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

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