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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1760, Sat Feb 3 21:13:22 2007 UTC
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1    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-10 to upload
4    
5            * tests/Class+Meth.R (tstMatrixClass): require coercions to
6            specific classes less unconditionally.
7    
8            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
9    
10            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
11    
12            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
13            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
14            R_to_CMatrix segfaults on one platform.
15            Eliminate most coercion method to *specific* classes, and replace
16            with virtual classes coercions.
17    
18    
19    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
20    
21            * src/init.c: export the CHM...._validate() placeholders, since
22            they *are* called.
23    
24            * tests/Class+Meth.R (classCanCoerce): and starting to test
25            all as(<from>, <to>)
26    
27    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
30            * tests/indexing.R: tested now
31            * tests/indexing.Rout.save: updated
32    
33            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
34            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
35            appropriate.
36    
37            * NAMESPACE: export a trivial
38            * R/Matrix.R: drop() Matrix-method
39    
40            * R/AllClass.R: moved all prototypes to virtual super classes.
41    
42            * R/Rsparse.R: many more coercions to have less exceptions in
43            * tests/Class+Meth.R:
44    
45            * R/Ops.R (Compare): tweak for case with NA
46            * tests/simpl.R: hence another 'FIXME' eliminated
47    
48    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
51            objects.
52    
53            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
54              and more of "!", "&", "|", all, any; coercions
55    
56            * R/Rsparse.R: many coercions (which enable quite a few other
57            methods), thanks to enhancements in
58            * src/dgCMatrix.c (R_to_CMatrix): new, and
59            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
60            symmetric & triangular and ..RMatrix objects.
61    
62            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
63            renamed file from src/dsTMatrix.c;
64            now dealing with symmetric and triangular Tsparse coercions, both
65            to dense and general.
66    
67    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
70    
71            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
72            where sensible when the <numeric> is of length > 1.
73    
74    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Matrix.R ([<-): for M[] <- value: fix length
77    
78    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
81            * R/ndenseMatrix.R: new coercions n* -> l*
82    
83    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
86    
87            * R/Ops.R ("Logic"): and other "Ops", many updates
88    
89    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/Mutils.h (SET_DimNames): new utility
92    
93            * R/Auxiliaries.R (nnzero): improved and now exported via
94    
95            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
96    
97    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/diagMatrix.R (!): fix typo.
100    
101    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Auxiliaries.R (as_Csparse): and quite a few others:
104                    allow to pass class definition --> speedup
105            * R/sparseMatrix.R: apply the above
106    
107            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
108    
109            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
110            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
111            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
112    
113            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
114    
115            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
116            and use it for "sparse*" as well, since it's faster than the
117            as_Csparse(.) way.
118    
119    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
122    
123    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
126            as method for   M[ ij ] <- v
127            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
128    
129            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
130            FALSE answer
131    
132            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
133            * tests/indexing.R: test it, and some of the above
134    
135    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Auxiliaries.R (is_duplicatedT): new utility
138    
139    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * src/init.c (R_init_Matrix): export cholmod_scale
142    
143    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
146            base::as.matrix to (x, ...)
147    
148    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
151            file; start using "Logic", hence
152    
153            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
154            * NAMESPACE: import and export "Logic"
155    
156    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
159            only needed previously to R version 2.5.0.
160    
161    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
164    
165            * R/Tsparse.R (replTmat): fix subassignment of triangular
166            * R/Csparse.R (replCmat): ditto
167            * tests/indexing.R: more tests, incl the above fix
168    
169    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (drop0): extend for non CSparse
172            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
173    
174            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
175                    use uplo correctly (!); other places: use uplo_P() macro
176    
177            * R/Csparse.R (replCmat): call diagU2N() when needed
178            * R/Tsparse.R (replTmat): ditto
179    
180            * src/dtCMatrix.c (tCMatrix_validate): new
181            * src/dtTMatrix.c (tTMatrix_validate): new, used in
182            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
183    
184            * R/diagMatrix.R (replDiag): to use in [<-
185    
186    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
189                    also more general diagU2N().
190    
191    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
194            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
195    
196    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * tests/bind.R: a few more cases
199            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
200    
201            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
202            * R/ddenseMatrix.R (cbind2/rbind2)
203            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
204            * tests/indexing.R
205            * tests/indexing.Rout.save: updated
206    
207    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
210            * tests/indexing.R
211    
212    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
215            align with proper position of "0", i.e., right for integers.
216            argument 'align' by default is "fancy".
217    
218    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
221            * R/Csparse.R: and fix "Compare" for more cases.
222            * tests/Class+Meth.R: test some of these (m == m, m != m)
223    
224    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/lsparseMatrix.R: all() and any() methods
227            * R/ldenseMatrix.R:      ditto
228            * NAMESPACE, R/Matrix.R: ditto
229    
230            * man/all-methods.Rd: document them minimally
231    
232            * tests/simple.R: add a few examples for these
233    
234    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R ([): fix long standing typo in symmetric case
237            * man/dsCMatrix-class.Rd: add example exhibiting the above case
238    
239    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
242            to LL before converting to a sparse matrix. (The LDL form can be
243            converted to a sparse matrix but it is implicitly a unit
244            triangular matrix and a diagonal matrix overwritten on the diagonal.)
245    
246    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
249    
250    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * DESCRIPTION (Version): updated -> release 0.9975-7
253            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
254    
255    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
258    
259    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
262            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
263            is exactly singular.
264    
265    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Date): updated -> release 0.9975-6
268    
269    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
272            now returns symmetric.
273    
274            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
275    
276            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
277            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
278    
279            * R/Auxiliaries.R (.type.kind): added
280    
281    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
284            running src/CSparse_install.sh
285    
286            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
287    
288    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
291            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
292    
293            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
294    
295            * tests/Class+Meth.R (tstMatrixClass): now assure
296            the (important in method programming) property :
297    
298                    ###>>  Every "Matrix" is either
299                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
300    
301                    (where "*" stands for "Matrix")
302    
303            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
304    
305            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
306            * tests/validObj.R: checks for "comparison"
307    
308            * R/sparseMatrix.R ([): improved indexing for sparse;
309                    trying to keep <symmetric>[ n, n] symmmetric
310    
311            * tests/indexing.R: indexing for logical sparse now ok
312    
313    
314    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * src/Tsparse.c: use xTsparse_validate() , and hence remove
317    
318            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
319    
320    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
323    
324            * tests/simple.R: validObject() checking the above.
325    
326            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
327            replacing both dgCMatrix_validate and lgCM*.
328    
329            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
330            fix dimnames setting in other places.
331            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
332    
333    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
336    
337            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
338            symmetry test, via
339            * R/Auxiliaries.R (.as.dgC.0.factors):
340    
341    2006-11-01  Douglas Bates  <bates@r-project.org>
342    
343            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
344            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
345            <CsparseMatrix>) added
346    
347    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * tests/matprod.R: add a variation of Harri's example
350    
351            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
352            recursive infinitely.
353    
354            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
355    
356            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
357    
358    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
361            matrix if possible; test m+m == 2*m; now test dgRMatrix.
362            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
363            satisfy the above test.
364    
365    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
368    
369            * R/dgCMatrix.R: solve(a, b="missing") based on
370            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
371            RHS = NULL.
372    
373            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
374            add more (needed) [t]crossprod() methods.
375    
376            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
377    
378            * R/Auxiliaries.R (as_CspClass): cleanup
379            (drop0): internal utility for "Csparse_drop(*, 0)"
380            (.bail.out.2): encourage active feedback
381    
382    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/dMatrix.R(Compare): new(), then slots [no validity check]
385    
386            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
387            non-valid or 'sorted' case).
388    
389            * R/dsparseMatrix.R: add "chol" method.
390            * R/ddenseMatrix.R: ditto
391    
392            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
393            * NAMESPACE (Ops)
394            * R/diagMatrix.R (diag2T): simple utility used "higher level"
395            coercion; deprecating direct lower level coercions.
396    
397            * R/*.R (seq): use seq_len() and seq_along() where possible.
398    
399    
400    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * DESCRIPTION (Version): 0.9975-5 ready for release
403    
404    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
405    
406            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
407    
408    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/AllClass.R (corMatrix): add 'validity' check;
411                    comment out unused "LDL" class definition
412            * NAMESPACE: mention, but do not export "LDL" class
413            * R/corMatrix.R: new (simple), needed for R-devel with
414            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
415              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
416    
417    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
418    
419            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
420            use Rprintf and R's error handling.
421    
422    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
425            * tests/matprod.R: add tests for the bug fixed.
426    
427    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
428    
429            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
430            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
431    
432    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
433    
434            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
435    
436    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * DESCRIPTION (Version): 0.9975-3
439    
440            * R/diagMatrix.R (bdiag): new function constructing block diagonal
441            (sparse) matrices.
442            * man/bdiag.Rd: docu + examples
443    
444            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
445    
446            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
447            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
448    
449            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
450            that result is sparse or diagonal (and not dense).
451    
452            * man/Subassign-methods.Rd: fix examples
453    
454            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
455            should always return a sparse (and not sometimes a diagonal) matrix.
456    
457    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
460    
461    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * DESCRIPTION (Version): 0.9975-2
464    
465            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
466    
467    2006-10-02  Douglas Bates  <bates@R-project.org>
468    
469            * tests/dg_Matrix.R: Simplify test taking into account new code.
470    
471    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
474    
475            * R/lsTMatrix.R: new files w/ missing methods
476            * R/nsTMatrix.R:  "  'for completeness'
477    
478            * tests/Class+Meth.R: a bit less 'not.ok.classes'
479    
480            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
481    
482    
483    2006-09-28  Douglas Bates  <bates@R-project.org>
484    
485            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
486            included.
487    
488            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
489            Export C-callable functions used in Zt_create in lme4.
490    
491    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * DESCRIPTION (Version): 0.9975-1
494    
495            * tests/simple.R: less checks fail; using NA, found that our
496                    kronecker() is not base-compatible with NA's.
497    
498            * R/dMatrix.R: "Compare" method now implemented for all cases
499    
500            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
501    
502            * man/dtpMatrix-class.Rd: mention length of 'x' slot
503    
504            * src/dtpMatrix.c (dtpMatrix_validate): fix check
505            * src/dspMatrix.c (dspMatrix_validate): ditto
506    
507            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
508              including coercion to [nl]tTMatrix.
509    
510            * R/diagMatrix.R (show): print a header line as for other classes.
511    
512    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * src/Makefile.win (SUBDIRS): fix typo
515    
516    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
519    
520    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
521    
522            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
523            symmetric and y missing in R code using %*% (cholmod_aat doesn't
524            accept a symmetric matrix).
525            * tests/group-methods.R: Uncomment test of crossprod applied to
526            lsCMatrix objects.
527    
528    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/AllClass.R (symmetricMatrix): add validity method (available
531            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
532    
533            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
534    
535            * tests/indexing.Rout.save:
536            * tests/indexing.R: additions, mainly for 'lsparse'
537    
538            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
539            case.
540    
541            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
542    
543    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
546                    as 'N' (1-letter - Ok?)
547    
548            * tests/group-methods.R: add test for logical + NAs
549    
550            * R/dMatrix.R ("Compare"): fix to work with NA's
551    
552            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
553    
554            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
555                    which is implemented.
556    
557    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * src/chm_common.c: coerce logical <-> double instead of
560            typecasting;  needed for "l" matrix handling in cholmod.
561    
562            * tests/other-pkgs.R (graph): small extension in "graph" checks.
563    
564            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
565            (Tsp2grNEL): other fixes needed
566    
567    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
570                    Matrices, since "lMatrix", also "lsparseM" can have NA
571            * R/ndenseMatrix.R, etc: new source files
572            * man/nsparseMatrix-classes.Rd, etc: new help files
573            * tests/: adaptions
574            * src/chm_common.c (chm_dense_to_SEXP): and others:
575                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
576            * src/Csparse.c, etc: ditto
577    
578    2006-09-11  Douglas Bates  <bates@R-project.org>
579    
580            * src/Mutils.[ch],init.c inst/include/*.h: Move the
581            alloc_d**Matrix functions to the lme4 package.
582    
583    2006-09-09  Douglas Bates  <bates@R-project.org>
584    
585            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
586            fixed
587    
588    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/lMatrix.R: new
591    
592            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
593    
594            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
595            * man/tcrossprod.Rd: ditto
596    
597    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
600            for exported functions
601            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
602            Remove partitioning algorithms for sparse matrix reordering.  The
603            copyright on the Metis code was problematic and the methods were
604            rarely used.
605            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
606            operations are now done entirely in CHOLMOD code.
607    
608    2006-09-06  Douglas Bates  <bates@R-project.org>
609    
610            * src/Mutils.h: Remove functions that are no longer used.
611    
612    2006-09-04  Douglas Bates  <bates@R-project.org>
613    
614            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
615            * src/DEPS.mkf: update
616    
617    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * created branches/Matrix-for-R-2.3.x;  on trunk: do
620            * DESCRIPTION (Version): 0.9975-0
621            (Depends): R (>= 2.4.0)
622    
623    2006-09-01  Douglas Bates  <bates@R-project.org>
624    
625            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
626    
627    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
630            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
631    
632            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
633    
634    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
637            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
638            * R/dsparseMatrix.R: ditto
639            * R/Csparse.R: ditto
640    
641    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/dMatrix.R (Compare): improve availability of "<", etc
644            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
645    
646    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
649            of a 0-index which was used as 1-index (..hmm)
650    
651            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
652    
653            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
654            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
655            (.is.diagonal): ditto
656    
657            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
658    
659            * R/Matrix.R (Matrix): also work for NA data
660    
661    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
664            in all cases.
665    
666    2006-08-27  Douglas Bates  <bates@R-project.org>
667    
668            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
669            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
670    
671    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
674            subclasses of "ddenseMatrix"
675            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
676            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
677            instead of half dozen specialized ones.
678    
679    2006-08-25  Douglas Bates  <bates@R-project.org>
680    
681            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
682            <tillard@cirad.fr> - ordering standard errors to match effects.
683    
684    2006-08-24  Douglas Bates  <bates@R-project.org>
685    
686            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
687            on R_ldl.
688            * R/lCholCMatrix.R,
689            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
690            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
691            * many files in ./R and ./src: Use more general version of
692            dup_mMatrix_as_dgeMatrix to simplify method definitions.
693            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
694            dtpMatrix, dspMatrix and dppMatrix conversions.
695    
696    
697    2006-08-23  Douglas Bates  <bates@R-project.org>
698    
699            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
700            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
701            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
702            dgeMatrix_crossprod (may need to do this in other places).
703            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
704            generic and method for dsCMatrix.  Use CHOLMOD for chol().
705    
706    2006-08-22  Douglas Bates  <bates@R-project.org>
707    
708            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
709            types of classed Matrices, matrices or numeric or logical vectors.
710            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
711            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
712            to Mutils.h (as an inline) and change name to Matrix_check_class;
713            fixes in as_cholmod_factor and chm_factor_to_SEXP.
714            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
715            dsCMatrix_matrix_solve.  Comment out vestigial functions.
716            * src/Csparse.c: use diag_P and uplo_P macros.
717    
718    2006-08-21  Douglas Bates  <bates@R-project.org>
719    
720            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
721            valgrind.
722            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
723            inverses.
724            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
725            -Wall warnings.
726            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
727            Use dup_mMatrix_as_dgeMatrix.
728    
729    2006-08-20  Douglas Bates  <bates@R-project.org>
730    
731            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
732            * tests/sparseQR.R: Added
733            * man/sparseQR-class.Rd: Document methods for qr.* generics
734            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
735    
736    2006-08-19  Douglas Bates  <bates@R-project.org>
737    
738            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
739            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
740            and qr.fitted.
741            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
742            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
743    
744    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
747            the base version has no "..." argument.
748    
749            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
750    
751            * R/Matrix.R: define and
752            * NAMESPACE: export as.numeric() and as.logical() methods.
753                    Let's hope these do not badly slow down something...
754            Finally export the zapsmall() method.
755    
756    2006-08-17  Douglas Bates  <bates@R-project.org>
757    
758            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
759            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
760            * src/dtCMatrix.c :Remove code that is no longer used
761            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
762    
763    2006-08-14  Douglas Bates  <bates@R-project.org>
764    
765            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
766            Csparse_to_logical and Csparse_symmetric_to_general.
767            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
768            coercion methods between CsparseMatrix and TsparseMatrix.
769    
770    2006-08-14  Douglas Bates  <bates@R-project.org>
771    
772            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
773            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
774            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
775            possible.
776    
777    2006-08-12  Douglas Bates  <bates@R-project.org>
778    
779            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
780              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
781              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
782              generalize conversions between TsparseMatrix, CsparseMatrix,
783              denseMatrix and matrix.  Preserve triangularity property and
784              propagate Dimnames in the easy cases.
785    
786    2006-08-10  Douglas Bates  <bates@R-project.org>
787    
788            * src/lmer.c: adjust checks in glmer_init for S4SXP
789            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
790            before S4SXP but for the wrong reasons.
791    
792    2006-08-08  Douglas Bates  <bates@R-project.org>
793    
794            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
795            Later modified to return the upper triangle only.
796            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
797    
798    2006-08-07  Douglas Bates  <bates@R-project.org>
799    
800            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
801            R-level conversion to a sparse symmetric class.
802            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
803            Remove conversion to sparse symmetric classes (now done in C code).
804    
805    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
808            * man/band.Rd:  adapt the \dontshow{} unit test.
809    
810    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * DESCRIPTION (Version): 0.995-14  for CRAN
813    
814            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
815    
816            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
817            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
818    
819            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
820            * R/Tsparse.R (tril, triu, band): methods
821            * R/dgRMatrix.R (tril, ...):    ditto
822            * man/band.Rd:                  ditto
823    
824    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * R/Matrix.R (head, tail): directly use utils:::head.matrix
827                    to be up-to-date automatically.
828    
829    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
832    
833            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
834            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
835            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
836            such that the S4 objects are always created by the current version
837            of R and 'Matrix' class definitions.
838    
839    2006-08-01  Douglas Bates  <bates@R-project.org>
840    
841            * R/lmer.R (LMEoptimize method), tests/lmer.R,
842            inst/external/test3comp.rda: Added warnings for convergence on
843            boundary and test cases.
844    
845            * src/lmer.c (mer_postVar): Modified to return the variances that
846            are marginal to the fixed effects, not conditional on them (which
847            is what the bVar slot contents represent).
848    
849    2006-07-31  Douglas Bates  <bates@R-project.org>
850    
851            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
852            function which calls the C function mer_hat_trace2.
853    
854            * man/ranef.Rd: Include description of "postVar" argument and
855            producing a caterpillar plot.
856    
857    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * NAMESPACE:    change  "correlation" to "corMatrix"
860            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
861            * R/dpoMatrix.R: ditto
862            * R/lmer.R:      ditto
863    
864    2006-07-28  Douglas Bates  <bates@R-project.org>
865    
866            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
867            RZXinv slot's contents into a separate internal function that can
868            be used in mer_hat_trace.
869    
870    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
873            via new smart
874            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
875            utility functions.
876    
877    
878    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/Csparse.R (tril, triu, band): do return *triangular* classed
881            matrices when appropriate; band() even symmetric ones.
882            (replCmat): extend to potentially all "CsparseMatrix"
883            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
884            allow subassignment for special sparse matrices.
885    
886            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
887    
888            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
889            argument; in glmer_*(): print only if(verbose).
890    
891            speed-optimize a few places by moving REAL(.) out of loops.
892    
893            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
894    
895    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
898                    since that wrongly triggers also for M[ logi , ]
899    
900            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
901            a symmetric matrix that results in a non-symmetric one.
902            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
903    
904            * R/dMatrix.R: make round(M) work as round(M, 0)
905    
906            * R/dgTMatrix.R (image): coordinate system and axis now use
907            1-based indices, not 0-based ones.
908    
909            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
910            * tests/indexing.R: test it.
911    
912            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
913            * man/isSymmetric-methods.Rd: and document it.
914    
915            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
916            * man/SparseM-conv.Rd: docu them
917    
918            * tests/other-pkgs.R: renamed from tests/graph.R and add example
919                    for 'SparseM' conversions
920    
921    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
922    
923            * R/Matrix.R (head): added head() and tail() methods.
924    
925    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * DESCRIPTION (Version): 0.995-12 released to CRAN
928    
929    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * tests/simple.R: add check for correct dsT -> dgT coercion;
932                    add check for correct printing of symmetric sparse matrices.
933    
934            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
935            for sparse symmetric matrices.
936    
937            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
938            diagonal twice.
939    
940    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
941    
942            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
943            being applied to the x slot (detected by Brian Ripley).
944    
945    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
948    
949            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
950    
951    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * src/lgCMatrix.c (lgCMatrix_diag): new function
954            * R/lgCMatrix.R (diag): for new method
955    
956            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
957                 ==> construction of illegal "*gTMatrix" via new() should
958                 now be much less easy:
959            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
960    
961            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
962                    directly.
963            * man/Matrix.Rd: documents it.
964    
965    2006-07-06  Douglas Bates  <bates@R-project.org>
966    
967            * src/pedigree.c (pedigree_inbreeding): Correction in
968            initialization.  This function is not currently being used and is
969            not fully tested.
970    
971            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
972            Introduced the glmer class.  Added code for mcmcmsamp on glmer
973            objects.  Modified validity check on pedigree objects to account
974            for nonparallel patterns of missingness of parents.
975    
976            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
977            class.
978    
979    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/pMatrix.R: coercion pMatrix -> Tsparse
982    
983    2006-06-12  Douglas Bates  <bates@R-project.org>
984    
985            * DESCRIPTION (Version): 0.995-11 released to CRAN
986    
987            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
988            the output from mcmcsamp.
989    
990    2006-06-10  Douglas Bates  <bates@R-project.org>
991    
992            * R/lmer.R (simulestimate): added C code for calculating the trace
993            of the hat matrix.
994    
995    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
998            classes.
999            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1000    
1001    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1002    
1003            * R/dgTMatrix.R (colSums): etc. All four of
1004            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1005            all "Matrices".
1006    
1007    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1008    
1009            * R/lmer.R (panel.ci): Add a reference line at zero and a
1010            background grid to the qqmath plot of ranef.lmer.
1011    
1012    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1013    
1014            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1015            grouping factors to be specified in the formula as (1|foo/bar).
1016    
1017    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1018    
1019            * R/lmer.R (findbars and others): Change check of is.numeric to
1020            !is.language to resolve the bug reported by Jacob Wegelin.
1021    
1022            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1023            code to evaluate inbreeding coefficients without calculating T,
1024            based on code in Sargolzaei and Iwaisaki's paper.
1025    
1026    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1027    
1028            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1029            generic and mer methods for isNested and denomDF. This denomDF was
1030            an attempt to emulate that in lme but I don't think that makes
1031            sense.  Use the trace of the hat matrix instead.
1032    
1033    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1034    
1035            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1036            the C code depending on a slot structure that's no longer valid.
1037            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1038    
1039    
1040    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1041    
1042            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1043            of lowerTriMatrix generic and methods to tril (also upper to triu)
1044            and added a general band extractor.
1045    
1046    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1047    
1048            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1049            allowable range with NAs. Added a corresponding check in the
1050            validity check for the pedigree class.
1051    
1052            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1053            crossprod methods now inherits from symmetricMatrix.
1054    
1055    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1056    
1057            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1058            generics lowerTriMatrix and upperTriMatrix along with methods for
1059            the Csparse virtual class.  Also added a C function Csparse_band
1060            that implements these methods by calling cholmod_band.
1061    
1062    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1065            erased when it was NULL.  This led to invalid subselections!
1066    
1067    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1068    
1069            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1070            in method for "t" so as not to lose the unit diagonal property.
1071    
1072    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1073    
1074            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1075            and methods.  This is now an option to the ranef method for the
1076            mer class.
1077    
1078            * src/cs_utils.c: Ensure that the nz component is -1 for a
1079            compressed column-oriented matrix.  Minor formatting cleanup.
1080    
1081            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1082            objects.
1083    
1084    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1087            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1088    
1089    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1090    
1091            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1092            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1093    
1094            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1095            for the dtCMatrix class.
1096    
1097    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1098    
1099            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1100            and methods for it.
1101    
1102    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1105            arguments, such that M %*% 1:6 now works
1106            * Tests/matprod.R: test the above
1107    
1108    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1109    
1110            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1111            the ranef.lmer class.
1112    
1113            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1114            methods to extract the posterior variances from the bVar slot.
1115    
1116    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1119            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1120    
1121            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1122            * tests/simple: (extended)
1123    
1124            * R/sparseMatrix.R (isTriangular): now using much improved
1125            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1126    
1127    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1128    
1129            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1130            (problem report from Franklin Parlamis).  This should be done
1131            generally.
1132    
1133    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1134    
1135            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1136            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1137            update the plot methods.
1138    
1139    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1140    
1141            * R/lmer.R (resid and ranef methods):  Added methods for the
1142            "residuals" and "resid" generic but only for linear mixed model
1143            fits.  Changed the ranef method to return a list of data frames so
1144            that the plot methods now work.
1145    
1146    2006-03-16  Douglas Bates  <bates@bates2>
1147    
1148            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1149            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1150    
1151            * DESCRIPTION (Date): New release
1152    
1153    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1156    
1157            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1158            * man/KNex.Rd: and other help files
1159            * tests/*.R: several ones needed adaption
1160            * inst/doc/Comparisons.Rnw: ditto
1161    
1162    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1165    
1166            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1167    
1168    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1171    
1172            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1173    
1174    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * R/dMatrix.R: enable things like  M [ M < 10 ]
1177            * R/dgeMatrix.R: implement it
1178    
1179    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * R/AllClass.R: define "summary.mer" and "*.lmer"
1182            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1183            * R/lmer.R (show): now works with summary()
1184    
1185    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1188            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1189                    support the above
1190    
1191  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1192    
1193          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 1361 
1361  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1362    
1363          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1364          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1365          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1366    
1367  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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