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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1803, Tue Mar 27 16:43:22 2007 UTC
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1    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: new file collecting kronecker() methods in one
4                    place.  Goal: become much faster!
5    
6    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
9            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
10            can be much faster.
11    
12            * tests/matprod.R: add regression tests for these (upper & lower).
13    
14    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Matrix.R (diff): method for our Matrices.
17    
18            * R/sparseMatrix.R (isDiagonal): check dim()!
19    
20    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (dim<-): new method for "reshape()" built on a
23            proposal from Tamas Papp.
24    
25    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
28    
29            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
30            rather define and export  cBind() and rBind() only.
31            --> useRs *must* change code that used to have cbind()/rbind() !!
32    
33            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
34            * R/bind.Rout.save: ditto
35    
36    2007-02-16  Douglas Bates  <bates@r-project.org>
37    
38            * DESCRIPTION (Date, Version): 0.9975-11 with new date
39            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
40            const modifier on declaration of the array 'valid'
41    
42    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
45    
46    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
49    
50            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
51            * tests/simple.R: test the above and some of these coercions:
52    
53            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
54                    be careful to avoid infinite recursion, using new coercions in
55            * R/ngCMatrix.R and nsC... and ntC...
56            * R/lsparseMatrix.R: ditto
57    
58            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
59    
60            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
61            * R/Rsparse.R: reactivate .Call()s
62    
63            * tests/Class+Meth.R: a bit more on actual classes
64    
65    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
68    
69    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.9975-10 to upload
72    
73            * tests/Class+Meth.R (tstMatrixClass): require coercions to
74            specific classes less unconditionally.
75    
76            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
77    
78            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
79    
80            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
81            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
82            R_to_CMatrix segfaults on one platform.
83            Eliminate most coercion method to *specific* classes, and replace
84            with virtual classes coercions.
85    
86    
87    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * src/init.c: export the CHM...._validate() placeholders, since
90            they *are* called.
91    
92            * tests/Class+Meth.R (classCanCoerce): and starting to test
93            all as(<from>, <to>)
94    
95    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
98            * tests/indexing.R: tested now
99            * tests/indexing.Rout.save: updated
100    
101            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
102            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
103            appropriate.
104    
105            * NAMESPACE: export a trivial
106            * R/Matrix.R: drop() Matrix-method
107    
108            * R/AllClass.R: moved all prototypes to virtual super classes.
109    
110            * R/Rsparse.R: many more coercions to have less exceptions in
111            * tests/Class+Meth.R:
112    
113            * R/Ops.R (Compare): tweak for case with NA
114            * tests/simpl.R: hence another 'FIXME' eliminated
115    
116    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
119            objects.
120    
121            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
122              and more of "!", "&", "|", all, any; coercions
123    
124            * R/Rsparse.R: many coercions (which enable quite a few other
125            methods), thanks to enhancements in
126            * src/dgCMatrix.c (R_to_CMatrix): new, and
127            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
128            symmetric & triangular and ..RMatrix objects.
129    
130            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
131            renamed file from src/dsTMatrix.c;
132            now dealing with symmetric and triangular Tsparse coercions, both
133            to dense and general.
134    
135    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
138    
139            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
140            where sensible when the <numeric> is of length > 1.
141    
142    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R ([<-): for M[] <- value: fix length
145    
146    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
149            * R/ndenseMatrix.R: new coercions n* -> l*
150    
151    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
154    
155            * R/Ops.R ("Logic"): and other "Ops", many updates
156    
157    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * src/Mutils.h (SET_DimNames): new utility
160    
161            * R/Auxiliaries.R (nnzero): improved and now exported via
162    
163            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
164    
165    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (!): fix typo.
168    
169    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (as_Csparse): and quite a few others:
172                    allow to pass class definition --> speedup
173            * R/sparseMatrix.R: apply the above
174    
175            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
176    
177            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
178            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
179            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
180    
181            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
182    
183            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
184            and use it for "sparse*" as well, since it's faster than the
185            as_Csparse(.) way.
186    
187    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
190    
191    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
194            as method for   M[ ij ] <- v
195            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
196    
197            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
198            FALSE answer
199    
200            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
201            * tests/indexing.R: test it, and some of the above
202    
203    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (is_duplicatedT): new utility
206    
207    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * src/init.c (R_init_Matrix): export cholmod_scale
210    
211    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
214            base::as.matrix to (x, ...)
215    
216    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
219            file; start using "Logic", hence
220    
221            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
222            * NAMESPACE: import and export "Logic"
223    
224    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
227            only needed previously to R version 2.5.0.
228    
229    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
232    
233            * R/Tsparse.R (replTmat): fix subassignment of triangular
234            * R/Csparse.R (replCmat): ditto
235            * tests/indexing.R: more tests, incl the above fix
236    
237    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Auxiliaries.R (drop0): extend for non CSparse
240            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
241    
242            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
243                    use uplo correctly (!); other places: use uplo_P() macro
244    
245            * R/Csparse.R (replCmat): call diagU2N() when needed
246            * R/Tsparse.R (replTmat): ditto
247    
248            * src/dtCMatrix.c (tCMatrix_validate): new
249            * src/dtTMatrix.c (tTMatrix_validate): new, used in
250            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
251    
252            * R/diagMatrix.R (replDiag): to use in [<-
253    
254    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
257                    also more general diagU2N().
258    
259    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
262            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
263    
264    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/bind.R: a few more cases
267            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
268    
269            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
270            * R/ddenseMatrix.R (cbind2/rbind2)
271            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
272            * tests/indexing.R
273            * tests/indexing.Rout.save: updated
274    
275    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
278            * tests/indexing.R
279    
280    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
283            align with proper position of "0", i.e., right for integers.
284            argument 'align' by default is "fancy".
285    
286    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
289            * R/Csparse.R: and fix "Compare" for more cases.
290            * tests/Class+Meth.R: test some of these (m == m, m != m)
291    
292    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/lsparseMatrix.R: all() and any() methods
295            * R/ldenseMatrix.R:      ditto
296            * NAMESPACE, R/Matrix.R: ditto
297    
298            * man/all-methods.Rd: document them minimally
299    
300            * tests/simple.R: add a few examples for these
301    
302    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Tsparse.R ([): fix long standing typo in symmetric case
305            * man/dsCMatrix-class.Rd: add example exhibiting the above case
306    
307    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
310            to LL before converting to a sparse matrix. (The LDL form can be
311            converted to a sparse matrix but it is implicitly a unit
312            triangular matrix and a diagonal matrix overwritten on the diagonal.)
313    
314    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
317    
318    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): updated -> release 0.9975-7
321            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
322    
323    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
326    
327    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
330            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
331            is exactly singular.
332    
333    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): updated -> release 0.9975-6
336    
337    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
340            now returns symmetric.
341    
342            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
343    
344            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
345            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
346    
347            * R/Auxiliaries.R (.type.kind): added
348    
349    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
352            running src/CSparse_install.sh
353    
354            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
355    
356    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
359            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
360    
361            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
362    
363            * tests/Class+Meth.R (tstMatrixClass): now assure
364            the (important in method programming) property :
365    
366                    ###>>  Every "Matrix" is either
367                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
368    
369                    (where "*" stands for "Matrix")
370    
371            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
372    
373            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
374            * tests/validObj.R: checks for "comparison"
375    
376            * R/sparseMatrix.R ([): improved indexing for sparse;
377                    trying to keep <symmetric>[ n, n] symmmetric
378    
379            * tests/indexing.R: indexing for logical sparse now ok
380    
381    
382    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/Tsparse.c: use xTsparse_validate() , and hence remove
385    
386            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
387    
388    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
391    
392            * tests/simple.R: validObject() checking the above.
393    
394            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
395            replacing both dgCMatrix_validate and lgCM*.
396    
397            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
398            fix dimnames setting in other places.
399            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
400    
401    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
404    
405            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
406            symmetry test, via
407            * R/Auxiliaries.R (.as.dgC.0.factors):
408    
409    2006-11-01  Douglas Bates  <bates@r-project.org>
410    
411            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
412            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
413            <CsparseMatrix>) added
414    
415    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * tests/matprod.R: add a variation of Harri's example
418    
419            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
420            recursive infinitely.
421    
422            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
423    
424            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
425    
426    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
429            matrix if possible; test m+m == 2*m; now test dgRMatrix.
430            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
431            satisfy the above test.
432    
433    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
436    
437            * R/dgCMatrix.R: solve(a, b="missing") based on
438            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
439            RHS = NULL.
440    
441            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
442            add more (needed) [t]crossprod() methods.
443    
444            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
445    
446            * R/Auxiliaries.R (as_CspClass): cleanup
447            (drop0): internal utility for "Csparse_drop(*, 0)"
448            (.bail.out.2): encourage active feedback
449    
450    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/dMatrix.R(Compare): new(), then slots [no validity check]
453    
454            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
455            non-valid or 'sorted' case).
456    
457            * R/dsparseMatrix.R: add "chol" method.
458            * R/ddenseMatrix.R: ditto
459    
460            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
461            * NAMESPACE (Ops)
462            * R/diagMatrix.R (diag2T): simple utility used "higher level"
463            coercion; deprecating direct lower level coercions.
464    
465            * R/*.R (seq): use seq_len() and seq_along() where possible.
466    
467    
468    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * DESCRIPTION (Version): 0.9975-5 ready for release
471    
472    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
475    
476    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllClass.R (corMatrix): add 'validity' check;
479                    comment out unused "LDL" class definition
480            * NAMESPACE: mention, but do not export "LDL" class
481            * R/corMatrix.R: new (simple), needed for R-devel with
482            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
483              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
484    
485    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
486    
487            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
488            use Rprintf and R's error handling.
489    
490    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
493            * tests/matprod.R: add tests for the bug fixed.
494    
495    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
496    
497            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
498            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
499    
500    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
501    
502            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
503    
504    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.9975-3
507    
508            * R/diagMatrix.R (bdiag): new function constructing block diagonal
509            (sparse) matrices.
510            * man/bdiag.Rd: docu + examples
511    
512            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
513    
514            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
515            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
516    
517            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
518            that result is sparse or diagonal (and not dense).
519    
520            * man/Subassign-methods.Rd: fix examples
521    
522            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
523            should always return a sparse (and not sometimes a diagonal) matrix.
524    
525    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
528    
529    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * DESCRIPTION (Version): 0.9975-2
532    
533            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
534    
535    2006-10-02  Douglas Bates  <bates@R-project.org>
536    
537            * tests/dg_Matrix.R: Simplify test taking into account new code.
538    
539    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
542    
543            * R/lsTMatrix.R: new files w/ missing methods
544            * R/nsTMatrix.R:  "  'for completeness'
545    
546            * tests/Class+Meth.R: a bit less 'not.ok.classes'
547    
548            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
549    
550    
551    2006-09-28  Douglas Bates  <bates@R-project.org>
552    
553            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
554            included.
555    
556            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
557            Export C-callable functions used in Zt_create in lme4.
558    
559    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * DESCRIPTION (Version): 0.9975-1
562    
563            * tests/simple.R: less checks fail; using NA, found that our
564                    kronecker() is not base-compatible with NA's.
565    
566            * R/dMatrix.R: "Compare" method now implemented for all cases
567    
568            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
569    
570            * man/dtpMatrix-class.Rd: mention length of 'x' slot
571    
572            * src/dtpMatrix.c (dtpMatrix_validate): fix check
573            * src/dspMatrix.c (dspMatrix_validate): ditto
574    
575            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
576              including coercion to [nl]tTMatrix.
577    
578            * R/diagMatrix.R (show): print a header line as for other classes.
579    
580    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/Makefile.win (SUBDIRS): fix typo
583    
584    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
587    
588    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
591            symmetric and y missing in R code using %*% (cholmod_aat doesn't
592            accept a symmetric matrix).
593            * tests/group-methods.R: Uncomment test of crossprod applied to
594            lsCMatrix objects.
595    
596    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/AllClass.R (symmetricMatrix): add validity method (available
599            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
600    
601            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
602    
603            * tests/indexing.Rout.save:
604            * tests/indexing.R: additions, mainly for 'lsparse'
605    
606            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
607            case.
608    
609            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
610    
611    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
614                    as 'N' (1-letter - Ok?)
615    
616            * tests/group-methods.R: add test for logical + NAs
617    
618            * R/dMatrix.R ("Compare"): fix to work with NA's
619    
620            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
621    
622            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
623                    which is implemented.
624    
625    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * src/chm_common.c: coerce logical <-> double instead of
628            typecasting;  needed for "l" matrix handling in cholmod.
629    
630            * tests/other-pkgs.R (graph): small extension in "graph" checks.
631    
632            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
633            (Tsp2grNEL): other fixes needed
634    
635    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
638                    Matrices, since "lMatrix", also "lsparseM" can have NA
639            * R/ndenseMatrix.R, etc: new source files
640            * man/nsparseMatrix-classes.Rd, etc: new help files
641            * tests/: adaptions
642            * src/chm_common.c (chm_dense_to_SEXP): and others:
643                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
644            * src/Csparse.c, etc: ditto
645    
646    2006-09-11  Douglas Bates  <bates@R-project.org>
647    
648            * src/Mutils.[ch],init.c inst/include/*.h: Move the
649            alloc_d**Matrix functions to the lme4 package.
650    
651    2006-09-09  Douglas Bates  <bates@R-project.org>
652    
653            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
654            fixed
655    
656    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/lMatrix.R: new
659    
660            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
661    
662            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
663            * man/tcrossprod.Rd: ditto
664    
665    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
666    
667            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
668            for exported functions
669            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
670            Remove partitioning algorithms for sparse matrix reordering.  The
671            copyright on the Metis code was problematic and the methods were
672            rarely used.
673            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
674            operations are now done entirely in CHOLMOD code.
675    
676    2006-09-06  Douglas Bates  <bates@R-project.org>
677    
678            * src/Mutils.h: Remove functions that are no longer used.
679    
680    2006-09-04  Douglas Bates  <bates@R-project.org>
681    
682            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
683            * src/DEPS.mkf: update
684    
685    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * created branches/Matrix-for-R-2.3.x;  on trunk: do
688            * DESCRIPTION (Version): 0.9975-0
689            (Depends): R (>= 2.4.0)
690    
691    2006-09-01  Douglas Bates  <bates@R-project.org>
692    
693            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
694    
695    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
698            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
699    
700            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
701    
702    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
705            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
706            * R/dsparseMatrix.R: ditto
707            * R/Csparse.R: ditto
708    
709    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/dMatrix.R (Compare): improve availability of "<", etc
712            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
713    
714    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
717            of a 0-index which was used as 1-index (..hmm)
718    
719            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
720    
721            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
722            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
723            (.is.diagonal): ditto
724    
725            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
726    
727            * R/Matrix.R (Matrix): also work for NA data
728    
729    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
732            in all cases.
733    
734    2006-08-27  Douglas Bates  <bates@R-project.org>
735    
736            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
737            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
738    
739    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
742            subclasses of "ddenseMatrix"
743            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
744            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
745            instead of half dozen specialized ones.
746    
747    2006-08-25  Douglas Bates  <bates@R-project.org>
748    
749            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
750            <tillard@cirad.fr> - ordering standard errors to match effects.
751    
752    2006-08-24  Douglas Bates  <bates@R-project.org>
753    
754            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
755            on R_ldl.
756            * R/lCholCMatrix.R,
757            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
758            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
759            * many files in ./R and ./src: Use more general version of
760            dup_mMatrix_as_dgeMatrix to simplify method definitions.
761            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
762            dtpMatrix, dspMatrix and dppMatrix conversions.
763    
764    
765    2006-08-23  Douglas Bates  <bates@R-project.org>
766    
767            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
768            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
769            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
770            dgeMatrix_crossprod (may need to do this in other places).
771            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
772            generic and method for dsCMatrix.  Use CHOLMOD for chol().
773    
774    2006-08-22  Douglas Bates  <bates@R-project.org>
775    
776            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
777            types of classed Matrices, matrices or numeric or logical vectors.
778            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
779            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
780            to Mutils.h (as an inline) and change name to Matrix_check_class;
781            fixes in as_cholmod_factor and chm_factor_to_SEXP.
782            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
783            dsCMatrix_matrix_solve.  Comment out vestigial functions.
784            * src/Csparse.c: use diag_P and uplo_P macros.
785    
786    2006-08-21  Douglas Bates  <bates@R-project.org>
787    
788            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
789            valgrind.
790            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
791            inverses.
792            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
793            -Wall warnings.
794            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
795            Use dup_mMatrix_as_dgeMatrix.
796    
797    2006-08-20  Douglas Bates  <bates@R-project.org>
798    
799            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
800            * tests/sparseQR.R: Added
801            * man/sparseQR-class.Rd: Document methods for qr.* generics
802            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
803    
804    2006-08-19  Douglas Bates  <bates@R-project.org>
805    
806            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
807            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
808            and qr.fitted.
809            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
810            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
811    
812    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
815            the base version has no "..." argument.
816    
817            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
818    
819            * R/Matrix.R: define and
820            * NAMESPACE: export as.numeric() and as.logical() methods.
821                    Let's hope these do not badly slow down something...
822            Finally export the zapsmall() method.
823    
824    2006-08-17  Douglas Bates  <bates@R-project.org>
825    
826            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
827            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
828            * src/dtCMatrix.c :Remove code that is no longer used
829            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
830    
831    2006-08-14  Douglas Bates  <bates@R-project.org>
832    
833            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
834            Csparse_to_logical and Csparse_symmetric_to_general.
835            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
836            coercion methods between CsparseMatrix and TsparseMatrix.
837    
838    2006-08-14  Douglas Bates  <bates@R-project.org>
839    
840            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
841            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
842            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
843            possible.
844    
845    2006-08-12  Douglas Bates  <bates@R-project.org>
846    
847            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
848              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
849              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
850              generalize conversions between TsparseMatrix, CsparseMatrix,
851              denseMatrix and matrix.  Preserve triangularity property and
852              propagate Dimnames in the easy cases.
853    
854    2006-08-10  Douglas Bates  <bates@R-project.org>
855    
856            * src/lmer.c: adjust checks in glmer_init for S4SXP
857            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
858            before S4SXP but for the wrong reasons.
859    
860    2006-08-08  Douglas Bates  <bates@R-project.org>
861    
862            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
863            Later modified to return the upper triangle only.
864            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
865    
866    2006-08-07  Douglas Bates  <bates@R-project.org>
867    
868            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
869            R-level conversion to a sparse symmetric class.
870            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
871            Remove conversion to sparse symmetric classes (now done in C code).
872    
873    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
876            * man/band.Rd:  adapt the \dontshow{} unit test.
877    
878    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * DESCRIPTION (Version): 0.995-14  for CRAN
881    
882            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
883    
884            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
885            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
886    
887            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
888            * R/Tsparse.R (tril, triu, band): methods
889            * R/dgRMatrix.R (tril, ...):    ditto
890            * man/band.Rd:                  ditto
891    
892    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * R/Matrix.R (head, tail): directly use utils:::head.matrix
895                    to be up-to-date automatically.
896    
897    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
900    
901            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
902            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
903            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
904            such that the S4 objects are always created by the current version
905            of R and 'Matrix' class definitions.
906    
907    2006-08-01  Douglas Bates  <bates@R-project.org>
908    
909            * R/lmer.R (LMEoptimize method), tests/lmer.R,
910            inst/external/test3comp.rda: Added warnings for convergence on
911            boundary and test cases.
912    
913            * src/lmer.c (mer_postVar): Modified to return the variances that
914            are marginal to the fixed effects, not conditional on them (which
915            is what the bVar slot contents represent).
916    
917    2006-07-31  Douglas Bates  <bates@R-project.org>
918    
919            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
920            function which calls the C function mer_hat_trace2.
921    
922            * man/ranef.Rd: Include description of "postVar" argument and
923            producing a caterpillar plot.
924    
925    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * NAMESPACE:    change  "correlation" to "corMatrix"
928            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
929            * R/dpoMatrix.R: ditto
930            * R/lmer.R:      ditto
931    
932    2006-07-28  Douglas Bates  <bates@R-project.org>
933    
934            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
935            RZXinv slot's contents into a separate internal function that can
936            be used in mer_hat_trace.
937    
938    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
941            via new smart
942            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
943            utility functions.
944    
945    
946    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/Csparse.R (tril, triu, band): do return *triangular* classed
949            matrices when appropriate; band() even symmetric ones.
950            (replCmat): extend to potentially all "CsparseMatrix"
951            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
952            allow subassignment for special sparse matrices.
953    
954            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
955    
956            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
957            argument; in glmer_*(): print only if(verbose).
958    
959            speed-optimize a few places by moving REAL(.) out of loops.
960    
961            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
962    
963    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
966                    since that wrongly triggers also for M[ logi , ]
967    
968            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
969            a symmetric matrix that results in a non-symmetric one.
970            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
971    
972            * R/dMatrix.R: make round(M) work as round(M, 0)
973    
974            * R/dgTMatrix.R (image): coordinate system and axis now use
975            1-based indices, not 0-based ones.
976    
977            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
978            * tests/indexing.R: test it.
979    
980            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
981            * man/isSymmetric-methods.Rd: and document it.
982    
983            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
984            * man/SparseM-conv.Rd: docu them
985    
986            * tests/other-pkgs.R: renamed from tests/graph.R and add example
987                    for 'SparseM' conversions
988    
989    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
990    
991            * R/Matrix.R (head): added head() and tail() methods.
992    
993    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * DESCRIPTION (Version): 0.995-12 released to CRAN
996    
997    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * tests/simple.R: add check for correct dsT -> dgT coercion;
1000                    add check for correct printing of symmetric sparse matrices.
1001    
1002            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1003            for sparse symmetric matrices.
1004    
1005            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1006            diagonal twice.
1007    
1008    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1009    
1010            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1011            being applied to the x slot (detected by Brian Ripley).
1012    
1013    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1016    
1017            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1018    
1019    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * src/lgCMatrix.c (lgCMatrix_diag): new function
1022            * R/lgCMatrix.R (diag): for new method
1023    
1024            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1025                 ==> construction of illegal "*gTMatrix" via new() should
1026                 now be much less easy:
1027            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1028    
1029            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1030                    directly.
1031            * man/Matrix.Rd: documents it.
1032    
1033    2006-07-06  Douglas Bates  <bates@R-project.org>
1034    
1035            * src/pedigree.c (pedigree_inbreeding): Correction in
1036            initialization.  This function is not currently being used and is
1037            not fully tested.
1038    
1039            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1040            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1041            objects.  Modified validity check on pedigree objects to account
1042            for nonparallel patterns of missingness of parents.
1043    
1044            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1045            class.
1046    
1047    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/pMatrix.R: coercion pMatrix -> Tsparse
1050    
1051    2006-06-12  Douglas Bates  <bates@R-project.org>
1052    
1053            * DESCRIPTION (Version): 0.995-11 released to CRAN
1054    
1055            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1056            the output from mcmcsamp.
1057    
1058    2006-06-10  Douglas Bates  <bates@R-project.org>
1059    
1060            * R/lmer.R (simulestimate): added C code for calculating the trace
1061            of the hat matrix.
1062    
1063    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1066            classes.
1067            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1068    
1069    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/dgTMatrix.R (colSums): etc. All four of
1072            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1073            all "Matrices".
1074    
1075  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1076    
1077          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 1102 
1102    
1103          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1104          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.
1105          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1106    
1107    
1108  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 1225 
1225          * 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)
1226          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1227          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1228          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1229    
1230  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
# Line 355  Line 1429 
1429  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1430    
1431          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1432          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1433          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1434    
1435  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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