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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1868, Mon Jun 4 17:15:09 2007 UTC
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1    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>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1226          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
1227          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1228    
1229    
1230  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 1347 
1347          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1348          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1349          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1350          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1351    
1352  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
# Line 329  Line 1551 
1551  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1552    
1553          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1554          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1555          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1556    
1557  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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