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

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