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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 2008, Thu Jul 19 19:47:59 2007 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
4              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
5              triplet_to_sparse, documentation, use typedefs
6    
7    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * man/dpoMatrix-class.Rd: added 'corMatrix' example
10    
11            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
12            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
13            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
14    
15            * R/lsparseMatrix.R: bug fix in "all" method
16            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
17    
18            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
19            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
20                    + matrix |-> nMatrix coercion
21            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
22            * man/pMatrix-class.Rd: ditto
23    
24            * R/Matrix.R (Summary): method for non-dMatrix
25    
26            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
27            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
28                    test all Summary methods.
29    
30    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
33    
34    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
37    
38            * R/pMatrix.R (t?crossprod): methods for pMatrix
39    
40    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
43    
44    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
47              trying to fix a subtle bug - which has been somewhere else.
48    
49    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
50    
51            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
52              solve the bug
53    
54    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/dgCMatrix.c (compressed_to_TMatrix):
57    
58    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * src/Csparse.c (Rsparse_validate): new, to have some validity
61            checking for RsparseMatrix
62            * src/dgCMatrix.c (xRMatrix_validate): ditto
63            * src/dtCMatrix.c (tRMatrix_validate): ditto
64    
65    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
68              lgRMatrix
69            * [r4568] DESCRIPTION: Prepare for bug-fix release
70            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
71              for declaration of cholmod_symmetry
72    
73    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
76            release.
77    
78    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
79    
80            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
81              functions - no longer used
82            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
83              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
84              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
85              Alloca
86    
87    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
90              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
91              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
92              src/t_gCMatrix_colSums.c: more R_CheckStack()s
93    
94    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
97              the required amount of memory then call M_numeric_as_chm_dense.
98            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
99              (like Calloc but calling alloca)
100    
101    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
104            and extended with more sophisticated 'col.names' option.
105            * NAMESPACE: export  printSparseMatrix()
106            * man/printSpMatrix.Rd: document, incl. examples
107    
108    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
109    
110            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
111              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
112              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
113    
114    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.99875-4
117    
118            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
119            some dimnames perservation.
120    
121            * R/dsTMatrix.R (t-method): keep dimnames
122            * R/dtTMatrix.R:  ditto
123    
124            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
125            and ncol(.) < 10
126    
127            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
128            from Mutils.h
129    
130            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
131            e.g. in as(<ngCMatrix>, "matrix")
132    
133    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
134    
135            * [r4529] .: Create a branch for the API changes from the 0.99875
136              series to the 0.999375 series
137            * [r4530] DESCRIPTION, inst/include/Matrix.h,
138              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
139              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
140              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
141              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
142              as_cholmod_x functions
143    
144    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
145    
146            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
147              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
148              to Comparisons
149    
150    >>>>>>> .merge-right.r4561
151    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.99875-3 ready to be released.
154    
155            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
156    
157            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
158            that should also work in a future version of R.
159    
160    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
163    
164            * R/sparseVector.R: more *sparseVector coercions, notably for
165            non - double ones.
166    
167    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
170              notably the new ones building on the new .Call(.)s:
171    
172            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
173            all 4 of [dlin]gCMatrix_colSums().
174    
175    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
178            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
179              result
180    
181    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/kronecker.R: fix typo (could lead to inf.recursion)
184            * test/simple.R: testing that
185    
186            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
187            method as well (which can have arguments, show() can't).
188    
189    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
190    
191            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
192              added dgCMatrix_colSums for [col,row][Sums,Means]
193    
194    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
195    
196            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
197              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
198              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
199            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
200              class
201            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
202              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
203              row names to store the levels - duh!  Added an example.
204    
205    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Csparse.c (Csparse_validate): check for *repeated* entries
208            thanks to example from Christian Buchta; with a test here:
209            * tests/simple.R:
210    
211    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
214            of colSums(*, sparseResult = TRUE)
215    
216    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
219            'na.rm = FALSE' as "everywhere" else in R.
220    
221    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4421] src/CSparse_install.sh: Modify for new organization of
224              CSparse package
225            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
226              SuiteSparse
227            * [r4426] src/Makefile: add ./UFconfig to the include path for
228              compilation
229            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
230            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
231              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
232    
233    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
236            * R/sparseMatrix.R (prSpMatrix): now gives a message about
237            suppressed column names.
238    
239    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
240    
241            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
242              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
243              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
244              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
245              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
246              Remove warnings after change to const char* CHAR
247    
248    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
249    
250            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
251              type of M_cholmod_ssmult
252    
253    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
254    
255            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
256              src/init.c: Yet another cholmod export - cholmod_ssmult
257    
258    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * NAMESPACE: exported drop0(), since
261            * man/drop0.Rd: I have seen several cases, I really wanted to use
262            it, so our users may want too.
263    
264    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * man/colSums.Rd: separately document colSums() etc, since these
267            have the extra argument 'sparseResult'.
268    
269    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
272            * man/spMatrix.Rd: docu., including examples
273    
274            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
275            in order to make colMeans() etc fast *and* correct.
276            * R/sparseVector.R (replSPvec): "[<-" functionality for
277            sparseVectors; tested in
278            * tests/simple.R:
279    
280    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
283            (very) sparse Matrices; output similar to Matlab's print().
284    
285    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
288            0-based, indices (Jose Quesada <quesada@gmail.com>).
289    
290    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
293    
294    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Auxiliaries.R (sparsapply): new utility, much faster than
297            tapply1() for large sparse matrices.
298    
299    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Matrix.R (dim<-): reshape now via sparseVector.
302    
303            * R/sparseVector.R: methods and function for
304            * R/AllClass.R: new "sparseVector" class and daughters.
305            * NAMESPACE: export new classes
306    
307    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * DESCRIPTION (Version): 0.99875-1
310            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
311    
312    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
315            indexing
316            * tests/indexing.R: test set for that.
317    
318    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
321            entries.
322            * tests/indexing.R(out): add regression test for it
323    
324    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
327            name for "!" method definitions.
328    
329    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Tsparse.R (intI): new utility, used for "[" :
332                    Cleanup up there, and fixes for duplicated indices - more TODO!
333    
334            * tests/indexing.R(out): more tests
335    
336    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
339            code that is now part of the R Lapack library.
340    
341            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
342            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
343    
344    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
347    
348    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
351            up with extraneous names '0'...'<n-1>'
352    
353    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/dgTMatrix.R (mat2dgT): care about NAs
356    
357    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/kronecker.R: triangularity preserving methods
360    
361    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/kronecker.R: new file collecting kronecker() methods in one
364                    place.  Goal: become much faster!
365    
366    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
369            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
370            can be much faster.
371    
372            * tests/matprod.R: add regression tests for these (upper & lower).
373    
374    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Matrix.R (diff): method for our Matrices.
377    
378            * R/sparseMatrix.R (isDiagonal): check dim()!
379    
380    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Matrix.R (dim<-): new method for "reshape()" built on a
383            proposal from Tamas Papp.
384    
385    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
388    
389            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
390            rather define and export  cBind() and rBind() only.
391            --> useRs *must* change code that used to have cbind()/rbind() !!
392    
393            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
394            * R/bind.Rout.save: ditto
395    
396    2007-02-16  Douglas Bates  <bates@r-project.org>
397    
398            * DESCRIPTION (Date, Version): 0.9975-11 with new date
399            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
400            const modifier on declaration of the array 'valid'
401    
402    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
405    
406    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
409    
410            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
411            * tests/simple.R: test the above and some of these coercions:
412    
413            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
414                    be careful to avoid infinite recursion, using new coercions in
415            * R/ngCMatrix.R and nsC... and ntC...
416            * R/lsparseMatrix.R: ditto
417    
418            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
419    
420            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
421            * R/Rsparse.R: reactivate .Call()s
422    
423            * tests/Class+Meth.R: a bit more on actual classes
424    
425    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
426    
427            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
428    
429    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * DESCRIPTION (Version): 0.9975-10 to upload
432    
433            * tests/Class+Meth.R (tstMatrixClass): require coercions to
434            specific classes less unconditionally.
435    
436            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
437    
438            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
439    
440            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
441            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
442            R_to_CMatrix segfaults on one platform.
443            Eliminate most coercion method to *specific* classes, and replace
444            with virtual classes coercions.
445    
446    
447    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
448    
449            * src/init.c: export the CHM...._validate() placeholders, since
450            they *are* called.
451    
452            * tests/Class+Meth.R (classCanCoerce): and starting to test
453            all as(<from>, <to>)
454    
455    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
458            * tests/indexing.R: tested now
459            * tests/indexing.Rout.save: updated
460    
461            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
462            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
463            appropriate.
464    
465            * NAMESPACE: export a trivial
466            * R/Matrix.R: drop() Matrix-method
467    
468            * R/AllClass.R: moved all prototypes to virtual super classes.
469    
470            * R/Rsparse.R: many more coercions to have less exceptions in
471            * tests/Class+Meth.R:
472    
473            * R/Ops.R (Compare): tweak for case with NA
474            * tests/simpl.R: hence another 'FIXME' eliminated
475    
476    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
479            objects.
480    
481            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
482              and more of "!", "&", "|", all, any; coercions
483    
484            * R/Rsparse.R: many coercions (which enable quite a few other
485            methods), thanks to enhancements in
486            * src/dgCMatrix.c (R_to_CMatrix): new, and
487            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
488            symmetric & triangular and ..RMatrix objects.
489    
490            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
491            renamed file from src/dsTMatrix.c;
492            now dealing with symmetric and triangular Tsparse coercions, both
493            to dense and general.
494    
495    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
498    
499            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
500            where sensible when the <numeric> is of length > 1.
501    
502    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/Matrix.R ([<-): for M[] <- value: fix length
505    
506    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
509            * R/ndenseMatrix.R: new coercions n* -> l*
510    
511    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
514    
515            * R/Ops.R ("Logic"): and other "Ops", many updates
516    
517    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * src/Mutils.h (SET_DimNames): new utility
520    
521            * R/Auxiliaries.R (nnzero): improved and now exported via
522    
523            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
524    
525    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/diagMatrix.R (!): fix typo.
528    
529    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/Auxiliaries.R (as_Csparse): and quite a few others:
532                    allow to pass class definition --> speedup
533            * R/sparseMatrix.R: apply the above
534    
535            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
536    
537            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
538            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
539            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
540    
541            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
542    
543            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
544            and use it for "sparse*" as well, since it's faster than the
545            as_Csparse(.) way.
546    
547    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
550    
551    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
554            as method for   M[ ij ] <- v
555            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
556    
557            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
558            FALSE answer
559    
560            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
561            * tests/indexing.R: test it, and some of the above
562    
563    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Auxiliaries.R (is_duplicatedT): new utility
566    
567    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
568    
569            * src/init.c (R_init_Matrix): export cholmod_scale
570    
571    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
574            base::as.matrix to (x, ...)
575    
576    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
579            file; start using "Logic", hence
580    
581            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
582            * NAMESPACE: import and export "Logic"
583    
584    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
587            only needed previously to R version 2.5.0.
588    
589    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
592    
593            * R/Tsparse.R (replTmat): fix subassignment of triangular
594            * R/Csparse.R (replCmat): ditto
595            * tests/indexing.R: more tests, incl the above fix
596    
597    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Auxiliaries.R (drop0): extend for non CSparse
600            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
601    
602            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
603                    use uplo correctly (!); other places: use uplo_P() macro
604    
605            * R/Csparse.R (replCmat): call diagU2N() when needed
606            * R/Tsparse.R (replTmat): ditto
607    
608            * src/dtCMatrix.c (tCMatrix_validate): new
609            * src/dtTMatrix.c (tTMatrix_validate): new, used in
610            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
611    
612            * R/diagMatrix.R (replDiag): to use in [<-
613    
614    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
617                    also more general diagU2N().
618    
619    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
622            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
623    
624    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * tests/bind.R: a few more cases
627            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
628    
629            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
630            * R/ddenseMatrix.R (cbind2/rbind2)
631            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
632            * tests/indexing.R
633            * tests/indexing.Rout.save: updated
634    
635    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
638            * tests/indexing.R
639    
640    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
643            align with proper position of "0", i.e., right for integers.
644            argument 'align' by default is "fancy".
645    
646    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
649            * R/Csparse.R: and fix "Compare" for more cases.
650            * tests/Class+Meth.R: test some of these (m == m, m != m)
651    
652    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/lsparseMatrix.R: all() and any() methods
655            * R/ldenseMatrix.R:      ditto
656            * NAMESPACE, R/Matrix.R: ditto
657    
658            * man/all-methods.Rd: document them minimally
659    
660            * tests/simple.R: add a few examples for these
661    
662    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/Tsparse.R ([): fix long standing typo in symmetric case
665            * man/dsCMatrix-class.Rd: add example exhibiting the above case
666    
667    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
670            to LL before converting to a sparse matrix. (The LDL form can be
671            converted to a sparse matrix but it is implicitly a unit
672            triangular matrix and a diagonal matrix overwritten on the diagonal.)
673    
674    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
675    
676            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
677    
678    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
679    
680            * DESCRIPTION (Version): updated -> release 0.9975-7
681            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
682    
683    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
686    
687    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
688    
689            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
690            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
691            is exactly singular.
692    
693    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * DESCRIPTION (Date): updated -> release 0.9975-6
696    
697    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
700            now returns symmetric.
701    
702            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
703    
704            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
705            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
706    
707            * R/Auxiliaries.R (.type.kind): added
708    
709    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
712            running src/CSparse_install.sh
713    
714            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
715    
716    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
719            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
720    
721            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
722    
723            * tests/Class+Meth.R (tstMatrixClass): now assure
724            the (important in method programming) property :
725    
726                    ###>>  Every "Matrix" is either
727                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
728    
729                    (where "*" stands for "Matrix")
730    
731            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
732    
733            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
734            * tests/validObj.R: checks for "comparison"
735    
736            * R/sparseMatrix.R ([): improved indexing for sparse;
737                    trying to keep <symmetric>[ n, n] symmmetric
738    
739            * tests/indexing.R: indexing for logical sparse now ok
740    
741    
742    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * src/Tsparse.c: use xTsparse_validate() , and hence remove
745    
746            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
747    
748    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
751    
752            * tests/simple.R: validObject() checking the above.
753    
754            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
755            replacing both dgCMatrix_validate and lgCM*.
756    
757            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
758            fix dimnames setting in other places.
759            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
760    
761    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
764    
765            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
766            symmetry test, via
767            * R/Auxiliaries.R (.as.dgC.0.factors):
768    
769    2006-11-01  Douglas Bates  <bates@r-project.org>
770    
771            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
772            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
773            <CsparseMatrix>) added
774    
775    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * tests/matprod.R: add a variation of Harri's example
778    
779            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
780            recursive infinitely.
781    
782            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
783    
784            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
785    
786    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
789            matrix if possible; test m+m == 2*m; now test dgRMatrix.
790            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
791            satisfy the above test.
792    
793    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
796    
797            * R/dgCMatrix.R: solve(a, b="missing") based on
798            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
799            RHS = NULL.
800    
801            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
802            add more (needed) [t]crossprod() methods.
803    
804            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
805    
806            * R/Auxiliaries.R (as_CspClass): cleanup
807            (drop0): internal utility for "Csparse_drop(*, 0)"
808            (.bail.out.2): encourage active feedback
809    
810    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/dMatrix.R(Compare): new(), then slots [no validity check]
813    
814            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
815            non-valid or 'sorted' case).
816    
817            * R/dsparseMatrix.R: add "chol" method.
818            * R/ddenseMatrix.R: ditto
819    
820            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
821            * NAMESPACE (Ops)
822            * R/diagMatrix.R (diag2T): simple utility used "higher level"
823            coercion; deprecating direct lower level coercions.
824    
825            * R/*.R (seq): use seq_len() and seq_along() where possible.
826    
827    
828    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * DESCRIPTION (Version): 0.9975-5 ready for release
831    
832    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
833    
834            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
835    
836    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/AllClass.R (corMatrix): add 'validity' check;
839                    comment out unused "LDL" class definition
840            * NAMESPACE: mention, but do not export "LDL" class
841            * R/corMatrix.R: new (simple), needed for R-devel with
842            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
843              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
844    
845    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
846    
847            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
848            use Rprintf and R's error handling.
849    
850    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
853            * tests/matprod.R: add tests for the bug fixed.
854    
855    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
856    
857            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
858            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
859    
860    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
861    
862            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
863    
864    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * DESCRIPTION (Version): 0.9975-3
867    
868            * R/diagMatrix.R (bdiag): new function constructing block diagonal
869            (sparse) matrices.
870            * man/bdiag.Rd: docu + examples
871    
872            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
873    
874            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
875            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
876    
877            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
878            that result is sparse or diagonal (and not dense).
879    
880            * man/Subassign-methods.Rd: fix examples
881    
882            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
883            should always return a sparse (and not sometimes a diagonal) matrix.
884    
885    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
888    
889    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
890    
891            * DESCRIPTION (Version): 0.9975-2
892    
893            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
894    
895    2006-10-02  Douglas Bates  <bates@R-project.org>
896    
897            * tests/dg_Matrix.R: Simplify test taking into account new code.
898    
899    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
902    
903            * R/lsTMatrix.R: new files w/ missing methods
904            * R/nsTMatrix.R:  "  'for completeness'
905    
906            * tests/Class+Meth.R: a bit less 'not.ok.classes'
907    
908            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
909    
910    
911    2006-09-28  Douglas Bates  <bates@R-project.org>
912    
913            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
914            included.
915    
916            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
917            Export C-callable functions used in Zt_create in lme4.
918    
919    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * DESCRIPTION (Version): 0.9975-1
922    
923            * tests/simple.R: less checks fail; using NA, found that our
924                    kronecker() is not base-compatible with NA's.
925    
926            * R/dMatrix.R: "Compare" method now implemented for all cases
927    
928            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
929    
930            * man/dtpMatrix-class.Rd: mention length of 'x' slot
931    
932            * src/dtpMatrix.c (dtpMatrix_validate): fix check
933            * src/dspMatrix.c (dspMatrix_validate): ditto
934    
935            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
936              including coercion to [nl]tTMatrix.
937    
938            * R/diagMatrix.R (show): print a header line as for other classes.
939    
940    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * src/Makefile.win (SUBDIRS): fix typo
943    
944    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
947    
948    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
949    
950            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
951            symmetric and y missing in R code using %*% (cholmod_aat doesn't
952            accept a symmetric matrix).
953            * tests/group-methods.R: Uncomment test of crossprod applied to
954            lsCMatrix objects.
955    
956    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * R/AllClass.R (symmetricMatrix): add validity method (available
959            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
960    
961            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
962    
963            * tests/indexing.Rout.save:
964            * tests/indexing.R: additions, mainly for 'lsparse'
965    
966            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
967            case.
968    
969            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
970    
971    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
974                    as 'N' (1-letter - Ok?)
975    
976            * tests/group-methods.R: add test for logical + NAs
977    
978            * R/dMatrix.R ("Compare"): fix to work with NA's
979    
980            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
981    
982            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
983                    which is implemented.
984    
985    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * src/chm_common.c: coerce logical <-> double instead of
988            typecasting;  needed for "l" matrix handling in cholmod.
989    
990            * tests/other-pkgs.R (graph): small extension in "graph" checks.
991    
992            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
993            (Tsp2grNEL): other fixes needed
994    
995    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
998                    Matrices, since "lMatrix", also "lsparseM" can have NA
999            * R/ndenseMatrix.R, etc: new source files
1000            * man/nsparseMatrix-classes.Rd, etc: new help files
1001            * tests/: adaptions
1002            * src/chm_common.c (chm_dense_to_SEXP): and others:
1003                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1004            * src/Csparse.c, etc: ditto
1005    
1006    2006-09-11  Douglas Bates  <bates@R-project.org>
1007    
1008            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1009            alloc_d**Matrix functions to the lme4 package.
1010    
1011    2006-09-09  Douglas Bates  <bates@R-project.org>
1012    
1013            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1014            fixed
1015    
1016    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/lMatrix.R: new
1019    
1020            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1021    
1022            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1023            * man/tcrossprod.Rd: ditto
1024    
1025    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1026    
1027            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1028            for exported functions
1029            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1030            Remove partitioning algorithms for sparse matrix reordering.  The
1031            copyright on the Metis code was problematic and the methods were
1032            rarely used.
1033            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1034            operations are now done entirely in CHOLMOD code.
1035    
1036    2006-09-06  Douglas Bates  <bates@R-project.org>
1037    
1038            * src/Mutils.h: Remove functions that are no longer used.
1039    
1040    2006-09-04  Douglas Bates  <bates@R-project.org>
1041    
1042            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1043            * src/DEPS.mkf: update
1044    
1045    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1048            * DESCRIPTION (Version): 0.9975-0
1049            (Depends): R (>= 2.4.0)
1050    
1051    2006-09-01  Douglas Bates  <bates@R-project.org>
1052    
1053            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1054    
1055    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1058            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1059    
1060            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1061    
1062    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1065            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1066            * R/dsparseMatrix.R: ditto
1067            * R/Csparse.R: ditto
1068    
1069    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/dMatrix.R (Compare): improve availability of "<", etc
1072            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1073    
1074    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1077            of a 0-index which was used as 1-index (..hmm)
1078    
1079            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1080    
1081            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1082            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1083            (.is.diagonal): ditto
1084    
1085            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1086    
1087            * R/Matrix.R (Matrix): also work for NA data
1088    
1089    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1092            in all cases.
1093    
1094    2006-08-27  Douglas Bates  <bates@R-project.org>
1095    
1096            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1097            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1098    
1099    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1102            subclasses of "ddenseMatrix"
1103            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1104            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1105            instead of half dozen specialized ones.
1106    
1107    2006-08-25  Douglas Bates  <bates@R-project.org>
1108    
1109            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1110            <tillard@cirad.fr> - ordering standard errors to match effects.
1111    
1112    2006-08-24  Douglas Bates  <bates@R-project.org>
1113    
1114            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1115            on R_ldl.
1116            * R/lCholCMatrix.R,
1117            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1118            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1119            * many files in ./R and ./src: Use more general version of
1120            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1121            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1122            dtpMatrix, dspMatrix and dppMatrix conversions.
1123    
1124    
1125    2006-08-23  Douglas Bates  <bates@R-project.org>
1126    
1127            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1128            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1129            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1130            dgeMatrix_crossprod (may need to do this in other places).
1131            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1132            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1133    
1134    2006-08-22  Douglas Bates  <bates@R-project.org>
1135    
1136            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1137            types of classed Matrices, matrices or numeric or logical vectors.
1138            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1139            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1140            to Mutils.h (as an inline) and change name to Matrix_check_class;
1141            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1142            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1143            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1144            * src/Csparse.c: use diag_P and uplo_P macros.
1145    
1146    2006-08-21  Douglas Bates  <bates@R-project.org>
1147    
1148            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1149            valgrind.
1150            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1151            inverses.
1152            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1153            -Wall warnings.
1154            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1155            Use dup_mMatrix_as_dgeMatrix.
1156    
1157    2006-08-20  Douglas Bates  <bates@R-project.org>
1158    
1159            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1160            * tests/sparseQR.R: Added
1161            * man/sparseQR-class.Rd: Document methods for qr.* generics
1162            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1163    
1164    2006-08-19  Douglas Bates  <bates@R-project.org>
1165    
1166            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1167            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1168            and qr.fitted.
1169            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1170            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1171    
1172    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1175            the base version has no "..." argument.
1176    
1177            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1178    
1179            * R/Matrix.R: define and
1180            * NAMESPACE: export as.numeric() and as.logical() methods.
1181                    Let's hope these do not badly slow down something...
1182            Finally export the zapsmall() method.
1183    
1184    2006-08-17  Douglas Bates  <bates@R-project.org>
1185    
1186            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1187            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1188            * src/dtCMatrix.c :Remove code that is no longer used
1189            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1190    
1191    2006-08-14  Douglas Bates  <bates@R-project.org>
1192    
1193            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1194            Csparse_to_logical and Csparse_symmetric_to_general.
1195            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1196            coercion methods between CsparseMatrix and TsparseMatrix.
1197    
1198    2006-08-14  Douglas Bates  <bates@R-project.org>
1199    
1200            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1201            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1202            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1203            possible.
1204    
1205    2006-08-12  Douglas Bates  <bates@R-project.org>
1206    
1207            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1208              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1209              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1210              generalize conversions between TsparseMatrix, CsparseMatrix,
1211              denseMatrix and matrix.  Preserve triangularity property and
1212              propagate Dimnames in the easy cases.
1213    
1214    2006-08-10  Douglas Bates  <bates@R-project.org>
1215    
1216            * src/lmer.c: adjust checks in glmer_init for S4SXP
1217            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1218            before S4SXP but for the wrong reasons.
1219    
1220    2006-08-08  Douglas Bates  <bates@R-project.org>
1221    
1222            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1223            Later modified to return the upper triangle only.
1224            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1225    
1226    2006-08-07  Douglas Bates  <bates@R-project.org>
1227    
1228            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1229            R-level conversion to a sparse symmetric class.
1230            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1231            Remove conversion to sparse symmetric classes (now done in C code).
1232    
1233    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1236            * man/band.Rd:  adapt the \dontshow{} unit test.
1237    
1238    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1239    
1240            * DESCRIPTION (Version): 0.995-14  for CRAN
1241    
1242            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1243    
1244            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1245            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1246    
1247            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1248            * R/Tsparse.R (tril, triu, band): methods
1249            * R/dgRMatrix.R (tril, ...):    ditto
1250            * man/band.Rd:                  ditto
1251    
1252    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1253    
1254            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1255                    to be up-to-date automatically.
1256    
1257    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1258    
1259            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1260    
1261            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1262            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1263            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1264            such that the S4 objects are always created by the current version
1265            of R and 'Matrix' class definitions.
1266    
1267    2006-08-01  Douglas Bates  <bates@R-project.org>
1268    
1269            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1270            inst/external/test3comp.rda: Added warnings for convergence on
1271            boundary and test cases.
1272    
1273            * src/lmer.c (mer_postVar): Modified to return the variances that
1274            are marginal to the fixed effects, not conditional on them (which
1275            is what the bVar slot contents represent).
1276    
1277    2006-07-31  Douglas Bates  <bates@R-project.org>
1278    
1279            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1280            function which calls the C function mer_hat_trace2.
1281    
1282            * man/ranef.Rd: Include description of "postVar" argument and
1283            producing a caterpillar plot.
1284    
1285    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * NAMESPACE:    change  "correlation" to "corMatrix"
1288            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1289            * R/dpoMatrix.R: ditto
1290            * R/lmer.R:      ditto
1291    
1292    2006-07-28  Douglas Bates  <bates@R-project.org>
1293    
1294            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1295            RZXinv slot's contents into a separate internal function that can
1296            be used in mer_hat_trace.
1297    
1298    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1299    
1300            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1301            via new smart
1302            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1303            utility functions.
1304    
1305    
1306    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1309            matrices when appropriate; band() even symmetric ones.
1310            (replCmat): extend to potentially all "CsparseMatrix"
1311            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1312            allow subassignment for special sparse matrices.
1313    
1314            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1315    
1316            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1317            argument; in glmer_*(): print only if(verbose).
1318    
1319            speed-optimize a few places by moving REAL(.) out of loops.
1320    
1321            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1322    
1323    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1324    
1325            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1326                    since that wrongly triggers also for M[ logi , ]
1327    
1328            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1329            a symmetric matrix that results in a non-symmetric one.
1330            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1331    
1332            * R/dMatrix.R: make round(M) work as round(M, 0)
1333    
1334            * R/dgTMatrix.R (image): coordinate system and axis now use
1335            1-based indices, not 0-based ones.
1336    
1337            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1338            * tests/indexing.R: test it.
1339    
1340            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1341            * man/isSymmetric-methods.Rd: and document it.
1342    
1343            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1344            * man/SparseM-conv.Rd: docu them
1345    
1346            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1347                    for 'SparseM' conversions
1348    
1349    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1350    
1351            * R/Matrix.R (head): added head() and tail() methods.
1352    
1353    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * DESCRIPTION (Version): 0.995-12 released to CRAN
1356    
1357    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * tests/simple.R: add check for correct dsT -> dgT coercion;
1360                    add check for correct printing of symmetric sparse matrices.
1361    
1362            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1363            for sparse symmetric matrices.
1364    
1365            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1366            diagonal twice.
1367    
1368    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1369    
1370            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1371            being applied to the x slot (detected by Brian Ripley).
1372    
1373    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1376    
1377            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1378    
1379    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1380    
1381            * src/lgCMatrix.c (lgCMatrix_diag): new function
1382            * R/lgCMatrix.R (diag): for new method
1383    
1384            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1385                 ==> construction of illegal "*gTMatrix" via new() should
1386                 now be much less easy:
1387            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1388    
1389            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1390                    directly.
1391            * man/Matrix.Rd: documents it.
1392    
1393    2006-07-06  Douglas Bates  <bates@R-project.org>
1394    
1395            * src/pedigree.c (pedigree_inbreeding): Correction in
1396            initialization.  This function is not currently being used and is
1397            not fully tested.
1398    
1399            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1400            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1401            objects.  Modified validity check on pedigree objects to account
1402            for nonparallel patterns of missingness of parents.
1403    
1404            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1405            class.
1406    
1407    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1408    
1409            * R/pMatrix.R: coercion pMatrix -> Tsparse
1410    
1411    2006-06-12  Douglas Bates  <bates@R-project.org>
1412    
1413            * DESCRIPTION (Version): 0.995-11 released to CRAN
1414    
1415            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1416            the output from mcmcsamp.
1417    
1418    2006-06-10  Douglas Bates  <bates@R-project.org>
1419    
1420            * R/lmer.R (simulestimate): added C code for calculating the trace
1421            of the hat matrix.
1422    
1423    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1424    
1425            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1426            classes.
1427            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1428    
1429    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1430    
1431            * R/dgTMatrix.R (colSums): etc. All four of
1432            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1433            all "Matrices".
1434    
1435    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1436    
1437            * R/lmer.R (panel.ci): Add a reference line at zero and a
1438            background grid to the qqmath plot of ranef.lmer.
1439    
1440    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1441    
1442            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1443            grouping factors to be specified in the formula as (1|foo/bar).
1444    
1445    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1446    
1447            * R/lmer.R (findbars and others): Change check of is.numeric to
1448            !is.language to resolve the bug reported by Jacob Wegelin.
1449    
1450            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1451            code to evaluate inbreeding coefficients without calculating T,
1452            based on code in Sargolzaei and Iwaisaki's paper.
1453    
1454    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1455    
1456            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1457            generic and mer methods for isNested and denomDF. This denomDF was
1458            an attempt to emulate that in lme but I don't think that makes
1459            sense.  Use the trace of the hat matrix instead.
1460    
1461    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1462    
1463            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1464            the C code depending on a slot structure that's no longer valid.
1465            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1466    
1467    
1468    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1469    
1470            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1471            of lowerTriMatrix generic and methods to tril (also upper to triu)
1472            and added a general band extractor.
1473    
1474    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1475    
1476            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1477            allowable range with NAs. Added a corresponding check in the
1478            validity check for the pedigree class.
1479    
1480            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1481            crossprod methods now inherits from symmetricMatrix.
1482    
1483    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1484    
1485            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1486            generics lowerTriMatrix and upperTriMatrix along with methods for
1487            the Csparse virtual class.  Also added a C function Csparse_band
1488            that implements these methods by calling cholmod_band.
1489    
1490    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1491    
1492            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1493            erased when it was NULL.  This led to invalid subselections!
1494    
1495    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1496    
1497            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1498            in method for "t" so as not to lose the unit diagonal property.
1499    
1500    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1501    
1502            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1503            and methods.  This is now an option to the ranef method for the
1504            mer class.
1505    
1506            * src/cs_utils.c: Ensure that the nz component is -1 for a
1507            compressed column-oriented matrix.  Minor formatting cleanup.
1508    
1509            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1510            objects.
1511    
1512    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1513    
1514            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1515            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1516    
1517    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1518    
1519            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1520            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1521    
1522            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1523            for the dtCMatrix class.
1524    
1525    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1526    
1527            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1528            and methods for it.
1529    
1530    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1531    
1532            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1533            arguments, such that M %*% 1:6 now works
1534            * Tests/matprod.R: test the above
1535    
1536    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1537    
1538            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1539            the ranef.lmer class.
1540    
1541            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1542            methods to extract the posterior variances from the bVar slot.
1543    
1544    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1545    
1546            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1547            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1548    
1549            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1550            * tests/simple: (extended)
1551    
1552            * R/sparseMatrix.R (isTriangular): now using much improved
1553            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1554    
1555    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1556    
1557            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1558            (problem report from Franklin Parlamis).  This should be done
1559            generally.
1560    
1561    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1562    
1563            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1564            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1565            update the plot methods.
1566    
1567    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1568    
1569            * R/lmer.R (resid and ranef methods):  Added methods for the
1570            "residuals" and "resid" generic but only for linear mixed model
1571            fits.  Changed the ranef method to return a list of data frames so
1572            that the plot methods now work.
1573    
1574    2006-03-16  Douglas Bates  <bates@bates2>
1575    
1576            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1577            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1578    
1579            * DESCRIPTION (Date): New release
1580    
1581    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1582    
1583            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1584    
1585            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1586            * man/KNex.Rd: and other help files
1587            * tests/*.R: several ones needed adaption
1588            * inst/doc/Comparisons.Rnw: ditto
1589    
1590    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1591    
1592            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1593    
1594            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1595    
1596    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1597    
1598            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1599    
1600            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1601    
1602    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1603    
1604            * R/dMatrix.R: enable things like  M [ M < 10 ]
1605            * R/dgeMatrix.R: implement it
1606    
1607    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1608    
1609            * R/AllClass.R: define "summary.mer" and "*.lmer"
1610            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1611            * R/lmer.R (show): now works with summary()
1612    
1613    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1614    
1615            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1616            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1617                    support the above
1618    
1619    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1620    
1621            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1622            Use glmFit$prior.weights for weights in a glmm.
1623            Allow an option usePQL = FALSE to skip the PQL steps for the
1624            Laplace method (and, in time, the AGQ method).
1625    
1626            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1627            into a separate function internal_mer_Xfactor to be able to call
1628            it from internal_bhat.
1629    
1630    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * tests/Class+Meth.R (tstMatrixClass): function for much better
1633            testing; now again of all actual classes.
1634    
1635            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1636                    use macros and define make_d_matrix_* and make_i_matrix_*
1637                    where _i_ is for the ldense routines:
1638    
1639            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1640            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1641    
1642            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1643    
1644    
1645    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1646    
1647            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1648                    many different kinds of matrices.
1649            * R/*.R: quite a few new methods were needed for R CMD check with
1650                    new Matrix().  Very good for users playing around.
1651    
1652    
1653    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1654    
1655            * src/dgeMatrix.c (dMatrix_validate): new
1656            * src/Mutils.c (dense_nonpacked_validate): new
1657    
1658            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1659    
1660    
1661    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1662    
1663            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1664    
1665    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1666    
1667            * DESCRIPTION (Version): 0.99-6 released to CRAN
1668    
1669            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1670            segfault in cases with multiple non-nested grouping factors.
1671    
1672    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1673    
1674            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1675                    (Depends): also on 'utils'
1676    
1677            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1678            * R/diagMatrix.R (Diagonal): constructor and methods for
1679            diagonal matrices
1680    
1681            * R/ltTMatrix.R: new "minimal methods"
1682    
1683    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1684    
1685            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1686            all methods (and help files).
1687    
1688    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1689    
1690            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1691                    for case (dimn.  op  no_dimn.)
1692    
1693    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1694    
1695            * DESCRIPTION (Version): 0.99-2  released to CRAN
1696    
1697    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1698    
1699            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1700            by Julian Faraway.
1701    
1702    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1703    
1704            * R/Auxiliaries.R (try_as): new utility
1705            * R/sparseMatrix.R: use try_as() in coercion to original class
1706    
1707    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1708    
1709            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1710    
1711    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1712    
1713            * R/Auxiliaries.R (dimNamesCheck): added
1714    
1715            * R/Matrix.R (as.array), (as.vector): new
1716    
1717    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1718    
1719            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1720                    default.
1721            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1722                    "pMatrix" now contains "sparseMatrix"
1723    
1724    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1725    
1726            * tests/Class+Meth.R: new tests; t(t(m)) == m
1727    
1728            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1729    
1730            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1731            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1732    
1733            * R/dspMatrix.R: typo in "t" method
1734    
1735    2005-09-18  Douglas Bates  <bates@wisc.edu>
1736    
1737            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1738            * R/Tsparse.R: instead of R/gTMatrix.R
1739            * R/Csparse.R: new
1740            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1741            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1742            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1743                            via cholmod
1744    
1745    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1746    
1747            * R/Auxiliaries.R (non0ind): new function using new C code
1748            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1749    
1750    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1751    
1752            * src/chm_common.h: header file required by all C sources that
1753            call CHOLMOD functions.  It defines a cholmod_common structure
1754            called 'c' whose address is passed as the last argument to
1755            (virtually) every CHOLMOD function.
1756    
1757            * src/Pattern.c: Simple example of the use of CHOLMOD.
1758    
1759            * src/init.c: initialize and finalize the cholmod_common structure.
1760    
1761            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1762            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1763    
1764    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1765    
1766            * inst/test-tools.R: new file collecting the utility functions used
1767                    in ./tests/*.R
1768    
1769            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1770            * R/Matrix.R (cbind2): methods for NULL and missing
1771    
1772    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1773    
1774            * R/AllClass.R: new "index" class for "[" and "[<-":
1775                    First cut at "symmetricMatrix" and "triangularMatrix"
1776            * R/gTMatrix.R (.ind.prep): new function;
1777                    Logical and character indexing now work too.
1778            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1779            * tests/indexing.R: new, including *.Rout.save
1780            * tests/dgTMatrix.R: new
1781    
1782    2005-08-29  Douglas Bates  <bates@wisc.edu>
1783    
1784            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1785            indicator pos not being updated.  Also enforced upper triangular
1786            for symmetric case.  Need to coerce edges component of elements of
1787            edge list - grr! (Why don't they define their classes cleanly?)
1788    
1789    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1790    
1791            * R/Matrix.R:  added first "[<-" methods; not yet functional
1792            * R/denseMatrix.R: ditto
1793            * man/Subassign-methods.Rd: new help file for these
1794    
1795    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1796    
1797            * DESCRIPTION (Version): 0.98-6
1798    
1799            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1800            matrices.
1801    
1802    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1803    
1804            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1805                    as( <logical>, "matrix")
1806    
1807            * R/pMatrix.R: coercion to "lgTMatrix"
1808    
1809            * R/gTMatrix.R: new virtual class to define "[" methods for.
1810            * man/gTMatrix-class.Rd:
1811            * General slight re-organization of where "[" methods are defined.
1812              more to come.
1813    
1814    2005-08-18  Douglas Bates  <bates@wisc.edu>
1815    
1816            * DESCRIPTION (Version): 0.98-5  released to CRAN
1817    
1818            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1819            * .....
1820    
1821    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1822    
1823            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1824            or glmer objects.
1825    
1826    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1827    
1828            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1829    
1830    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1831    
1832            * R/HBMM.R: finish re-writing R-only code.
1833    
1834    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1835    
1836            * man/externalFormats.Rd: move documentation for writeHB and
1837            writeMM here.
1838    
1839            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1840            (suggested by Paul Roecker).
1841    
1842            * tests/validObj.R (assertError): Comment out test that is failing
1843            after recent changes in r-devel.
1844    
1845    
1846    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1847    
1848            * R/AllClass.R: intermediate virtual class "denseMatrix"
1849            * man/denseMatrix-class.Rd
1850            * NAMESPACE: export it, and also export
1851            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1852    
1853    2005-08-10  Douglas Bates  <bates@wisc.edu>
1854    
1855            * DESCRIPTION (Version): 0.98-3 to CRAN
1856    
1857            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1858            matrix_solve code (which was really, really wrong).
1859    
1860    2005-08-07  Douglas Bates  <bates@wisc.edu>
1861    
1862            * DESCRIPTION (Version): 0.98-2
1863    
1864            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1865    
1866            * R/lmer.R (abbrvNms): new
1867            * R/lmer.R (mcmcsamp): allow transformed parameters
1868            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1869            for the Harwell-Boeing and the MatrixMarket formats.
1870    
1871    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1872    
1873            * man/dtrMatrix-class.Rd: add examples
1874            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1875    
1876            * TODO: note the dtpMatrix (docu) bug
1877    
1878            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1879            in order to ensure that new as.matrix() is used by old functions,
1880            e.g., svd(), qr(), eigen(), dist(),..;
1881                  apply(), also matplot() or pairs().
1882    
1883    
1884    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1885    
1886            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1887              add comments about 'control' / lmerControl() arguments
1888    
1889    2005-07-27  Douglas Bates  <bates@wisc.edu>
1890    
1891            * man/sleepstudy.Rd: Added the sleep data set.
1892            * DESCRIPTION (Version): 0.98-1  released to CRAN
1893    
1894    2005-07-12  Douglas Bates  <bates@wisc.edu>
1895            * man/sleepstudy.Rd: Added the sleep data set.
1896    
1897            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1898            .Call calls that were producing spurious output.
1899    
1900    2005-07-05  Douglas Bates  <bates@wisc.edu>
1901    
1902            * R/lmer.R (lmer): stored updated variance component estimates in
1903            mer object for the generalized model.  (Bug reported by Renaud
1904            Lancelot).
1905    
1906    2005-07-03  Douglas Bates  <bates@wisc.edu>
1907    
1908            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1909            unidimensional case.
1910    
1911    2005-06-08  Douglas Bates  <bates@wisc.edu>
1912    
1913            * DESCRIPTION (Version): 0.96-1
1914    
1915            * moved  lmer-class' R and C code moved from lme4 to here
1916    
1917    2005-06-04  Douglas Bates  <bates@wisc.edu>
1918    
1919            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1920            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1921    
1922    2005-06-02  Douglas Bates  <bates@wisc.edu>
1923    
1924            * src/Makefile.win: Forgot to update this when Makefile changed.
1925    
1926    2005-05-11  Douglas Bates  <bates@wisc.edu>
1927    
1928            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1929            bug reported by Kurt Hornik and Michael Hahsler.
1930    
1931    2005-05-10  Douglas Bates  <bates@wisc.edu>
1932    
1933            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1934            logical sparse matrices.  These will also be used in the symbolic
1935            analysis for lmer objects.
1936    
1937            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1938            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1939    
1940    2005-05-06  Douglas Bates  <bates@wisc.edu>
1941    
1942            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1943            colMeans, colSums, rowMeans and rowSums.
1944    
1945    2005-04-18  Douglas Bates  <bates@wisc.edu>
1946    
1947            * src/lgCMatrix.[ch]: code for _validate method and stub for
1948            multiplication operation.
1949    
1950            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1951            to dgetrs.
1952    
1953            * src/init.c: Fix cut-and-paste error in definition of
1954            dgeMatrix_matrix_solve
1955    
1956            * src/{many files}: Tighten code by using ALLOC_SLOT.
1957    
1958    2005-04-15  Douglas Bates  <bates@wisc.edu>
1959    
1960            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1961    
1962            * DESCRIPTION: Eliminate import of stats.
1963    
1964    
1965    2005-04-06  Douglas Bates  <bates@wisc.edu>
1966    
1967            * R/AllClass.R : add logical sparse matrix classes
1968    
1969    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1970    
1971            * R/dgTMatrix.R: add "[" method for triplet matrices
1972            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1973    
1974    2005-03-31  Douglas Bates  <bates@wisc.edu>
1975    
1976            * DESCRIPTION (Version): release 0.95-5 to CRAN
1977    
1978            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1979            * R/sparseMatrix.R: %*%, crossprod()
1980            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1981            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1982            * src/lmer.c (lmer_fitted): fix thinko
1983    
1984    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1985    
1986            * R/AllClass.R: add two virtual sparse classes ``on top''
1987    
1988    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1989    
1990            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1991                    correspondingly fix examples and tests/ since new()
1992                    doesn't work for virtual classes.
1993    
1994    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1995    
1996            * R/Matrix.R (as.matrix): method and one for unname()
1997            * tests/dpoMatrix.R: tests should now be less platform dependent;
1998              also run for R 2.1.0; using as.matrix()
1999    
2000    2005-03-15  Douglas Bates  <bates@wisc.edu>
2001    
2002            * R/pMatrix.R: "pMatrix" class added
2003            * ....
2004    
2005    2005-03-14  Douglas Bates  <bates@wisc.edu>
2006    
2007            * R/dtpMatrix.R: Add unpack method and an example.
2008    
2009            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2010            of general symmetric matrices and associated S4 methods.
2011    
2012    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2013            +
2014    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2015    
2016            * R/dgeMatrix.R (setAs): and many other files: more coercion,
2017              crossprod() and "%*%" methods added; tests, too.
2018            * tests/matprod.R: new, for testing these
2019    
2020    2005-03-03  Douglas Bates  <bates@wisc.edu>
2021    
2022            * src/lmer.c (lmer_fitted): Added.
2023    
2024    2005-03-02  Douglas Bates  <bates@wisc.edu>
2025    
2026            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2027    
2028    2005-02-28  Douglas Bates  <bates@wisc.edu>
2029    
2030            * src/*.c,po/,inst/po: Internationalization and localization of
2031            the package.
2032    
2033            * src/ldl.[ch]: Removed these as their contents are referenced in the
2034            R_ldl.c file.
2035    
2036            * src/flame.[ch]: Removed these source files.
2037    
2038            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2039    
2040            * src/LU.[ch],src/init.c: absorb in factorizations
2041    
2042            * src/Mutils.h: prepare for internationalization
2043    
2044            * src/cblas.h: move the enum definitions to Mutils.h and remove
2045            this file
2046    
2047    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2048    
2049            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2050    
2051            * R/dtrMatrix.R: fix t() method
2052    
2053            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2054            * NAMESPACE: export them (and import generics from "methods")
2055            * tests/group-methods.R : and test them.
2056    
2057            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2058            border case
2059    
2060    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
2061    
2062            * DESCRIPTION (Version): 0.95-2  released to CRAN
2063    
2064            * src/dgBCMatrix.c:
2065            * src/lmer.c: many changes
2066            * ...
2067    
2068    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2069    
2070            * R/Matrix.R: add more sophisticated show() method.
2071    
2072    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
2073    
2074            * */* : almost complete reorganization of classes.
2075    
2076    2005-01-26  Douglas Bates  <bates@wisc.edu>
2077    
2078            * R/AllGeneric.R: Added matrix exponential generic expm and a method
2079            for the geMatrix class.
2080    
2081    2005-01-24  Douglas Bates  <bates@wisc.edu>
2082    
2083            * src/Makefile (clean): Remove *.a and *.so
2084    
2085            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2086    
2087    2005-01-23  Douglas Bates  <bates@wisc.edu>
2088    
2089            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2090            had an effect in cases with more than 2 grouping factors.
2091    
2092    2005-01-03  Douglas Bates  <bates@wisc.edu>
2093    
2094            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2095    
2096    2004-12-23  Douglas Bates  <bates@wisc.edu>
2097    
2098            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2099            and R_useDynamicSymbols (suggested by B.D.Ripley).
2100    
2101    2004-12-14  Douglas Bates  <bates@wisc.edu>
2102    
2103          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
2104    
2105          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2106          for tripletMatrix to matrix.          for tripletMatrix to matrix.
2107    
2108  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
2109    
2110          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2111          no longer used.          no longer used.
# Line 17  Line 2117 
2117          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
2118          Fixes part but not all of #15.          Fixes part but not all of #15.
2119    
2120  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
2121    
2122          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2123          scalar grouping factors corrected.          scalar grouping factors corrected.
2124    
2125  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
2126    
2127          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
2128    
2129  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
2130    
2131          * 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
2132          .h file can be included.          .h file can be included.
2133    
2134  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2135    
2136          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2137          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2138    
2139          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2140    
2141  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2142    
2143          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2144    
2145  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2146    
2147          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2148    
2149  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2150    
2151          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2152    
2153  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2154    
2155          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2156    
2157  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2158    
2159          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2160          routines.          routines.
2161    
2162  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2163    
2164          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2165    
2166  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2167    
2168          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2169    

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