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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1837, Mon May 14 13:17:37 2007 UTC
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1    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.99875-1
4            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
5    
6    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
9            indexing
10            * tests/indexing.R: test set for that.
11    
12    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
15            entries.
16            * tests/indexing.R(out): add regression test for it
17    
18    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
21            name for "!" method definitions.
22    
23    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R (intI): new utility, used for "[" :
26                    Cleanup up there, and fixes for duplicated indices - more TODO!
27    
28            * tests/indexing.R(out): more tests
29    
30    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
33            code that is now part of the R Lapack library.
34    
35            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
36            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
37    
38    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
41    
42    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
45            up with extraneous names '0'...'<n-1>'
46    
47    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dgTMatrix.R (mat2dgT): care about NAs
50    
51    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/kronecker.R: triangularity preserving methods
54    
55    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/kronecker.R: new file collecting kronecker() methods in one
58                    place.  Goal: become much faster!
59    
60    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
63            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
64            can be much faster.
65    
66            * tests/matprod.R: add regression tests for these (upper & lower).
67    
68    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R (diff): method for our Matrices.
71    
72            * R/sparseMatrix.R (isDiagonal): check dim()!
73    
74    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Matrix.R (dim<-): new method for "reshape()" built on a
77            proposal from Tamas Papp.
78    
79    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
82    
83            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
84            rather define and export  cBind() and rBind() only.
85            --> useRs *must* change code that used to have cbind()/rbind() !!
86    
87            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
88            * R/bind.Rout.save: ditto
89    
90    2007-02-16  Douglas Bates  <bates@r-project.org>
91    
92            * DESCRIPTION (Date, Version): 0.9975-11 with new date
93            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
94            const modifier on declaration of the array 'valid'
95    
96    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
99    
100    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
103    
104            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
105            * tests/simple.R: test the above and some of these coercions:
106    
107            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
108                    be careful to avoid infinite recursion, using new coercions in
109            * R/ngCMatrix.R and nsC... and ntC...
110            * R/lsparseMatrix.R: ditto
111    
112            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
113    
114            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
115            * R/Rsparse.R: reactivate .Call()s
116    
117            * tests/Class+Meth.R: a bit more on actual classes
118    
119    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
122    
123    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * DESCRIPTION (Version): 0.9975-10 to upload
126    
127            * tests/Class+Meth.R (tstMatrixClass): require coercions to
128            specific classes less unconditionally.
129    
130            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
131    
132            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
133    
134            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
135            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
136            R_to_CMatrix segfaults on one platform.
137            Eliminate most coercion method to *specific* classes, and replace
138            with virtual classes coercions.
139    
140    
141    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
142    
143            * src/init.c: export the CHM...._validate() placeholders, since
144            they *are* called.
145    
146            * tests/Class+Meth.R (classCanCoerce): and starting to test
147            all as(<from>, <to>)
148    
149    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
152            * tests/indexing.R: tested now
153            * tests/indexing.Rout.save: updated
154    
155            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
156            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
157            appropriate.
158    
159            * NAMESPACE: export a trivial
160            * R/Matrix.R: drop() Matrix-method
161    
162            * R/AllClass.R: moved all prototypes to virtual super classes.
163    
164            * R/Rsparse.R: many more coercions to have less exceptions in
165            * tests/Class+Meth.R:
166    
167            * R/Ops.R (Compare): tweak for case with NA
168            * tests/simpl.R: hence another 'FIXME' eliminated
169    
170    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
173            objects.
174    
175            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
176              and more of "!", "&", "|", all, any; coercions
177    
178            * R/Rsparse.R: many coercions (which enable quite a few other
179            methods), thanks to enhancements in
180            * src/dgCMatrix.c (R_to_CMatrix): new, and
181            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
182            symmetric & triangular and ..RMatrix objects.
183    
184            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
185            renamed file from src/dsTMatrix.c;
186            now dealing with symmetric and triangular Tsparse coercions, both
187            to dense and general.
188    
189    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
192    
193            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
194            where sensible when the <numeric> is of length > 1.
195    
196    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/Matrix.R ([<-): for M[] <- value: fix length
199    
200    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
203            * R/ndenseMatrix.R: new coercions n* -> l*
204    
205    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
208    
209            * R/Ops.R ("Logic"): and other "Ops", many updates
210    
211    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/Mutils.h (SET_DimNames): new utility
214    
215            * R/Auxiliaries.R (nnzero): improved and now exported via
216    
217            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
218    
219    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/diagMatrix.R (!): fix typo.
222    
223    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Auxiliaries.R (as_Csparse): and quite a few others:
226                    allow to pass class definition --> speedup
227            * R/sparseMatrix.R: apply the above
228    
229            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
230    
231            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
232            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
233            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
234    
235            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
236    
237            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
238            and use it for "sparse*" as well, since it's faster than the
239            as_Csparse(.) way.
240    
241    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
244    
245    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
248            as method for   M[ ij ] <- v
249            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
250    
251            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
252            FALSE answer
253    
254            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
255            * tests/indexing.R: test it, and some of the above
256    
257    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Auxiliaries.R (is_duplicatedT): new utility
260    
261    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/init.c (R_init_Matrix): export cholmod_scale
264    
265    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
268            base::as.matrix to (x, ...)
269    
270    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
273            file; start using "Logic", hence
274    
275            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
276            * NAMESPACE: import and export "Logic"
277    
278    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
281            only needed previously to R version 2.5.0.
282    
283    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
286    
287            * R/Tsparse.R (replTmat): fix subassignment of triangular
288            * R/Csparse.R (replCmat): ditto
289            * tests/indexing.R: more tests, incl the above fix
290    
291    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (drop0): extend for non CSparse
294            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
295    
296            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
297                    use uplo correctly (!); other places: use uplo_P() macro
298    
299            * R/Csparse.R (replCmat): call diagU2N() when needed
300            * R/Tsparse.R (replTmat): ditto
301    
302            * src/dtCMatrix.c (tCMatrix_validate): new
303            * src/dtTMatrix.c (tTMatrix_validate): new, used in
304            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
305    
306            * R/diagMatrix.R (replDiag): to use in [<-
307    
308    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
311                    also more general diagU2N().
312    
313    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
316            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
317    
318    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * tests/bind.R: a few more cases
321            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
322    
323            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
324            * R/ddenseMatrix.R (cbind2/rbind2)
325            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
326            * tests/indexing.R
327            * tests/indexing.Rout.save: updated
328    
329    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
332            * tests/indexing.R
333    
334    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
337            align with proper position of "0", i.e., right for integers.
338            argument 'align' by default is "fancy".
339    
340    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
343            * R/Csparse.R: and fix "Compare" for more cases.
344            * tests/Class+Meth.R: test some of these (m == m, m != m)
345    
346    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/lsparseMatrix.R: all() and any() methods
349            * R/ldenseMatrix.R:      ditto
350            * NAMESPACE, R/Matrix.R: ditto
351    
352            * man/all-methods.Rd: document them minimally
353    
354            * tests/simple.R: add a few examples for these
355    
356    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Tsparse.R ([): fix long standing typo in symmetric case
359            * man/dsCMatrix-class.Rd: add example exhibiting the above case
360    
361    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
364            to LL before converting to a sparse matrix. (The LDL form can be
365            converted to a sparse matrix but it is implicitly a unit
366            triangular matrix and a diagonal matrix overwritten on the diagonal.)
367    
368    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
369    
370            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
371    
372    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * DESCRIPTION (Version): updated -> release 0.9975-7
375            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
376    
377    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
380    
381    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
384            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
385            is exactly singular.
386    
387    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * DESCRIPTION (Date): updated -> release 0.9975-6
390    
391    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
394            now returns symmetric.
395    
396            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
397    
398            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
399            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
400    
401            * R/Auxiliaries.R (.type.kind): added
402    
403    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
406            running src/CSparse_install.sh
407    
408            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
409    
410    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
413            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
414    
415            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
416    
417            * tests/Class+Meth.R (tstMatrixClass): now assure
418            the (important in method programming) property :
419    
420                    ###>>  Every "Matrix" is either
421                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
422    
423                    (where "*" stands for "Matrix")
424    
425            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
426    
427            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
428            * tests/validObj.R: checks for "comparison"
429    
430            * R/sparseMatrix.R ([): improved indexing for sparse;
431                    trying to keep <symmetric>[ n, n] symmmetric
432    
433            * tests/indexing.R: indexing for logical sparse now ok
434    
435    
436    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * src/Tsparse.c: use xTsparse_validate() , and hence remove
439    
440            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
441    
442    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
445    
446            * tests/simple.R: validObject() checking the above.
447    
448            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
449            replacing both dgCMatrix_validate and lgCM*.
450    
451            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
452            fix dimnames setting in other places.
453            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
454    
455    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
458    
459            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
460            symmetry test, via
461            * R/Auxiliaries.R (.as.dgC.0.factors):
462    
463    2006-11-01  Douglas Bates  <bates@r-project.org>
464    
465            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
466            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
467            <CsparseMatrix>) added
468    
469    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/matprod.R: add a variation of Harri's example
472    
473            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
474            recursive infinitely.
475    
476            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
477    
478            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
479    
480    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
483            matrix if possible; test m+m == 2*m; now test dgRMatrix.
484            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
485            satisfy the above test.
486    
487    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
490    
491            * R/dgCMatrix.R: solve(a, b="missing") based on
492            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
493            RHS = NULL.
494    
495            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
496            add more (needed) [t]crossprod() methods.
497    
498            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
499    
500            * R/Auxiliaries.R (as_CspClass): cleanup
501            (drop0): internal utility for "Csparse_drop(*, 0)"
502            (.bail.out.2): encourage active feedback
503    
504    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/dMatrix.R(Compare): new(), then slots [no validity check]
507    
508            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
509            non-valid or 'sorted' case).
510    
511            * R/dsparseMatrix.R: add "chol" method.
512            * R/ddenseMatrix.R: ditto
513    
514            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
515            * NAMESPACE (Ops)
516            * R/diagMatrix.R (diag2T): simple utility used "higher level"
517            coercion; deprecating direct lower level coercions.
518    
519            * R/*.R (seq): use seq_len() and seq_along() where possible.
520    
521    
522    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * DESCRIPTION (Version): 0.9975-5 ready for release
525    
526    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
527    
528            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
529    
530    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/AllClass.R (corMatrix): add 'validity' check;
533                    comment out unused "LDL" class definition
534            * NAMESPACE: mention, but do not export "LDL" class
535            * R/corMatrix.R: new (simple), needed for R-devel with
536            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
537              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
538    
539    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
540    
541            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
542            use Rprintf and R's error handling.
543    
544    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
547            * tests/matprod.R: add tests for the bug fixed.
548    
549    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
552            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
553    
554    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
555    
556            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
557    
558    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * DESCRIPTION (Version): 0.9975-3
561    
562            * R/diagMatrix.R (bdiag): new function constructing block diagonal
563            (sparse) matrices.
564            * man/bdiag.Rd: docu + examples
565    
566            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
567    
568            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
569            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
570    
571            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
572            that result is sparse or diagonal (and not dense).
573    
574            * man/Subassign-methods.Rd: fix examples
575    
576            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
577            should always return a sparse (and not sometimes a diagonal) matrix.
578    
579    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
582    
583    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
584    
585            * DESCRIPTION (Version): 0.9975-2
586    
587            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
588    
589    2006-10-02  Douglas Bates  <bates@R-project.org>
590    
591            * tests/dg_Matrix.R: Simplify test taking into account new code.
592    
593    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
596    
597            * R/lsTMatrix.R: new files w/ missing methods
598            * R/nsTMatrix.R:  "  'for completeness'
599    
600            * tests/Class+Meth.R: a bit less 'not.ok.classes'
601    
602            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
603    
604    
605    2006-09-28  Douglas Bates  <bates@R-project.org>
606    
607            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
608            included.
609    
610            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
611            Export C-callable functions used in Zt_create in lme4.
612    
613    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * DESCRIPTION (Version): 0.9975-1
616    
617            * tests/simple.R: less checks fail; using NA, found that our
618                    kronecker() is not base-compatible with NA's.
619    
620            * R/dMatrix.R: "Compare" method now implemented for all cases
621    
622            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
623    
624            * man/dtpMatrix-class.Rd: mention length of 'x' slot
625    
626            * src/dtpMatrix.c (dtpMatrix_validate): fix check
627            * src/dspMatrix.c (dspMatrix_validate): ditto
628    
629            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
630              including coercion to [nl]tTMatrix.
631    
632            * R/diagMatrix.R (show): print a header line as for other classes.
633    
634    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * src/Makefile.win (SUBDIRS): fix typo
637    
638    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
641    
642    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
643    
644            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
645            symmetric and y missing in R code using %*% (cholmod_aat doesn't
646            accept a symmetric matrix).
647            * tests/group-methods.R: Uncomment test of crossprod applied to
648            lsCMatrix objects.
649    
650    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/AllClass.R (symmetricMatrix): add validity method (available
653            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
654    
655            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
656    
657            * tests/indexing.Rout.save:
658            * tests/indexing.R: additions, mainly for 'lsparse'
659    
660            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
661            case.
662    
663            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
664    
665    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
668                    as 'N' (1-letter - Ok?)
669    
670            * tests/group-methods.R: add test for logical + NAs
671    
672            * R/dMatrix.R ("Compare"): fix to work with NA's
673    
674            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
675    
676            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
677                    which is implemented.
678    
679    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * src/chm_common.c: coerce logical <-> double instead of
682            typecasting;  needed for "l" matrix handling in cholmod.
683    
684            * tests/other-pkgs.R (graph): small extension in "graph" checks.
685    
686            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
687            (Tsp2grNEL): other fixes needed
688    
689    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
692                    Matrices, since "lMatrix", also "lsparseM" can have NA
693            * R/ndenseMatrix.R, etc: new source files
694            * man/nsparseMatrix-classes.Rd, etc: new help files
695            * tests/: adaptions
696            * src/chm_common.c (chm_dense_to_SEXP): and others:
697                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
698            * src/Csparse.c, etc: ditto
699    
700    2006-09-11  Douglas Bates  <bates@R-project.org>
701    
702            * src/Mutils.[ch],init.c inst/include/*.h: Move the
703            alloc_d**Matrix functions to the lme4 package.
704    
705    2006-09-09  Douglas Bates  <bates@R-project.org>
706    
707            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
708            fixed
709    
710    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/lMatrix.R: new
713    
714            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
715    
716            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
717            * man/tcrossprod.Rd: ditto
718    
719    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
720    
721            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
722            for exported functions
723            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
724            Remove partitioning algorithms for sparse matrix reordering.  The
725            copyright on the Metis code was problematic and the methods were
726            rarely used.
727            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
728            operations are now done entirely in CHOLMOD code.
729    
730    2006-09-06  Douglas Bates  <bates@R-project.org>
731    
732            * src/Mutils.h: Remove functions that are no longer used.
733    
734    2006-09-04  Douglas Bates  <bates@R-project.org>
735    
736            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
737            * src/DEPS.mkf: update
738    
739    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * created branches/Matrix-for-R-2.3.x;  on trunk: do
742            * DESCRIPTION (Version): 0.9975-0
743            (Depends): R (>= 2.4.0)
744    
745    2006-09-01  Douglas Bates  <bates@R-project.org>
746    
747            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
748    
749    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
752            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
753    
754            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
755    
756    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
759            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
760            * R/dsparseMatrix.R: ditto
761            * R/Csparse.R: ditto
762    
763    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/dMatrix.R (Compare): improve availability of "<", etc
766            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
767    
768    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
771            of a 0-index which was used as 1-index (..hmm)
772    
773            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
774    
775            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
776            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
777            (.is.diagonal): ditto
778    
779            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
780    
781            * R/Matrix.R (Matrix): also work for NA data
782    
783    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
786            in all cases.
787    
788    2006-08-27  Douglas Bates  <bates@R-project.org>
789    
790            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
791            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
792    
793    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
796            subclasses of "ddenseMatrix"
797            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
798            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
799            instead of half dozen specialized ones.
800    
801    2006-08-25  Douglas Bates  <bates@R-project.org>
802    
803            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
804            <tillard@cirad.fr> - ordering standard errors to match effects.
805    
806    2006-08-24  Douglas Bates  <bates@R-project.org>
807    
808            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
809            on R_ldl.
810            * R/lCholCMatrix.R,
811            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
812            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
813            * many files in ./R and ./src: Use more general version of
814            dup_mMatrix_as_dgeMatrix to simplify method definitions.
815            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
816            dtpMatrix, dspMatrix and dppMatrix conversions.
817    
818    
819    2006-08-23  Douglas Bates  <bates@R-project.org>
820    
821            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
822            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
823            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
824            dgeMatrix_crossprod (may need to do this in other places).
825            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
826            generic and method for dsCMatrix.  Use CHOLMOD for chol().
827    
828    2006-08-22  Douglas Bates  <bates@R-project.org>
829    
830            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
831            types of classed Matrices, matrices or numeric or logical vectors.
832            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
833            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
834            to Mutils.h (as an inline) and change name to Matrix_check_class;
835            fixes in as_cholmod_factor and chm_factor_to_SEXP.
836            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
837            dsCMatrix_matrix_solve.  Comment out vestigial functions.
838            * src/Csparse.c: use diag_P and uplo_P macros.
839    
840    2006-08-21  Douglas Bates  <bates@R-project.org>
841    
842            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
843            valgrind.
844            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
845            inverses.
846            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
847            -Wall warnings.
848            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
849            Use dup_mMatrix_as_dgeMatrix.
850    
851    2006-08-20  Douglas Bates  <bates@R-project.org>
852    
853            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
854            * tests/sparseQR.R: Added
855            * man/sparseQR-class.Rd: Document methods for qr.* generics
856            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
857    
858    2006-08-19  Douglas Bates  <bates@R-project.org>
859    
860            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
861            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
862            and qr.fitted.
863            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
864            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
865    
866    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
869            the base version has no "..." argument.
870    
871            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
872    
873            * R/Matrix.R: define and
874            * NAMESPACE: export as.numeric() and as.logical() methods.
875                    Let's hope these do not badly slow down something...
876            Finally export the zapsmall() method.
877    
878    2006-08-17  Douglas Bates  <bates@R-project.org>
879    
880            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
881            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
882            * src/dtCMatrix.c :Remove code that is no longer used
883            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
884    
885    2006-08-14  Douglas Bates  <bates@R-project.org>
886    
887            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
888            Csparse_to_logical and Csparse_symmetric_to_general.
889            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
890            coercion methods between CsparseMatrix and TsparseMatrix.
891    
892    2006-08-14  Douglas Bates  <bates@R-project.org>
893    
894            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
895            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
896            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
897            possible.
898    
899    2006-08-12  Douglas Bates  <bates@R-project.org>
900    
901            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
902              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
903              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
904              generalize conversions between TsparseMatrix, CsparseMatrix,
905              denseMatrix and matrix.  Preserve triangularity property and
906              propagate Dimnames in the easy cases.
907    
908    2006-08-10  Douglas Bates  <bates@R-project.org>
909    
910            * src/lmer.c: adjust checks in glmer_init for S4SXP
911            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
912            before S4SXP but for the wrong reasons.
913    
914    2006-08-08  Douglas Bates  <bates@R-project.org>
915    
916            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
917            Later modified to return the upper triangle only.
918            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
919    
920    2006-08-07  Douglas Bates  <bates@R-project.org>
921    
922            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
923            R-level conversion to a sparse symmetric class.
924            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
925            Remove conversion to sparse symmetric classes (now done in C code).
926    
927    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
928    
929            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
930            * man/band.Rd:  adapt the \dontshow{} unit test.
931    
932    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * DESCRIPTION (Version): 0.995-14  for CRAN
935    
936            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
937    
938            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
939            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
940    
941            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
942            * R/Tsparse.R (tril, triu, band): methods
943            * R/dgRMatrix.R (tril, ...):    ditto
944            * man/band.Rd:                  ditto
945    
946    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/Matrix.R (head, tail): directly use utils:::head.matrix
949                    to be up-to-date automatically.
950    
951    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
954    
955            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
956            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
957            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
958            such that the S4 objects are always created by the current version
959            of R and 'Matrix' class definitions.
960    
961    2006-08-01  Douglas Bates  <bates@R-project.org>
962    
963            * R/lmer.R (LMEoptimize method), tests/lmer.R,
964            inst/external/test3comp.rda: Added warnings for convergence on
965            boundary and test cases.
966    
967            * src/lmer.c (mer_postVar): Modified to return the variances that
968            are marginal to the fixed effects, not conditional on them (which
969            is what the bVar slot contents represent).
970    
971    2006-07-31  Douglas Bates  <bates@R-project.org>
972    
973            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
974            function which calls the C function mer_hat_trace2.
975    
976            * man/ranef.Rd: Include description of "postVar" argument and
977            producing a caterpillar plot.
978    
979    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * NAMESPACE:    change  "correlation" to "corMatrix"
982            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
983            * R/dpoMatrix.R: ditto
984            * R/lmer.R:      ditto
985    
986    2006-07-28  Douglas Bates  <bates@R-project.org>
987    
988            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
989            RZXinv slot's contents into a separate internal function that can
990            be used in mer_hat_trace.
991    
992    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
995            via new smart
996            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
997            utility functions.
998    
999    
1000    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1003            matrices when appropriate; band() even symmetric ones.
1004            (replCmat): extend to potentially all "CsparseMatrix"
1005            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1006            allow subassignment for special sparse matrices.
1007    
1008            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1009    
1010            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1011            argument; in glmer_*(): print only if(verbose).
1012    
1013            speed-optimize a few places by moving REAL(.) out of loops.
1014    
1015            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1016    
1017    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1020                    since that wrongly triggers also for M[ logi , ]
1021    
1022            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1023            a symmetric matrix that results in a non-symmetric one.
1024            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1025    
1026            * R/dMatrix.R: make round(M) work as round(M, 0)
1027    
1028            * R/dgTMatrix.R (image): coordinate system and axis now use
1029            1-based indices, not 0-based ones.
1030    
1031            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1032            * tests/indexing.R: test it.
1033    
1034            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1035            * man/isSymmetric-methods.Rd: and document it.
1036    
1037            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1038            * man/SparseM-conv.Rd: docu them
1039    
1040            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1041                    for 'SparseM' conversions
1042    
1043    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1044    
1045            * R/Matrix.R (head): added head() and tail() methods.
1046    
1047    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * DESCRIPTION (Version): 0.995-12 released to CRAN
1050    
1051    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * tests/simple.R: add check for correct dsT -> dgT coercion;
1054                    add check for correct printing of symmetric sparse matrices.
1055    
1056            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1057            for sparse symmetric matrices.
1058    
1059            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1060            diagonal twice.
1061    
1062    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1063    
1064            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1065            being applied to the x slot (detected by Brian Ripley).
1066    
1067    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1070    
1071            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1072    
1073    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1074    
1075            * src/lgCMatrix.c (lgCMatrix_diag): new function
1076            * R/lgCMatrix.R (diag): for new method
1077    
1078            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1079                 ==> construction of illegal "*gTMatrix" via new() should
1080                 now be much less easy:
1081            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1082    
1083            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1084                    directly.
1085            * man/Matrix.Rd: documents it.
1086    
1087    2006-07-06  Douglas Bates  <bates@R-project.org>
1088    
1089            * src/pedigree.c (pedigree_inbreeding): Correction in
1090            initialization.  This function is not currently being used and is
1091            not fully tested.
1092    
1093            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1094            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1095            objects.  Modified validity check on pedigree objects to account
1096            for nonparallel patterns of missingness of parents.
1097    
1098            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1099            class.
1100    
1101    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/pMatrix.R: coercion pMatrix -> Tsparse
1104    
1105    2006-06-12  Douglas Bates  <bates@R-project.org>
1106    
1107            * DESCRIPTION (Version): 0.995-11 released to CRAN
1108    
1109            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1110            the output from mcmcsamp.
1111    
1112  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
1113    
1114          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
1115            of the hat matrix.
1116    
1117  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1120          classes.          classes.
1121            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1122    
1123  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
# Line 43  Line 1156 
1156    
1157          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1158          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.
1159          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1160    
1161    
1162  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 1279 
1279          * 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)
1280          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1281          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1282          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1283    
1284  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
# Line 370  Line 1483 
1483  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1484    
1485          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1486          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1487          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1488    
1489  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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