
331    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
332    
333            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
334            0-based, indices (Jose Quesada <quesada@gmail.com>).
335    
336    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
339    
340    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/Auxiliaries.R (sparsapply): new utility, much faster than
343            tapply1() for large sparse matrices.
344    
345    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Matrix.R (dim<-): reshape now via sparseVector.
348    
349            * R/sparseVector.R: methods and function for
350            * R/AllClass.R: new "sparseVector" class and daughters.
351            * NAMESPACE: export new classes
352    
353    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Version): 0.99875-1
356            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
357    
358    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
361            indexing
362            * tests/indexing.R: test set for that.
363    
364    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
367            entries.
368            * tests/indexing.R(out): add regression test for it
369    
370    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
373            name for "!" method definitions.
374    
375    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Tsparse.R (intI): new utility, used for "[" :
378                    Cleanup up there, and fixes for duplicated indices - more TODO!
379    
380            * tests/indexing.R(out): more tests
381    
382    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
383    
384            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
385            code that is now part of the R Lapack library.
386    
387            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
388            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
389    
390    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
393    
394    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
397            up with extraneous names '0'...'<n-1>'
398    
399    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/dgTMatrix.R (mat2dgT): care about NAs
402    
403    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/kronecker.R: triangularity preserving methods
406    
407    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/kronecker.R: new file collecting kronecker() methods in one
410                    place.  Goal: become much faster!
411    
412    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
415            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
416            can be much faster.
417    
418            * tests/matprod.R: add regression tests for these (upper & lower).
419    
420    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/Matrix.R (diff): method for our Matrices.
423    
424            * R/sparseMatrix.R (isDiagonal): check dim()!
425    
426    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Matrix.R (dim<-): new method for "reshape()" built on a
429            proposal from Tamas Papp.
430    
431    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
434    
435            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
436            rather define and export  cBind() and rBind() only.
437            --> useRs *must* change code that used to have cbind()/rbind() !!
438    
439            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
440            * R/bind.Rout.save: ditto
441    
442    2007-02-16  Douglas Bates  <bates@r-project.org>
443    
444            * DESCRIPTION (Date, Version): 0.9975-11 with new date
445            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
446            const modifier on declaration of the array 'valid'
447    
448    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
451    
452    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
455    
456            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
457            * tests/simple.R: test the above and some of these coercions:
458    
459            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
460                    be careful to avoid infinite recursion, using new coercions in
461            * R/ngCMatrix.R and nsC... and ntC...
462            * R/lsparseMatrix.R: ditto
463    
464            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
465    
466            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
467            * R/Rsparse.R: reactivate .Call()s
468    
469            * tests/Class+Meth.R: a bit more on actual classes
470    
471    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
474    
475    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * DESCRIPTION (Version): 0.9975-10 to upload
478    
479            * tests/Class+Meth.R (tstMatrixClass): require coercions to
480            specific classes less unconditionally.
481    
482            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
483    
484            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
485    
486            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
487            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
488            R_to_CMatrix segfaults on one platform.
489            Eliminate most coercion method to *specific* classes, and replace
490            with virtual classes coercions.
491    
492    
493    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
494    
495            * src/init.c: export the CHM...._validate() placeholders, since
496            they *are* called.
497    
498            * tests/Class+Meth.R (classCanCoerce): and starting to test
499            all as(<from>, <to>)
500    
501    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
504            * tests/indexing.R: tested now
505            * tests/indexing.Rout.save: updated
506    
507            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
508            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
509            appropriate.
510    
511            * NAMESPACE: export a trivial
512            * R/Matrix.R: drop() Matrix-method
513    
514            * R/AllClass.R: moved all prototypes to virtual super classes.
515    
516            * R/Rsparse.R: many more coercions to have less exceptions in
517            * tests/Class+Meth.R:
518    
519            * R/Ops.R (Compare): tweak for case with NA
520            * tests/simpl.R: hence another 'FIXME' eliminated
521    
522    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
525            objects.
526    
527            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
528              and more of "!", "&", "|", all, any; coercions
529    
530            * R/Rsparse.R: many coercions (which enable quite a few other
531            methods), thanks to enhancements in
532            * src/dgCMatrix.c (R_to_CMatrix): new, and
533            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
534            symmetric & triangular and ..RMatrix objects.
535    
536            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
537            renamed file from src/dsTMatrix.c;
538            now dealing with symmetric and triangular Tsparse coercions, both
539            to dense and general.
540    
541    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
544    
545            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
546            where sensible when the <numeric> is of length > 1.
547    
548    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/Matrix.R ([<-): for M[] <- value: fix length
551    
552    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
555            * R/ndenseMatrix.R: new coercions n* -> l*
556    
557    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
560    
561            * R/Ops.R ("Logic"): and other "Ops", many updates
562    
563    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * src/Mutils.h (SET_DimNames): new utility
566    
567            * R/Auxiliaries.R (nnzero): improved and now exported via
568    
569            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
570    
571    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/diagMatrix.R (!): fix typo.
574    
575    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Auxiliaries.R (as_Csparse): and quite a few others:
578                    allow to pass class definition --> speedup
579            * R/sparseMatrix.R: apply the above
580    
581            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
582    
583            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
584            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
585            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
586    
587            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
588    
589            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
590            and use it for "sparse*" as well, since it's faster than the
591            as_Csparse(.) way.
592    
593    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
596    
597    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
600            as method for   M[ ij ] <- v
601            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
602    
603            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
604            FALSE answer
605    
606            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
607            * tests/indexing.R: test it, and some of the above
608    
609    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Auxiliaries.R (is_duplicatedT): new utility
612    
613    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
614    
615            * src/init.c (R_init_Matrix): export cholmod_scale
616    
617    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
620            base::as.matrix to (x, ...)
621    
622    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
625            file; start using "Logic", hence
626    
627            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
628            * NAMESPACE: import and export "Logic"
629    
630    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
633            only needed previously to R version 2.5.0.
634    
635    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
638    
639            * R/Tsparse.R (replTmat): fix subassignment of triangular
640            * R/Csparse.R (replCmat): ditto
641            * tests/indexing.R: more tests, incl the above fix
642    
643    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Auxiliaries.R (drop0): extend for non CSparse
646            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
647    
648            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
649                    use uplo correctly (!); other places: use uplo_P() macro
650    
651            * R/Csparse.R (replCmat): call diagU2N() when needed
652            * R/Tsparse.R (replTmat): ditto
653    
654            * src/dtCMatrix.c (tCMatrix_validate): new
655            * src/dtTMatrix.c (tTMatrix_validate): new, used in
656            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
657    
658            * R/diagMatrix.R (replDiag): to use in [<-
659    
660    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
663                    also more general diagU2N().
664    
665    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
668            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
669    
670    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * tests/bind.R: a few more cases
673            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
674    
675            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
676            * R/ddenseMatrix.R (cbind2/rbind2)
677            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
678            * tests/indexing.R
679            * tests/indexing.Rout.save: updated
680    
681    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
684            * tests/indexing.R
685    
686    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
689            align with proper position of "0", i.e., right for integers.
690            argument 'align' by default is "fancy".
691    
692    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
695            * R/Csparse.R: and fix "Compare" for more cases.
696            * tests/Class+Meth.R: test some of these (m == m, m != m)
697    
698    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/lsparseMatrix.R: all() and any() methods
701            * R/ldenseMatrix.R:      ditto
702            * NAMESPACE, R/Matrix.R: ditto
703    
704            * man/all-methods.Rd: document them minimally
705    
706            * tests/simple.R: add a few examples for these
707    
708    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Tsparse.R ([): fix long standing typo in symmetric case
711            * man/dsCMatrix-class.Rd: add example exhibiting the above case
712    
713    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
714    
715            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
716            to LL before converting to a sparse matrix. (The LDL form can be
717            converted to a sparse matrix but it is implicitly a unit
718            triangular matrix and a diagonal matrix overwritten on the diagonal.)
719    
720    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
721    
722            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
723    
724    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
725    
726            * DESCRIPTION (Version): updated -> release 0.9975-7
727            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
728    
729    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
732    
733    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
734    
735            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
736            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
737            is exactly singular.
738    
739    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * DESCRIPTION (Date): updated -> release 0.9975-6
742    
743    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
746            now returns symmetric.
747    
748            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
749    
750            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
751            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
752    
753            * R/Auxiliaries.R (.type.kind): added
754    
755    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
758            running src/CSparse_install.sh
759    
760            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
761    
762    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
765            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
766    
767            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
768    
769            * tests/Class+Meth.R (tstMatrixClass): now assure
770            the (important in method programming) property :
771    
772                    ###>>  Every "Matrix" is either
773                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
774    
775                    (where "*" stands for "Matrix")
776    
777            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
778    
779            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
780            * tests/validObj.R: checks for "comparison"
781    
782            * R/sparseMatrix.R ([): improved indexing for sparse;
783                    trying to keep <symmetric>[ n, n] symmmetric
784    
785            * tests/indexing.R: indexing for logical sparse now ok
786    
787    
788    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * src/Tsparse.c: use xTsparse_validate() , and hence remove
791    
792            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
793    
794    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
797    
798            * tests/simple.R: validObject() checking the above.
799    
800            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
801            replacing both dgCMatrix_validate and lgCM*.
802    
803            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
804            fix dimnames setting in other places.
805            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
806    
807    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
810    
811            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
812            symmetry test, via
813            * R/Auxiliaries.R (.as.dgC.0.factors):
814    
815    2006-11-01  Douglas Bates  <bates@r-project.org>
816    
817            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
818            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
819            <CsparseMatrix>) added
820    
821    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * tests/matprod.R: add a variation of Harri's example
824    
825            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
826            recursive infinitely.
827    
828            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
829    
830            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
831    
832    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
835            matrix if possible; test m+m == 2*m; now test dgRMatrix.
836            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
837            satisfy the above test.
838    
839    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
842    
843            * R/dgCMatrix.R: solve(a, b="missing") based on
844            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
845            RHS = NULL.
846    
847            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
848            add more (needed) [t]crossprod() methods.
849    
850            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
851    
852            * R/Auxiliaries.R (as_CspClass): cleanup
853            (drop0): internal utility for "Csparse_drop(*, 0)"
854            (.bail.out.2): encourage active feedback
855    
856    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/dMatrix.R(Compare): new(), then slots [no validity check]
859    
860            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
861            non-valid or 'sorted' case).
862    
863            * R/dsparseMatrix.R: add "chol" method.
864            * R/ddenseMatrix.R: ditto
865    
866            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
867            * NAMESPACE (Ops)
868            * R/diagMatrix.R (diag2T): simple utility used "higher level"
869            coercion; deprecating direct lower level coercions.
870    
871            * R/*.R (seq): use seq_len() and seq_along() where possible.
872    
873    
874    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * DESCRIPTION (Version): 0.9975-5 ready for release
877    
878    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
879    
880            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
881    
882    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/AllClass.R (corMatrix): add 'validity' check;
885                    comment out unused "LDL" class definition
886            * NAMESPACE: mention, but do not export "LDL" class
887            * R/corMatrix.R: new (simple), needed for R-devel with
888            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
889              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
890    
891    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
892    
893            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
894            use Rprintf and R's error handling.
895    
896    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
899            * tests/matprod.R: add tests for the bug fixed.
900    
901    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
902    
903            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
904            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
905    
906    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
907    
908            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
909    
910    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * DESCRIPTION (Version): 0.9975-3
913    
914            * R/diagMatrix.R (bdiag): new function constructing block diagonal
915            (sparse) matrices.
916            * man/bdiag.Rd: docu + examples
917    
918            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
919    
920            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
921            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
922    
923            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
924            that result is sparse or diagonal (and not dense).
925    
926            * man/Subassign-methods.Rd: fix examples
927    
928            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
929            should always return a sparse (and not sometimes a diagonal) matrix.
930    
931    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
934    
935    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
936    
937            * DESCRIPTION (Version): 0.9975-2
938    
939            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
940    
941    2006-10-02  Douglas Bates  <bates@R-project.org>
942    
943            * tests/dg_Matrix.R: Simplify test taking into account new code.
944    
945    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
948    
949            * R/lsTMatrix.R: new files w/ missing methods
950            * R/nsTMatrix.R:  "  'for completeness'
951    
952            * tests/Class+Meth.R: a bit less 'not.ok.classes'
953    
954            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
955    
956    
957    2006-09-28  Douglas Bates  <bates@R-project.org>
958    
959            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
960            included.
961    
962            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
963            Export C-callable functions used in Zt_create in lme4.
964    
965    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * DESCRIPTION (Version): 0.9975-1
968    
969            * tests/simple.R: less checks fail; using NA, found that our
970                    kronecker() is not base-compatible with NA's.
971    
972            * R/dMatrix.R: "Compare" method now implemented for all cases
973    
974            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
975    
976            * man/dtpMatrix-class.Rd: mention length of 'x' slot
977    
978            * src/dtpMatrix.c (dtpMatrix_validate): fix check
979            * src/dspMatrix.c (dspMatrix_validate): ditto
980    
981            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
982              including coercion to [nl]tTMatrix.
983    
984            * R/diagMatrix.R (show): print a header line as for other classes.
985    
986    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * src/Makefile.win (SUBDIRS): fix typo
989    
990    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
993    
994    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
995    
996            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
997            symmetric and y missing in R code using %*% (cholmod_aat doesn't
998            accept a symmetric matrix).
999            * tests/group-methods.R: Uncomment test of crossprod applied to
1000            lsCMatrix objects.
1001    
1002    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/AllClass.R (symmetricMatrix): add validity method (available
1005            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1006    
1007            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1008    
1009            * tests/indexing.Rout.save:
1010            * tests/indexing.R: additions, mainly for 'lsparse'
1011    
1012            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1013            case.
1014    
1015            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1016    
1017    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1020                    as 'N' (1-letter - Ok?)
1021    
1022            * tests/group-methods.R: add test for logical + NAs
1023    
1024            * R/dMatrix.R ("Compare"): fix to work with NA's
1025    
1026            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1027    
1028            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1029                    which is implemented.
1030    
1031    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * src/chm_common.c: coerce logical <-> double instead of
1034            typecasting;  needed for "l" matrix handling in cholmod.
1035    
1036            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1037    
1038            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1039            (Tsp2grNEL): other fixes needed
1040    
1041    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1044                    Matrices, since "lMatrix", also "lsparseM" can have NA
1045            * R/ndenseMatrix.R, etc: new source files
1046            * man/nsparseMatrix-classes.Rd, etc: new help files
1047            * tests/: adaptions
1048            * src/chm_common.c (chm_dense_to_SEXP): and others:
1049                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1050            * src/Csparse.c, etc: ditto
1051    
1052    2006-09-11  Douglas Bates  <bates@R-project.org>
1053    
1054            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1055            alloc_d**Matrix functions to the lme4 package.
1056    
1057    2006-09-09  Douglas Bates  <bates@R-project.org>
1058    
1059            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1060            fixed
1061    
1062    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/lMatrix.R: new
1065    
1066            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1067    
1068            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1069            * man/tcrossprod.Rd: ditto
1070    
1071    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1072    
1073            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1074            for exported functions
1075            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1076            Remove partitioning algorithms for sparse matrix reordering.  The
1077            copyright on the Metis code was problematic and the methods were
1078            rarely used.
1079            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1080            operations are now done entirely in CHOLMOD code.
1081    
1082    2006-09-06  Douglas Bates  <bates@R-project.org>
1083    
1084            * src/Mutils.h: Remove functions that are no longer used.
1085    
1086    2006-09-04  Douglas Bates  <bates@R-project.org>
1087    
1088            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1089            * src/DEPS.mkf: update
1090    
1091    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1092    
1093            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1094            * DESCRIPTION (Version): 0.9975-0
1095            (Depends): R (>= 2.4.0)
1096    
1097    2006-09-01  Douglas Bates  <bates@R-project.org>
1098    
1099            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1100    
1101    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1104            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1105    
1106            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1107    
1108    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1111            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1112            * R/dsparseMatrix.R: ditto
1113            * R/Csparse.R: ditto
1114    
1115    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * R/dMatrix.R (Compare): improve availability of "<", etc
1118            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1119    
1120    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1123            of a 0-index which was used as 1-index (..hmm)
1124    
1125            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1126    
1127            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1128            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1129            (.is.diagonal): ditto
1130    
1131            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1132    
1133            * R/Matrix.R (Matrix): also work for NA data
1134    
1135    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1138            in all cases.
1139    
1140    2006-08-27  Douglas Bates  <bates@R-project.org>
1141    
1142            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1143            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1144    
1145    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1146    
1147            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1148            subclasses of "ddenseMatrix"
1149            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1150            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1151            instead of half dozen specialized ones.
1152    
1153    2006-08-25  Douglas Bates  <bates@R-project.org>
1154    
1155            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1156            <tillard@cirad.fr> - ordering standard errors to match effects.
1157    
1158    2006-08-24  Douglas Bates  <bates@R-project.org>
1159    
1160            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1161            on R_ldl.
1162            * R/lCholCMatrix.R,
1163            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1164            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1165            * many files in ./R and ./src: Use more general version of
1166            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1167            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1168            dtpMatrix, dspMatrix and dppMatrix conversions.
1169    
1170    
1171    2006-08-23  Douglas Bates  <bates@R-project.org>
1172    
1173            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1174            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1175            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1176            dgeMatrix_crossprod (may need to do this in other places).
1177            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1178            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1179    
1180    2006-08-22  Douglas Bates  <bates@R-project.org>
1181    
1182            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1183            types of classed Matrices, matrices or numeric or logical vectors.
1184            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1185            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1186            to Mutils.h (as an inline) and change name to Matrix_check_class;
1187            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1188            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1189            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1190            * src/Csparse.c: use diag_P and uplo_P macros.
1191    
1192    2006-08-21  Douglas Bates  <bates@R-project.org>
1193    
1194            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1195            valgrind.
1196            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1197            inverses.
1198            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1199            -Wall warnings.
1200            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1201            Use dup_mMatrix_as_dgeMatrix.
1202    
1203    2006-08-20  Douglas Bates  <bates@R-project.org>
1204    
1205            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1206            * tests/sparseQR.R: Added
1207            * man/sparseQR-class.Rd: Document methods for qr.* generics
1208            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1209    
1210    2006-08-19  Douglas Bates  <bates@R-project.org>
1211    
1212            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1213            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1214            and qr.fitted.
1215            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1216            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1217    
1218    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1221            the base version has no "..." argument.
1222    
1223            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1224    
1225            * R/Matrix.R: define and
1226            * NAMESPACE: export as.numeric() and as.logical() methods.
1227                    Let's hope these do not badly slow down something...
1228            Finally export the zapsmall() method.
1229    
1230    2006-08-17  Douglas Bates  <bates@R-project.org>
1231    
1232            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1233            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1234            * src/dtCMatrix.c :Remove code that is no longer used
1235            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1236    
1237    2006-08-14  Douglas Bates  <bates@R-project.org>
1238    
1239            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1240            Csparse_to_logical and Csparse_symmetric_to_general.
1241            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1242            coercion methods between CsparseMatrix and TsparseMatrix.
1243    
1244    2006-08-14  Douglas Bates  <bates@R-project.org>
1245    
1246            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1247            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1248            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1249            possible.
1250    
1251    2006-08-12  Douglas Bates  <bates@R-project.org>
1252    
1253            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1254              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1255              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1256              generalize conversions between TsparseMatrix, CsparseMatrix,
1257              denseMatrix and matrix.  Preserve triangularity property and
1258              propagate Dimnames in the easy cases.
1259    
1260    2006-08-10  Douglas Bates  <bates@R-project.org>
1261    
1262            * src/lmer.c: adjust checks in glmer_init for S4SXP
1263            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1264            before S4SXP but for the wrong reasons.
1265    
1266    2006-08-08  Douglas Bates  <bates@R-project.org>
1267    
1268            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1269            Later modified to return the upper triangle only.
1270            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1271    
1272    2006-08-07  Douglas Bates  <bates@R-project.org>
1273    
1274            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1275            R-level conversion to a sparse symmetric class.
1276            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1277            Remove conversion to sparse symmetric classes (now done in C code).
1278    
1279    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1282            * man/band.Rd:  adapt the \dontshow{} unit test.
1283    
1284    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
1286            * DESCRIPTION (Version): 0.995-14  for CRAN
1287    
1288            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1289    
1290            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1291            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1292    
1293            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1294            * R/Tsparse.R (tril, triu, band): methods
1295            * R/dgRMatrix.R (tril, ...):    ditto
1296            * man/band.Rd:                  ditto
1297    
1298    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1299    
1300            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1301                    to be up-to-date automatically.
1302    
1303    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1304    
1305            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1306    
1307            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1308            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1309            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1310            such that the S4 objects are always created by the current version
1311            of R and 'Matrix' class definitions.
1312    
1313    2006-08-01  Douglas Bates  <bates@R-project.org>
1314    
1315            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1316            inst/external/test3comp.rda: Added warnings for convergence on
1317            boundary and test cases.
1318    
1319            * src/lmer.c (mer_postVar): Modified to return the variances that
1320            are marginal to the fixed effects, not conditional on them (which
1321            is what the bVar slot contents represent).
1322    
1323    2006-07-31  Douglas Bates  <bates@R-project.org>
1324    
1325            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1326            function which calls the C function mer_hat_trace2.
1327    
1328            * man/ranef.Rd: Include description of "postVar" argument and
1329            producing a caterpillar plot.
1330    
1331    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1332    
1333            * NAMESPACE:    change  "correlation" to "corMatrix"
1334            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1335            * R/dpoMatrix.R: ditto
1336            * R/lmer.R:      ditto
1337    
1338    2006-07-28  Douglas Bates  <bates@R-project.org>
1339    
1340            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1341            RZXinv slot's contents into a separate internal function that can
1342            be used in mer_hat_trace.
1343    
1344    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1345    
1346            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1347            via new smart
1348            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1349            utility functions.
1350    
1351    
1352    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1355            matrices when appropriate; band() even symmetric ones.
1356            (replCmat): extend to potentially all "CsparseMatrix"
1357            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1358            allow subassignment for special sparse matrices.
1359    
1360            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1361    
1362            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1363            argument; in glmer_*(): print only if(verbose).
1364    
1365            speed-optimize a few places by moving REAL(.) out of loops.
1366    
1367            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1368    
1369    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1370    
1371            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1372                    since that wrongly triggers also for M[ logi , ]
1373    
1374            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1375            a symmetric matrix that results in a non-symmetric one.
1376            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1377    
1378            * R/dMatrix.R: make round(M) work as round(M, 0)
1379    
1380            * R/dgTMatrix.R (image): coordinate system and axis now use
1381            1-based indices, not 0-based ones.
1382    
1383            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1384            * tests/indexing.R: test it.
1385    
1386            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1387            * man/isSymmetric-methods.Rd: and document it.
1388    
1389            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1390            * man/SparseM-conv.Rd: docu them
1391    
1392            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1393                    for 'SparseM' conversions
1394    
1395    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1396    
1397            * R/Matrix.R (head): added head() and tail() methods.
1398    
1399    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1400    
1401            * DESCRIPTION (Version): 0.995-12 released to CRAN
1402    
1403    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1404    
1405            * tests/simple.R: add check for correct dsT -> dgT coercion;
1406                    add check for correct printing of symmetric sparse matrices.
1407    
1408            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1409            for sparse symmetric matrices.
1410    
1411            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1412            diagonal twice.
1413    
1414    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1415    
1416            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1417            being applied to the x slot (detected by Brian Ripley).
1418    
1419    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1420    
1421            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1422    
1423            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1424    
1425    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1426    
1427            * src/lgCMatrix.c (lgCMatrix_diag): new function
1428            * R/lgCMatrix.R (diag): for new method
1429    
1430            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1431                 ==> construction of illegal "*gTMatrix" via new() should
1432                 now be much less easy:
1433            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1434    
1435            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1436                    directly.
1437            * man/Matrix.Rd: documents it.
1438    
1439    2006-07-06  Douglas Bates  <bates@R-project.org>
1440    
1441            * src/pedigree.c (pedigree_inbreeding): Correction in
1442            initialization.  This function is not currently being used and is
1443            not fully tested.
1444    
1445            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1446            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1447            objects.  Modified validity check on pedigree objects to account
1448            for nonparallel patterns of missingness of parents.
1449    
1450            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1451            class.
1452    
1453    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1454    
1455            * R/pMatrix.R: coercion pMatrix -> Tsparse
1456    
1457    2006-06-12  Douglas Bates  <bates@R-project.org>
1458    
1459            * DESCRIPTION (Version): 0.995-11 released to CRAN
1460    
1461            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1462            the output from mcmcsamp.
1463    
1464    2006-06-10  Douglas Bates  <bates@R-project.org>
1465    
1466            * R/lmer.R (simulestimate): added C code for calculating the trace
1467            of the hat matrix.
1468    
1469    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1470    
1471            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1472            classes.
1473            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1474    
1475    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1476    
1477            * R/dgTMatrix.R (colSums): etc. All four of
1478            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1479            all "Matrices".
1480    
1481    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1482    
1483            * R/lmer.R (panel.ci): Add a reference line at zero and a
1484            background grid to the qqmath plot of ranef.lmer.
1485    
1486    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1487    
1488            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1489            grouping factors to be specified in the formula as (1|foo/bar).
1490    
1491    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1492    
1493            * R/lmer.R (findbars and others): Change check of is.numeric to
1494            !is.language to resolve the bug reported by Jacob Wegelin.
1495    
1496            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1497            code to evaluate inbreeding coefficients without calculating T,
1498            based on code in Sargolzaei and Iwaisaki's paper.
1499    
1500    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1501    
1502            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1503            generic and mer methods for isNested and denomDF. This denomDF was
1504            an attempt to emulate that in lme but I don't think that makes
1505            sense.  Use the trace of the hat matrix instead.
1506    
1507    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1508    
1509            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1510            the C code depending on a slot structure that's no longer valid.
1511            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1512    
1513    
1514    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1515    
1516            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1517            of lowerTriMatrix generic and methods to tril (also upper to triu)
1518            and added a general band extractor.
1519    
1520    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1521    
1522            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1523            allowable range with NAs. Added a corresponding check in the
1524            validity check for the pedigree class.
1525    
1526            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1527            crossprod methods now inherits from symmetricMatrix.
1528    
1529    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1530    
1531            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1532            generics lowerTriMatrix and upperTriMatrix along with methods for
1533            the Csparse virtual class.  Also added a C function Csparse_band
1534            that implements these methods by calling cholmod_band.
1535    
1536    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1537    
1538            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1539            erased when it was NULL.  This led to invalid subselections!
1540    
1541    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1542    
1543            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1544            in method for "t" so as not to lose the unit diagonal property.
1545    
1546    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1547    
1548            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1549            and methods.  This is now an option to the ranef method for the
1550            mer class.
1551    
1552            * src/cs_utils.c: Ensure that the nz component is -1 for a
1553            compressed column-oriented matrix.  Minor formatting cleanup.
1554    
1555            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1556            objects.
1557    
1558    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1559    
1560            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1561            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1562    
1563    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1564    
1565            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1566            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1567    
1568            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1569            for the dtCMatrix class.
1570    
1571    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1572    
1573            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1574            and methods for it.
1575    
1576    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1577    
1578            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1579            arguments, such that M %*% 1:6 now works
1580            * Tests/matprod.R: test the above
1581    
1582    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1583    
1584            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1585            the ranef.lmer class.
1586    
1587            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1588            methods to extract the posterior variances from the bVar slot.
1589    
1590    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1591    
1592            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1593            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1594    
1595            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1596            * tests/simple: (extended)
1597    
1598            * R/sparseMatrix.R (isTriangular): now using much improved
1599            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1600    
1601    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1602    
1603            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1604            (problem report from Franklin Parlamis).  This should be done
1605            generally.
1606    
1607    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1608    
1609            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1610            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1611            update the plot methods.
1612    
1613    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1614    
1615            * R/lmer.R (resid and ranef methods):  Added methods for the
1616            "residuals" and "resid" generic but only for linear mixed model
1617            fits.  Changed the ranef method to return a list of data frames so
1618            that the plot methods now work.
1619    
1620    2006-03-16  Douglas Bates  <bates@bates2>
1621    
1622            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1623            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1624    
1625            * DESCRIPTION (Date): New release
1626    
1627    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1628    
1629            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1630    
1631            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1632            * man/KNex.Rd: and other help files
1633            * tests/*.R: several ones needed adaption
1634            * inst/doc/Comparisons.Rnw: ditto
1635    
1636    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1637    
1638            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1639    
1640            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1641    
1642    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1643    
1644            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1645    
1646            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1647    
1648    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1649    
1650            * R/dMatrix.R: enable things like  M [ M < 10 ]
1651            * R/dgeMatrix.R: implement it
1652    
1653    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1654    
1655            * R/AllClass.R: define "summary.mer" and "*.lmer"
1656            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1657            * R/lmer.R (show): now works with summary()
1658    
1659    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1660    
1661            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1662            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1663                    support the above
1664    
1665    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1666    
1667            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1668            Use glmFit$prior.weights for weights in a glmm.
1669            Allow an option usePQL = FALSE to skip the PQL steps for the
1670            Laplace method (and, in time, the AGQ method).
1671    
1672            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1673            into a separate function internal_mer_Xfactor to be able to call
1674            it from internal_bhat.
1675    
1676    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1677    
1678            * tests/Class+Meth.R (tstMatrixClass): function for much better
1679            testing; now again of all actual classes.
1680    
1681            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1682                    use macros and define make_d_matrix_* and make_i_matrix_*
1683                    where _i_ is for the ldense routines:
1684    
1685            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1686            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1687    
1688            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1689    
1690    
1691    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1692    
1693            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1694                    many different kinds of matrices.
1695            * R/*.R: quite a few new methods were needed for R CMD check with
1696                    new Matrix().  Very good for users playing around.
1697    
1698    
1699    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1700    
1701            * src/dgeMatrix.c (dMatrix_validate): new
1702            * src/Mutils.c (dense_nonpacked_validate): new
1703    
1704            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1705    
1706    
1707    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1708    
1709            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1710    
1711    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1712    
1713            * DESCRIPTION (Version): 0.99-6 released to CRAN
1714    
1715            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1716            segfault in cases with multiple non-nested grouping factors.
1717    
1718    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1719    
1720            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1721                    (Depends): also on 'utils'
1722    
1723            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1724            * R/diagMatrix.R (Diagonal): constructor and methods for
1725            diagonal matrices
1726    
1727            * R/ltTMatrix.R: new "minimal methods"
1728    
1729    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1730    
1731            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1732            all methods (and help files).
1733    
1734    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1735    
1736            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1737                    for case (dimn.  op  no_dimn.)
1738    
1739    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1740    
1741            * DESCRIPTION (Version): 0.99-2  released to CRAN
1742    
1743    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1744    
1745            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1746            by Julian Faraway.
1747    
1748    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1749    
1750            * R/Auxiliaries.R (try_as): new utility
1751            * R/sparseMatrix.R: use try_as() in coercion to original class
1752    
1753    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1754    
1755            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1756    
1757    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1758    
1759            * R/Auxiliaries.R (dimNamesCheck): added
1760    
1761            * R/Matrix.R (as.array), (as.vector): new
1762    
1763    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1764    
1765            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1766                    default.
1767            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1768                    "pMatrix" now contains "sparseMatrix"
1769    
1770    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1771    
1772            * tests/Class+Meth.R: new tests; t(t(m)) == m
1773    
1774            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1775    
1776            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1777            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1778    
1779            * R/dspMatrix.R: typo in "t" method
1780    
1781    2005-09-18  Douglas Bates  <bates@wisc.edu>
1782    
1783            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1784            * R/Tsparse.R: instead of R/gTMatrix.R
1785            * R/Csparse.R: new
1786            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1787            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1788            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1789                            via cholmod
1790    
1791    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1792    
1793            * R/Auxiliaries.R (non0ind): new function using new C code
1794            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1795    
1796    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1797    
1798            * src/chm_common.h: header file required by all C sources that
1799            call CHOLMOD functions.  It defines a cholmod_common structure
1800            called 'c' whose address is passed as the last argument to
1801            (virtually) every CHOLMOD function.
1802    
1803            * src/Pattern.c: Simple example of the use of CHOLMOD.
1804    
1805            * src/init.c: initialize and finalize the cholmod_common structure.
1806    
1807            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1808            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1809    
1810    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1811    
1812            * inst/test-tools.R: new file collecting the utility functions used
1813                    in ./tests/*.R
1814    
1815            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1816            * R/Matrix.R (cbind2): methods for NULL and missing
1817    
1818    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1819    
1820            * R/AllClass.R: new "index" class for "[" and "[<-":
1821                    First cut at "symmetricMatrix" and "triangularMatrix"
1822            * R/gTMatrix.R (.ind.prep): new function;
1823                    Logical and character indexing now work too.
1824            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1825            * tests/indexing.R: new, including *.Rout.save
1826            * tests/dgTMatrix.R: new
1827    
1828    2005-08-29  Douglas Bates  <bates@wisc.edu>
1829    
1830            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1831            indicator pos not being updated.  Also enforced upper triangular
1832            for symmetric case.  Need to coerce edges component of elements of
1833            edge list - grr! (Why don't they define their classes cleanly?)
1834    
1835    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1836    
1837            * R/Matrix.R:  added first "[<-" methods; not yet functional
1838            * R/denseMatrix.R: ditto
1839            * man/Subassign-methods.Rd: new help file for these
1840    
1841    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1842    
1843            * DESCRIPTION (Version): 0.98-6
1844    
1845            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1846            matrices.
1847    
1848    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1849    
1850            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1851                    as( <logical>, "matrix")
1852    
1853            * R/pMatrix.R: coercion to "lgTMatrix"
1854    
1855            * R/gTMatrix.R: new virtual class to define "[" methods for.
1856            * man/gTMatrix-class.Rd:
1857            * General slight re-organization of where "[" methods are defined.
1858              more to come.
1859    
1860    2005-08-18  Douglas Bates  <bates@wisc.edu>
1861    
1862            * DESCRIPTION (Version): 0.98-5  released to CRAN
1863    
1864            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1865            * .....
1866    
1867    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1868    
1869            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1870            or glmer objects.
1871    
1872    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1873    
1874            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1875    
1876    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1877    
1878            * R/HBMM.R: finish re-writing R-only code.
1879    
1880    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1881    
1882            * man/externalFormats.Rd: move documentation for writeHB and
1883            writeMM here.
1884    
1885            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1886            (suggested by Paul Roecker).
1887    
1888            * tests/validObj.R (assertError): Comment out test that is failing
1889            after recent changes in r-devel.
1890    
1891    
1892    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1893    
1894            * R/AllClass.R: intermediate virtual class "denseMatrix"
1895            * man/denseMatrix-class.Rd
1896            * NAMESPACE: export it, and also export
1897            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1898    
1899    2005-08-10  Douglas Bates  <bates@wisc.edu>
1900    
1901            * DESCRIPTION (Version): 0.98-3 to CRAN
1902    
1903            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1904            matrix_solve code (which was really, really wrong).
1905    
1906    2005-08-07  Douglas Bates  <bates@wisc.edu>
1907    
1908            * DESCRIPTION (Version): 0.98-2
1909    
1910            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1911    
1912            * R/lmer.R (abbrvNms): new
1913            * R/lmer.R (mcmcsamp): allow transformed parameters
1914            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1915            for the Harwell-Boeing and the MatrixMarket formats.
1916    
1917    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1918    
1919            * man/dtrMatrix-class.Rd: add examples
1920            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1921    
1922            * TODO: note the dtpMatrix (docu) bug
1923    
1924            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1925            in order to ensure that new as.matrix() is used by old functions,
1926            e.g., svd(), qr(), eigen(), dist(),..;
1927                  apply(), also matplot() or pairs().
1928    
1929    
1930    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1931    
1932            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1933              add comments about 'control' / lmerControl() arguments
1934    
1935    2005-07-27  Douglas Bates  <bates@wisc.edu>
1936    
1937            * man/sleepstudy.Rd: Added the sleep data set.
1938            * DESCRIPTION (Version): 0.98-1  released to CRAN
1939    
1940    2005-07-12  Douglas Bates  <bates@wisc.edu>
1941            * man/sleepstudy.Rd: Added the sleep data set.
1942    
1943            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1944            .Call calls that were producing spurious output.
1945    
1946    2005-07-05  Douglas Bates  <bates@wisc.edu>
1947    
1948            * R/lmer.R (lmer): stored updated variance component estimates in
1949            mer object for the generalized model.  (Bug reported by Renaud
1950            Lancelot).
1951    
1952    2005-07-03  Douglas Bates  <bates@wisc.edu>
1953    
1954            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1955            unidimensional case.
1956    
1957    2005-06-08  Douglas Bates  <bates@wisc.edu>
1958    
1959            * DESCRIPTION (Version): 0.96-1
1960    
1961            * moved  lmer-class' R and C code moved from lme4 to here
1962    
1963    2005-06-04  Douglas Bates  <bates@wisc.edu>
1964    
1965            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1966            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1967    
1968    2005-06-02  Douglas Bates  <bates@wisc.edu>
1969    
1970            * src/Makefile.win: Forgot to update this when Makefile changed.
1971    
1972    2005-05-11  Douglas Bates  <bates@wisc.edu>
1973    
1974            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1975            bug reported by Kurt Hornik and Michael Hahsler.
1976    
1977    2005-05-10  Douglas Bates  <bates@wisc.edu>
1978    
1979            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1980            logical sparse matrices.  These will also be used in the symbolic
1981            analysis for lmer objects.
1982    
1983            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1984            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1985    
1986    2005-05-06  Douglas Bates  <bates@wisc.edu>
1987    
1988            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1989            colMeans, colSums, rowMeans and rowSums.
1990    
1991    2005-04-18  Douglas Bates  <bates@wisc.edu>
1992    
1993            * src/lgCMatrix.[ch]: code for _validate method and stub for
1994            multiplication operation.
1995    
1996            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1997            to dgetrs.
1998    
1999            * src/init.c: Fix cut-and-paste error in definition of
2000            dgeMatrix_matrix_solve
2001    
2002            * src/{many files}: Tighten code by using ALLOC_SLOT.
2003    
2004    2005-04-15  Douglas Bates  <bates@wisc.edu>
2005    
2006            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2007    
2008            * DESCRIPTION: Eliminate import of stats.
2009    
2010    
2011    2005-04-06  Douglas Bates  <bates@wisc.edu>
2012    
2013            * R/AllClass.R : add logical sparse matrix classes
2014    
2015    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2016    
2017            * R/dgTMatrix.R: add "[" method for triplet matrices
2018            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2019    
2020    2005-03-31  Douglas Bates  <bates@wisc.edu>
2021    
2022            * DESCRIPTION (Version): release 0.95-5 to CRAN
2023    
2024            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2025            * R/sparseMatrix.R: %*%, crossprod()
2026            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2027            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2028            * src/lmer.c (lmer_fitted): fix thinko
2029    
2030    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2031    
2032            * R/AllClass.R: add two virtual sparse classes ``on top''
2033    
2034    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2035    
2036            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2037                    correspondingly fix examples and tests/ since new()
2038                    doesn't work for virtual classes.
2039    
2040    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2041    
2042            * R/Matrix.R (as.matrix): method and one for unname()
2043            * tests/dpoMatrix.R: tests should now be less platform dependent;
2044              also run for R 2.1.0; using as.matrix()
2045    
2046    2005-03-15  Douglas Bates  <bates@wisc.edu>
2047    
2048            * R/pMatrix.R: "pMatrix" class added
2049            * ....
2050    
2051    2005-03-14  Douglas Bates  <bates@wisc.edu>
2052    
2053            * R/dtpMatrix.R: Add unpack method and an example.
2054    
2055            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2056            of general symmetric matrices and associated S4 methods.
2057    
2058    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2059            +
2060    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2061    
2062            * R/dgeMatrix.R (setAs): and many other files: more coercion,
2063              crossprod() and "%*%" methods added; tests, too.
2064            * tests/matprod.R: new, for testing these
2065    
2066    2005-03-03  Douglas Bates  <bates@wisc.edu>
2067    
2068            * src/lmer.c (lmer_fitted): Added.
2069    
2070    2005-03-02  Douglas Bates  <bates@wisc.edu>
2071    
2072            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2073    
2074    2005-02-28  Douglas Bates  <bates@wisc.edu>
2075    
2076            * src/*.c,po/,inst/po: Internationalization and localization of
2077            the package.
2078    
2079            * src/ldl.[ch]: Removed these as their contents are referenced in the
2080            R_ldl.c file.
2081    
2082            * src/flame.[ch]: Removed these source files.
2083    
2084            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2085    
2086            * src/LU.[ch],src/init.c: absorb in factorizations
2087    
2088            * src/Mutils.h: prepare for internationalization
2089    
2090            * src/cblas.h: move the enum definitions to Mutils.h and remove
2091            this file
2092    
2093    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2094    
2095            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2096    
2097            * R/dtrMatrix.R: fix t() method
2098    
2099            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2100            * NAMESPACE: export them (and import generics from "methods")
2101            * tests/group-methods.R : and test them.
2102    
2103            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2104            border case
2105    
2106    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
2107    
2108            * DESCRIPTION (Version): 0.95-2  released to CRAN
2109    
2110            * src/dgBCMatrix.c:
2111            * src/lmer.c: many changes
2112            * ...
2113    
2114    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2115    
2116            * R/Matrix.R: add more sophisticated show() method.
2117    
2118    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
2119    
2120            * */* : almost complete reorganization of classes.
2121    
2122    2005-01-26  Douglas Bates  <bates@wisc.edu>
2123    
2124            * R/AllGeneric.R: Added matrix exponential generic expm and a method
2125            for the geMatrix class.
2126    
2127    2005-01-24  Douglas Bates  <bates@wisc.edu>
2128    
2129            * src/Makefile (clean): Remove *.a and *.so
2130    
2131            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2132    
2133    2005-01-23  Douglas Bates  <bates@wisc.edu>
2134    
2135            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2136            had an effect in cases with more than 2 grouping factors.
2137    
2138    2005-01-03  Douglas Bates  <bates@wisc.edu>
2139    
2140            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2141    
2142    2004-12-23  Douglas Bates  <bates@wisc.edu>
2143    
2144            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2145            and R_useDynamicSymbols (suggested by B.D.Ripley).
2146    
2147    2004-12-14  Douglas Bates  <bates@wisc.edu>
2148    
2149          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
2150    
2151          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2152          for tripletMatrix to matrix.          for tripletMatrix to matrix.
2153    
2154  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
2155    
2156          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2157          no longer used.          no longer used.
# Line 17  Line 2163 
2163          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
2164          Fixes part but not all of #15.          Fixes part but not all of #15.
2165    
2166  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
2167    
2168          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2169          scalar grouping factors corrected.          scalar grouping factors corrected.
2170    
2171  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
2172    
2173          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
2174    
2175  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
2176    
2177          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
2178          .h file can be included.          .h file can be included.
2179    
2180  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2181    
2182          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2183          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2184    
2185          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2186    
2187  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2188    
2189          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2190    
2191  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2192    
2193          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2194    
2195  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2196    
2197          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2198    
2199  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2200    
2201          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2202    
2203  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2204    
2205          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2206          routines.          routines.
2207    
2208  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2209    
2210          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2211    
2212  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2213    
2214          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2215    

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