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revision 1236, Thu Mar 23 15:16:17 2006 UTC revision 2005, Wed Jul 18 14:46:20 2007 UTC
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1    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * man/dpoMatrix-class.Rd: added 'corMatrix' example
4    
5            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
6            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
7            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
8    
9            * R/lsparseMatrix.R: bug fix in "all" method
10            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
11    
12            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
13            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
14                    + matrix |-> nMatrix coercion
15            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
16            * man/pMatrix-class.Rd: ditto
17    
18            * R/Matrix.R (Summary): method for non-dMatrix
19    
20            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
21            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
22                    test all Summary methods.
23    
24    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
27    
28    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
31    
32            * R/pMatrix.R (t?crossprod): methods for pMatrix
33    
34    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
35    
36            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
37    
38    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
39    
40            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
41              trying to fix a subtle bug - which has been somewhere else.
42    
43    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
44    
45            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
46              solve the bug
47    
48    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/dgCMatrix.c (compressed_to_TMatrix):
51    
52    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/Csparse.c (Rsparse_validate): new, to have some validity
55            checking for RsparseMatrix
56            * src/dgCMatrix.c (xRMatrix_validate): ditto
57            * src/dtCMatrix.c (tRMatrix_validate): ditto
58    
59    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
60    
61            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
62              lgRMatrix
63            * [r4568] DESCRIPTION: Prepare for bug-fix release
64            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
65              for declaration of cholmod_symmetry
66    
67    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
70            release.
71    
72    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
73    
74            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
75              functions - no longer used
76            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
77              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
78              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
79              Alloca
80    
81    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
82    
83            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
84              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
85              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
86              src/t_gCMatrix_colSums.c: more R_CheckStack()s
87    
88    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
89    
90            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
91              the required amount of memory then call M_numeric_as_chm_dense.
92            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
93              (like Calloc but calling alloca)
94    
95    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
98            and extended with more sophisticated 'col.names' option.
99            * NAMESPACE: export  printSparseMatrix()
100            * man/printSpMatrix.Rd: document, incl. examples
101    
102    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
103    
104            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
105              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
106              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
107    
108    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.99875-4
111    
112            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
113            some dimnames perservation.
114    
115            * R/dsTMatrix.R (t-method): keep dimnames
116            * R/dtTMatrix.R:  ditto
117    
118            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
119            and ncol(.) < 10
120    
121            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
122            from Mutils.h
123    
124            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
125            e.g. in as(<ngCMatrix>, "matrix")
126    
127    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
128    
129            * [r4529] .: Create a branch for the API changes from the 0.99875
130              series to the 0.999375 series
131            * [r4530] DESCRIPTION, inst/include/Matrix.h,
132              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
133              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
134              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
135              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
136              as_cholmod_x functions
137    
138    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
139    
140            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
141              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
142              to Comparisons
143    
144    >>>>>>> .merge-right.r4561
145    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.99875-3 ready to be released.
148    
149            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
150    
151            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
152            that should also work in a future version of R.
153    
154    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
157    
158            * R/sparseVector.R: more *sparseVector coercions, notably for
159            non - double ones.
160    
161    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
164              notably the new ones building on the new .Call(.)s:
165    
166            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
167            all 4 of [dlin]gCMatrix_colSums().
168    
169    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
170    
171            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
172            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
173              result
174    
175    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/kronecker.R: fix typo (could lead to inf.recursion)
178            * test/simple.R: testing that
179    
180            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
181            method as well (which can have arguments, show() can't).
182    
183    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
184    
185            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
186              added dgCMatrix_colSums for [col,row][Sums,Means]
187    
188    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
189    
190            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
191              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
192              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
193            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
194              class
195            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
196              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
197              row names to store the levels - duh!  Added an example.
198    
199    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/Csparse.c (Csparse_validate): check for *repeated* entries
202            thanks to example from Christian Buchta; with a test here:
203            * tests/simple.R:
204    
205    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
208            of colSums(*, sparseResult = TRUE)
209    
210    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
213            'na.rm = FALSE' as "everywhere" else in R.
214    
215    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
216    
217            * [r4421] src/CSparse_install.sh: Modify for new organization of
218              CSparse package
219            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
220              SuiteSparse
221            * [r4426] src/Makefile: add ./UFconfig to the include path for
222              compilation
223            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
224            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
225              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
226    
227    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
230            * R/sparseMatrix.R (prSpMatrix): now gives a message about
231            suppressed column names.
232    
233    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
234    
235            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
236              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
237              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
238              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
239              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
240              Remove warnings after change to const char* CHAR
241    
242    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
243    
244            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
245              type of M_cholmod_ssmult
246    
247    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
248    
249            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
250              src/init.c: Yet another cholmod export - cholmod_ssmult
251    
252    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * NAMESPACE: exported drop0(), since
255            * man/drop0.Rd: I have seen several cases, I really wanted to use
256            it, so our users may want too.
257    
258    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * man/colSums.Rd: separately document colSums() etc, since these
261            have the extra argument 'sparseResult'.
262    
263    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
266            * man/spMatrix.Rd: docu., including examples
267    
268            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
269            in order to make colMeans() etc fast *and* correct.
270            * R/sparseVector.R (replSPvec): "[<-" functionality for
271            sparseVectors; tested in
272            * tests/simple.R:
273    
274    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
277            (very) sparse Matrices; output similar to Matlab's print().
278    
279    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
282            0-based, indices (Jose Quesada <quesada@gmail.com>).
283    
284    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
287    
288    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/Auxiliaries.R (sparsapply): new utility, much faster than
291            tapply1() for large sparse matrices.
292    
293    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/Matrix.R (dim<-): reshape now via sparseVector.
296    
297            * R/sparseVector.R: methods and function for
298            * R/AllClass.R: new "sparseVector" class and daughters.
299            * NAMESPACE: export new classes
300    
301    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * DESCRIPTION (Version): 0.99875-1
304            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
305    
306    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
309            indexing
310            * tests/indexing.R: test set for that.
311    
312    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
315            entries.
316            * tests/indexing.R(out): add regression test for it
317    
318    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
321            name for "!" method definitions.
322    
323    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Tsparse.R (intI): new utility, used for "[" :
326                    Cleanup up there, and fixes for duplicated indices - more TODO!
327    
328            * tests/indexing.R(out): more tests
329    
330    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
333            code that is now part of the R Lapack library.
334    
335            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
336            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
337    
338    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
341    
342    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
345            up with extraneous names '0'...'<n-1>'
346    
347    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/dgTMatrix.R (mat2dgT): care about NAs
350    
351    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/kronecker.R: triangularity preserving methods
354    
355    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/kronecker.R: new file collecting kronecker() methods in one
358                    place.  Goal: become much faster!
359    
360    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
363            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
364            can be much faster.
365    
366            * tests/matprod.R: add regression tests for these (upper & lower).
367    
368    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Matrix.R (diff): method for our Matrices.
371    
372            * R/sparseMatrix.R (isDiagonal): check dim()!
373    
374    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Matrix.R (dim<-): new method for "reshape()" built on a
377            proposal from Tamas Papp.
378    
379    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
382    
383            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
384            rather define and export  cBind() and rBind() only.
385            --> useRs *must* change code that used to have cbind()/rbind() !!
386    
387            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
388            * R/bind.Rout.save: ditto
389    
390    2007-02-16  Douglas Bates  <bates@r-project.org>
391    
392            * DESCRIPTION (Date, Version): 0.9975-11 with new date
393            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
394            const modifier on declaration of the array 'valid'
395    
396    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
397    
398            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
399    
400    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
403    
404            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
405            * tests/simple.R: test the above and some of these coercions:
406    
407            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
408                    be careful to avoid infinite recursion, using new coercions in
409            * R/ngCMatrix.R and nsC... and ntC...
410            * R/lsparseMatrix.R: ditto
411    
412            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
413    
414            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
415            * R/Rsparse.R: reactivate .Call()s
416    
417            * tests/Class+Meth.R: a bit more on actual classes
418    
419    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
420    
421            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
422    
423    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * DESCRIPTION (Version): 0.9975-10 to upload
426    
427            * tests/Class+Meth.R (tstMatrixClass): require coercions to
428            specific classes less unconditionally.
429    
430            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
431    
432            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
433    
434            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
435            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
436            R_to_CMatrix segfaults on one platform.
437            Eliminate most coercion method to *specific* classes, and replace
438            with virtual classes coercions.
439    
440    
441    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
442    
443            * src/init.c: export the CHM...._validate() placeholders, since
444            they *are* called.
445    
446            * tests/Class+Meth.R (classCanCoerce): and starting to test
447            all as(<from>, <to>)
448    
449    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
452            * tests/indexing.R: tested now
453            * tests/indexing.Rout.save: updated
454    
455            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
456            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
457            appropriate.
458    
459            * NAMESPACE: export a trivial
460            * R/Matrix.R: drop() Matrix-method
461    
462            * R/AllClass.R: moved all prototypes to virtual super classes.
463    
464            * R/Rsparse.R: many more coercions to have less exceptions in
465            * tests/Class+Meth.R:
466    
467            * R/Ops.R (Compare): tweak for case with NA
468            * tests/simpl.R: hence another 'FIXME' eliminated
469    
470    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
473            objects.
474    
475            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
476              and more of "!", "&", "|", all, any; coercions
477    
478            * R/Rsparse.R: many coercions (which enable quite a few other
479            methods), thanks to enhancements in
480            * src/dgCMatrix.c (R_to_CMatrix): new, and
481            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
482            symmetric & triangular and ..RMatrix objects.
483    
484            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
485            renamed file from src/dsTMatrix.c;
486            now dealing with symmetric and triangular Tsparse coercions, both
487            to dense and general.
488    
489    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
492    
493            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
494            where sensible when the <numeric> is of length > 1.
495    
496    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Matrix.R ([<-): for M[] <- value: fix length
499    
500    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
503            * R/ndenseMatrix.R: new coercions n* -> l*
504    
505    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
508    
509            * R/Ops.R ("Logic"): and other "Ops", many updates
510    
511    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * src/Mutils.h (SET_DimNames): new utility
514    
515            * R/Auxiliaries.R (nnzero): improved and now exported via
516    
517            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
518    
519    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/diagMatrix.R (!): fix typo.
522    
523    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Auxiliaries.R (as_Csparse): and quite a few others:
526                    allow to pass class definition --> speedup
527            * R/sparseMatrix.R: apply the above
528    
529            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
530    
531            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
532            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
533            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
534    
535            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
536    
537            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
538            and use it for "sparse*" as well, since it's faster than the
539            as_Csparse(.) way.
540    
541    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
544    
545    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
548            as method for   M[ ij ] <- v
549            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
550    
551            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
552            FALSE answer
553    
554            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
555            * tests/indexing.R: test it, and some of the above
556    
557    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Auxiliaries.R (is_duplicatedT): new utility
560    
561    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * src/init.c (R_init_Matrix): export cholmod_scale
564    
565    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
568            base::as.matrix to (x, ...)
569    
570    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
573            file; start using "Logic", hence
574    
575            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
576            * NAMESPACE: import and export "Logic"
577    
578    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
581            only needed previously to R version 2.5.0.
582    
583    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
586    
587            * R/Tsparse.R (replTmat): fix subassignment of triangular
588            * R/Csparse.R (replCmat): ditto
589            * tests/indexing.R: more tests, incl the above fix
590    
591    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/Auxiliaries.R (drop0): extend for non CSparse
594            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
595    
596            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
597                    use uplo correctly (!); other places: use uplo_P() macro
598    
599            * R/Csparse.R (replCmat): call diagU2N() when needed
600            * R/Tsparse.R (replTmat): ditto
601    
602            * src/dtCMatrix.c (tCMatrix_validate): new
603            * src/dtTMatrix.c (tTMatrix_validate): new, used in
604            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
605    
606            * R/diagMatrix.R (replDiag): to use in [<-
607    
608    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
611                    also more general diagU2N().
612    
613    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
616            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
617    
618    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * tests/bind.R: a few more cases
621            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
622    
623            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
624            * R/ddenseMatrix.R (cbind2/rbind2)
625            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
626            * tests/indexing.R
627            * tests/indexing.Rout.save: updated
628    
629    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
632            * tests/indexing.R
633    
634    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
637            align with proper position of "0", i.e., right for integers.
638            argument 'align' by default is "fancy".
639    
640    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
643            * R/Csparse.R: and fix "Compare" for more cases.
644            * tests/Class+Meth.R: test some of these (m == m, m != m)
645    
646    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/lsparseMatrix.R: all() and any() methods
649            * R/ldenseMatrix.R:      ditto
650            * NAMESPACE, R/Matrix.R: ditto
651    
652            * man/all-methods.Rd: document them minimally
653    
654            * tests/simple.R: add a few examples for these
655    
656    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Tsparse.R ([): fix long standing typo in symmetric case
659            * man/dsCMatrix-class.Rd: add example exhibiting the above case
660    
661    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
664            to LL before converting to a sparse matrix. (The LDL form can be
665            converted to a sparse matrix but it is implicitly a unit
666            triangular matrix and a diagonal matrix overwritten on the diagonal.)
667    
668    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
671    
672    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * DESCRIPTION (Version): updated -> release 0.9975-7
675            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
676    
677    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
680    
681    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
684            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
685            is exactly singular.
686    
687    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * DESCRIPTION (Date): updated -> release 0.9975-6
690    
691    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
694            now returns symmetric.
695    
696            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
697    
698            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
699            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
700    
701            * R/Auxiliaries.R (.type.kind): added
702    
703    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
706            running src/CSparse_install.sh
707    
708            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
709    
710    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
713            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
714    
715            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
716    
717            * tests/Class+Meth.R (tstMatrixClass): now assure
718            the (important in method programming) property :
719    
720                    ###>>  Every "Matrix" is either
721                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
722    
723                    (where "*" stands for "Matrix")
724    
725            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
726    
727            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
728            * tests/validObj.R: checks for "comparison"
729    
730            * R/sparseMatrix.R ([): improved indexing for sparse;
731                    trying to keep <symmetric>[ n, n] symmmetric
732    
733            * tests/indexing.R: indexing for logical sparse now ok
734    
735    
736    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * src/Tsparse.c: use xTsparse_validate() , and hence remove
739    
740            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
741    
742    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
745    
746            * tests/simple.R: validObject() checking the above.
747    
748            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
749            replacing both dgCMatrix_validate and lgCM*.
750    
751            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
752            fix dimnames setting in other places.
753            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
754    
755    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
758    
759            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
760            symmetry test, via
761            * R/Auxiliaries.R (.as.dgC.0.factors):
762    
763    2006-11-01  Douglas Bates  <bates@r-project.org>
764    
765            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
766            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
767            <CsparseMatrix>) added
768    
769    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * tests/matprod.R: add a variation of Harri's example
772    
773            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
774            recursive infinitely.
775    
776            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
777    
778            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
779    
780    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
783            matrix if possible; test m+m == 2*m; now test dgRMatrix.
784            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
785            satisfy the above test.
786    
787    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
790    
791            * R/dgCMatrix.R: solve(a, b="missing") based on
792            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
793            RHS = NULL.
794    
795            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
796            add more (needed) [t]crossprod() methods.
797    
798            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
799    
800            * R/Auxiliaries.R (as_CspClass): cleanup
801            (drop0): internal utility for "Csparse_drop(*, 0)"
802            (.bail.out.2): encourage active feedback
803    
804    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/dMatrix.R(Compare): new(), then slots [no validity check]
807    
808            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
809            non-valid or 'sorted' case).
810    
811            * R/dsparseMatrix.R: add "chol" method.
812            * R/ddenseMatrix.R: ditto
813    
814            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
815            * NAMESPACE (Ops)
816            * R/diagMatrix.R (diag2T): simple utility used "higher level"
817            coercion; deprecating direct lower level coercions.
818    
819            * R/*.R (seq): use seq_len() and seq_along() where possible.
820    
821    
822    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * DESCRIPTION (Version): 0.9975-5 ready for release
825    
826    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
827    
828            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
829    
830    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/AllClass.R (corMatrix): add 'validity' check;
833                    comment out unused "LDL" class definition
834            * NAMESPACE: mention, but do not export "LDL" class
835            * R/corMatrix.R: new (simple), needed for R-devel with
836            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
837              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
838    
839    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
840    
841            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
842            use Rprintf and R's error handling.
843    
844    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
847            * tests/matprod.R: add tests for the bug fixed.
848    
849    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
850    
851            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
852            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
853    
854    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
855    
856            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
857    
858    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * DESCRIPTION (Version): 0.9975-3
861    
862            * R/diagMatrix.R (bdiag): new function constructing block diagonal
863            (sparse) matrices.
864            * man/bdiag.Rd: docu + examples
865    
866            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
867    
868            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
869            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
870    
871            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
872            that result is sparse or diagonal (and not dense).
873    
874            * man/Subassign-methods.Rd: fix examples
875    
876            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
877            should always return a sparse (and not sometimes a diagonal) matrix.
878    
879    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
882    
883    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
884    
885            * DESCRIPTION (Version): 0.9975-2
886    
887            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
888    
889    2006-10-02  Douglas Bates  <bates@R-project.org>
890    
891            * tests/dg_Matrix.R: Simplify test taking into account new code.
892    
893    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
896    
897            * R/lsTMatrix.R: new files w/ missing methods
898            * R/nsTMatrix.R:  "  'for completeness'
899    
900            * tests/Class+Meth.R: a bit less 'not.ok.classes'
901    
902            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
903    
904    
905    2006-09-28  Douglas Bates  <bates@R-project.org>
906    
907            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
908            included.
909    
910            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
911            Export C-callable functions used in Zt_create in lme4.
912    
913    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * DESCRIPTION (Version): 0.9975-1
916    
917            * tests/simple.R: less checks fail; using NA, found that our
918                    kronecker() is not base-compatible with NA's.
919    
920            * R/dMatrix.R: "Compare" method now implemented for all cases
921    
922            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
923    
924            * man/dtpMatrix-class.Rd: mention length of 'x' slot
925    
926            * src/dtpMatrix.c (dtpMatrix_validate): fix check
927            * src/dspMatrix.c (dspMatrix_validate): ditto
928    
929            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
930              including coercion to [nl]tTMatrix.
931    
932            * R/diagMatrix.R (show): print a header line as for other classes.
933    
934    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * src/Makefile.win (SUBDIRS): fix typo
937    
938    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
941    
942    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
943    
944            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
945            symmetric and y missing in R code using %*% (cholmod_aat doesn't
946            accept a symmetric matrix).
947            * tests/group-methods.R: Uncomment test of crossprod applied to
948            lsCMatrix objects.
949    
950    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/AllClass.R (symmetricMatrix): add validity method (available
953            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
954    
955            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
956    
957            * tests/indexing.Rout.save:
958            * tests/indexing.R: additions, mainly for 'lsparse'
959    
960            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
961            case.
962    
963            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
964    
965    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
968                    as 'N' (1-letter - Ok?)
969    
970            * tests/group-methods.R: add test for logical + NAs
971    
972            * R/dMatrix.R ("Compare"): fix to work with NA's
973    
974            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
975    
976            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
977                    which is implemented.
978    
979    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * src/chm_common.c: coerce logical <-> double instead of
982            typecasting;  needed for "l" matrix handling in cholmod.
983    
984            * tests/other-pkgs.R (graph): small extension in "graph" checks.
985    
986            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
987            (Tsp2grNEL): other fixes needed
988    
989    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
992                    Matrices, since "lMatrix", also "lsparseM" can have NA
993            * R/ndenseMatrix.R, etc: new source files
994            * man/nsparseMatrix-classes.Rd, etc: new help files
995            * tests/: adaptions
996            * src/chm_common.c (chm_dense_to_SEXP): and others:
997                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
998            * src/Csparse.c, etc: ditto
999    
1000    2006-09-11  Douglas Bates  <bates@R-project.org>
1001    
1002            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1003            alloc_d**Matrix functions to the lme4 package.
1004    
1005    2006-09-09  Douglas Bates  <bates@R-project.org>
1006    
1007            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1008            fixed
1009    
1010    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/lMatrix.R: new
1013    
1014            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1015    
1016            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1017            * man/tcrossprod.Rd: ditto
1018    
1019    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1020    
1021            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1022            for exported functions
1023            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1024            Remove partitioning algorithms for sparse matrix reordering.  The
1025            copyright on the Metis code was problematic and the methods were
1026            rarely used.
1027            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1028            operations are now done entirely in CHOLMOD code.
1029    
1030    2006-09-06  Douglas Bates  <bates@R-project.org>
1031    
1032            * src/Mutils.h: Remove functions that are no longer used.
1033    
1034    2006-09-04  Douglas Bates  <bates@R-project.org>
1035    
1036            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1037            * src/DEPS.mkf: update
1038    
1039    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1042            * DESCRIPTION (Version): 0.9975-0
1043            (Depends): R (>= 2.4.0)
1044    
1045    2006-09-01  Douglas Bates  <bates@R-project.org>
1046    
1047            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1048    
1049    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1052            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1053    
1054            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1055    
1056    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1059            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1060            * R/dsparseMatrix.R: ditto
1061            * R/Csparse.R: ditto
1062    
1063    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/dMatrix.R (Compare): improve availability of "<", etc
1066            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1067    
1068    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1071            of a 0-index which was used as 1-index (..hmm)
1072    
1073            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1074    
1075            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1076            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1077            (.is.diagonal): ditto
1078    
1079            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1080    
1081            * R/Matrix.R (Matrix): also work for NA data
1082    
1083    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1086            in all cases.
1087    
1088    2006-08-27  Douglas Bates  <bates@R-project.org>
1089    
1090            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1091            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1092    
1093    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1096            subclasses of "ddenseMatrix"
1097            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1098            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1099            instead of half dozen specialized ones.
1100    
1101    2006-08-25  Douglas Bates  <bates@R-project.org>
1102    
1103            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1104            <tillard@cirad.fr> - ordering standard errors to match effects.
1105    
1106    2006-08-24  Douglas Bates  <bates@R-project.org>
1107    
1108            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1109            on R_ldl.
1110            * R/lCholCMatrix.R,
1111            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1112            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1113            * many files in ./R and ./src: Use more general version of
1114            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1115            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1116            dtpMatrix, dspMatrix and dppMatrix conversions.
1117    
1118    
1119    2006-08-23  Douglas Bates  <bates@R-project.org>
1120    
1121            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1122            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1123            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1124            dgeMatrix_crossprod (may need to do this in other places).
1125            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1126            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1127    
1128    2006-08-22  Douglas Bates  <bates@R-project.org>
1129    
1130            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1131            types of classed Matrices, matrices or numeric or logical vectors.
1132            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1133            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1134            to Mutils.h (as an inline) and change name to Matrix_check_class;
1135            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1136            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1137            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1138            * src/Csparse.c: use diag_P and uplo_P macros.
1139    
1140    2006-08-21  Douglas Bates  <bates@R-project.org>
1141    
1142            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1143            valgrind.
1144            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1145            inverses.
1146            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1147            -Wall warnings.
1148            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1149            Use dup_mMatrix_as_dgeMatrix.
1150    
1151    2006-08-20  Douglas Bates  <bates@R-project.org>
1152    
1153            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1154            * tests/sparseQR.R: Added
1155            * man/sparseQR-class.Rd: Document methods for qr.* generics
1156            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1157    
1158    2006-08-19  Douglas Bates  <bates@R-project.org>
1159    
1160            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1161            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1162            and qr.fitted.
1163            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1164            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1165    
1166    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1169            the base version has no "..." argument.
1170    
1171            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1172    
1173            * R/Matrix.R: define and
1174            * NAMESPACE: export as.numeric() and as.logical() methods.
1175                    Let's hope these do not badly slow down something...
1176            Finally export the zapsmall() method.
1177    
1178    2006-08-17  Douglas Bates  <bates@R-project.org>
1179    
1180            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1181            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1182            * src/dtCMatrix.c :Remove code that is no longer used
1183            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1184    
1185    2006-08-14  Douglas Bates  <bates@R-project.org>
1186    
1187            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1188            Csparse_to_logical and Csparse_symmetric_to_general.
1189            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1190            coercion methods between CsparseMatrix and TsparseMatrix.
1191    
1192    2006-08-14  Douglas Bates  <bates@R-project.org>
1193    
1194            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1195            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1196            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1197            possible.
1198    
1199    2006-08-12  Douglas Bates  <bates@R-project.org>
1200    
1201            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1202              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1203              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1204              generalize conversions between TsparseMatrix, CsparseMatrix,
1205              denseMatrix and matrix.  Preserve triangularity property and
1206              propagate Dimnames in the easy cases.
1207    
1208    2006-08-10  Douglas Bates  <bates@R-project.org>
1209    
1210            * src/lmer.c: adjust checks in glmer_init for S4SXP
1211            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1212            before S4SXP but for the wrong reasons.
1213    
1214    2006-08-08  Douglas Bates  <bates@R-project.org>
1215    
1216            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1217            Later modified to return the upper triangle only.
1218            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1219    
1220    2006-08-07  Douglas Bates  <bates@R-project.org>
1221    
1222            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1223            R-level conversion to a sparse symmetric class.
1224            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1225            Remove conversion to sparse symmetric classes (now done in C code).
1226    
1227    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1230            * man/band.Rd:  adapt the \dontshow{} unit test.
1231    
1232    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * DESCRIPTION (Version): 0.995-14  for CRAN
1235    
1236            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1237    
1238            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1239            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1240    
1241            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1242            * R/Tsparse.R (tril, triu, band): methods
1243            * R/dgRMatrix.R (tril, ...):    ditto
1244            * man/band.Rd:                  ditto
1245    
1246    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1249                    to be up-to-date automatically.
1250    
1251    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1254    
1255            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1256            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1257            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1258            such that the S4 objects are always created by the current version
1259            of R and 'Matrix' class definitions.
1260    
1261    2006-08-01  Douglas Bates  <bates@R-project.org>
1262    
1263            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1264            inst/external/test3comp.rda: Added warnings for convergence on
1265            boundary and test cases.
1266    
1267            * src/lmer.c (mer_postVar): Modified to return the variances that
1268            are marginal to the fixed effects, not conditional on them (which
1269            is what the bVar slot contents represent).
1270    
1271    2006-07-31  Douglas Bates  <bates@R-project.org>
1272    
1273            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1274            function which calls the C function mer_hat_trace2.
1275    
1276            * man/ranef.Rd: Include description of "postVar" argument and
1277            producing a caterpillar plot.
1278    
1279    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * NAMESPACE:    change  "correlation" to "corMatrix"
1282            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1283            * R/dpoMatrix.R: ditto
1284            * R/lmer.R:      ditto
1285    
1286    2006-07-28  Douglas Bates  <bates@R-project.org>
1287    
1288            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1289            RZXinv slot's contents into a separate internal function that can
1290            be used in mer_hat_trace.
1291    
1292    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1295            via new smart
1296            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1297            utility functions.
1298    
1299    
1300    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1303            matrices when appropriate; band() even symmetric ones.
1304            (replCmat): extend to potentially all "CsparseMatrix"
1305            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1306            allow subassignment for special sparse matrices.
1307    
1308            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1309    
1310            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1311            argument; in glmer_*(): print only if(verbose).
1312    
1313            speed-optimize a few places by moving REAL(.) out of loops.
1314    
1315            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1316    
1317    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1320                    since that wrongly triggers also for M[ logi , ]
1321    
1322            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1323            a symmetric matrix that results in a non-symmetric one.
1324            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1325    
1326            * R/dMatrix.R: make round(M) work as round(M, 0)
1327    
1328            * R/dgTMatrix.R (image): coordinate system and axis now use
1329            1-based indices, not 0-based ones.
1330    
1331            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1332            * tests/indexing.R: test it.
1333    
1334            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1335            * man/isSymmetric-methods.Rd: and document it.
1336    
1337            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1338            * man/SparseM-conv.Rd: docu them
1339    
1340            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1341                    for 'SparseM' conversions
1342    
1343    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1344    
1345            * R/Matrix.R (head): added head() and tail() methods.
1346    
1347    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * DESCRIPTION (Version): 0.995-12 released to CRAN
1350    
1351    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1352    
1353            * tests/simple.R: add check for correct dsT -> dgT coercion;
1354                    add check for correct printing of symmetric sparse matrices.
1355    
1356            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1357            for sparse symmetric matrices.
1358    
1359            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1360            diagonal twice.
1361    
1362    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1363    
1364            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1365            being applied to the x slot (detected by Brian Ripley).
1366    
1367    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
1369            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1370    
1371            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1372    
1373    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * src/lgCMatrix.c (lgCMatrix_diag): new function
1376            * R/lgCMatrix.R (diag): for new method
1377    
1378            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1379                 ==> construction of illegal "*gTMatrix" via new() should
1380                 now be much less easy:
1381            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1382    
1383            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1384                    directly.
1385            * man/Matrix.Rd: documents it.
1386    
1387    2006-07-06  Douglas Bates  <bates@R-project.org>
1388    
1389            * src/pedigree.c (pedigree_inbreeding): Correction in
1390            initialization.  This function is not currently being used and is
1391            not fully tested.
1392    
1393            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1394            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1395            objects.  Modified validity check on pedigree objects to account
1396            for nonparallel patterns of missingness of parents.
1397    
1398            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1399            class.
1400    
1401    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * R/pMatrix.R: coercion pMatrix -> Tsparse
1404    
1405    2006-06-12  Douglas Bates  <bates@R-project.org>
1406    
1407            * DESCRIPTION (Version): 0.995-11 released to CRAN
1408    
1409            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1410            the output from mcmcsamp.
1411    
1412    2006-06-10  Douglas Bates  <bates@R-project.org>
1413    
1414            * R/lmer.R (simulestimate): added C code for calculating the trace
1415            of the hat matrix.
1416    
1417    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1420            classes.
1421            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1422    
1423    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1424    
1425            * R/dgTMatrix.R (colSums): etc. All four of
1426            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1427            all "Matrices".
1428    
1429    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1430    
1431            * R/lmer.R (panel.ci): Add a reference line at zero and a
1432            background grid to the qqmath plot of ranef.lmer.
1433    
1434    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1435    
1436            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1437            grouping factors to be specified in the formula as (1|foo/bar).
1438    
1439    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1440    
1441            * R/lmer.R (findbars and others): Change check of is.numeric to
1442            !is.language to resolve the bug reported by Jacob Wegelin.
1443    
1444            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1445            code to evaluate inbreeding coefficients without calculating T,
1446            based on code in Sargolzaei and Iwaisaki's paper.
1447    
1448    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1449    
1450            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1451            generic and mer methods for isNested and denomDF. This denomDF was
1452            an attempt to emulate that in lme but I don't think that makes
1453            sense.  Use the trace of the hat matrix instead.
1454    
1455    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1456    
1457            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1458            the C code depending on a slot structure that's no longer valid.
1459            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1460    
1461    
1462    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1463    
1464            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1465            of lowerTriMatrix generic and methods to tril (also upper to triu)
1466            and added a general band extractor.
1467    
1468    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1469    
1470            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1471            allowable range with NAs. Added a corresponding check in the
1472            validity check for the pedigree class.
1473    
1474            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1475            crossprod methods now inherits from symmetricMatrix.
1476    
1477    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1478    
1479            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1480            generics lowerTriMatrix and upperTriMatrix along with methods for
1481            the Csparse virtual class.  Also added a C function Csparse_band
1482            that implements these methods by calling cholmod_band.
1483    
1484    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1485    
1486            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1487            erased when it was NULL.  This led to invalid subselections!
1488    
1489    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1490    
1491            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1492            in method for "t" so as not to lose the unit diagonal property.
1493    
1494    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1495    
1496            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1497            and methods.  This is now an option to the ranef method for the
1498            mer class.
1499    
1500            * src/cs_utils.c: Ensure that the nz component is -1 for a
1501            compressed column-oriented matrix.  Minor formatting cleanup.
1502    
1503            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1504            objects.
1505    
1506    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1509            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1510    
1511    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1512    
1513            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1514            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1515    
1516            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1517            for the dtCMatrix class.
1518    
1519    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1520    
1521            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1522            and methods for it.
1523    
1524    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1527            arguments, such that M %*% 1:6 now works
1528            * Tests/matprod.R: test the above
1529    
1530    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1531    
1532            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1533            the ranef.lmer class.
1534    
1535            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1536            methods to extract the posterior variances from the bVar slot.
1537    
1538    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1539    
1540            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1541            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1542    
1543            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1544            * tests/simple: (extended)
1545    
1546            * R/sparseMatrix.R (isTriangular): now using much improved
1547            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1548    
1549  2006-03-23  Douglas Bates  <bates@stat.wisc.edu>  2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1550    
1551          * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames          * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
# Line 31  Line 1579 
1579          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1580          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1581          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1582          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1583    
1584  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1585    
# Line 235  Line 1783 
1783  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1784    
1785          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1786          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1787          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1788    
1789  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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