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

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