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revision 726, Thu May 12 14:59:04 2005 UTC revision 2018, Wed Aug 1 15:22:05 2007 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
4            * tests/matprod.R: regr.test for it
5    
6    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
9            * tests/group-methods.R: and regression-test it
10    
11    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
12    
13            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
15              triplet_to_sparse, documentation, use typedefs
16    
17    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/dpoMatrix-class.Rd: added 'corMatrix' example
20    
21            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
22            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
23            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
24    
25            * R/lsparseMatrix.R: bug fix in "all" method
26            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
27    
28            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
29            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
30                    + matrix |-> nMatrix coercion
31            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
32            * man/pMatrix-class.Rd: ditto
33    
34            * R/Matrix.R (Summary): method for non-dMatrix
35    
36            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
37            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
38                    test all Summary methods.
39    
40    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
43    
44    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
47    
48            * R/pMatrix.R (t?crossprod): methods for pMatrix
49    
50    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
53    
54    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
55    
56            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
57              trying to fix a subtle bug - which has been somewhere else.
58    
59    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
60    
61            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
62              solve the bug
63    
64    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dgCMatrix.c (compressed_to_TMatrix):
67    
68    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * src/Csparse.c (Rsparse_validate): new, to have some validity
71            checking for RsparseMatrix
72            * src/dgCMatrix.c (xRMatrix_validate): ditto
73            * src/dtCMatrix.c (tRMatrix_validate): ditto
74    
75    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
76    
77            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
78              lgRMatrix
79            * [r4568] DESCRIPTION: Prepare for bug-fix release
80            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
81              for declaration of cholmod_symmetry
82    
83    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
86            release.
87    
88    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
89    
90            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
91              functions - no longer used
92            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
93              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
94              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
95              Alloca
96    
97    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
98    
99            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
100              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
101              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
102              src/t_gCMatrix_colSums.c: more R_CheckStack()s
103    
104    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
105    
106            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
107              the required amount of memory then call M_numeric_as_chm_dense.
108            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
109              (like Calloc but calling alloca)
110    
111    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
114            and extended with more sophisticated 'col.names' option.
115            * NAMESPACE: export  printSparseMatrix()
116            * man/printSpMatrix.Rd: document, incl. examples
117    
118    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
119    
120            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
121              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
122              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
123    
124    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.99875-4
127    
128            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
129            some dimnames perservation.
130    
131            * R/dsTMatrix.R (t-method): keep dimnames
132            * R/dtTMatrix.R:  ditto
133    
134            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
135            and ncol(.) < 10
136    
137            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
138            from Mutils.h
139    
140            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
141            e.g. in as(<ngCMatrix>, "matrix")
142    
143    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
144    
145            * [r4529] .: Create a branch for the API changes from the 0.99875
146              series to the 0.999375 series
147            * [r4530] DESCRIPTION, inst/include/Matrix.h,
148              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
149              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
150              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
151              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
152              as_cholmod_x functions
153    
154    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
155    
156            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
157              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
158              to Comparisons
159    
160    >>>>>>> .merge-right.r4561
161    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Version): 0.99875-3 ready to be released.
164    
165            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
166    
167            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
168            that should also work in a future version of R.
169    
170    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
173    
174            * R/sparseVector.R: more *sparseVector coercions, notably for
175            non - double ones.
176    
177    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
180              notably the new ones building on the new .Call(.)s:
181    
182            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
183            all 4 of [dlin]gCMatrix_colSums().
184    
185    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
186    
187            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
188            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
189              result
190    
191    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/kronecker.R: fix typo (could lead to inf.recursion)
194            * test/simple.R: testing that
195    
196            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
197            method as well (which can have arguments, show() can't).
198    
199    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
200    
201            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
202              added dgCMatrix_colSums for [col,row][Sums,Means]
203    
204    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
205    
206            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
207              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
208              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
209            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
210              class
211            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
212              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
213              row names to store the levels - duh!  Added an example.
214    
215    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Csparse.c (Csparse_validate): check for *repeated* entries
218            thanks to example from Christian Buchta; with a test here:
219            * tests/simple.R:
220    
221    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
224            of colSums(*, sparseResult = TRUE)
225    
226    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
229            'na.rm = FALSE' as "everywhere" else in R.
230    
231    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
232    
233            * [r4421] src/CSparse_install.sh: Modify for new organization of
234              CSparse package
235            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
236              SuiteSparse
237            * [r4426] src/Makefile: add ./UFconfig to the include path for
238              compilation
239            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
240            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
241              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
242    
243    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
246            * R/sparseMatrix.R (prSpMatrix): now gives a message about
247            suppressed column names.
248    
249    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
250    
251            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
252              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
253              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
254              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
255              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
256              Remove warnings after change to const char* CHAR
257    
258    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
261              type of M_cholmod_ssmult
262    
263    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
264    
265            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
266              src/init.c: Yet another cholmod export - cholmod_ssmult
267    
268    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * NAMESPACE: exported drop0(), since
271            * man/drop0.Rd: I have seen several cases, I really wanted to use
272            it, so our users may want too.
273    
274    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * man/colSums.Rd: separately document colSums() etc, since these
277            have the extra argument 'sparseResult'.
278    
279    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
282            * man/spMatrix.Rd: docu., including examples
283    
284            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
285            in order to make colMeans() etc fast *and* correct.
286            * R/sparseVector.R (replSPvec): "[<-" functionality for
287            sparseVectors; tested in
288            * tests/simple.R:
289    
290    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
293            (very) sparse Matrices; output similar to Matlab's print().
294    
295    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
298            0-based, indices (Jose Quesada <quesada@gmail.com>).
299    
300    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
303    
304    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Auxiliaries.R (sparsapply): new utility, much faster than
307            tapply1() for large sparse matrices.
308    
309    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Matrix.R (dim<-): reshape now via sparseVector.
312    
313            * R/sparseVector.R: methods and function for
314            * R/AllClass.R: new "sparseVector" class and daughters.
315            * NAMESPACE: export new classes
316    
317    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * DESCRIPTION (Version): 0.99875-1
320            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
321    
322    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
325            indexing
326            * tests/indexing.R: test set for that.
327    
328    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
331            entries.
332            * tests/indexing.R(out): add regression test for it
333    
334    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
337            name for "!" method definitions.
338    
339    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Tsparse.R (intI): new utility, used for "[" :
342                    Cleanup up there, and fixes for duplicated indices - more TODO!
343    
344            * tests/indexing.R(out): more tests
345    
346    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
349            code that is now part of the R Lapack library.
350    
351            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
352            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
353    
354    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
357    
358    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
361            up with extraneous names '0'...'<n-1>'
362    
363    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/dgTMatrix.R (mat2dgT): care about NAs
366    
367    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/kronecker.R: triangularity preserving methods
370    
371    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/kronecker.R: new file collecting kronecker() methods in one
374                    place.  Goal: become much faster!
375    
376    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
379            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
380            can be much faster.
381    
382            * tests/matprod.R: add regression tests for these (upper & lower).
383    
384    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/Matrix.R (diff): method for our Matrices.
387    
388            * R/sparseMatrix.R (isDiagonal): check dim()!
389    
390    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (dim<-): new method for "reshape()" built on a
393            proposal from Tamas Papp.
394    
395    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
398    
399            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
400            rather define and export  cBind() and rBind() only.
401            --> useRs *must* change code that used to have cbind()/rbind() !!
402    
403            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
404            * R/bind.Rout.save: ditto
405    
406    2007-02-16  Douglas Bates  <bates@r-project.org>
407    
408            * DESCRIPTION (Date, Version): 0.9975-11 with new date
409            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
410            const modifier on declaration of the array 'valid'
411    
412    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
415    
416    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
419    
420            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
421            * tests/simple.R: test the above and some of these coercions:
422    
423            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
424                    be careful to avoid infinite recursion, using new coercions in
425            * R/ngCMatrix.R and nsC... and ntC...
426            * R/lsparseMatrix.R: ditto
427    
428            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
429    
430            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
431            * R/Rsparse.R: reactivate .Call()s
432    
433            * tests/Class+Meth.R: a bit more on actual classes
434    
435    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
438    
439    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * DESCRIPTION (Version): 0.9975-10 to upload
442    
443            * tests/Class+Meth.R (tstMatrixClass): require coercions to
444            specific classes less unconditionally.
445    
446            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
447    
448            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
449    
450            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
451            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
452            R_to_CMatrix segfaults on one platform.
453            Eliminate most coercion method to *specific* classes, and replace
454            with virtual classes coercions.
455    
456    
457    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
458    
459            * src/init.c: export the CHM...._validate() placeholders, since
460            they *are* called.
461    
462            * tests/Class+Meth.R (classCanCoerce): and starting to test
463            all as(<from>, <to>)
464    
465    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
468            * tests/indexing.R: tested now
469            * tests/indexing.Rout.save: updated
470    
471            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
472            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
473            appropriate.
474    
475            * NAMESPACE: export a trivial
476            * R/Matrix.R: drop() Matrix-method
477    
478            * R/AllClass.R: moved all prototypes to virtual super classes.
479    
480            * R/Rsparse.R: many more coercions to have less exceptions in
481            * tests/Class+Meth.R:
482    
483            * R/Ops.R (Compare): tweak for case with NA
484            * tests/simpl.R: hence another 'FIXME' eliminated
485    
486    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
489            objects.
490    
491            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
492              and more of "!", "&", "|", all, any; coercions
493    
494            * R/Rsparse.R: many coercions (which enable quite a few other
495            methods), thanks to enhancements in
496            * src/dgCMatrix.c (R_to_CMatrix): new, and
497            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
498            symmetric & triangular and ..RMatrix objects.
499    
500            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
501            renamed file from src/dsTMatrix.c;
502            now dealing with symmetric and triangular Tsparse coercions, both
503            to dense and general.
504    
505    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
508    
509            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
510            where sensible when the <numeric> is of length > 1.
511    
512    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Matrix.R ([<-): for M[] <- value: fix length
515    
516    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
519            * R/ndenseMatrix.R: new coercions n* -> l*
520    
521    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
524    
525            * R/Ops.R ("Logic"): and other "Ops", many updates
526    
527    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * src/Mutils.h (SET_DimNames): new utility
530    
531            * R/Auxiliaries.R (nnzero): improved and now exported via
532    
533            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
534    
535    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/diagMatrix.R (!): fix typo.
538    
539    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Auxiliaries.R (as_Csparse): and quite a few others:
542                    allow to pass class definition --> speedup
543            * R/sparseMatrix.R: apply the above
544    
545            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
546    
547            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
548            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
549            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
550    
551            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
552    
553            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
554            and use it for "sparse*" as well, since it's faster than the
555            as_Csparse(.) way.
556    
557    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
560    
561    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
564            as method for   M[ ij ] <- v
565            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
566    
567            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
568            FALSE answer
569    
570            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
571            * tests/indexing.R: test it, and some of the above
572    
573    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/Auxiliaries.R (is_duplicatedT): new utility
576    
577    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
578    
579            * src/init.c (R_init_Matrix): export cholmod_scale
580    
581    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
584            base::as.matrix to (x, ...)
585    
586    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
589            file; start using "Logic", hence
590    
591            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
592            * NAMESPACE: import and export "Logic"
593    
594    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
597            only needed previously to R version 2.5.0.
598    
599    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
602    
603            * R/Tsparse.R (replTmat): fix subassignment of triangular
604            * R/Csparse.R (replCmat): ditto
605            * tests/indexing.R: more tests, incl the above fix
606    
607    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/Auxiliaries.R (drop0): extend for non CSparse
610            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
611    
612            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
613                    use uplo correctly (!); other places: use uplo_P() macro
614    
615            * R/Csparse.R (replCmat): call diagU2N() when needed
616            * R/Tsparse.R (replTmat): ditto
617    
618            * src/dtCMatrix.c (tCMatrix_validate): new
619            * src/dtTMatrix.c (tTMatrix_validate): new, used in
620            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
621    
622            * R/diagMatrix.R (replDiag): to use in [<-
623    
624    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
627                    also more general diagU2N().
628    
629    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
632            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
633    
634    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * tests/bind.R: a few more cases
637            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
638    
639            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
640            * R/ddenseMatrix.R (cbind2/rbind2)
641            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
642            * tests/indexing.R
643            * tests/indexing.Rout.save: updated
644    
645    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
648            * tests/indexing.R
649    
650    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
653            align with proper position of "0", i.e., right for integers.
654            argument 'align' by default is "fancy".
655    
656    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
659            * R/Csparse.R: and fix "Compare" for more cases.
660            * tests/Class+Meth.R: test some of these (m == m, m != m)
661    
662    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/lsparseMatrix.R: all() and any() methods
665            * R/ldenseMatrix.R:      ditto
666            * NAMESPACE, R/Matrix.R: ditto
667    
668            * man/all-methods.Rd: document them minimally
669    
670            * tests/simple.R: add a few examples for these
671    
672    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Tsparse.R ([): fix long standing typo in symmetric case
675            * man/dsCMatrix-class.Rd: add example exhibiting the above case
676    
677    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
680            to LL before converting to a sparse matrix. (The LDL form can be
681            converted to a sparse matrix but it is implicitly a unit
682            triangular matrix and a diagonal matrix overwritten on the diagonal.)
683    
684    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
685    
686            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
687    
688    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
689    
690            * DESCRIPTION (Version): updated -> release 0.9975-7
691            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
692    
693    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
696    
697    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
698    
699            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
700            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
701            is exactly singular.
702    
703    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * DESCRIPTION (Date): updated -> release 0.9975-6
706    
707    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
710            now returns symmetric.
711    
712            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
713    
714            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
715            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
716    
717            * R/Auxiliaries.R (.type.kind): added
718    
719    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
722            running src/CSparse_install.sh
723    
724            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
725    
726    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
729            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
730    
731            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
732    
733            * tests/Class+Meth.R (tstMatrixClass): now assure
734            the (important in method programming) property :
735    
736                    ###>>  Every "Matrix" is either
737                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
738    
739                    (where "*" stands for "Matrix")
740    
741            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
742    
743            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
744            * tests/validObj.R: checks for "comparison"
745    
746            * R/sparseMatrix.R ([): improved indexing for sparse;
747                    trying to keep <symmetric>[ n, n] symmmetric
748    
749            * tests/indexing.R: indexing for logical sparse now ok
750    
751    
752    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * src/Tsparse.c: use xTsparse_validate() , and hence remove
755    
756            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
757    
758    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
761    
762            * tests/simple.R: validObject() checking the above.
763    
764            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
765            replacing both dgCMatrix_validate and lgCM*.
766    
767            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
768            fix dimnames setting in other places.
769            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
770    
771    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
774    
775            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
776            symmetry test, via
777            * R/Auxiliaries.R (.as.dgC.0.factors):
778    
779    2006-11-01  Douglas Bates  <bates@r-project.org>
780    
781            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
782            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
783            <CsparseMatrix>) added
784    
785    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * tests/matprod.R: add a variation of Harri's example
788    
789            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
790            recursive infinitely.
791    
792            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
793    
794            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
795    
796    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
799            matrix if possible; test m+m == 2*m; now test dgRMatrix.
800            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
801            satisfy the above test.
802    
803    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
806    
807            * R/dgCMatrix.R: solve(a, b="missing") based on
808            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
809            RHS = NULL.
810    
811            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
812            add more (needed) [t]crossprod() methods.
813    
814            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
815    
816            * R/Auxiliaries.R (as_CspClass): cleanup
817            (drop0): internal utility for "Csparse_drop(*, 0)"
818            (.bail.out.2): encourage active feedback
819    
820    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/dMatrix.R(Compare): new(), then slots [no validity check]
823    
824            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
825            non-valid or 'sorted' case).
826    
827            * R/dsparseMatrix.R: add "chol" method.
828            * R/ddenseMatrix.R: ditto
829    
830            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
831            * NAMESPACE (Ops)
832            * R/diagMatrix.R (diag2T): simple utility used "higher level"
833            coercion; deprecating direct lower level coercions.
834    
835            * R/*.R (seq): use seq_len() and seq_along() where possible.
836    
837    
838    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * DESCRIPTION (Version): 0.9975-5 ready for release
841    
842    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
843    
844            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
845    
846    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/AllClass.R (corMatrix): add 'validity' check;
849                    comment out unused "LDL" class definition
850            * NAMESPACE: mention, but do not export "LDL" class
851            * R/corMatrix.R: new (simple), needed for R-devel with
852            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
853              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
854    
855    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
856    
857            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
858            use Rprintf and R's error handling.
859    
860    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
863            * tests/matprod.R: add tests for the bug fixed.
864    
865    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
868            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
869    
870    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
871    
872            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
873    
874    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * DESCRIPTION (Version): 0.9975-3
877    
878            * R/diagMatrix.R (bdiag): new function constructing block diagonal
879            (sparse) matrices.
880            * man/bdiag.Rd: docu + examples
881    
882            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
883    
884            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
885            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
886    
887            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
888            that result is sparse or diagonal (and not dense).
889    
890            * man/Subassign-methods.Rd: fix examples
891    
892            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
893            should always return a sparse (and not sometimes a diagonal) matrix.
894    
895    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
898    
899    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * DESCRIPTION (Version): 0.9975-2
902    
903            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
904    
905    2006-10-02  Douglas Bates  <bates@R-project.org>
906    
907            * tests/dg_Matrix.R: Simplify test taking into account new code.
908    
909    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
912    
913            * R/lsTMatrix.R: new files w/ missing methods
914            * R/nsTMatrix.R:  "  'for completeness'
915    
916            * tests/Class+Meth.R: a bit less 'not.ok.classes'
917    
918            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
919    
920    
921    2006-09-28  Douglas Bates  <bates@R-project.org>
922    
923            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
924            included.
925    
926            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
927            Export C-callable functions used in Zt_create in lme4.
928    
929    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * DESCRIPTION (Version): 0.9975-1
932    
933            * tests/simple.R: less checks fail; using NA, found that our
934                    kronecker() is not base-compatible with NA's.
935    
936            * R/dMatrix.R: "Compare" method now implemented for all cases
937    
938            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
939    
940            * man/dtpMatrix-class.Rd: mention length of 'x' slot
941    
942            * src/dtpMatrix.c (dtpMatrix_validate): fix check
943            * src/dspMatrix.c (dspMatrix_validate): ditto
944    
945            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
946              including coercion to [nl]tTMatrix.
947    
948            * R/diagMatrix.R (show): print a header line as for other classes.
949    
950    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * src/Makefile.win (SUBDIRS): fix typo
953    
954    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
957    
958    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
959    
960            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
961            symmetric and y missing in R code using %*% (cholmod_aat doesn't
962            accept a symmetric matrix).
963            * tests/group-methods.R: Uncomment test of crossprod applied to
964            lsCMatrix objects.
965    
966    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/AllClass.R (symmetricMatrix): add validity method (available
969            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
970    
971            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
972    
973            * tests/indexing.Rout.save:
974            * tests/indexing.R: additions, mainly for 'lsparse'
975    
976            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
977            case.
978    
979            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
980    
981    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
984                    as 'N' (1-letter - Ok?)
985    
986            * tests/group-methods.R: add test for logical + NAs
987    
988            * R/dMatrix.R ("Compare"): fix to work with NA's
989    
990            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
991    
992            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
993                    which is implemented.
994    
995    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * src/chm_common.c: coerce logical <-> double instead of
998            typecasting;  needed for "l" matrix handling in cholmod.
999    
1000            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1001    
1002            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1003            (Tsp2grNEL): other fixes needed
1004    
1005    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1008                    Matrices, since "lMatrix", also "lsparseM" can have NA
1009            * R/ndenseMatrix.R, etc: new source files
1010            * man/nsparseMatrix-classes.Rd, etc: new help files
1011            * tests/: adaptions
1012            * src/chm_common.c (chm_dense_to_SEXP): and others:
1013                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1014            * src/Csparse.c, etc: ditto
1015    
1016    2006-09-11  Douglas Bates  <bates@R-project.org>
1017    
1018            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1019            alloc_d**Matrix functions to the lme4 package.
1020    
1021    2006-09-09  Douglas Bates  <bates@R-project.org>
1022    
1023            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1024            fixed
1025    
1026    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/lMatrix.R: new
1029    
1030            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1031    
1032            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1033            * man/tcrossprod.Rd: ditto
1034    
1035    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1036    
1037            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1038            for exported functions
1039            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1040            Remove partitioning algorithms for sparse matrix reordering.  The
1041            copyright on the Metis code was problematic and the methods were
1042            rarely used.
1043            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1044            operations are now done entirely in CHOLMOD code.
1045    
1046    2006-09-06  Douglas Bates  <bates@R-project.org>
1047    
1048            * src/Mutils.h: Remove functions that are no longer used.
1049    
1050    2006-09-04  Douglas Bates  <bates@R-project.org>
1051    
1052            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1053            * src/DEPS.mkf: update
1054    
1055    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1058            * DESCRIPTION (Version): 0.9975-0
1059            (Depends): R (>= 2.4.0)
1060    
1061    2006-09-01  Douglas Bates  <bates@R-project.org>
1062    
1063            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1064    
1065    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1068            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1069    
1070            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1071    
1072    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1075            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1076            * R/dsparseMatrix.R: ditto
1077            * R/Csparse.R: ditto
1078    
1079    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/dMatrix.R (Compare): improve availability of "<", etc
1082            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1083    
1084    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1087            of a 0-index which was used as 1-index (..hmm)
1088    
1089            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1090    
1091            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1092            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1093            (.is.diagonal): ditto
1094    
1095            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1096    
1097            * R/Matrix.R (Matrix): also work for NA data
1098    
1099    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1102            in all cases.
1103    
1104    2006-08-27  Douglas Bates  <bates@R-project.org>
1105    
1106            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1107            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1108    
1109    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1112            subclasses of "ddenseMatrix"
1113            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1114            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1115            instead of half dozen specialized ones.
1116    
1117    2006-08-25  Douglas Bates  <bates@R-project.org>
1118    
1119            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1120            <tillard@cirad.fr> - ordering standard errors to match effects.
1121    
1122    2006-08-24  Douglas Bates  <bates@R-project.org>
1123    
1124            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1125            on R_ldl.
1126            * R/lCholCMatrix.R,
1127            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1128            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1129            * many files in ./R and ./src: Use more general version of
1130            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1131            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1132            dtpMatrix, dspMatrix and dppMatrix conversions.
1133    
1134    
1135    2006-08-23  Douglas Bates  <bates@R-project.org>
1136    
1137            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1138            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1139            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1140            dgeMatrix_crossprod (may need to do this in other places).
1141            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1142            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1143    
1144    2006-08-22  Douglas Bates  <bates@R-project.org>
1145    
1146            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1147            types of classed Matrices, matrices or numeric or logical vectors.
1148            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1149            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1150            to Mutils.h (as an inline) and change name to Matrix_check_class;
1151            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1152            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1153            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1154            * src/Csparse.c: use diag_P and uplo_P macros.
1155    
1156    2006-08-21  Douglas Bates  <bates@R-project.org>
1157    
1158            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1159            valgrind.
1160            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1161            inverses.
1162            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1163            -Wall warnings.
1164            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1165            Use dup_mMatrix_as_dgeMatrix.
1166    
1167    2006-08-20  Douglas Bates  <bates@R-project.org>
1168    
1169            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1170            * tests/sparseQR.R: Added
1171            * man/sparseQR-class.Rd: Document methods for qr.* generics
1172            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1173    
1174    2006-08-19  Douglas Bates  <bates@R-project.org>
1175    
1176            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1177            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1178            and qr.fitted.
1179            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1180            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1181    
1182    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1183    
1184            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1185            the base version has no "..." argument.
1186    
1187            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1188    
1189            * R/Matrix.R: define and
1190            * NAMESPACE: export as.numeric() and as.logical() methods.
1191                    Let's hope these do not badly slow down something...
1192            Finally export the zapsmall() method.
1193    
1194    2006-08-17  Douglas Bates  <bates@R-project.org>
1195    
1196            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1197            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1198            * src/dtCMatrix.c :Remove code that is no longer used
1199            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1200    
1201    2006-08-14  Douglas Bates  <bates@R-project.org>
1202    
1203            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1204            Csparse_to_logical and Csparse_symmetric_to_general.
1205            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1206            coercion methods between CsparseMatrix and TsparseMatrix.
1207    
1208    2006-08-14  Douglas Bates  <bates@R-project.org>
1209    
1210            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1211            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1212            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1213            possible.
1214    
1215    2006-08-12  Douglas Bates  <bates@R-project.org>
1216    
1217            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1218              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1219              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1220              generalize conversions between TsparseMatrix, CsparseMatrix,
1221              denseMatrix and matrix.  Preserve triangularity property and
1222              propagate Dimnames in the easy cases.
1223    
1224    2006-08-10  Douglas Bates  <bates@R-project.org>
1225    
1226            * src/lmer.c: adjust checks in glmer_init for S4SXP
1227            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1228            before S4SXP but for the wrong reasons.
1229    
1230    2006-08-08  Douglas Bates  <bates@R-project.org>
1231    
1232            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1233            Later modified to return the upper triangle only.
1234            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1235    
1236    2006-08-07  Douglas Bates  <bates@R-project.org>
1237    
1238            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1239            R-level conversion to a sparse symmetric class.
1240            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1241            Remove conversion to sparse symmetric classes (now done in C code).
1242    
1243    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1244    
1245            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1246            * man/band.Rd:  adapt the \dontshow{} unit test.
1247    
1248    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * DESCRIPTION (Version): 0.995-14  for CRAN
1251    
1252            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1253    
1254            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1255            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1256    
1257            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1258            * R/Tsparse.R (tril, triu, band): methods
1259            * R/dgRMatrix.R (tril, ...):    ditto
1260            * man/band.Rd:                  ditto
1261    
1262    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1263    
1264            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1265                    to be up-to-date automatically.
1266    
1267    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1270    
1271            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1272            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1273            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1274            such that the S4 objects are always created by the current version
1275            of R and 'Matrix' class definitions.
1276    
1277    2006-08-01  Douglas Bates  <bates@R-project.org>
1278    
1279            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1280            inst/external/test3comp.rda: Added warnings for convergence on
1281            boundary and test cases.
1282    
1283            * src/lmer.c (mer_postVar): Modified to return the variances that
1284            are marginal to the fixed effects, not conditional on them (which
1285            is what the bVar slot contents represent).
1286    
1287    2006-07-31  Douglas Bates  <bates@R-project.org>
1288    
1289            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1290            function which calls the C function mer_hat_trace2.
1291    
1292            * man/ranef.Rd: Include description of "postVar" argument and
1293            producing a caterpillar plot.
1294    
1295    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1296    
1297            * NAMESPACE:    change  "correlation" to "corMatrix"
1298            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1299            * R/dpoMatrix.R: ditto
1300            * R/lmer.R:      ditto
1301    
1302    2006-07-28  Douglas Bates  <bates@R-project.org>
1303    
1304            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1305            RZXinv slot's contents into a separate internal function that can
1306            be used in mer_hat_trace.
1307    
1308    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1309    
1310            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1311            via new smart
1312            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1313            utility functions.
1314    
1315    
1316    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1319            matrices when appropriate; band() even symmetric ones.
1320            (replCmat): extend to potentially all "CsparseMatrix"
1321            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1322            allow subassignment for special sparse matrices.
1323    
1324            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1325    
1326            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1327            argument; in glmer_*(): print only if(verbose).
1328    
1329            speed-optimize a few places by moving REAL(.) out of loops.
1330    
1331            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1332    
1333    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1334    
1335            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1336                    since that wrongly triggers also for M[ logi , ]
1337    
1338            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1339            a symmetric matrix that results in a non-symmetric one.
1340            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1341    
1342            * R/dMatrix.R: make round(M) work as round(M, 0)
1343    
1344            * R/dgTMatrix.R (image): coordinate system and axis now use
1345            1-based indices, not 0-based ones.
1346    
1347            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1348            * tests/indexing.R: test it.
1349    
1350            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1351            * man/isSymmetric-methods.Rd: and document it.
1352    
1353            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1354            * man/SparseM-conv.Rd: docu them
1355    
1356            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1357                    for 'SparseM' conversions
1358    
1359    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1360    
1361            * R/Matrix.R (head): added head() and tail() methods.
1362    
1363    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1364    
1365            * DESCRIPTION (Version): 0.995-12 released to CRAN
1366    
1367    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
1369            * tests/simple.R: add check for correct dsT -> dgT coercion;
1370                    add check for correct printing of symmetric sparse matrices.
1371    
1372            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1373            for sparse symmetric matrices.
1374    
1375            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1376            diagonal twice.
1377    
1378    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1379    
1380            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1381            being applied to the x slot (detected by Brian Ripley).
1382    
1383    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1384    
1385            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1386    
1387            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1388    
1389    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1390    
1391            * src/lgCMatrix.c (lgCMatrix_diag): new function
1392            * R/lgCMatrix.R (diag): for new method
1393    
1394            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1395                 ==> construction of illegal "*gTMatrix" via new() should
1396                 now be much less easy:
1397            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1398    
1399            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1400                    directly.
1401            * man/Matrix.Rd: documents it.
1402    
1403    2006-07-06  Douglas Bates  <bates@R-project.org>
1404    
1405            * src/pedigree.c (pedigree_inbreeding): Correction in
1406            initialization.  This function is not currently being used and is
1407            not fully tested.
1408    
1409            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1410            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1411            objects.  Modified validity check on pedigree objects to account
1412            for nonparallel patterns of missingness of parents.
1413    
1414            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1415            class.
1416    
1417    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * R/pMatrix.R: coercion pMatrix -> Tsparse
1420    
1421    2006-06-12  Douglas Bates  <bates@R-project.org>
1422    
1423            * DESCRIPTION (Version): 0.995-11 released to CRAN
1424    
1425            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1426            the output from mcmcsamp.
1427    
1428    2006-06-10  Douglas Bates  <bates@R-project.org>
1429    
1430            * R/lmer.R (simulestimate): added C code for calculating the trace
1431            of the hat matrix.
1432    
1433    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1434    
1435            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1436            classes.
1437            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1438    
1439    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1440    
1441            * R/dgTMatrix.R (colSums): etc. All four of
1442            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1443            all "Matrices".
1444    
1445    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1446    
1447            * R/lmer.R (panel.ci): Add a reference line at zero and a
1448            background grid to the qqmath plot of ranef.lmer.
1449    
1450    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1451    
1452            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1453            grouping factors to be specified in the formula as (1|foo/bar).
1454    
1455    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1456    
1457            * R/lmer.R (findbars and others): Change check of is.numeric to
1458            !is.language to resolve the bug reported by Jacob Wegelin.
1459    
1460            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1461            code to evaluate inbreeding coefficients without calculating T,
1462            based on code in Sargolzaei and Iwaisaki's paper.
1463    
1464    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1465    
1466            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1467            generic and mer methods for isNested and denomDF. This denomDF was
1468            an attempt to emulate that in lme but I don't think that makes
1469            sense.  Use the trace of the hat matrix instead.
1470    
1471    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1472    
1473            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1474            the C code depending on a slot structure that's no longer valid.
1475            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1476    
1477    
1478    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1479    
1480            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1481            of lowerTriMatrix generic and methods to tril (also upper to triu)
1482            and added a general band extractor.
1483    
1484    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1485    
1486            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1487            allowable range with NAs. Added a corresponding check in the
1488            validity check for the pedigree class.
1489    
1490            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1491            crossprod methods now inherits from symmetricMatrix.
1492    
1493    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1494    
1495            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1496            generics lowerTriMatrix and upperTriMatrix along with methods for
1497            the Csparse virtual class.  Also added a C function Csparse_band
1498            that implements these methods by calling cholmod_band.
1499    
1500    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1501    
1502            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1503            erased when it was NULL.  This led to invalid subselections!
1504    
1505    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1506    
1507            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1508            in method for "t" so as not to lose the unit diagonal property.
1509    
1510    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1511    
1512            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1513            and methods.  This is now an option to the ranef method for the
1514            mer class.
1515    
1516            * src/cs_utils.c: Ensure that the nz component is -1 for a
1517            compressed column-oriented matrix.  Minor formatting cleanup.
1518    
1519            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1520            objects.
1521    
1522    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1523    
1524            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1525            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1526    
1527    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1528    
1529            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1530            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1531    
1532            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1533            for the dtCMatrix class.
1534    
1535    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1536    
1537            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1538            and methods for it.
1539    
1540    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1541    
1542            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1543            arguments, such that M %*% 1:6 now works
1544            * Tests/matprod.R: test the above
1545    
1546    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1547    
1548            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1549            the ranef.lmer class.
1550    
1551            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1552            methods to extract the posterior variances from the bVar slot.
1553    
1554    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1555    
1556            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1557            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1558    
1559            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1560            * tests/simple: (extended)
1561    
1562            * R/sparseMatrix.R (isTriangular): now using much improved
1563            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1564    
1565    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1566    
1567            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1568            (problem report from Franklin Parlamis).  This should be done
1569            generally.
1570    
1571    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1572    
1573            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1574            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1575            update the plot methods.
1576    
1577    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1578    
1579            * R/lmer.R (resid and ranef methods):  Added methods for the
1580            "residuals" and "resid" generic but only for linear mixed model
1581            fits.  Changed the ranef method to return a list of data frames so
1582            that the plot methods now work.
1583    
1584    2006-03-16  Douglas Bates  <bates@bates2>
1585    
1586            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1587            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1588    
1589            * DESCRIPTION (Date): New release
1590    
1591    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1592    
1593            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1594    
1595            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1596            * man/KNex.Rd: and other help files
1597            * tests/*.R: several ones needed adaption
1598            * inst/doc/Comparisons.Rnw: ditto
1599    
1600    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1601    
1602            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1603    
1604            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1605    
1606    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1607    
1608            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1609    
1610            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1611    
1612    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1613    
1614            * R/dMatrix.R: enable things like  M [ M < 10 ]
1615            * R/dgeMatrix.R: implement it
1616    
1617    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1618    
1619            * R/AllClass.R: define "summary.mer" and "*.lmer"
1620            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1621            * R/lmer.R (show): now works with summary()
1622    
1623    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1624    
1625            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1626            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1627                    support the above
1628    
1629    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1630    
1631            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1632            Use glmFit$prior.weights for weights in a glmm.
1633            Allow an option usePQL = FALSE to skip the PQL steps for the
1634            Laplace method (and, in time, the AGQ method).
1635    
1636            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1637            into a separate function internal_mer_Xfactor to be able to call
1638            it from internal_bhat.
1639    
1640    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1641    
1642            * tests/Class+Meth.R (tstMatrixClass): function for much better
1643            testing; now again of all actual classes.
1644    
1645            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1646                    use macros and define make_d_matrix_* and make_i_matrix_*
1647                    where _i_ is for the ldense routines:
1648    
1649            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1650            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1651    
1652            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1653    
1654    
1655    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1656    
1657            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1658                    many different kinds of matrices.
1659            * R/*.R: quite a few new methods were needed for R CMD check with
1660                    new Matrix().  Very good for users playing around.
1661    
1662    
1663    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1664    
1665            * src/dgeMatrix.c (dMatrix_validate): new
1666            * src/Mutils.c (dense_nonpacked_validate): new
1667    
1668            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1669    
1670    
1671    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1672    
1673            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1674    
1675    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1676    
1677            * DESCRIPTION (Version): 0.99-6 released to CRAN
1678    
1679            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1680            segfault in cases with multiple non-nested grouping factors.
1681    
1682    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1683    
1684            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1685                    (Depends): also on 'utils'
1686    
1687            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1688            * R/diagMatrix.R (Diagonal): constructor and methods for
1689            diagonal matrices
1690    
1691            * R/ltTMatrix.R: new "minimal methods"
1692    
1693    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1694    
1695            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1696            all methods (and help files).
1697    
1698    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1699    
1700            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1701                    for case (dimn.  op  no_dimn.)
1702    
1703    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1704    
1705            * DESCRIPTION (Version): 0.99-2  released to CRAN
1706    
1707    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1708    
1709            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1710            by Julian Faraway.
1711    
1712    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1713    
1714            * R/Auxiliaries.R (try_as): new utility
1715            * R/sparseMatrix.R: use try_as() in coercion to original class
1716    
1717    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1718    
1719            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1720    
1721    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1722    
1723            * R/Auxiliaries.R (dimNamesCheck): added
1724    
1725            * R/Matrix.R (as.array), (as.vector): new
1726    
1727    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1728    
1729            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1730                    default.
1731            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1732                    "pMatrix" now contains "sparseMatrix"
1733    
1734    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1735    
1736            * tests/Class+Meth.R: new tests; t(t(m)) == m
1737    
1738            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1739    
1740            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1741            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1742    
1743            * R/dspMatrix.R: typo in "t" method
1744    
1745    2005-09-18  Douglas Bates  <bates@wisc.edu>
1746    
1747            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1748            * R/Tsparse.R: instead of R/gTMatrix.R
1749            * R/Csparse.R: new
1750            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1751            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1752            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1753                            via cholmod
1754    
1755    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1756    
1757            * R/Auxiliaries.R (non0ind): new function using new C code
1758            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1759    
1760    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1761    
1762            * src/chm_common.h: header file required by all C sources that
1763            call CHOLMOD functions.  It defines a cholmod_common structure
1764            called 'c' whose address is passed as the last argument to
1765            (virtually) every CHOLMOD function.
1766    
1767            * src/Pattern.c: Simple example of the use of CHOLMOD.
1768    
1769            * src/init.c: initialize and finalize the cholmod_common structure.
1770    
1771            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1772            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1773    
1774    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1775    
1776            * inst/test-tools.R: new file collecting the utility functions used
1777                    in ./tests/*.R
1778    
1779            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1780            * R/Matrix.R (cbind2): methods for NULL and missing
1781    
1782    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1783    
1784            * R/AllClass.R: new "index" class for "[" and "[<-":
1785                    First cut at "symmetricMatrix" and "triangularMatrix"
1786            * R/gTMatrix.R (.ind.prep): new function;
1787                    Logical and character indexing now work too.
1788            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1789            * tests/indexing.R: new, including *.Rout.save
1790            * tests/dgTMatrix.R: new
1791    
1792    2005-08-29  Douglas Bates  <bates@wisc.edu>
1793    
1794            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1795            indicator pos not being updated.  Also enforced upper triangular
1796            for symmetric case.  Need to coerce edges component of elements of
1797            edge list - grr! (Why don't they define their classes cleanly?)
1798    
1799    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1800    
1801            * R/Matrix.R:  added first "[<-" methods; not yet functional
1802            * R/denseMatrix.R: ditto
1803            * man/Subassign-methods.Rd: new help file for these
1804    
1805    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1806    
1807            * DESCRIPTION (Version): 0.98-6
1808    
1809            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1810            matrices.
1811    
1812    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1813    
1814            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1815                    as( <logical>, "matrix")
1816    
1817            * R/pMatrix.R: coercion to "lgTMatrix"
1818    
1819            * R/gTMatrix.R: new virtual class to define "[" methods for.
1820            * man/gTMatrix-class.Rd:
1821            * General slight re-organization of where "[" methods are defined.
1822              more to come.
1823    
1824    2005-08-18  Douglas Bates  <bates@wisc.edu>
1825    
1826            * DESCRIPTION (Version): 0.98-5  released to CRAN
1827    
1828            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1829            * .....
1830    
1831    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1832    
1833            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1834            or glmer objects.
1835    
1836    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1837    
1838            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1839    
1840    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1841    
1842            * R/HBMM.R: finish re-writing R-only code.
1843    
1844    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1845    
1846            * man/externalFormats.Rd: move documentation for writeHB and
1847            writeMM here.
1848    
1849            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1850            (suggested by Paul Roecker).
1851    
1852            * tests/validObj.R (assertError): Comment out test that is failing
1853            after recent changes in r-devel.
1854    
1855    
1856    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1857    
1858            * R/AllClass.R: intermediate virtual class "denseMatrix"
1859            * man/denseMatrix-class.Rd
1860            * NAMESPACE: export it, and also export
1861            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1862    
1863    2005-08-10  Douglas Bates  <bates@wisc.edu>
1864    
1865            * DESCRIPTION (Version): 0.98-3 to CRAN
1866    
1867            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1868            matrix_solve code (which was really, really wrong).
1869    
1870    2005-08-07  Douglas Bates  <bates@wisc.edu>
1871    
1872            * DESCRIPTION (Version): 0.98-2
1873    
1874            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1875    
1876            * R/lmer.R (abbrvNms): new
1877            * R/lmer.R (mcmcsamp): allow transformed parameters
1878            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1879            for the Harwell-Boeing and the MatrixMarket formats.
1880    
1881    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1882    
1883            * man/dtrMatrix-class.Rd: add examples
1884            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1885    
1886            * TODO: note the dtpMatrix (docu) bug
1887    
1888            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1889            in order to ensure that new as.matrix() is used by old functions,
1890            e.g., svd(), qr(), eigen(), dist(),..;
1891                  apply(), also matplot() or pairs().
1892    
1893    
1894    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1895    
1896            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1897              add comments about 'control' / lmerControl() arguments
1898    
1899    2005-07-27  Douglas Bates  <bates@wisc.edu>
1900    
1901            * man/sleepstudy.Rd: Added the sleep data set.
1902            * DESCRIPTION (Version): 0.98-1  released to CRAN
1903    
1904    2005-07-12  Douglas Bates  <bates@wisc.edu>
1905            * man/sleepstudy.Rd: Added the sleep data set.
1906    
1907            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1908            .Call calls that were producing spurious output.
1909    
1910    2005-07-05  Douglas Bates  <bates@wisc.edu>
1911    
1912            * R/lmer.R (lmer): stored updated variance component estimates in
1913            mer object for the generalized model.  (Bug reported by Renaud
1914            Lancelot).
1915    
1916    2005-07-03  Douglas Bates  <bates@wisc.edu>
1917    
1918            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1919            unidimensional case.
1920    
1921    2005-06-08  Douglas Bates  <bates@wisc.edu>
1922    
1923            * DESCRIPTION (Version): 0.96-1
1924    
1925            * moved  lmer-class' R and C code moved from lme4 to here
1926    
1927    2005-06-04  Douglas Bates  <bates@wisc.edu>
1928    
1929            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1930            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1931    
1932    2005-06-02  Douglas Bates  <bates@wisc.edu>
1933    
1934            * src/Makefile.win: Forgot to update this when Makefile changed.
1935    
1936    2005-05-11  Douglas Bates  <bates@wisc.edu>
1937    
1938          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1939          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1940    
1941  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1942    
1943          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1944          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1947 
1947          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1948          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1949    
1950  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1951    
1952          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1953          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1954    
1955  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1956    
1957          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1958          multiplication operation.          multiplication operation.
# Line 30  Line 1965 
1965    
1966          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1967    
1968  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1969    
1970          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1971    
1972          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1973    
1974    
1975  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1976    
1977          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1978    
# Line 46  Line 1981 
1981          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1982          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1983    
1984  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1985    
1986          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1987    
# Line 72  Line 2007 
2007          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
2008            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
2009    
2010  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
2011    
2012          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
2013          * ....          * ....
2014    
2015  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
2016    
2017          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
2018    
# Line 92  Line 2027 
2027            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
2028          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
2029    
2030  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
2031    
2032          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
2033    
2034  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
2035    
2036          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2037    
2038  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
2039    
2040          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
2041          the package.          the package.
# Line 148  Line 2083 
2083    
2084          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
2085    
2086  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
2087    
2088          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
2089          for the geMatrix class.          for the geMatrix class.
2090    
2091  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
2092    
2093          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
2094    
2095          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2096    
2097  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
2098    
2099          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2100          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
2101    
2102  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
2103    
2104          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2105    
2106  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
2107    
2108          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2109          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
2110    
2111  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
2112    
2113          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
2114    
2115          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2116          for tripletMatrix to matrix.          for tripletMatrix to matrix.
2117    
2118  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
2119    
2120          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2121          no longer used.          no longer used.
# Line 192  Line 2127 
2127          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
2128          Fixes part but not all of #15.          Fixes part but not all of #15.
2129    
2130  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
2131    
2132          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2133          scalar grouping factors corrected.          scalar grouping factors corrected.
2134    
2135  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
2136    
2137          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
2138    
2139  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
2140    
2141          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
2142          .h file can be included.          .h file can be included.
2143    
2144  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2145    
2146          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2147          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2148    
2149          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2150    
2151  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2152    
2153          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2154    
2155  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2156    
2157          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2158    
2159  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2160    
2161          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2162    
2163  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2164    
2165          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2166    
2167  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2168    
2169          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2170          routines.          routines.
2171    
2172  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2173    
2174          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2175    
2176  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2177    
2178          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2179    

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