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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1868, Mon Jun 4 17:15:09 2007 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
4              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
5              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
6              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
7              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
8              Remove warnings after change to const char* CHAR
9    
10    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
11    
12            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
13              type of M_cholmod_ssmult
14    
15    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
16    
17            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
18              src/init.c: Yet another cholmod export - cholmod_ssmult
19    
20    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * NAMESPACE: exported drop0(), since
23            * man/drop0.Rd: I have seen several cases, I really wanted to use
24            it, so our users may want too.
25    
26    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * man/colSums.Rd: separately document colSums() etc, since these
29            have the extra argument 'sparseResult'.
30    
31    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
34            * man/spMatrix.Rd: docu., including examples
35    
36            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
37            in order to make colMeans() etc fast *and* correct.
38            * R/sparseVector.R (replSPvec): "[<-" functionality for
39            sparseVectors; tested in
40            * tests/simple.R:
41    
42    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
45            (very) sparse Matrices; output similar to Matlab's print().
46    
47    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
50            0-based, indices (Jose Quesada <quesada@gmail.com>).
51    
52    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
55    
56    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Auxiliaries.R (sparsapply): new utility, much faster than
59            tapply1() for large sparse matrices.
60    
61    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Matrix.R (dim<-): reshape now via sparseVector.
64    
65            * R/sparseVector.R: methods and function for
66            * R/AllClass.R: new "sparseVector" class and daughters.
67            * NAMESPACE: export new classes
68    
69    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.99875-1
72            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
73    
74    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
77            indexing
78            * tests/indexing.R: test set for that.
79    
80    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
83            entries.
84            * tests/indexing.R(out): add regression test for it
85    
86    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
89            name for "!" method definitions.
90    
91    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R (intI): new utility, used for "[" :
94                    Cleanup up there, and fixes for duplicated indices - more TODO!
95    
96            * tests/indexing.R(out): more tests
97    
98    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
101            code that is now part of the R Lapack library.
102    
103            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
104            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
105    
106    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
109    
110    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
113            up with extraneous names '0'...'<n-1>'
114    
115    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/dgTMatrix.R (mat2dgT): care about NAs
118    
119    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/kronecker.R: triangularity preserving methods
122    
123    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/kronecker.R: new file collecting kronecker() methods in one
126                    place.  Goal: become much faster!
127    
128    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
131            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
132            can be much faster.
133    
134            * tests/matprod.R: add regression tests for these (upper & lower).
135    
136    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Matrix.R (diff): method for our Matrices.
139    
140            * R/sparseMatrix.R (isDiagonal): check dim()!
141    
142    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (dim<-): new method for "reshape()" built on a
145            proposal from Tamas Papp.
146    
147    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
150    
151            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
152            rather define and export  cBind() and rBind() only.
153            --> useRs *must* change code that used to have cbind()/rbind() !!
154    
155            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
156            * R/bind.Rout.save: ditto
157    
158    2007-02-16  Douglas Bates  <bates@r-project.org>
159    
160            * DESCRIPTION (Date, Version): 0.9975-11 with new date
161            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
162            const modifier on declaration of the array 'valid'
163    
164    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
167    
168    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
171    
172            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
173            * tests/simple.R: test the above and some of these coercions:
174    
175            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
176                    be careful to avoid infinite recursion, using new coercions in
177            * R/ngCMatrix.R and nsC... and ntC...
178            * R/lsparseMatrix.R: ditto
179    
180            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
181    
182            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
183            * R/Rsparse.R: reactivate .Call()s
184    
185            * tests/Class+Meth.R: a bit more on actual classes
186    
187    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
190    
191    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * DESCRIPTION (Version): 0.9975-10 to upload
194    
195            * tests/Class+Meth.R (tstMatrixClass): require coercions to
196            specific classes less unconditionally.
197    
198            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
199    
200            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
201    
202            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
203            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
204            R_to_CMatrix segfaults on one platform.
205            Eliminate most coercion method to *specific* classes, and replace
206            with virtual classes coercions.
207    
208    
209    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
210    
211            * src/init.c: export the CHM...._validate() placeholders, since
212            they *are* called.
213    
214            * tests/Class+Meth.R (classCanCoerce): and starting to test
215            all as(<from>, <to>)
216    
217    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
220            * tests/indexing.R: tested now
221            * tests/indexing.Rout.save: updated
222    
223            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
224            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
225            appropriate.
226    
227            * NAMESPACE: export a trivial
228            * R/Matrix.R: drop() Matrix-method
229    
230            * R/AllClass.R: moved all prototypes to virtual super classes.
231    
232            * R/Rsparse.R: many more coercions to have less exceptions in
233            * tests/Class+Meth.R:
234    
235            * R/Ops.R (Compare): tweak for case with NA
236            * tests/simpl.R: hence another 'FIXME' eliminated
237    
238    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
241            objects.
242    
243            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
244              and more of "!", "&", "|", all, any; coercions
245    
246            * R/Rsparse.R: many coercions (which enable quite a few other
247            methods), thanks to enhancements in
248            * src/dgCMatrix.c (R_to_CMatrix): new, and
249            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
250            symmetric & triangular and ..RMatrix objects.
251    
252            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
253            renamed file from src/dsTMatrix.c;
254            now dealing with symmetric and triangular Tsparse coercions, both
255            to dense and general.
256    
257    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
260    
261            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
262            where sensible when the <numeric> is of length > 1.
263    
264    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Matrix.R ([<-): for M[] <- value: fix length
267    
268    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
271            * R/ndenseMatrix.R: new coercions n* -> l*
272    
273    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
276    
277            * R/Ops.R ("Logic"): and other "Ops", many updates
278    
279    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/Mutils.h (SET_DimNames): new utility
282    
283            * R/Auxiliaries.R (nnzero): improved and now exported via
284    
285            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
286    
287    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/diagMatrix.R (!): fix typo.
290    
291    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (as_Csparse): and quite a few others:
294                    allow to pass class definition --> speedup
295            * R/sparseMatrix.R: apply the above
296    
297            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
298    
299            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
300            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
301            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
302    
303            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
304    
305            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
306            and use it for "sparse*" as well, since it's faster than the
307            as_Csparse(.) way.
308    
309    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
312    
313    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
316            as method for   M[ ij ] <- v
317            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
318    
319            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
320            FALSE answer
321    
322            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
323            * tests/indexing.R: test it, and some of the above
324    
325    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Auxiliaries.R (is_duplicatedT): new utility
328    
329    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * src/init.c (R_init_Matrix): export cholmod_scale
332    
333    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
336            base::as.matrix to (x, ...)
337    
338    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
341            file; start using "Logic", hence
342    
343            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
344            * NAMESPACE: import and export "Logic"
345    
346    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
349            only needed previously to R version 2.5.0.
350    
351    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
354    
355            * R/Tsparse.R (replTmat): fix subassignment of triangular
356            * R/Csparse.R (replCmat): ditto
357            * tests/indexing.R: more tests, incl the above fix
358    
359    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Auxiliaries.R (drop0): extend for non CSparse
362            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
363    
364            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
365                    use uplo correctly (!); other places: use uplo_P() macro
366    
367            * R/Csparse.R (replCmat): call diagU2N() when needed
368            * R/Tsparse.R (replTmat): ditto
369    
370            * src/dtCMatrix.c (tCMatrix_validate): new
371            * src/dtTMatrix.c (tTMatrix_validate): new, used in
372            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
373    
374            * R/diagMatrix.R (replDiag): to use in [<-
375    
376    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
379                    also more general diagU2N().
380    
381    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
384            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
385    
386    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * tests/bind.R: a few more cases
389            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
390    
391            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
392            * R/ddenseMatrix.R (cbind2/rbind2)
393            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
394            * tests/indexing.R
395            * tests/indexing.Rout.save: updated
396    
397    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
400            * tests/indexing.R
401    
402    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
405            align with proper position of "0", i.e., right for integers.
406            argument 'align' by default is "fancy".
407    
408    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
411            * R/Csparse.R: and fix "Compare" for more cases.
412            * tests/Class+Meth.R: test some of these (m == m, m != m)
413    
414    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/lsparseMatrix.R: all() and any() methods
417            * R/ldenseMatrix.R:      ditto
418            * NAMESPACE, R/Matrix.R: ditto
419    
420            * man/all-methods.Rd: document them minimally
421    
422            * tests/simple.R: add a few examples for these
423    
424    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/Tsparse.R ([): fix long standing typo in symmetric case
427            * man/dsCMatrix-class.Rd: add example exhibiting the above case
428    
429    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
432            to LL before converting to a sparse matrix. (The LDL form can be
433            converted to a sparse matrix but it is implicitly a unit
434            triangular matrix and a diagonal matrix overwritten on the diagonal.)
435    
436    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
437    
438            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
439    
440    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
441    
442            * DESCRIPTION (Version): updated -> release 0.9975-7
443            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
444    
445    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
448    
449    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
450    
451            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
452            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
453            is exactly singular.
454    
455    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * DESCRIPTION (Date): updated -> release 0.9975-6
458    
459    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
462            now returns symmetric.
463    
464            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
465    
466            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
467            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
468    
469            * R/Auxiliaries.R (.type.kind): added
470    
471    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
474            running src/CSparse_install.sh
475    
476            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
477    
478    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
481            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
482    
483            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
484    
485            * tests/Class+Meth.R (tstMatrixClass): now assure
486            the (important in method programming) property :
487    
488                    ###>>  Every "Matrix" is either
489                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
490    
491                    (where "*" stands for "Matrix")
492    
493            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
494    
495            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
496            * tests/validObj.R: checks for "comparison"
497    
498            * R/sparseMatrix.R ([): improved indexing for sparse;
499                    trying to keep <symmetric>[ n, n] symmmetric
500    
501            * tests/indexing.R: indexing for logical sparse now ok
502    
503    
504    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * src/Tsparse.c: use xTsparse_validate() , and hence remove
507    
508            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
509    
510    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
513    
514            * tests/simple.R: validObject() checking the above.
515    
516            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
517            replacing both dgCMatrix_validate and lgCM*.
518    
519            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
520            fix dimnames setting in other places.
521            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
522    
523    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
526    
527            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
528            symmetry test, via
529            * R/Auxiliaries.R (.as.dgC.0.factors):
530    
531    2006-11-01  Douglas Bates  <bates@r-project.org>
532    
533            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
534            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
535            <CsparseMatrix>) added
536    
537    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * tests/matprod.R: add a variation of Harri's example
540    
541            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
542            recursive infinitely.
543    
544            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
545    
546            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
547    
548    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
551            matrix if possible; test m+m == 2*m; now test dgRMatrix.
552            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
553            satisfy the above test.
554    
555    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
558    
559            * R/dgCMatrix.R: solve(a, b="missing") based on
560            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
561            RHS = NULL.
562    
563            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
564            add more (needed) [t]crossprod() methods.
565    
566            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
567    
568            * R/Auxiliaries.R (as_CspClass): cleanup
569            (drop0): internal utility for "Csparse_drop(*, 0)"
570            (.bail.out.2): encourage active feedback
571    
572    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/dMatrix.R(Compare): new(), then slots [no validity check]
575    
576            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
577            non-valid or 'sorted' case).
578    
579            * R/dsparseMatrix.R: add "chol" method.
580            * R/ddenseMatrix.R: ditto
581    
582            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
583            * NAMESPACE (Ops)
584            * R/diagMatrix.R (diag2T): simple utility used "higher level"
585            coercion; deprecating direct lower level coercions.
586    
587            * R/*.R (seq): use seq_len() and seq_along() where possible.
588    
589    
590    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * DESCRIPTION (Version): 0.9975-5 ready for release
593    
594    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
595    
596            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
597    
598    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/AllClass.R (corMatrix): add 'validity' check;
601                    comment out unused "LDL" class definition
602            * NAMESPACE: mention, but do not export "LDL" class
603            * R/corMatrix.R: new (simple), needed for R-devel with
604            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
605              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
606    
607    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
610            use Rprintf and R's error handling.
611    
612    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
615            * tests/matprod.R: add tests for the bug fixed.
616    
617    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
618    
619            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
620            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
621    
622    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
623    
624            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
625    
626    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * DESCRIPTION (Version): 0.9975-3
629    
630            * R/diagMatrix.R (bdiag): new function constructing block diagonal
631            (sparse) matrices.
632            * man/bdiag.Rd: docu + examples
633    
634            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
635    
636            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
637            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
638    
639            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
640            that result is sparse or diagonal (and not dense).
641    
642            * man/Subassign-methods.Rd: fix examples
643    
644            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
645            should always return a sparse (and not sometimes a diagonal) matrix.
646    
647    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
650    
651    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
652    
653            * DESCRIPTION (Version): 0.9975-2
654    
655            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
656    
657    2006-10-02  Douglas Bates  <bates@R-project.org>
658    
659            * tests/dg_Matrix.R: Simplify test taking into account new code.
660    
661    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
664    
665            * R/lsTMatrix.R: new files w/ missing methods
666            * R/nsTMatrix.R:  "  'for completeness'
667    
668            * tests/Class+Meth.R: a bit less 'not.ok.classes'
669    
670            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
671    
672    
673    2006-09-28  Douglas Bates  <bates@R-project.org>
674    
675            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
676            included.
677    
678            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
679            Export C-callable functions used in Zt_create in lme4.
680    
681    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * DESCRIPTION (Version): 0.9975-1
684    
685            * tests/simple.R: less checks fail; using NA, found that our
686                    kronecker() is not base-compatible with NA's.
687    
688            * R/dMatrix.R: "Compare" method now implemented for all cases
689    
690            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
691    
692            * man/dtpMatrix-class.Rd: mention length of 'x' slot
693    
694            * src/dtpMatrix.c (dtpMatrix_validate): fix check
695            * src/dspMatrix.c (dspMatrix_validate): ditto
696    
697            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
698              including coercion to [nl]tTMatrix.
699    
700            * R/diagMatrix.R (show): print a header line as for other classes.
701    
702    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * src/Makefile.win (SUBDIRS): fix typo
705    
706    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
709    
710    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
713            symmetric and y missing in R code using %*% (cholmod_aat doesn't
714            accept a symmetric matrix).
715            * tests/group-methods.R: Uncomment test of crossprod applied to
716            lsCMatrix objects.
717    
718    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/AllClass.R (symmetricMatrix): add validity method (available
721            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
722    
723            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
724    
725            * tests/indexing.Rout.save:
726            * tests/indexing.R: additions, mainly for 'lsparse'
727    
728            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
729            case.
730    
731            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
732    
733    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
736                    as 'N' (1-letter - Ok?)
737    
738            * tests/group-methods.R: add test for logical + NAs
739    
740            * R/dMatrix.R ("Compare"): fix to work with NA's
741    
742            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
743    
744            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
745                    which is implemented.
746    
747    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * src/chm_common.c: coerce logical <-> double instead of
750            typecasting;  needed for "l" matrix handling in cholmod.
751    
752            * tests/other-pkgs.R (graph): small extension in "graph" checks.
753    
754            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
755            (Tsp2grNEL): other fixes needed
756    
757    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
760                    Matrices, since "lMatrix", also "lsparseM" can have NA
761            * R/ndenseMatrix.R, etc: new source files
762            * man/nsparseMatrix-classes.Rd, etc: new help files
763            * tests/: adaptions
764            * src/chm_common.c (chm_dense_to_SEXP): and others:
765                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
766            * src/Csparse.c, etc: ditto
767    
768    2006-09-11  Douglas Bates  <bates@R-project.org>
769    
770            * src/Mutils.[ch],init.c inst/include/*.h: Move the
771            alloc_d**Matrix functions to the lme4 package.
772    
773    2006-09-09  Douglas Bates  <bates@R-project.org>
774    
775            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
776            fixed
777    
778    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/lMatrix.R: new
781    
782            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
783    
784            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
785            * man/tcrossprod.Rd: ditto
786    
787    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
788    
789            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
790            for exported functions
791            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
792            Remove partitioning algorithms for sparse matrix reordering.  The
793            copyright on the Metis code was problematic and the methods were
794            rarely used.
795            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
796            operations are now done entirely in CHOLMOD code.
797    
798    2006-09-06  Douglas Bates  <bates@R-project.org>
799    
800            * src/Mutils.h: Remove functions that are no longer used.
801    
802    2006-09-04  Douglas Bates  <bates@R-project.org>
803    
804            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
805            * src/DEPS.mkf: update
806    
807    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * created branches/Matrix-for-R-2.3.x;  on trunk: do
810            * DESCRIPTION (Version): 0.9975-0
811            (Depends): R (>= 2.4.0)
812    
813    2006-09-01  Douglas Bates  <bates@R-project.org>
814    
815            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
816    
817    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
820            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
821    
822            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
823    
824    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
827            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
828            * R/dsparseMatrix.R: ditto
829            * R/Csparse.R: ditto
830    
831    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/dMatrix.R (Compare): improve availability of "<", etc
834            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
835    
836    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
839            of a 0-index which was used as 1-index (..hmm)
840    
841            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
842    
843            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
844            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
845            (.is.diagonal): ditto
846    
847            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
848    
849            * R/Matrix.R (Matrix): also work for NA data
850    
851    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
854            in all cases.
855    
856    2006-08-27  Douglas Bates  <bates@R-project.org>
857    
858            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
859            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
860    
861    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
864            subclasses of "ddenseMatrix"
865            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
866            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
867            instead of half dozen specialized ones.
868    
869    2006-08-25  Douglas Bates  <bates@R-project.org>
870    
871            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
872            <tillard@cirad.fr> - ordering standard errors to match effects.
873    
874    2006-08-24  Douglas Bates  <bates@R-project.org>
875    
876            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
877            on R_ldl.
878            * R/lCholCMatrix.R,
879            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
880            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
881            * many files in ./R and ./src: Use more general version of
882            dup_mMatrix_as_dgeMatrix to simplify method definitions.
883            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
884            dtpMatrix, dspMatrix and dppMatrix conversions.
885    
886    
887    2006-08-23  Douglas Bates  <bates@R-project.org>
888    
889            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
890            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
891            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
892            dgeMatrix_crossprod (may need to do this in other places).
893            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
894            generic and method for dsCMatrix.  Use CHOLMOD for chol().
895    
896    2006-08-22  Douglas Bates  <bates@R-project.org>
897    
898            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
899            types of classed Matrices, matrices or numeric or logical vectors.
900            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
901            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
902            to Mutils.h (as an inline) and change name to Matrix_check_class;
903            fixes in as_cholmod_factor and chm_factor_to_SEXP.
904            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
905            dsCMatrix_matrix_solve.  Comment out vestigial functions.
906            * src/Csparse.c: use diag_P and uplo_P macros.
907    
908    2006-08-21  Douglas Bates  <bates@R-project.org>
909    
910            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
911            valgrind.
912            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
913            inverses.
914            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
915            -Wall warnings.
916            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
917            Use dup_mMatrix_as_dgeMatrix.
918    
919    2006-08-20  Douglas Bates  <bates@R-project.org>
920    
921            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
922            * tests/sparseQR.R: Added
923            * man/sparseQR-class.Rd: Document methods for qr.* generics
924            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
925    
926    2006-08-19  Douglas Bates  <bates@R-project.org>
927    
928            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
929            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
930            and qr.fitted.
931            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
932            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
933    
934    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
937            the base version has no "..." argument.
938    
939            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
940    
941            * R/Matrix.R: define and
942            * NAMESPACE: export as.numeric() and as.logical() methods.
943                    Let's hope these do not badly slow down something...
944            Finally export the zapsmall() method.
945    
946    2006-08-17  Douglas Bates  <bates@R-project.org>
947    
948            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
949            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
950            * src/dtCMatrix.c :Remove code that is no longer used
951            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
952    
953    2006-08-14  Douglas Bates  <bates@R-project.org>
954    
955            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
956            Csparse_to_logical and Csparse_symmetric_to_general.
957            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
958            coercion methods between CsparseMatrix and TsparseMatrix.
959    
960    2006-08-14  Douglas Bates  <bates@R-project.org>
961    
962            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
963            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
964            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
965            possible.
966    
967    2006-08-12  Douglas Bates  <bates@R-project.org>
968    
969            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
970              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
971              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
972              generalize conversions between TsparseMatrix, CsparseMatrix,
973              denseMatrix and matrix.  Preserve triangularity property and
974              propagate Dimnames in the easy cases.
975    
976    2006-08-10  Douglas Bates  <bates@R-project.org>
977    
978            * src/lmer.c: adjust checks in glmer_init for S4SXP
979            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
980            before S4SXP but for the wrong reasons.
981    
982    2006-08-08  Douglas Bates  <bates@R-project.org>
983    
984            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
985            Later modified to return the upper triangle only.
986            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
987    
988    2006-08-07  Douglas Bates  <bates@R-project.org>
989    
990            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
991            R-level conversion to a sparse symmetric class.
992            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
993            Remove conversion to sparse symmetric classes (now done in C code).
994    
995    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
998            * man/band.Rd:  adapt the \dontshow{} unit test.
999    
1000    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * DESCRIPTION (Version): 0.995-14  for CRAN
1003    
1004            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1005    
1006            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1007            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1008    
1009            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1010            * R/Tsparse.R (tril, triu, band): methods
1011            * R/dgRMatrix.R (tril, ...):    ditto
1012            * man/band.Rd:                  ditto
1013    
1014    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1017                    to be up-to-date automatically.
1018    
1019    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1022    
1023            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1024            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1025            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1026            such that the S4 objects are always created by the current version
1027            of R and 'Matrix' class definitions.
1028    
1029    2006-08-01  Douglas Bates  <bates@R-project.org>
1030    
1031            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1032            inst/external/test3comp.rda: Added warnings for convergence on
1033            boundary and test cases.
1034    
1035            * src/lmer.c (mer_postVar): Modified to return the variances that
1036            are marginal to the fixed effects, not conditional on them (which
1037            is what the bVar slot contents represent).
1038    
1039    2006-07-31  Douglas Bates  <bates@R-project.org>
1040    
1041            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1042            function which calls the C function mer_hat_trace2.
1043    
1044            * man/ranef.Rd: Include description of "postVar" argument and
1045            producing a caterpillar plot.
1046    
1047    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * NAMESPACE:    change  "correlation" to "corMatrix"
1050            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1051            * R/dpoMatrix.R: ditto
1052            * R/lmer.R:      ditto
1053    
1054    2006-07-28  Douglas Bates  <bates@R-project.org>
1055    
1056            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1057            RZXinv slot's contents into a separate internal function that can
1058            be used in mer_hat_trace.
1059    
1060    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1063            via new smart
1064            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1065            utility functions.
1066    
1067    
1068    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1071            matrices when appropriate; band() even symmetric ones.
1072            (replCmat): extend to potentially all "CsparseMatrix"
1073            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1074            allow subassignment for special sparse matrices.
1075    
1076            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1077    
1078            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1079            argument; in glmer_*(): print only if(verbose).
1080    
1081            speed-optimize a few places by moving REAL(.) out of loops.
1082    
1083            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1084    
1085    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1088                    since that wrongly triggers also for M[ logi , ]
1089    
1090            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1091            a symmetric matrix that results in a non-symmetric one.
1092            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1093    
1094            * R/dMatrix.R: make round(M) work as round(M, 0)
1095    
1096            * R/dgTMatrix.R (image): coordinate system and axis now use
1097            1-based indices, not 0-based ones.
1098    
1099            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1100            * tests/indexing.R: test it.
1101    
1102            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1103            * man/isSymmetric-methods.Rd: and document it.
1104    
1105            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1106            * man/SparseM-conv.Rd: docu them
1107    
1108            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1109                    for 'SparseM' conversions
1110    
1111    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1112    
1113            * R/Matrix.R (head): added head() and tail() methods.
1114    
1115    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * DESCRIPTION (Version): 0.995-12 released to CRAN
1118    
1119    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1120    
1121            * tests/simple.R: add check for correct dsT -> dgT coercion;
1122                    add check for correct printing of symmetric sparse matrices.
1123    
1124            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1125            for sparse symmetric matrices.
1126    
1127            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1128            diagonal twice.
1129    
1130    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1131    
1132            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1133            being applied to the x slot (detected by Brian Ripley).
1134    
1135    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1138    
1139            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1140    
1141    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * src/lgCMatrix.c (lgCMatrix_diag): new function
1144            * R/lgCMatrix.R (diag): for new method
1145    
1146            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1147                 ==> construction of illegal "*gTMatrix" via new() should
1148                 now be much less easy:
1149            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1150    
1151            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1152                    directly.
1153            * man/Matrix.Rd: documents it.
1154    
1155    2006-07-06  Douglas Bates  <bates@R-project.org>
1156    
1157            * src/pedigree.c (pedigree_inbreeding): Correction in
1158            initialization.  This function is not currently being used and is
1159            not fully tested.
1160    
1161            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1162            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1163            objects.  Modified validity check on pedigree objects to account
1164            for nonparallel patterns of missingness of parents.
1165    
1166            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1167            class.
1168    
1169    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171            * R/pMatrix.R: coercion pMatrix -> Tsparse
1172    
1173    2006-06-12  Douglas Bates  <bates@R-project.org>
1174    
1175            * DESCRIPTION (Version): 0.995-11 released to CRAN
1176    
1177            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1178            the output from mcmcsamp.
1179    
1180    2006-06-10  Douglas Bates  <bates@R-project.org>
1181    
1182            * R/lmer.R (simulestimate): added C code for calculating the trace
1183            of the hat matrix.
1184    
1185    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1188            classes.
1189            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1190    
1191    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1192    
1193            * R/dgTMatrix.R (colSums): etc. All four of
1194            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1195            all "Matrices".
1196    
1197    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1198    
1199            * R/lmer.R (panel.ci): Add a reference line at zero and a
1200            background grid to the qqmath plot of ranef.lmer.
1201    
1202    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1203    
1204            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1205            grouping factors to be specified in the formula as (1|foo/bar).
1206    
1207    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1208    
1209            * R/lmer.R (findbars and others): Change check of is.numeric to
1210            !is.language to resolve the bug reported by Jacob Wegelin.
1211    
1212            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1213            code to evaluate inbreeding coefficients without calculating T,
1214            based on code in Sargolzaei and Iwaisaki's paper.
1215    
1216    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1217    
1218            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1219            generic and mer methods for isNested and denomDF. This denomDF was
1220            an attempt to emulate that in lme but I don't think that makes
1221            sense.  Use the trace of the hat matrix instead.
1222    
1223    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1226            the C code depending on a slot structure that's no longer valid.
1227            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1228    
1229    
1230    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1231    
1232            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1233            of lowerTriMatrix generic and methods to tril (also upper to triu)
1234            and added a general band extractor.
1235    
1236    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1237    
1238            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1239            allowable range with NAs. Added a corresponding check in the
1240            validity check for the pedigree class.
1241    
1242            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1243            crossprod methods now inherits from symmetricMatrix.
1244    
1245    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1246    
1247            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1248            generics lowerTriMatrix and upperTriMatrix along with methods for
1249            the Csparse virtual class.  Also added a C function Csparse_band
1250            that implements these methods by calling cholmod_band.
1251    
1252    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1253    
1254            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1255            erased when it was NULL.  This led to invalid subselections!
1256    
1257    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1258    
1259            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1260            in method for "t" so as not to lose the unit diagonal property.
1261    
1262    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1263    
1264            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1265            and methods.  This is now an option to the ranef method for the
1266            mer class.
1267    
1268            * src/cs_utils.c: Ensure that the nz component is -1 for a
1269            compressed column-oriented matrix.  Minor formatting cleanup.
1270    
1271            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1272            objects.
1273    
1274    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1277            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1278    
1279    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1280    
1281            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1282            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1283    
1284            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1285            for the dtCMatrix class.
1286    
1287    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1288    
1289            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1290            and methods for it.
1291    
1292    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1295            arguments, such that M %*% 1:6 now works
1296            * Tests/matprod.R: test the above
1297    
1298    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1299    
1300            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1301            the ranef.lmer class.
1302    
1303            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1304            methods to extract the posterior variances from the bVar slot.
1305    
1306    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1309            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1310    
1311            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1312            * tests/simple: (extended)
1313    
1314            * R/sparseMatrix.R (isTriangular): now using much improved
1315            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1316    
1317    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1318    
1319            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1320            (problem report from Franklin Parlamis).  This should be done
1321            generally.
1322    
1323    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1324    
1325            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1326            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1327            update the plot methods.
1328    
1329    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1330    
1331            * R/lmer.R (resid and ranef methods):  Added methods for the
1332            "residuals" and "resid" generic but only for linear mixed model
1333            fits.  Changed the ranef method to return a list of data frames so
1334            that the plot methods now work.
1335    
1336    2006-03-16  Douglas Bates  <bates@bates2>
1337    
1338            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1339            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1340    
1341            * DESCRIPTION (Date): New release
1342    
1343    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1344    
1345            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1346    
1347            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1348            * man/KNex.Rd: and other help files
1349            * tests/*.R: several ones needed adaption
1350            * inst/doc/Comparisons.Rnw: ditto
1351    
1352    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1355    
1356            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1357    
1358    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1361    
1362            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1363    
1364    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1365    
1366            * R/dMatrix.R: enable things like  M [ M < 10 ]
1367            * R/dgeMatrix.R: implement it
1368    
1369    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1370    
1371            * R/AllClass.R: define "summary.mer" and "*.lmer"
1372            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1373            * R/lmer.R (show): now works with summary()
1374    
1375    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1376    
1377            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1378            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1379                    support the above
1380    
1381    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1382    
1383            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1384            Use glmFit$prior.weights for weights in a glmm.
1385            Allow an option usePQL = FALSE to skip the PQL steps for the
1386            Laplace method (and, in time, the AGQ method).
1387    
1388            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1389            into a separate function internal_mer_Xfactor to be able to call
1390            it from internal_bhat.
1391    
1392    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1393    
1394            * tests/Class+Meth.R (tstMatrixClass): function for much better
1395            testing; now again of all actual classes.
1396    
1397            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1398                    use macros and define make_d_matrix_* and make_i_matrix_*
1399                    where _i_ is for the ldense routines:
1400    
1401            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1402            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1403    
1404            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1405    
1406    
1407    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1408    
1409            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1410                    many different kinds of matrices.
1411            * R/*.R: quite a few new methods were needed for R CMD check with
1412                    new Matrix().  Very good for users playing around.
1413    
1414    
1415    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1416    
1417            * src/dgeMatrix.c (dMatrix_validate): new
1418            * src/Mutils.c (dense_nonpacked_validate): new
1419    
1420            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1421    
1422    
1423    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1424    
1425            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1426    
1427    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1428    
1429            * DESCRIPTION (Version): 0.99-6 released to CRAN
1430    
1431            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1432            segfault in cases with multiple non-nested grouping factors.
1433    
1434    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1437                    (Depends): also on 'utils'
1438    
1439            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1440            * R/diagMatrix.R (Diagonal): constructor and methods for
1441            diagonal matrices
1442    
1443            * R/ltTMatrix.R: new "minimal methods"
1444    
1445    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1448            all methods (and help files).
1449    
1450    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1451    
1452            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1453                    for case (dimn.  op  no_dimn.)
1454    
1455    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1456    
1457            * DESCRIPTION (Version): 0.99-2  released to CRAN
1458    
1459    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1460    
1461            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1462            by Julian Faraway.
1463    
1464    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1465    
1466            * R/Auxiliaries.R (try_as): new utility
1467            * R/sparseMatrix.R: use try_as() in coercion to original class
1468    
1469    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1470    
1471            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1472    
1473    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1474    
1475            * R/Auxiliaries.R (dimNamesCheck): added
1476    
1477            * R/Matrix.R (as.array), (as.vector): new
1478    
1479    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1482                    default.
1483            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1484                    "pMatrix" now contains "sparseMatrix"
1485    
1486    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1487    
1488            * tests/Class+Meth.R: new tests; t(t(m)) == m
1489    
1490            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1491    
1492            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1493            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1494    
1495            * R/dspMatrix.R: typo in "t" method
1496    
1497    2005-09-18  Douglas Bates  <bates@wisc.edu>
1498    
1499            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1500            * R/Tsparse.R: instead of R/gTMatrix.R
1501            * R/Csparse.R: new
1502            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1503            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1504            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1505                            via cholmod
1506    
1507    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1508    
1509            * R/Auxiliaries.R (non0ind): new function using new C code
1510            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1511    
1512    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1513    
1514            * src/chm_common.h: header file required by all C sources that
1515            call CHOLMOD functions.  It defines a cholmod_common structure
1516            called 'c' whose address is passed as the last argument to
1517            (virtually) every CHOLMOD function.
1518    
1519            * src/Pattern.c: Simple example of the use of CHOLMOD.
1520    
1521            * src/init.c: initialize and finalize the cholmod_common structure.
1522    
1523            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1524            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1525    
1526    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1527    
1528            * inst/test-tools.R: new file collecting the utility functions used
1529                    in ./tests/*.R
1530    
1531            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1532            * R/Matrix.R (cbind2): methods for NULL and missing
1533    
1534    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1535    
1536            * R/AllClass.R: new "index" class for "[" and "[<-":
1537                    First cut at "symmetricMatrix" and "triangularMatrix"
1538            * R/gTMatrix.R (.ind.prep): new function;
1539                    Logical and character indexing now work too.
1540            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1541            * tests/indexing.R: new, including *.Rout.save
1542            * tests/dgTMatrix.R: new
1543    
1544    2005-08-29  Douglas Bates  <bates@wisc.edu>
1545    
1546            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1547            indicator pos not being updated.  Also enforced upper triangular
1548            for symmetric case.  Need to coerce edges component of elements of
1549            edge list - grr! (Why don't they define their classes cleanly?)
1550    
1551    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1552    
1553            * R/Matrix.R:  added first "[<-" methods; not yet functional
1554            * R/denseMatrix.R: ditto
1555            * man/Subassign-methods.Rd: new help file for these
1556    
1557    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
1559            * DESCRIPTION (Version): 0.98-6
1560    
1561            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1562            matrices.
1563    
1564    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1565    
1566            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1567                    as( <logical>, "matrix")
1568    
1569            * R/pMatrix.R: coercion to "lgTMatrix"
1570    
1571            * R/gTMatrix.R: new virtual class to define "[" methods for.
1572            * man/gTMatrix-class.Rd:
1573            * General slight re-organization of where "[" methods are defined.
1574              more to come.
1575    
1576    2005-08-18  Douglas Bates  <bates@wisc.edu>
1577    
1578            * DESCRIPTION (Version): 0.98-5  released to CRAN
1579    
1580            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1581            * .....
1582    
1583    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1584    
1585            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1586            or glmer objects.
1587    
1588    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1589    
1590            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1591    
1592    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1593    
1594            * R/HBMM.R: finish re-writing R-only code.
1595    
1596    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1597    
1598            * man/externalFormats.Rd: move documentation for writeHB and
1599            writeMM here.
1600    
1601            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1602            (suggested by Paul Roecker).
1603    
1604            * tests/validObj.R (assertError): Comment out test that is failing
1605            after recent changes in r-devel.
1606    
1607    
1608    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1609    
1610            * R/AllClass.R: intermediate virtual class "denseMatrix"
1611            * man/denseMatrix-class.Rd
1612            * NAMESPACE: export it, and also export
1613            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1614    
1615    2005-08-10  Douglas Bates  <bates@wisc.edu>
1616    
1617            * DESCRIPTION (Version): 0.98-3 to CRAN
1618    
1619            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1620            matrix_solve code (which was really, really wrong).
1621    
1622    2005-08-07  Douglas Bates  <bates@wisc.edu>
1623    
1624            * DESCRIPTION (Version): 0.98-2
1625    
1626            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1627    
1628            * R/lmer.R (abbrvNms): new
1629            * R/lmer.R (mcmcsamp): allow transformed parameters
1630            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1631            for the Harwell-Boeing and the MatrixMarket formats.
1632    
1633    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1634    
1635            * man/dtrMatrix-class.Rd: add examples
1636            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1637    
1638            * TODO: note the dtpMatrix (docu) bug
1639    
1640            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1641            in order to ensure that new as.matrix() is used by old functions,
1642            e.g., svd(), qr(), eigen(), dist(),..;
1643                  apply(), also matplot() or pairs().
1644    
1645    
1646    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1647    
1648            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1649              add comments about 'control' / lmerControl() arguments
1650    
1651    2005-07-27  Douglas Bates  <bates@wisc.edu>
1652    
1653            * man/sleepstudy.Rd: Added the sleep data set.
1654            * DESCRIPTION (Version): 0.98-1  released to CRAN
1655    
1656    2005-07-12  Douglas Bates  <bates@wisc.edu>
1657            * man/sleepstudy.Rd: Added the sleep data set.
1658    
1659            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1660            .Call calls that were producing spurious output.
1661    
1662    2005-07-05  Douglas Bates  <bates@wisc.edu>
1663    
1664            * R/lmer.R (lmer): stored updated variance component estimates in
1665            mer object for the generalized model.  (Bug reported by Renaud
1666            Lancelot).
1667    
1668    2005-07-03  Douglas Bates  <bates@wisc.edu>
1669    
1670            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1671            unidimensional case.
1672    
1673    2005-06-08  Douglas Bates  <bates@wisc.edu>
1674    
1675            * DESCRIPTION (Version): 0.96-1
1676    
1677            * moved  lmer-class' R and C code moved from lme4 to here
1678    
1679    2005-06-04  Douglas Bates  <bates@wisc.edu>
1680    
1681            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1682            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1683    
1684    2005-06-02  Douglas Bates  <bates@wisc.edu>
1685    
1686            * src/Makefile.win: Forgot to update this when Makefile changed.
1687    
1688    2005-05-11  Douglas Bates  <bates@wisc.edu>
1689    
1690            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1691            bug reported by Kurt Hornik and Michael Hahsler.
1692    
1693    2005-05-10  Douglas Bates  <bates@wisc.edu>
1694    
1695            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1696            logical sparse matrices.  These will also be used in the symbolic
1697            analysis for lmer objects.
1698    
1699            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1700            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1701    
1702    2005-05-06  Douglas Bates  <bates@wisc.edu>
1703    
1704            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1705            colMeans, colSums, rowMeans and rowSums.
1706    
1707    2005-04-18  Douglas Bates  <bates@wisc.edu>
1708    
1709            * src/lgCMatrix.[ch]: code for _validate method and stub for
1710            multiplication operation.
1711    
1712            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1713            to dgetrs.
1714    
1715            * src/init.c: Fix cut-and-paste error in definition of
1716            dgeMatrix_matrix_solve
1717    
1718            * src/{many files}: Tighten code by using ALLOC_SLOT.
1719    
1720    2005-04-15  Douglas Bates  <bates@wisc.edu>
1721    
1722            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1723    
1724            * DESCRIPTION: Eliminate import of stats.
1725    
1726    
1727    2005-04-06  Douglas Bates  <bates@wisc.edu>
1728    
1729            * R/AllClass.R : add logical sparse matrix classes
1730    
1731    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1732    
1733            * R/dgTMatrix.R: add "[" method for triplet matrices
1734            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1735    
1736    2005-03-31  Douglas Bates  <bates@wisc.edu>
1737    
1738            * DESCRIPTION (Version): release 0.95-5 to CRAN
1739    
1740            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1741            * R/sparseMatrix.R: %*%, crossprod()
1742            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1743            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1744            * src/lmer.c (lmer_fitted): fix thinko
1745    
1746    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1747    
1748            * R/AllClass.R: add two virtual sparse classes ``on top''
1749    
1750    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1751    
1752            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1753                    correspondingly fix examples and tests/ since new()
1754                    doesn't work for virtual classes.
1755    
1756    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1757    
1758            * R/Matrix.R (as.matrix): method and one for unname()
1759            * tests/dpoMatrix.R: tests should now be less platform dependent;
1760              also run for R 2.1.0; using as.matrix()
1761    
1762    2005-03-15  Douglas Bates  <bates@wisc.edu>
1763    
1764            * R/pMatrix.R: "pMatrix" class added
1765            * ....
1766    
1767    2005-03-14  Douglas Bates  <bates@wisc.edu>
1768    
1769            * R/dtpMatrix.R: Add unpack method and an example.
1770    
1771            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1772            of general symmetric matrices and associated S4 methods.
1773    
1774    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1775            +
1776    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1777    
1778            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1779              crossprod() and "%*%" methods added; tests, too.
1780            * tests/matprod.R: new, for testing these
1781    
1782    2005-03-03  Douglas Bates  <bates@wisc.edu>
1783    
1784            * src/lmer.c (lmer_fitted): Added.
1785    
1786    2005-03-02  Douglas Bates  <bates@wisc.edu>
1787    
1788            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1789    
1790    2005-02-28  Douglas Bates  <bates@wisc.edu>
1791    
1792            * src/*.c,po/,inst/po: Internationalization and localization of
1793            the package.
1794    
1795            * src/ldl.[ch]: Removed these as their contents are referenced in the
1796            R_ldl.c file.
1797    
1798            * src/flame.[ch]: Removed these source files.
1799    
1800            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1801    
1802            * src/LU.[ch],src/init.c: absorb in factorizations
1803    
1804            * src/Mutils.h: prepare for internationalization
1805    
1806            * src/cblas.h: move the enum definitions to Mutils.h and remove
1807            this file
1808    
1809    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1810    
1811            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1812    
1813            * R/dtrMatrix.R: fix t() method
1814    
1815            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1816            * NAMESPACE: export them (and import generics from "methods")
1817            * tests/group-methods.R : and test them.
1818    
1819            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1820            border case
1821    
1822    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1823    
1824            * DESCRIPTION (Version): 0.95-2  released to CRAN
1825    
1826            * src/dgBCMatrix.c:
1827            * src/lmer.c: many changes
1828            * ...
1829    
1830    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1831    
1832            * R/Matrix.R: add more sophisticated show() method.
1833    
1834    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1835    
1836            * */* : almost complete reorganization of classes.
1837    
1838    2005-01-26  Douglas Bates  <bates@wisc.edu>
1839    
1840            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1841            for the geMatrix class.
1842    
1843    2005-01-24  Douglas Bates  <bates@wisc.edu>
1844    
1845            * src/Makefile (clean): Remove *.a and *.so
1846    
1847            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1848    
1849    2005-01-23  Douglas Bates  <bates@wisc.edu>
1850    
1851            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1852            had an effect in cases with more than 2 grouping factors.
1853    
1854    2005-01-03  Douglas Bates  <bates@wisc.edu>
1855    
1856            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1857    
1858    2004-12-23  Douglas Bates  <bates@wisc.edu>
1859    
1860            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1861            and R_useDynamicSymbols (suggested by B.D.Ripley).
1862    
1863    2004-12-14  Douglas Bates  <bates@wisc.edu>
1864    
1865            * R/sscMatrix.R: Add determinant methods
1866    
1867            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1868            for tripletMatrix to matrix.
1869    
1870    2004-12-13  Douglas Bates  <bates@wisc.edu>
1871    
1872            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1873            no longer used.
1874    
1875          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1876          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1879 
1879          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1880          Fixes part but not all of #15.          Fixes part but not all of #15.
1881    
1882  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1883    
1884          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1885          scalar grouping factors corrected.          scalar grouping factors corrected.
1886    
1887  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1888    
1889          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1890    
1891  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1892    
1893          * 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
1894          .h file can be included.          .h file can be included.
1895    
1896  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1897    
1898          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1899          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1900    
1901          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1902    
1903  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1904    
1905          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1906    
1907  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1908    
1909          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1910    
1911  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1912    
1913          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1914    
1915  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1916    
1917          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1918    
1919  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1920    
1921          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1922          routines.          routines.
1923    
1924  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1925    
1926          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1927    
1928  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1929    
1930          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1931    

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