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

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