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revision 10, Mon Mar 22 20:20:05 2004 UTC revision 1968, Sat Jul 7 22:49:12 2007 UTC
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1    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (compressed_to_TMatrix):
4    
5    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * src/Csparse.c (Rsparse_validate): new, to have some validity
8            checking for RsparseMatrix
9            * src/dgCMatrix.c (xRMatrix_validate): ditto
10            * src/dtCMatrix.c (tRMatrix_validate): ditto
11    
12    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
13    
14            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
15              lgRMatrix
16            * [r4568] DESCRIPTION: Prepare for bug-fix release
17            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
18              for declaration of cholmod_symmetry
19    
20    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
23            release.
24    
25    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
28              functions - no longer used
29            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
30              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
31              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
32              Alloca
33    
34    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
35    
36            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
37              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
38              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
39              src/t_gCMatrix_colSums.c: more R_CheckStack()s
40    
41    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
44              the required amount of memory then call M_numeric_as_chm_dense.
45            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
46              (like Calloc but calling alloca)
47    
48    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
51            and extended with more sophisticated 'col.names' option.
52            * NAMESPACE: export  printSparseMatrix()
53            * man/printSpMatrix.Rd: document, incl. examples
54    
55    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
58              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
59              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
60    
61    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.99875-4
64    
65            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
66            some dimnames perservation.
67    
68            * R/dsTMatrix.R (t-method): keep dimnames
69            * R/dtTMatrix.R:  ditto
70    
71            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
72            and ncol(.) < 10
73    
74            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
75            from Mutils.h
76    
77            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
78            e.g. in as(<ngCMatrix>, "matrix")
79    
80    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r4529] .: Create a branch for the API changes from the 0.99875
83              series to the 0.999375 series
84            * [r4530] DESCRIPTION, inst/include/Matrix.h,
85              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
86              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
87              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
88              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
89              as_cholmod_x functions
90    
91    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
92    
93            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
94              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
95              to Comparisons
96    
97    >>>>>>> .merge-right.r4561
98    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): 0.99875-3 ready to be released.
101    
102            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
103    
104            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
105            that should also work in a future version of R.
106    
107    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
110    
111            * R/sparseVector.R: more *sparseVector coercions, notably for
112            non - double ones.
113    
114    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
117              notably the new ones building on the new .Call(.)s:
118    
119            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
120            all 4 of [dlin]gCMatrix_colSums().
121    
122    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
123    
124            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
125            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
126              result
127    
128    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/kronecker.R: fix typo (could lead to inf.recursion)
131            * test/simple.R: testing that
132    
133            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
134            method as well (which can have arguments, show() can't).
135    
136    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
139              added dgCMatrix_colSums for [col,row][Sums,Means]
140    
141    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
142    
143            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
144              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
145              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
146            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
147              class
148            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
149              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
150              row names to store the levels - duh!  Added an example.
151    
152    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Csparse.c (Csparse_validate): check for *repeated* entries
155            thanks to example from Christian Buchta; with a test here:
156            * tests/simple.R:
157    
158    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
161            of colSums(*, sparseResult = TRUE)
162    
163    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
166            'na.rm = FALSE' as "everywhere" else in R.
167    
168    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
169    
170            * [r4421] src/CSparse_install.sh: Modify for new organization of
171              CSparse package
172            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
173              SuiteSparse
174            * [r4426] src/Makefile: add ./UFconfig to the include path for
175              compilation
176            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
177            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
178              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
179    
180    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
183            * R/sparseMatrix.R (prSpMatrix): now gives a message about
184            suppressed column names.
185    
186    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
187    
188            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
189              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
190              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
191              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
192              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
193              Remove warnings after change to const char* CHAR
194    
195    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
198              type of M_cholmod_ssmult
199    
200    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
203              src/init.c: Yet another cholmod export - cholmod_ssmult
204    
205    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * NAMESPACE: exported drop0(), since
208            * man/drop0.Rd: I have seen several cases, I really wanted to use
209            it, so our users may want too.
210    
211    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * man/colSums.Rd: separately document colSums() etc, since these
214            have the extra argument 'sparseResult'.
215    
216    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
219            * man/spMatrix.Rd: docu., including examples
220    
221            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
222            in order to make colMeans() etc fast *and* correct.
223            * R/sparseVector.R (replSPvec): "[<-" functionality for
224            sparseVectors; tested in
225            * tests/simple.R:
226    
227    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
230            (very) sparse Matrices; output similar to Matlab's print().
231    
232    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
235            0-based, indices (Jose Quesada <quesada@gmail.com>).
236    
237    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
240    
241    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Auxiliaries.R (sparsapply): new utility, much faster than
244            tapply1() for large sparse matrices.
245    
246    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R (dim<-): reshape now via sparseVector.
249    
250            * R/sparseVector.R: methods and function for
251            * R/AllClass.R: new "sparseVector" class and daughters.
252            * NAMESPACE: export new classes
253    
254    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * DESCRIPTION (Version): 0.99875-1
257            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
258    
259    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
262            indexing
263            * tests/indexing.R: test set for that.
264    
265    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
268            entries.
269            * tests/indexing.R(out): add regression test for it
270    
271    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
274            name for "!" method definitions.
275    
276    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Tsparse.R (intI): new utility, used for "[" :
279                    Cleanup up there, and fixes for duplicated indices - more TODO!
280    
281            * tests/indexing.R(out): more tests
282    
283    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
286            code that is now part of the R Lapack library.
287    
288            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
289            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
290    
291    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
294    
295    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
298            up with extraneous names '0'...'<n-1>'
299    
300    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgTMatrix.R (mat2dgT): care about NAs
303    
304    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/kronecker.R: triangularity preserving methods
307    
308    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/kronecker.R: new file collecting kronecker() methods in one
311                    place.  Goal: become much faster!
312    
313    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
316            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
317            can be much faster.
318    
319            * tests/matprod.R: add regression tests for these (upper & lower).
320    
321    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/Matrix.R (diff): method for our Matrices.
324    
325            * R/sparseMatrix.R (isDiagonal): check dim()!
326    
327    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/Matrix.R (dim<-): new method for "reshape()" built on a
330            proposal from Tamas Papp.
331    
332    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
335    
336            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
337            rather define and export  cBind() and rBind() only.
338            --> useRs *must* change code that used to have cbind()/rbind() !!
339    
340            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
341            * R/bind.Rout.save: ditto
342    
343    2007-02-16  Douglas Bates  <bates@r-project.org>
344    
345            * DESCRIPTION (Date, Version): 0.9975-11 with new date
346            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
347            const modifier on declaration of the array 'valid'
348    
349    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
352    
353    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
356    
357            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
358            * tests/simple.R: test the above and some of these coercions:
359    
360            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
361                    be careful to avoid infinite recursion, using new coercions in
362            * R/ngCMatrix.R and nsC... and ntC...
363            * R/lsparseMatrix.R: ditto
364    
365            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
366    
367            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
368            * R/Rsparse.R: reactivate .Call()s
369    
370            * tests/Class+Meth.R: a bit more on actual classes
371    
372    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
375    
376    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version): 0.9975-10 to upload
379    
380            * tests/Class+Meth.R (tstMatrixClass): require coercions to
381            specific classes less unconditionally.
382    
383            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
384    
385            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
386    
387            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
388            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
389            R_to_CMatrix segfaults on one platform.
390            Eliminate most coercion method to *specific* classes, and replace
391            with virtual classes coercions.
392    
393    
394    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * src/init.c: export the CHM...._validate() placeholders, since
397            they *are* called.
398    
399            * tests/Class+Meth.R (classCanCoerce): and starting to test
400            all as(<from>, <to>)
401    
402    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
405            * tests/indexing.R: tested now
406            * tests/indexing.Rout.save: updated
407    
408            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
409            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
410            appropriate.
411    
412            * NAMESPACE: export a trivial
413            * R/Matrix.R: drop() Matrix-method
414    
415            * R/AllClass.R: moved all prototypes to virtual super classes.
416    
417            * R/Rsparse.R: many more coercions to have less exceptions in
418            * tests/Class+Meth.R:
419    
420            * R/Ops.R (Compare): tweak for case with NA
421            * tests/simpl.R: hence another 'FIXME' eliminated
422    
423    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
426            objects.
427    
428            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
429              and more of "!", "&", "|", all, any; coercions
430    
431            * R/Rsparse.R: many coercions (which enable quite a few other
432            methods), thanks to enhancements in
433            * src/dgCMatrix.c (R_to_CMatrix): new, and
434            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
435            symmetric & triangular and ..RMatrix objects.
436    
437            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
438            renamed file from src/dsTMatrix.c;
439            now dealing with symmetric and triangular Tsparse coercions, both
440            to dense and general.
441    
442    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
445    
446            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
447            where sensible when the <numeric> is of length > 1.
448    
449    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R ([<-): for M[] <- value: fix length
452    
453    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
456            * R/ndenseMatrix.R: new coercions n* -> l*
457    
458    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
461    
462            * R/Ops.R ("Logic"): and other "Ops", many updates
463    
464    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * src/Mutils.h (SET_DimNames): new utility
467    
468            * R/Auxiliaries.R (nnzero): improved and now exported via
469    
470            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
471    
472    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/diagMatrix.R (!): fix typo.
475    
476    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Auxiliaries.R (as_Csparse): and quite a few others:
479                    allow to pass class definition --> speedup
480            * R/sparseMatrix.R: apply the above
481    
482            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
483    
484            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
485            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
486            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
487    
488            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
489    
490            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
491            and use it for "sparse*" as well, since it's faster than the
492            as_Csparse(.) way.
493    
494    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
497    
498    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
501            as method for   M[ ij ] <- v
502            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
503    
504            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
505            FALSE answer
506    
507            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
508            * tests/indexing.R: test it, and some of the above
509    
510    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/Auxiliaries.R (is_duplicatedT): new utility
513    
514    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * src/init.c (R_init_Matrix): export cholmod_scale
517    
518    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
521            base::as.matrix to (x, ...)
522    
523    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
526            file; start using "Logic", hence
527    
528            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
529            * NAMESPACE: import and export "Logic"
530    
531    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
534            only needed previously to R version 2.5.0.
535    
536    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
539    
540            * R/Tsparse.R (replTmat): fix subassignment of triangular
541            * R/Csparse.R (replCmat): ditto
542            * tests/indexing.R: more tests, incl the above fix
543    
544    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/Auxiliaries.R (drop0): extend for non CSparse
547            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
548    
549            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
550                    use uplo correctly (!); other places: use uplo_P() macro
551    
552            * R/Csparse.R (replCmat): call diagU2N() when needed
553            * R/Tsparse.R (replTmat): ditto
554    
555            * src/dtCMatrix.c (tCMatrix_validate): new
556            * src/dtTMatrix.c (tTMatrix_validate): new, used in
557            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
558    
559            * R/diagMatrix.R (replDiag): to use in [<-
560    
561    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
564                    also more general diagU2N().
565    
566    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
569            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
570    
571    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * tests/bind.R: a few more cases
574            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
575    
576            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
577            * R/ddenseMatrix.R (cbind2/rbind2)
578            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
579            * tests/indexing.R
580            * tests/indexing.Rout.save: updated
581    
582    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
585            * tests/indexing.R
586    
587    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
590            align with proper position of "0", i.e., right for integers.
591            argument 'align' by default is "fancy".
592    
593    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
596            * R/Csparse.R: and fix "Compare" for more cases.
597            * tests/Class+Meth.R: test some of these (m == m, m != m)
598    
599    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/lsparseMatrix.R: all() and any() methods
602            * R/ldenseMatrix.R:      ditto
603            * NAMESPACE, R/Matrix.R: ditto
604    
605            * man/all-methods.Rd: document them minimally
606    
607            * tests/simple.R: add a few examples for these
608    
609    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Tsparse.R ([): fix long standing typo in symmetric case
612            * man/dsCMatrix-class.Rd: add example exhibiting the above case
613    
614    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
617            to LL before converting to a sparse matrix. (The LDL form can be
618            converted to a sparse matrix but it is implicitly a unit
619            triangular matrix and a diagonal matrix overwritten on the diagonal.)
620    
621    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
622    
623            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
624    
625    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * DESCRIPTION (Version): updated -> release 0.9975-7
628            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
629    
630    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
633    
634    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
637            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
638            is exactly singular.
639    
640    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Date): updated -> release 0.9975-6
643    
644    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
647            now returns symmetric.
648    
649            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
650    
651            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
652            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
653    
654            * R/Auxiliaries.R (.type.kind): added
655    
656    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
659            running src/CSparse_install.sh
660    
661            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
662    
663    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
666            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
667    
668            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
669    
670            * tests/Class+Meth.R (tstMatrixClass): now assure
671            the (important in method programming) property :
672    
673                    ###>>  Every "Matrix" is either
674                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
675    
676                    (where "*" stands for "Matrix")
677    
678            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
679    
680            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
681            * tests/validObj.R: checks for "comparison"
682    
683            * R/sparseMatrix.R ([): improved indexing for sparse;
684                    trying to keep <symmetric>[ n, n] symmmetric
685    
686            * tests/indexing.R: indexing for logical sparse now ok
687    
688    
689    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * src/Tsparse.c: use xTsparse_validate() , and hence remove
692    
693            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
694    
695    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
698    
699            * tests/simple.R: validObject() checking the above.
700    
701            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
702            replacing both dgCMatrix_validate and lgCM*.
703    
704            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
705            fix dimnames setting in other places.
706            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
707    
708    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
711    
712            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
713            symmetry test, via
714            * R/Auxiliaries.R (.as.dgC.0.factors):
715    
716    2006-11-01  Douglas Bates  <bates@r-project.org>
717    
718            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
719            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
720            <CsparseMatrix>) added
721    
722    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * tests/matprod.R: add a variation of Harri's example
725    
726            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
727            recursive infinitely.
728    
729            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
730    
731            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
732    
733    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
736            matrix if possible; test m+m == 2*m; now test dgRMatrix.
737            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
738            satisfy the above test.
739    
740    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
743    
744            * R/dgCMatrix.R: solve(a, b="missing") based on
745            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
746            RHS = NULL.
747    
748            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
749            add more (needed) [t]crossprod() methods.
750    
751            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
752    
753            * R/Auxiliaries.R (as_CspClass): cleanup
754            (drop0): internal utility for "Csparse_drop(*, 0)"
755            (.bail.out.2): encourage active feedback
756    
757    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/dMatrix.R(Compare): new(), then slots [no validity check]
760    
761            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
762            non-valid or 'sorted' case).
763    
764            * R/dsparseMatrix.R: add "chol" method.
765            * R/ddenseMatrix.R: ditto
766    
767            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
768            * NAMESPACE (Ops)
769            * R/diagMatrix.R (diag2T): simple utility used "higher level"
770            coercion; deprecating direct lower level coercions.
771    
772            * R/*.R (seq): use seq_len() and seq_along() where possible.
773    
774    
775    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * DESCRIPTION (Version): 0.9975-5 ready for release
778    
779    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
782    
783    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/AllClass.R (corMatrix): add 'validity' check;
786                    comment out unused "LDL" class definition
787            * NAMESPACE: mention, but do not export "LDL" class
788            * R/corMatrix.R: new (simple), needed for R-devel with
789            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
790              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
791    
792    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
795            use Rprintf and R's error handling.
796    
797    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
800            * tests/matprod.R: add tests for the bug fixed.
801    
802    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
803    
804            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
805            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
806    
807    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
808    
809            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
810    
811    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * DESCRIPTION (Version): 0.9975-3
814    
815            * R/diagMatrix.R (bdiag): new function constructing block diagonal
816            (sparse) matrices.
817            * man/bdiag.Rd: docu + examples
818    
819            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
820    
821            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
822            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
823    
824            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
825            that result is sparse or diagonal (and not dense).
826    
827            * man/Subassign-methods.Rd: fix examples
828    
829            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
830            should always return a sparse (and not sometimes a diagonal) matrix.
831    
832    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
835    
836    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
837    
838            * DESCRIPTION (Version): 0.9975-2
839    
840            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
841    
842    2006-10-02  Douglas Bates  <bates@R-project.org>
843    
844            * tests/dg_Matrix.R: Simplify test taking into account new code.
845    
846    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
849    
850            * R/lsTMatrix.R: new files w/ missing methods
851            * R/nsTMatrix.R:  "  'for completeness'
852    
853            * tests/Class+Meth.R: a bit less 'not.ok.classes'
854    
855            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
856    
857    
858    2006-09-28  Douglas Bates  <bates@R-project.org>
859    
860            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
861            included.
862    
863            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
864            Export C-callable functions used in Zt_create in lme4.
865    
866    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * DESCRIPTION (Version): 0.9975-1
869    
870            * tests/simple.R: less checks fail; using NA, found that our
871                    kronecker() is not base-compatible with NA's.
872    
873            * R/dMatrix.R: "Compare" method now implemented for all cases
874    
875            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
876    
877            * man/dtpMatrix-class.Rd: mention length of 'x' slot
878    
879            * src/dtpMatrix.c (dtpMatrix_validate): fix check
880            * src/dspMatrix.c (dspMatrix_validate): ditto
881    
882            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
883              including coercion to [nl]tTMatrix.
884    
885            * R/diagMatrix.R (show): print a header line as for other classes.
886    
887    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * src/Makefile.win (SUBDIRS): fix typo
890    
891    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
894    
895    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
896    
897            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
898            symmetric and y missing in R code using %*% (cholmod_aat doesn't
899            accept a symmetric matrix).
900            * tests/group-methods.R: Uncomment test of crossprod applied to
901            lsCMatrix objects.
902    
903    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/AllClass.R (symmetricMatrix): add validity method (available
906            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
907    
908            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
909    
910            * tests/indexing.Rout.save:
911            * tests/indexing.R: additions, mainly for 'lsparse'
912    
913            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
914            case.
915    
916            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
917    
918    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
921                    as 'N' (1-letter - Ok?)
922    
923            * tests/group-methods.R: add test for logical + NAs
924    
925            * R/dMatrix.R ("Compare"): fix to work with NA's
926    
927            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
928    
929            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
930                    which is implemented.
931    
932    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * src/chm_common.c: coerce logical <-> double instead of
935            typecasting;  needed for "l" matrix handling in cholmod.
936    
937            * tests/other-pkgs.R (graph): small extension in "graph" checks.
938    
939            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
940            (Tsp2grNEL): other fixes needed
941    
942    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
945                    Matrices, since "lMatrix", also "lsparseM" can have NA
946            * R/ndenseMatrix.R, etc: new source files
947            * man/nsparseMatrix-classes.Rd, etc: new help files
948            * tests/: adaptions
949            * src/chm_common.c (chm_dense_to_SEXP): and others:
950                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
951            * src/Csparse.c, etc: ditto
952    
953    2006-09-11  Douglas Bates  <bates@R-project.org>
954    
955            * src/Mutils.[ch],init.c inst/include/*.h: Move the
956            alloc_d**Matrix functions to the lme4 package.
957    
958    2006-09-09  Douglas Bates  <bates@R-project.org>
959    
960            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
961            fixed
962    
963    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/lMatrix.R: new
966    
967            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
968    
969            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
970            * man/tcrossprod.Rd: ditto
971    
972    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
973    
974            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
975            for exported functions
976            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
977            Remove partitioning algorithms for sparse matrix reordering.  The
978            copyright on the Metis code was problematic and the methods were
979            rarely used.
980            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
981            operations are now done entirely in CHOLMOD code.
982    
983    2006-09-06  Douglas Bates  <bates@R-project.org>
984    
985            * src/Mutils.h: Remove functions that are no longer used.
986    
987    2006-09-04  Douglas Bates  <bates@R-project.org>
988    
989            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
990            * src/DEPS.mkf: update
991    
992    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * created branches/Matrix-for-R-2.3.x;  on trunk: do
995            * DESCRIPTION (Version): 0.9975-0
996            (Depends): R (>= 2.4.0)
997    
998    2006-09-01  Douglas Bates  <bates@R-project.org>
999    
1000            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1001    
1002    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1005            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1006    
1007            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1008    
1009    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1012            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1013            * R/dsparseMatrix.R: ditto
1014            * R/Csparse.R: ditto
1015    
1016    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/dMatrix.R (Compare): improve availability of "<", etc
1019            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1020    
1021    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1024            of a 0-index which was used as 1-index (..hmm)
1025    
1026            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1027    
1028            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1029            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1030            (.is.diagonal): ditto
1031    
1032            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1033    
1034            * R/Matrix.R (Matrix): also work for NA data
1035    
1036    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1039            in all cases.
1040    
1041    2006-08-27  Douglas Bates  <bates@R-project.org>
1042    
1043            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1044            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1045    
1046    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1049            subclasses of "ddenseMatrix"
1050            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1051            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1052            instead of half dozen specialized ones.
1053    
1054    2006-08-25  Douglas Bates  <bates@R-project.org>
1055    
1056            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1057            <tillard@cirad.fr> - ordering standard errors to match effects.
1058    
1059    2006-08-24  Douglas Bates  <bates@R-project.org>
1060    
1061            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1062            on R_ldl.
1063            * R/lCholCMatrix.R,
1064            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1065            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1066            * many files in ./R and ./src: Use more general version of
1067            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1068            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1069            dtpMatrix, dspMatrix and dppMatrix conversions.
1070    
1071    
1072    2006-08-23  Douglas Bates  <bates@R-project.org>
1073    
1074            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1075            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1076            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1077            dgeMatrix_crossprod (may need to do this in other places).
1078            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1079            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1080    
1081    2006-08-22  Douglas Bates  <bates@R-project.org>
1082    
1083            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1084            types of classed Matrices, matrices or numeric or logical vectors.
1085            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1086            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1087            to Mutils.h (as an inline) and change name to Matrix_check_class;
1088            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1089            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1090            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1091            * src/Csparse.c: use diag_P and uplo_P macros.
1092    
1093    2006-08-21  Douglas Bates  <bates@R-project.org>
1094    
1095            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1096            valgrind.
1097            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1098            inverses.
1099            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1100            -Wall warnings.
1101            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1102            Use dup_mMatrix_as_dgeMatrix.
1103    
1104    2006-08-20  Douglas Bates  <bates@R-project.org>
1105    
1106            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1107            * tests/sparseQR.R: Added
1108            * man/sparseQR-class.Rd: Document methods for qr.* generics
1109            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1110    
1111    2006-08-19  Douglas Bates  <bates@R-project.org>
1112    
1113            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1114            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1115            and qr.fitted.
1116            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1117            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1118    
1119    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1120    
1121            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1122            the base version has no "..." argument.
1123    
1124            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1125    
1126            * R/Matrix.R: define and
1127            * NAMESPACE: export as.numeric() and as.logical() methods.
1128                    Let's hope these do not badly slow down something...
1129            Finally export the zapsmall() method.
1130    
1131    2006-08-17  Douglas Bates  <bates@R-project.org>
1132    
1133            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1134            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1135            * src/dtCMatrix.c :Remove code that is no longer used
1136            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1137    
1138    2006-08-14  Douglas Bates  <bates@R-project.org>
1139    
1140            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1141            Csparse_to_logical and Csparse_symmetric_to_general.
1142            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1143            coercion methods between CsparseMatrix and TsparseMatrix.
1144    
1145    2006-08-14  Douglas Bates  <bates@R-project.org>
1146    
1147            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1148            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1149            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1150            possible.
1151    
1152    2006-08-12  Douglas Bates  <bates@R-project.org>
1153    
1154            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1155              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1156              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1157              generalize conversions between TsparseMatrix, CsparseMatrix,
1158              denseMatrix and matrix.  Preserve triangularity property and
1159              propagate Dimnames in the easy cases.
1160    
1161    2006-08-10  Douglas Bates  <bates@R-project.org>
1162    
1163            * src/lmer.c: adjust checks in glmer_init for S4SXP
1164            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1165            before S4SXP but for the wrong reasons.
1166    
1167    2006-08-08  Douglas Bates  <bates@R-project.org>
1168    
1169            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1170            Later modified to return the upper triangle only.
1171            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1172    
1173    2006-08-07  Douglas Bates  <bates@R-project.org>
1174    
1175            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1176            R-level conversion to a sparse symmetric class.
1177            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1178            Remove conversion to sparse symmetric classes (now done in C code).
1179    
1180    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1183            * man/band.Rd:  adapt the \dontshow{} unit test.
1184    
1185    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * DESCRIPTION (Version): 0.995-14  for CRAN
1188    
1189            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1190    
1191            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1192            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1193    
1194            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1195            * R/Tsparse.R (tril, triu, band): methods
1196            * R/dgRMatrix.R (tril, ...):    ditto
1197            * man/band.Rd:                  ditto
1198    
1199    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1202                    to be up-to-date automatically.
1203    
1204    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1207    
1208            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1209            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1210            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1211            such that the S4 objects are always created by the current version
1212            of R and 'Matrix' class definitions.
1213    
1214    2006-08-01  Douglas Bates  <bates@R-project.org>
1215    
1216            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1217            inst/external/test3comp.rda: Added warnings for convergence on
1218            boundary and test cases.
1219    
1220            * src/lmer.c (mer_postVar): Modified to return the variances that
1221            are marginal to the fixed effects, not conditional on them (which
1222            is what the bVar slot contents represent).
1223    
1224    2006-07-31  Douglas Bates  <bates@R-project.org>
1225    
1226            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1227            function which calls the C function mer_hat_trace2.
1228    
1229            * man/ranef.Rd: Include description of "postVar" argument and
1230            producing a caterpillar plot.
1231    
1232    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * NAMESPACE:    change  "correlation" to "corMatrix"
1235            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1236            * R/dpoMatrix.R: ditto
1237            * R/lmer.R:      ditto
1238    
1239    2006-07-28  Douglas Bates  <bates@R-project.org>
1240    
1241            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1242            RZXinv slot's contents into a separate internal function that can
1243            be used in mer_hat_trace.
1244    
1245    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1248            via new smart
1249            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1250            utility functions.
1251    
1252    
1253    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1256            matrices when appropriate; band() even symmetric ones.
1257            (replCmat): extend to potentially all "CsparseMatrix"
1258            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1259            allow subassignment for special sparse matrices.
1260    
1261            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1262    
1263            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1264            argument; in glmer_*(): print only if(verbose).
1265    
1266            speed-optimize a few places by moving REAL(.) out of loops.
1267    
1268            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1269    
1270    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1273                    since that wrongly triggers also for M[ logi , ]
1274    
1275            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1276            a symmetric matrix that results in a non-symmetric one.
1277            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1278    
1279            * R/dMatrix.R: make round(M) work as round(M, 0)
1280    
1281            * R/dgTMatrix.R (image): coordinate system and axis now use
1282            1-based indices, not 0-based ones.
1283    
1284            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1285            * tests/indexing.R: test it.
1286    
1287            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1288            * man/isSymmetric-methods.Rd: and document it.
1289    
1290            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1291            * man/SparseM-conv.Rd: docu them
1292    
1293            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1294                    for 'SparseM' conversions
1295    
1296    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1297    
1298            * R/Matrix.R (head): added head() and tail() methods.
1299    
1300    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * DESCRIPTION (Version): 0.995-12 released to CRAN
1303    
1304    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1305    
1306            * tests/simple.R: add check for correct dsT -> dgT coercion;
1307                    add check for correct printing of symmetric sparse matrices.
1308    
1309            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1310            for sparse symmetric matrices.
1311    
1312            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1313            diagonal twice.
1314    
1315    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1316    
1317            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1318            being applied to the x slot (detected by Brian Ripley).
1319    
1320    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1321    
1322            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1323    
1324            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1325    
1326    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * src/lgCMatrix.c (lgCMatrix_diag): new function
1329            * R/lgCMatrix.R (diag): for new method
1330    
1331            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1332                 ==> construction of illegal "*gTMatrix" via new() should
1333                 now be much less easy:
1334            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1335    
1336            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1337                    directly.
1338            * man/Matrix.Rd: documents it.
1339    
1340    2006-07-06  Douglas Bates  <bates@R-project.org>
1341    
1342            * src/pedigree.c (pedigree_inbreeding): Correction in
1343            initialization.  This function is not currently being used and is
1344            not fully tested.
1345    
1346            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1347            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1348            objects.  Modified validity check on pedigree objects to account
1349            for nonparallel patterns of missingness of parents.
1350    
1351            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1352            class.
1353    
1354    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1355    
1356            * R/pMatrix.R: coercion pMatrix -> Tsparse
1357    
1358    2006-06-12  Douglas Bates  <bates@R-project.org>
1359    
1360            * DESCRIPTION (Version): 0.995-11 released to CRAN
1361    
1362            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1363            the output from mcmcsamp.
1364    
1365    2006-06-10  Douglas Bates  <bates@R-project.org>
1366    
1367            * R/lmer.R (simulestimate): added C code for calculating the trace
1368            of the hat matrix.
1369    
1370    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1371    
1372            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1373            classes.
1374            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1375    
1376    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * R/dgTMatrix.R (colSums): etc. All four of
1379            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1380            all "Matrices".
1381    
1382    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1383    
1384            * R/lmer.R (panel.ci): Add a reference line at zero and a
1385            background grid to the qqmath plot of ranef.lmer.
1386    
1387    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1388    
1389            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1390            grouping factors to be specified in the formula as (1|foo/bar).
1391    
1392    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1393    
1394            * R/lmer.R (findbars and others): Change check of is.numeric to
1395            !is.language to resolve the bug reported by Jacob Wegelin.
1396    
1397            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1398            code to evaluate inbreeding coefficients without calculating T,
1399            based on code in Sargolzaei and Iwaisaki's paper.
1400    
1401    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1402    
1403            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1404            generic and mer methods for isNested and denomDF. This denomDF was
1405            an attempt to emulate that in lme but I don't think that makes
1406            sense.  Use the trace of the hat matrix instead.
1407    
1408    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1409    
1410            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1411            the C code depending on a slot structure that's no longer valid.
1412            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1413    
1414    
1415    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1416    
1417            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1418            of lowerTriMatrix generic and methods to tril (also upper to triu)
1419            and added a general band extractor.
1420    
1421    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1422    
1423            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1424            allowable range with NAs. Added a corresponding check in the
1425            validity check for the pedigree class.
1426    
1427            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1428            crossprod methods now inherits from symmetricMatrix.
1429    
1430    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1431    
1432            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1433            generics lowerTriMatrix and upperTriMatrix along with methods for
1434            the Csparse virtual class.  Also added a C function Csparse_band
1435            that implements these methods by calling cholmod_band.
1436    
1437    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1438    
1439            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1440            erased when it was NULL.  This led to invalid subselections!
1441    
1442    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1443    
1444            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1445            in method for "t" so as not to lose the unit diagonal property.
1446    
1447    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1448    
1449            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1450            and methods.  This is now an option to the ranef method for the
1451            mer class.
1452    
1453            * src/cs_utils.c: Ensure that the nz component is -1 for a
1454            compressed column-oriented matrix.  Minor formatting cleanup.
1455    
1456            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1457            objects.
1458    
1459    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1460    
1461            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1462            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1463    
1464    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1465    
1466            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1467            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1468    
1469            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1470            for the dtCMatrix class.
1471    
1472    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1473    
1474            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1475            and methods for it.
1476    
1477    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1478    
1479            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1480            arguments, such that M %*% 1:6 now works
1481            * Tests/matprod.R: test the above
1482    
1483    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1484    
1485            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1486            the ranef.lmer class.
1487    
1488            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1489            methods to extract the posterior variances from the bVar slot.
1490    
1491    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1492    
1493            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1494            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1495    
1496            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1497            * tests/simple: (extended)
1498    
1499            * R/sparseMatrix.R (isTriangular): now using much improved
1500            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1501    
1502    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1503    
1504            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1505            (problem report from Franklin Parlamis).  This should be done
1506            generally.
1507    
1508    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1509    
1510            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1511            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1512            update the plot methods.
1513    
1514    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1515    
1516            * R/lmer.R (resid and ranef methods):  Added methods for the
1517            "residuals" and "resid" generic but only for linear mixed model
1518            fits.  Changed the ranef method to return a list of data frames so
1519            that the plot methods now work.
1520    
1521    2006-03-16  Douglas Bates  <bates@bates2>
1522    
1523            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1524            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1525    
1526            * DESCRIPTION (Date): New release
1527    
1528    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1529    
1530            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1531    
1532            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1533            * man/KNex.Rd: and other help files
1534            * tests/*.R: several ones needed adaption
1535            * inst/doc/Comparisons.Rnw: ditto
1536    
1537    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1538    
1539            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1540    
1541            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1542    
1543    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1546    
1547            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1548    
1549    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1550    
1551            * R/dMatrix.R: enable things like  M [ M < 10 ]
1552            * R/dgeMatrix.R: implement it
1553    
1554    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1555    
1556            * R/AllClass.R: define "summary.mer" and "*.lmer"
1557            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1558            * R/lmer.R (show): now works with summary()
1559    
1560    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1561    
1562            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1563            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1564                    support the above
1565    
1566    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1567    
1568            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1569            Use glmFit$prior.weights for weights in a glmm.
1570            Allow an option usePQL = FALSE to skip the PQL steps for the
1571            Laplace method (and, in time, the AGQ method).
1572    
1573            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1574            into a separate function internal_mer_Xfactor to be able to call
1575            it from internal_bhat.
1576    
1577    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1578    
1579            * tests/Class+Meth.R (tstMatrixClass): function for much better
1580            testing; now again of all actual classes.
1581    
1582            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1583                    use macros and define make_d_matrix_* and make_i_matrix_*
1584                    where _i_ is for the ldense routines:
1585    
1586            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1587            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1588    
1589            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1590    
1591    
1592    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1593    
1594            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1595                    many different kinds of matrices.
1596            * R/*.R: quite a few new methods were needed for R CMD check with
1597                    new Matrix().  Very good for users playing around.
1598    
1599    
1600    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1601    
1602            * src/dgeMatrix.c (dMatrix_validate): new
1603            * src/Mutils.c (dense_nonpacked_validate): new
1604    
1605            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1606    
1607    
1608    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1609    
1610            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1611    
1612    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1613    
1614            * DESCRIPTION (Version): 0.99-6 released to CRAN
1615    
1616            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1617            segfault in cases with multiple non-nested grouping factors.
1618    
1619    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1620    
1621            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1622                    (Depends): also on 'utils'
1623    
1624            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1625            * R/diagMatrix.R (Diagonal): constructor and methods for
1626            diagonal matrices
1627    
1628            * R/ltTMatrix.R: new "minimal methods"
1629    
1630    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1633            all methods (and help files).
1634    
1635    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1636    
1637            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1638                    for case (dimn.  op  no_dimn.)
1639    
1640    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1641    
1642            * DESCRIPTION (Version): 0.99-2  released to CRAN
1643    
1644    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1645    
1646            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1647            by Julian Faraway.
1648    
1649    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1650    
1651            * R/Auxiliaries.R (try_as): new utility
1652            * R/sparseMatrix.R: use try_as() in coercion to original class
1653    
1654    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1655    
1656            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1657    
1658    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1659    
1660            * R/Auxiliaries.R (dimNamesCheck): added
1661    
1662            * R/Matrix.R (as.array), (as.vector): new
1663    
1664    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1665    
1666            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1667                    default.
1668            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1669                    "pMatrix" now contains "sparseMatrix"
1670    
1671    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1672    
1673            * tests/Class+Meth.R: new tests; t(t(m)) == m
1674    
1675            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1676    
1677            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1678            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1679    
1680            * R/dspMatrix.R: typo in "t" method
1681    
1682    2005-09-18  Douglas Bates  <bates@wisc.edu>
1683    
1684            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1685            * R/Tsparse.R: instead of R/gTMatrix.R
1686            * R/Csparse.R: new
1687            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1688            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1689            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1690                            via cholmod
1691    
1692    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1693    
1694            * R/Auxiliaries.R (non0ind): new function using new C code
1695            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1696    
1697    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1698    
1699            * src/chm_common.h: header file required by all C sources that
1700            call CHOLMOD functions.  It defines a cholmod_common structure
1701            called 'c' whose address is passed as the last argument to
1702            (virtually) every CHOLMOD function.
1703    
1704            * src/Pattern.c: Simple example of the use of CHOLMOD.
1705    
1706            * src/init.c: initialize and finalize the cholmod_common structure.
1707    
1708            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1709            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1710    
1711    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1712    
1713            * inst/test-tools.R: new file collecting the utility functions used
1714                    in ./tests/*.R
1715    
1716            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1717            * R/Matrix.R (cbind2): methods for NULL and missing
1718    
1719    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1720    
1721            * R/AllClass.R: new "index" class for "[" and "[<-":
1722                    First cut at "symmetricMatrix" and "triangularMatrix"
1723            * R/gTMatrix.R (.ind.prep): new function;
1724                    Logical and character indexing now work too.
1725            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1726            * tests/indexing.R: new, including *.Rout.save
1727            * tests/dgTMatrix.R: new
1728    
1729    2005-08-29  Douglas Bates  <bates@wisc.edu>
1730    
1731            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1732            indicator pos not being updated.  Also enforced upper triangular
1733            for symmetric case.  Need to coerce edges component of elements of
1734            edge list - grr! (Why don't they define their classes cleanly?)
1735    
1736    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1737    
1738            * R/Matrix.R:  added first "[<-" methods; not yet functional
1739            * R/denseMatrix.R: ditto
1740            * man/Subassign-methods.Rd: new help file for these
1741    
1742    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1743    
1744            * DESCRIPTION (Version): 0.98-6
1745    
1746            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1747            matrices.
1748    
1749    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1750    
1751            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1752                    as( <logical>, "matrix")
1753    
1754            * R/pMatrix.R: coercion to "lgTMatrix"
1755    
1756            * R/gTMatrix.R: new virtual class to define "[" methods for.
1757            * man/gTMatrix-class.Rd:
1758            * General slight re-organization of where "[" methods are defined.
1759              more to come.
1760    
1761    2005-08-18  Douglas Bates  <bates@wisc.edu>
1762    
1763            * DESCRIPTION (Version): 0.98-5  released to CRAN
1764    
1765            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1766            * .....
1767    
1768    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1769    
1770            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1771            or glmer objects.
1772    
1773    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1774    
1775            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1776    
1777    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1778    
1779            * R/HBMM.R: finish re-writing R-only code.
1780    
1781    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1782    
1783            * man/externalFormats.Rd: move documentation for writeHB and
1784            writeMM here.
1785    
1786            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1787            (suggested by Paul Roecker).
1788    
1789            * tests/validObj.R (assertError): Comment out test that is failing
1790            after recent changes in r-devel.
1791    
1792    
1793    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1794    
1795            * R/AllClass.R: intermediate virtual class "denseMatrix"
1796            * man/denseMatrix-class.Rd
1797            * NAMESPACE: export it, and also export
1798            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1799    
1800    2005-08-10  Douglas Bates  <bates@wisc.edu>
1801    
1802            * DESCRIPTION (Version): 0.98-3 to CRAN
1803    
1804            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1805            matrix_solve code (which was really, really wrong).
1806    
1807    2005-08-07  Douglas Bates  <bates@wisc.edu>
1808    
1809            * DESCRIPTION (Version): 0.98-2
1810    
1811            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1812    
1813            * R/lmer.R (abbrvNms): new
1814            * R/lmer.R (mcmcsamp): allow transformed parameters
1815            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1816            for the Harwell-Boeing and the MatrixMarket formats.
1817    
1818    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1819    
1820            * man/dtrMatrix-class.Rd: add examples
1821            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1822    
1823            * TODO: note the dtpMatrix (docu) bug
1824    
1825            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1826            in order to ensure that new as.matrix() is used by old functions,
1827            e.g., svd(), qr(), eigen(), dist(),..;
1828                  apply(), also matplot() or pairs().
1829    
1830    
1831    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1832    
1833            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1834              add comments about 'control' / lmerControl() arguments
1835    
1836    2005-07-27  Douglas Bates  <bates@wisc.edu>
1837    
1838            * man/sleepstudy.Rd: Added the sleep data set.
1839            * DESCRIPTION (Version): 0.98-1  released to CRAN
1840    
1841    2005-07-12  Douglas Bates  <bates@wisc.edu>
1842            * man/sleepstudy.Rd: Added the sleep data set.
1843    
1844            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1845            .Call calls that were producing spurious output.
1846    
1847    2005-07-05  Douglas Bates  <bates@wisc.edu>
1848    
1849            * R/lmer.R (lmer): stored updated variance component estimates in
1850            mer object for the generalized model.  (Bug reported by Renaud
1851            Lancelot).
1852    
1853    2005-07-03  Douglas Bates  <bates@wisc.edu>
1854    
1855            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1856            unidimensional case.
1857    
1858    2005-06-08  Douglas Bates  <bates@wisc.edu>
1859    
1860            * DESCRIPTION (Version): 0.96-1
1861    
1862            * moved  lmer-class' R and C code moved from lme4 to here
1863    
1864    2005-06-04  Douglas Bates  <bates@wisc.edu>
1865    
1866            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1867            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1868    
1869    2005-06-02  Douglas Bates  <bates@wisc.edu>
1870    
1871            * src/Makefile.win: Forgot to update this when Makefile changed.
1872    
1873    2005-05-11  Douglas Bates  <bates@wisc.edu>
1874    
1875            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1876            bug reported by Kurt Hornik and Michael Hahsler.
1877    
1878    2005-05-10  Douglas Bates  <bates@wisc.edu>
1879    
1880            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1881            logical sparse matrices.  These will also be used in the symbolic
1882            analysis for lmer objects.
1883    
1884            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1885            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1886    
1887    2005-05-06  Douglas Bates  <bates@wisc.edu>
1888    
1889            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1890            colMeans, colSums, rowMeans and rowSums.
1891    
1892    2005-04-18  Douglas Bates  <bates@wisc.edu>
1893    
1894            * src/lgCMatrix.[ch]: code for _validate method and stub for
1895            multiplication operation.
1896    
1897            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1898            to dgetrs.
1899    
1900            * src/init.c: Fix cut-and-paste error in definition of
1901            dgeMatrix_matrix_solve
1902    
1903            * src/{many files}: Tighten code by using ALLOC_SLOT.
1904    
1905    2005-04-15  Douglas Bates  <bates@wisc.edu>
1906    
1907            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1908    
1909            * DESCRIPTION: Eliminate import of stats.
1910    
1911    
1912    2005-04-06  Douglas Bates  <bates@wisc.edu>
1913    
1914            * R/AllClass.R : add logical sparse matrix classes
1915    
1916    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1917    
1918            * R/dgTMatrix.R: add "[" method for triplet matrices
1919            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1920    
1921    2005-03-31  Douglas Bates  <bates@wisc.edu>
1922    
1923            * DESCRIPTION (Version): release 0.95-5 to CRAN
1924    
1925            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1926            * R/sparseMatrix.R: %*%, crossprod()
1927            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1928            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1929            * src/lmer.c (lmer_fitted): fix thinko
1930    
1931    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1932    
1933            * R/AllClass.R: add two virtual sparse classes ``on top''
1934    
1935    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1936    
1937            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1938                    correspondingly fix examples and tests/ since new()
1939                    doesn't work for virtual classes.
1940    
1941    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1942    
1943            * R/Matrix.R (as.matrix): method and one for unname()
1944            * tests/dpoMatrix.R: tests should now be less platform dependent;
1945              also run for R 2.1.0; using as.matrix()
1946    
1947    2005-03-15  Douglas Bates  <bates@wisc.edu>
1948    
1949            * R/pMatrix.R: "pMatrix" class added
1950            * ....
1951    
1952    2005-03-14  Douglas Bates  <bates@wisc.edu>
1953    
1954            * R/dtpMatrix.R: Add unpack method and an example.
1955    
1956            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1957            of general symmetric matrices and associated S4 methods.
1958    
1959    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1960            +
1961    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1962    
1963            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1964              crossprod() and "%*%" methods added; tests, too.
1965            * tests/matprod.R: new, for testing these
1966    
1967    2005-03-03  Douglas Bates  <bates@wisc.edu>
1968    
1969            * src/lmer.c (lmer_fitted): Added.
1970    
1971    2005-03-02  Douglas Bates  <bates@wisc.edu>
1972    
1973            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1974    
1975    2005-02-28  Douglas Bates  <bates@wisc.edu>
1976    
1977            * src/*.c,po/,inst/po: Internationalization and localization of
1978            the package.
1979    
1980            * src/ldl.[ch]: Removed these as their contents are referenced in the
1981            R_ldl.c file.
1982    
1983            * src/flame.[ch]: Removed these source files.
1984    
1985            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1986    
1987            * src/LU.[ch],src/init.c: absorb in factorizations
1988    
1989            * src/Mutils.h: prepare for internationalization
1990    
1991            * src/cblas.h: move the enum definitions to Mutils.h and remove
1992            this file
1993    
1994    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1995    
1996            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1997    
1998            * R/dtrMatrix.R: fix t() method
1999    
2000            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2001            * NAMESPACE: export them (and import generics from "methods")
2002            * tests/group-methods.R : and test them.
2003    
2004            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2005            border case
2006    
2007    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
2008    
2009            * DESCRIPTION (Version): 0.95-2  released to CRAN
2010    
2011            * src/dgBCMatrix.c:
2012            * src/lmer.c: many changes
2013            * ...
2014    
2015    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2016    
2017            * R/Matrix.R: add more sophisticated show() method.
2018    
2019    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
2020    
2021            * */* : almost complete reorganization of classes.
2022    
2023    2005-01-26  Douglas Bates  <bates@wisc.edu>
2024    
2025            * R/AllGeneric.R: Added matrix exponential generic expm and a method
2026            for the geMatrix class.
2027    
2028    2005-01-24  Douglas Bates  <bates@wisc.edu>
2029    
2030            * src/Makefile (clean): Remove *.a and *.so
2031    
2032            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2033    
2034    2005-01-23  Douglas Bates  <bates@wisc.edu>
2035    
2036            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2037            had an effect in cases with more than 2 grouping factors.
2038    
2039    2005-01-03  Douglas Bates  <bates@wisc.edu>
2040    
2041            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2042    
2043    2004-12-23  Douglas Bates  <bates@wisc.edu>
2044    
2045            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2046            and R_useDynamicSymbols (suggested by B.D.Ripley).
2047    
2048    2004-12-14  Douglas Bates  <bates@wisc.edu>
2049    
2050            * R/sscMatrix.R: Add determinant methods
2051    
2052            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2053            for tripletMatrix to matrix.
2054    
2055    2004-12-13  Douglas Bates  <bates@wisc.edu>
2056    
2057            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2058            no longer used.
2059    
2060            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2061            with dynamic allocation of scratch arrays.
2062    
2063            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2064            for multivariate random effects with multiple grouping factors.
2065            Fixes part but not all of #15.
2066    
2067    2004-12-03  Douglas Bates  <bates@wisc.edu>
2068    
2069            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2070            scalar grouping factors corrected.
2071    
2072    2004-11-29  Douglas Bates  <bates@wisc.edu>
2073    
2074            * src/bCrosstab.c: remove diag_update which is no longer used
2075    
2076    2004-11-16  Douglas Bates  <bates@wisc.edu>
2077    
2078            * src/Metis_utils.c: Move metis.h include to C sources so that the
2079            .h file can be included.
2080    
2081    2004-11-12  Douglas Bates  <bates@wisc.edu>
2082    
2083            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2084            Complete allocation of slots in NEW_OBJECT.
2085    
2086            * src/Mutils.h: Moved list of symbols to an include file
2087    
2088    2004-11-11  Douglas Bates  <bates@wisc.edu>
2089    
2090            * src/geMutils.c (Matrix_init): remove unused function
2091    
2092    2004-11-10  Douglas Bates  <bates@wisc.edu>
2093    
2094            * src/cscMatrix.c (csc_to_imagemat): removed unused function
2095    
2096    2004-11-05  Douglas Bates  <bates@wisc.edu>
2097    
2098            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2099    
2100    2004-10-27  Douglas Bates  <bates@wisc.edu>
2101    
2102            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2103    
2104    2004-10-04  Douglas Bates  <bates@wisc.edu>
2105    
2106            * src/init.c: Created R_init_Matrix and added registration of C
2107            routines.
2108    
2109    2004-10-02  Douglas Bates  <bates@wisc.edu>
2110    
2111            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2112    
2113    2004-06-15  Douglas Bates  <bates@wisc.edu>
2114    
2115            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2116    
2117    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
2118    
2119            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2120    
2121    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
2122    
2123            * src/ssclme.c (ssclme_update_mm): fix logic error in
2124            ssclme_update_mm
2125    
2126    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
2127    
2128            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2129            in the order of unconstrained and constrained parameters.
2130            (ssclme_gradient): Added the gradients (not yet correct for
2131            multidimensional, unconstrained case).
2132    
2133    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
2134    
2135            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2136    
2137            * src/Makefile.win: Remove unneeded ranlib call
2138    
2139    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
2140    
2141            * DESCRIPTION (Version): New release
2142    
2143            * src/Makefile.win: Update Makefile.win to umfpack removal.
2144    
2145    2004-04-05  Douglas Bates  <bates@bates2_home>
2146    
2147            * src/triplet_to_col.c: Create triplet_to_col as a native
2148            function, not the version from umfpack.  There were problems with
2149            the configuration of UMFPACK for 64-bit processors and there was
2150            only one umfpack routine being used so I moved it here.
2151    
2152    2004-04-04  Douglas Bates  <bates@bates2_home>
2153    
2154            * src/ssclme.c (ssclme_variances): New function.
2155    
2156    2004-03-28  Douglas Bates  <bates@bates2_home>
2157    
2158            * src/ssclme.c (ssclme_fitted): Added function.
2159    
2160    2004-03-27  Douglas Bates  <bates@bates2_home>
2161    
2162            * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2163            store the dimnames in the XtX and bVar slots
2164            (ssclme_update_mm): Change the dimensions of the bVar slot
2165            components and the returned value from ssclme_ranef.
2166    
2167  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>
2168    
2169          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},

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