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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1767, Mon Feb 5 16:53:17 2007 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
4            * tests/simple.R: test the above and some of these coercions:
5    
6            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
7                    be careful to avoid infinite recursion, using new coercions in
8            * R/ngCMatrix.R and nsC... and ntC...
9            * R/lsparseMatrix.R: ditto
10    
11            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
12    
13            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
14            * R/Rsparse.R: reactivate .Call()s
15    
16            * tests/Class+Meth.R: a bit more on actual classes
17    
18    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
21    
22    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * DESCRIPTION (Version): 0.9975-10 to upload
25    
26            * tests/Class+Meth.R (tstMatrixClass): require coercions to
27            specific classes less unconditionally.
28    
29            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
30    
31            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
32    
33            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
34            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
35            R_to_CMatrix segfaults on one platform.
36            Eliminate most coercion method to *specific* classes, and replace
37            with virtual classes coercions.
38    
39    
40    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
41    
42            * src/init.c: export the CHM...._validate() placeholders, since
43            they *are* called.
44    
45            * tests/Class+Meth.R (classCanCoerce): and starting to test
46            all as(<from>, <to>)
47    
48    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
51            * tests/indexing.R: tested now
52            * tests/indexing.Rout.save: updated
53    
54            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
55            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
56            appropriate.
57    
58            * NAMESPACE: export a trivial
59            * R/Matrix.R: drop() Matrix-method
60    
61            * R/AllClass.R: moved all prototypes to virtual super classes.
62    
63            * R/Rsparse.R: many more coercions to have less exceptions in
64            * tests/Class+Meth.R:
65    
66            * R/Ops.R (Compare): tweak for case with NA
67            * tests/simpl.R: hence another 'FIXME' eliminated
68    
69    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
72            objects.
73    
74            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
75              and more of "!", "&", "|", all, any; coercions
76    
77            * R/Rsparse.R: many coercions (which enable quite a few other
78            methods), thanks to enhancements in
79            * src/dgCMatrix.c (R_to_CMatrix): new, and
80            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
81            symmetric & triangular and ..RMatrix objects.
82    
83            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
84            renamed file from src/dsTMatrix.c;
85            now dealing with symmetric and triangular Tsparse coercions, both
86            to dense and general.
87    
88    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
91    
92            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
93            where sensible when the <numeric> is of length > 1.
94    
95    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R ([<-): for M[] <- value: fix length
98    
99    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
102            * R/ndenseMatrix.R: new coercions n* -> l*
103    
104    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
107    
108            * R/Ops.R ("Logic"): and other "Ops", many updates
109    
110    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * src/Mutils.h (SET_DimNames): new utility
113    
114            * R/Auxiliaries.R (nnzero): improved and now exported via
115    
116            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
117    
118    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/diagMatrix.R (!): fix typo.
121    
122    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (as_Csparse): and quite a few others:
125                    allow to pass class definition --> speedup
126            * R/sparseMatrix.R: apply the above
127    
128            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
129    
130            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
131            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
132            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
133    
134            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
135    
136            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
137            and use it for "sparse*" as well, since it's faster than the
138            as_Csparse(.) way.
139    
140    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
143    
144    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
147            as method for   M[ ij ] <- v
148            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
149    
150            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
151            FALSE answer
152    
153            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
154            * tests/indexing.R: test it, and some of the above
155    
156    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (is_duplicatedT): new utility
159    
160    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
161    
162            * src/init.c (R_init_Matrix): export cholmod_scale
163    
164    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
167            base::as.matrix to (x, ...)
168    
169    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
172            file; start using "Logic", hence
173    
174            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
175            * NAMESPACE: import and export "Logic"
176    
177    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
180            only needed previously to R version 2.5.0.
181    
182    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
185    
186            * R/Tsparse.R (replTmat): fix subassignment of triangular
187            * R/Csparse.R (replCmat): ditto
188            * tests/indexing.R: more tests, incl the above fix
189    
190    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (drop0): extend for non CSparse
193            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
194    
195            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
196                    use uplo correctly (!); other places: use uplo_P() macro
197    
198            * R/Csparse.R (replCmat): call diagU2N() when needed
199            * R/Tsparse.R (replTmat): ditto
200    
201            * src/dtCMatrix.c (tCMatrix_validate): new
202            * src/dtTMatrix.c (tTMatrix_validate): new, used in
203            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
204    
205            * R/diagMatrix.R (replDiag): to use in [<-
206    
207    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
210                    also more general diagU2N().
211    
212    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
215            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
216    
217    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * tests/bind.R: a few more cases
220            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
221    
222            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
223            * R/ddenseMatrix.R (cbind2/rbind2)
224            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
225            * tests/indexing.R
226            * tests/indexing.Rout.save: updated
227    
228    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
231            * tests/indexing.R
232    
233    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
236            align with proper position of "0", i.e., right for integers.
237            argument 'align' by default is "fancy".
238    
239    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
242            * R/Csparse.R: and fix "Compare" for more cases.
243            * tests/Class+Meth.R: test some of these (m == m, m != m)
244    
245    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/lsparseMatrix.R: all() and any() methods
248            * R/ldenseMatrix.R:      ditto
249            * NAMESPACE, R/Matrix.R: ditto
250    
251            * man/all-methods.Rd: document them minimally
252    
253            * tests/simple.R: add a few examples for these
254    
255    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/Tsparse.R ([): fix long standing typo in symmetric case
258            * man/dsCMatrix-class.Rd: add example exhibiting the above case
259    
260    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
261    
262            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
263            to LL before converting to a sparse matrix. (The LDL form can be
264            converted to a sparse matrix but it is implicitly a unit
265            triangular matrix and a diagonal matrix overwritten on the diagonal.)
266    
267    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
268    
269            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
270    
271    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * DESCRIPTION (Version): updated -> release 0.9975-7
274            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
275    
276    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
279    
280    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
283            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
284            is exactly singular.
285    
286    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * DESCRIPTION (Date): updated -> release 0.9975-6
289    
290    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
293            now returns symmetric.
294    
295            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
296    
297            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
298            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
299    
300            * R/Auxiliaries.R (.type.kind): added
301    
302    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
305            running src/CSparse_install.sh
306    
307            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
308    
309    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
312            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
313    
314            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
315    
316            * tests/Class+Meth.R (tstMatrixClass): now assure
317            the (important in method programming) property :
318    
319                    ###>>  Every "Matrix" is either
320                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
321    
322                    (where "*" stands for "Matrix")
323    
324            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
325    
326            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
327            * tests/validObj.R: checks for "comparison"
328    
329            * R/sparseMatrix.R ([): improved indexing for sparse;
330                    trying to keep <symmetric>[ n, n] symmmetric
331    
332            * tests/indexing.R: indexing for logical sparse now ok
333    
334    
335    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * src/Tsparse.c: use xTsparse_validate() , and hence remove
338    
339            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
340    
341    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
344    
345            * tests/simple.R: validObject() checking the above.
346    
347            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
348            replacing both dgCMatrix_validate and lgCM*.
349    
350            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
351            fix dimnames setting in other places.
352            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
353    
354    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
357    
358            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
359            symmetry test, via
360            * R/Auxiliaries.R (.as.dgC.0.factors):
361    
362    2006-11-01  Douglas Bates  <bates@r-project.org>
363    
364            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
365            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
366            <CsparseMatrix>) added
367    
368    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * tests/matprod.R: add a variation of Harri's example
371    
372            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
373            recursive infinitely.
374    
375            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
376    
377            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
378    
379    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
382            matrix if possible; test m+m == 2*m; now test dgRMatrix.
383            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
384            satisfy the above test.
385    
386    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
389    
390            * R/dgCMatrix.R: solve(a, b="missing") based on
391            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
392            RHS = NULL.
393    
394            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
395            add more (needed) [t]crossprod() methods.
396    
397            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
398    
399            * R/Auxiliaries.R (as_CspClass): cleanup
400            (drop0): internal utility for "Csparse_drop(*, 0)"
401            (.bail.out.2): encourage active feedback
402    
403    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/dMatrix.R(Compare): new(), then slots [no validity check]
406    
407            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
408            non-valid or 'sorted' case).
409    
410            * R/dsparseMatrix.R: add "chol" method.
411            * R/ddenseMatrix.R: ditto
412    
413            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
414            * NAMESPACE (Ops)
415            * R/diagMatrix.R (diag2T): simple utility used "higher level"
416            coercion; deprecating direct lower level coercions.
417    
418            * R/*.R (seq): use seq_len() and seq_along() where possible.
419    
420    
421    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * DESCRIPTION (Version): 0.9975-5 ready for release
424    
425    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
426    
427            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
428    
429    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/AllClass.R (corMatrix): add 'validity' check;
432                    comment out unused "LDL" class definition
433            * NAMESPACE: mention, but do not export "LDL" class
434            * R/corMatrix.R: new (simple), needed for R-devel with
435            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
436              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
437    
438    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
441            use Rprintf and R's error handling.
442    
443    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
446            * tests/matprod.R: add tests for the bug fixed.
447    
448    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
451            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
452    
453    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
456    
457    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * DESCRIPTION (Version): 0.9975-3
460    
461            * R/diagMatrix.R (bdiag): new function constructing block diagonal
462            (sparse) matrices.
463            * man/bdiag.Rd: docu + examples
464    
465            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
466    
467            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
468            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
469    
470            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
471            that result is sparse or diagonal (and not dense).
472    
473            * man/Subassign-methods.Rd: fix examples
474    
475            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
476            should always return a sparse (and not sometimes a diagonal) matrix.
477    
478    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
481    
482    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * DESCRIPTION (Version): 0.9975-2
485    
486            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
487    
488    2006-10-02  Douglas Bates  <bates@R-project.org>
489    
490            * tests/dg_Matrix.R: Simplify test taking into account new code.
491    
492    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
495    
496            * R/lsTMatrix.R: new files w/ missing methods
497            * R/nsTMatrix.R:  "  'for completeness'
498    
499            * tests/Class+Meth.R: a bit less 'not.ok.classes'
500    
501            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
502    
503    
504    2006-09-28  Douglas Bates  <bates@R-project.org>
505    
506            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
507            included.
508    
509            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
510            Export C-callable functions used in Zt_create in lme4.
511    
512    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * DESCRIPTION (Version): 0.9975-1
515    
516            * tests/simple.R: less checks fail; using NA, found that our
517                    kronecker() is not base-compatible with NA's.
518    
519            * R/dMatrix.R: "Compare" method now implemented for all cases
520    
521            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
522    
523            * man/dtpMatrix-class.Rd: mention length of 'x' slot
524    
525            * src/dtpMatrix.c (dtpMatrix_validate): fix check
526            * src/dspMatrix.c (dspMatrix_validate): ditto
527    
528            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
529              including coercion to [nl]tTMatrix.
530    
531            * R/diagMatrix.R (show): print a header line as for other classes.
532    
533    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * src/Makefile.win (SUBDIRS): fix typo
536    
537    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
540    
541    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
542    
543            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
544            symmetric and y missing in R code using %*% (cholmod_aat doesn't
545            accept a symmetric matrix).
546            * tests/group-methods.R: Uncomment test of crossprod applied to
547            lsCMatrix objects.
548    
549    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/AllClass.R (symmetricMatrix): add validity method (available
552            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
553    
554            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
555    
556            * tests/indexing.Rout.save:
557            * tests/indexing.R: additions, mainly for 'lsparse'
558    
559            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
560            case.
561    
562            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
563    
564    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
567                    as 'N' (1-letter - Ok?)
568    
569            * tests/group-methods.R: add test for logical + NAs
570    
571            * R/dMatrix.R ("Compare"): fix to work with NA's
572    
573            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
574    
575            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
576                    which is implemented.
577    
578    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * src/chm_common.c: coerce logical <-> double instead of
581            typecasting;  needed for "l" matrix handling in cholmod.
582    
583            * tests/other-pkgs.R (graph): small extension in "graph" checks.
584    
585            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
586            (Tsp2grNEL): other fixes needed
587    
588    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
591                    Matrices, since "lMatrix", also "lsparseM" can have NA
592            * R/ndenseMatrix.R, etc: new source files
593            * man/nsparseMatrix-classes.Rd, etc: new help files
594            * tests/: adaptions
595            * src/chm_common.c (chm_dense_to_SEXP): and others:
596                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
597            * src/Csparse.c, etc: ditto
598    
599    2006-09-11  Douglas Bates  <bates@R-project.org>
600    
601            * src/Mutils.[ch],init.c inst/include/*.h: Move the
602            alloc_d**Matrix functions to the lme4 package.
603    
604    2006-09-09  Douglas Bates  <bates@R-project.org>
605    
606            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
607            fixed
608    
609    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/lMatrix.R: new
612    
613            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
614    
615            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
616            * man/tcrossprod.Rd: ditto
617    
618    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
621            for exported functions
622            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
623            Remove partitioning algorithms for sparse matrix reordering.  The
624            copyright on the Metis code was problematic and the methods were
625            rarely used.
626            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
627            operations are now done entirely in CHOLMOD code.
628    
629    2006-09-06  Douglas Bates  <bates@R-project.org>
630    
631            * src/Mutils.h: Remove functions that are no longer used.
632    
633    2006-09-04  Douglas Bates  <bates@R-project.org>
634    
635            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
636            * src/DEPS.mkf: update
637    
638    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * created branches/Matrix-for-R-2.3.x;  on trunk: do
641            * DESCRIPTION (Version): 0.9975-0
642            (Depends): R (>= 2.4.0)
643    
644    2006-09-01  Douglas Bates  <bates@R-project.org>
645    
646            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
647    
648    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
651            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
652    
653            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
654    
655    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
658            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
659            * R/dsparseMatrix.R: ditto
660            * R/Csparse.R: ditto
661    
662    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dMatrix.R (Compare): improve availability of "<", etc
665            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
666    
667    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
670            of a 0-index which was used as 1-index (..hmm)
671    
672            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
673    
674            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
675            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
676            (.is.diagonal): ditto
677    
678            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
679    
680            * R/Matrix.R (Matrix): also work for NA data
681    
682    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
685            in all cases.
686    
687    2006-08-27  Douglas Bates  <bates@R-project.org>
688    
689            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
690            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
691    
692    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
695            subclasses of "ddenseMatrix"
696            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
697            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
698            instead of half dozen specialized ones.
699    
700    2006-08-25  Douglas Bates  <bates@R-project.org>
701    
702            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
703            <tillard@cirad.fr> - ordering standard errors to match effects.
704    
705    2006-08-24  Douglas Bates  <bates@R-project.org>
706    
707            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
708            on R_ldl.
709            * R/lCholCMatrix.R,
710            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
711            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
712            * many files in ./R and ./src: Use more general version of
713            dup_mMatrix_as_dgeMatrix to simplify method definitions.
714            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
715            dtpMatrix, dspMatrix and dppMatrix conversions.
716    
717    
718    2006-08-23  Douglas Bates  <bates@R-project.org>
719    
720            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
721            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
722            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
723            dgeMatrix_crossprod (may need to do this in other places).
724            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
725            generic and method for dsCMatrix.  Use CHOLMOD for chol().
726    
727    2006-08-22  Douglas Bates  <bates@R-project.org>
728    
729            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
730            types of classed Matrices, matrices or numeric or logical vectors.
731            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
732            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
733            to Mutils.h (as an inline) and change name to Matrix_check_class;
734            fixes in as_cholmod_factor and chm_factor_to_SEXP.
735            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
736            dsCMatrix_matrix_solve.  Comment out vestigial functions.
737            * src/Csparse.c: use diag_P and uplo_P macros.
738    
739    2006-08-21  Douglas Bates  <bates@R-project.org>
740    
741            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
742            valgrind.
743            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
744            inverses.
745            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
746            -Wall warnings.
747            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
748            Use dup_mMatrix_as_dgeMatrix.
749    
750    2006-08-20  Douglas Bates  <bates@R-project.org>
751    
752            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
753            * tests/sparseQR.R: Added
754            * man/sparseQR-class.Rd: Document methods for qr.* generics
755            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
756    
757    2006-08-19  Douglas Bates  <bates@R-project.org>
758    
759            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
760            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
761            and qr.fitted.
762            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
763            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
764    
765    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
768            the base version has no "..." argument.
769    
770            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
771    
772            * R/Matrix.R: define and
773            * NAMESPACE: export as.numeric() and as.logical() methods.
774                    Let's hope these do not badly slow down something...
775            Finally export the zapsmall() method.
776    
777    2006-08-17  Douglas Bates  <bates@R-project.org>
778    
779            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
780            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
781            * src/dtCMatrix.c :Remove code that is no longer used
782            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
783    
784    2006-08-14  Douglas Bates  <bates@R-project.org>
785    
786            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
787            Csparse_to_logical and Csparse_symmetric_to_general.
788            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
789            coercion methods between CsparseMatrix and TsparseMatrix.
790    
791    2006-08-14  Douglas Bates  <bates@R-project.org>
792    
793            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
794            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
795            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
796            possible.
797    
798    2006-08-12  Douglas Bates  <bates@R-project.org>
799    
800            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
801              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
802              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
803              generalize conversions between TsparseMatrix, CsparseMatrix,
804              denseMatrix and matrix.  Preserve triangularity property and
805              propagate Dimnames in the easy cases.
806    
807    2006-08-10  Douglas Bates  <bates@R-project.org>
808    
809            * src/lmer.c: adjust checks in glmer_init for S4SXP
810            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
811            before S4SXP but for the wrong reasons.
812    
813    2006-08-08  Douglas Bates  <bates@R-project.org>
814    
815            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
816            Later modified to return the upper triangle only.
817            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
818    
819    2006-08-07  Douglas Bates  <bates@R-project.org>
820    
821            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
822            R-level conversion to a sparse symmetric class.
823            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
824            Remove conversion to sparse symmetric classes (now done in C code).
825    
826    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
829            * man/band.Rd:  adapt the \dontshow{} unit test.
830    
831    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * DESCRIPTION (Version): 0.995-14  for CRAN
834    
835            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
836    
837            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
838            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
839    
840            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
841            * R/Tsparse.R (tril, triu, band): methods
842            * R/dgRMatrix.R (tril, ...):    ditto
843            * man/band.Rd:                  ditto
844    
845    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/Matrix.R (head, tail): directly use utils:::head.matrix
848                    to be up-to-date automatically.
849    
850    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
853    
854            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
855            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
856            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
857            such that the S4 objects are always created by the current version
858            of R and 'Matrix' class definitions.
859    
860    2006-08-01  Douglas Bates  <bates@R-project.org>
861    
862            * R/lmer.R (LMEoptimize method), tests/lmer.R,
863            inst/external/test3comp.rda: Added warnings for convergence on
864            boundary and test cases.
865    
866            * src/lmer.c (mer_postVar): Modified to return the variances that
867            are marginal to the fixed effects, not conditional on them (which
868            is what the bVar slot contents represent).
869    
870    2006-07-31  Douglas Bates  <bates@R-project.org>
871    
872            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
873            function which calls the C function mer_hat_trace2.
874    
875            * man/ranef.Rd: Include description of "postVar" argument and
876            producing a caterpillar plot.
877    
878    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * NAMESPACE:    change  "correlation" to "corMatrix"
881            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
882            * R/dpoMatrix.R: ditto
883            * R/lmer.R:      ditto
884    
885    2006-07-28  Douglas Bates  <bates@R-project.org>
886    
887            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
888            RZXinv slot's contents into a separate internal function that can
889            be used in mer_hat_trace.
890    
891    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
894            via new smart
895            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
896            utility functions.
897    
898    
899    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Csparse.R (tril, triu, band): do return *triangular* classed
902            matrices when appropriate; band() even symmetric ones.
903            (replCmat): extend to potentially all "CsparseMatrix"
904            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
905            allow subassignment for special sparse matrices.
906    
907            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
908    
909            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
910            argument; in glmer_*(): print only if(verbose).
911    
912            speed-optimize a few places by moving REAL(.) out of loops.
913    
914            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
915    
916    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
919                    since that wrongly triggers also for M[ logi , ]
920    
921            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
922            a symmetric matrix that results in a non-symmetric one.
923            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
924    
925            * R/dMatrix.R: make round(M) work as round(M, 0)
926    
927            * R/dgTMatrix.R (image): coordinate system and axis now use
928            1-based indices, not 0-based ones.
929    
930            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
931            * tests/indexing.R: test it.
932    
933            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
934            * man/isSymmetric-methods.Rd: and document it.
935    
936            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
937            * man/SparseM-conv.Rd: docu them
938    
939            * tests/other-pkgs.R: renamed from tests/graph.R and add example
940                    for 'SparseM' conversions
941    
942    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
943    
944            * R/Matrix.R (head): added head() and tail() methods.
945    
946    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * DESCRIPTION (Version): 0.995-12 released to CRAN
949    
950    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * tests/simple.R: add check for correct dsT -> dgT coercion;
953                    add check for correct printing of symmetric sparse matrices.
954    
955            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
956            for sparse symmetric matrices.
957    
958            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
959            diagonal twice.
960    
961    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
962    
963            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
964            being applied to the x slot (detected by Brian Ripley).
965    
966    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
969    
970            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
971    
972    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * src/lgCMatrix.c (lgCMatrix_diag): new function
975            * R/lgCMatrix.R (diag): for new method
976    
977            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
978                 ==> construction of illegal "*gTMatrix" via new() should
979                 now be much less easy:
980            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
981    
982            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
983                    directly.
984            * man/Matrix.Rd: documents it.
985    
986    2006-07-06  Douglas Bates  <bates@R-project.org>
987    
988            * src/pedigree.c (pedigree_inbreeding): Correction in
989            initialization.  This function is not currently being used and is
990            not fully tested.
991    
992            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
993            Introduced the glmer class.  Added code for mcmcmsamp on glmer
994            objects.  Modified validity check on pedigree objects to account
995            for nonparallel patterns of missingness of parents.
996    
997            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
998            class.
999    
1000    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/pMatrix.R: coercion pMatrix -> Tsparse
1003    
1004    2006-06-12  Douglas Bates  <bates@R-project.org>
1005    
1006            * DESCRIPTION (Version): 0.995-11 released to CRAN
1007    
1008            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1009            the output from mcmcsamp.
1010    
1011    2006-06-10  Douglas Bates  <bates@R-project.org>
1012    
1013            * R/lmer.R (simulestimate): added C code for calculating the trace
1014            of the hat matrix.
1015    
1016    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1019            classes.
1020            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1021    
1022    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/dgTMatrix.R (colSums): etc. All four of
1025            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1026            all "Matrices".
1027    
1028    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1029    
1030            * R/lmer.R (panel.ci): Add a reference line at zero and a
1031            background grid to the qqmath plot of ranef.lmer.
1032    
1033    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1034    
1035            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1036            grouping factors to be specified in the formula as (1|foo/bar).
1037    
1038    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1039    
1040            * R/lmer.R (findbars and others): Change check of is.numeric to
1041            !is.language to resolve the bug reported by Jacob Wegelin.
1042    
1043            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1044            code to evaluate inbreeding coefficients without calculating T,
1045            based on code in Sargolzaei and Iwaisaki's paper.
1046    
1047    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1048    
1049            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1050            generic and mer methods for isNested and denomDF. This denomDF was
1051            an attempt to emulate that in lme but I don't think that makes
1052            sense.  Use the trace of the hat matrix instead.
1053    
1054    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1055    
1056            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1057            the C code depending on a slot structure that's no longer valid.
1058            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1059    
1060    
1061    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1062    
1063            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1064            of lowerTriMatrix generic and methods to tril (also upper to triu)
1065            and added a general band extractor.
1066    
1067    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1068    
1069            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1070            allowable range with NAs. Added a corresponding check in the
1071            validity check for the pedigree class.
1072    
1073            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1074            crossprod methods now inherits from symmetricMatrix.
1075    
1076    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1077    
1078            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1079            generics lowerTriMatrix and upperTriMatrix along with methods for
1080            the Csparse virtual class.  Also added a C function Csparse_band
1081            that implements these methods by calling cholmod_band.
1082    
1083    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1086            erased when it was NULL.  This led to invalid subselections!
1087    
1088    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1089    
1090            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1091            in method for "t" so as not to lose the unit diagonal property.
1092    
1093    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1094    
1095            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1096            and methods.  This is now an option to the ranef method for the
1097            mer class.
1098    
1099            * src/cs_utils.c: Ensure that the nz component is -1 for a
1100            compressed column-oriented matrix.  Minor formatting cleanup.
1101    
1102            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1103            objects.
1104    
1105    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1108            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1109    
1110    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1111    
1112            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1113            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1114    
1115            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1116            for the dtCMatrix class.
1117    
1118    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1119    
1120            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1121            and methods for it.
1122    
1123    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1126            arguments, such that M %*% 1:6 now works
1127            * Tests/matprod.R: test the above
1128    
1129    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1130    
1131            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1132            the ranef.lmer class.
1133    
1134            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1135            methods to extract the posterior variances from the bVar slot.
1136    
1137    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1138    
1139            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1140            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1141    
1142            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1143            * tests/simple: (extended)
1144    
1145            * R/sparseMatrix.R (isTriangular): now using much improved
1146            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1147    
1148    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1149    
1150            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1151            (problem report from Franklin Parlamis).  This should be done
1152            generally.
1153    
1154    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1155    
1156            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1157            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1158            update the plot methods.
1159    
1160    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1161    
1162            * R/lmer.R (resid and ranef methods):  Added methods for the
1163            "residuals" and "resid" generic but only for linear mixed model
1164            fits.  Changed the ranef method to return a list of data frames so
1165            that the plot methods now work.
1166    
1167    2006-03-16  Douglas Bates  <bates@bates2>
1168    
1169            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1170            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1171    
1172            * DESCRIPTION (Date): New release
1173    
1174    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1177    
1178            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1179            * man/KNex.Rd: and other help files
1180            * tests/*.R: several ones needed adaption
1181            * inst/doc/Comparisons.Rnw: ditto
1182    
1183    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1186    
1187            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1188    
1189    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1190    
1191            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1192    
1193            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1194    
1195    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/dMatrix.R: enable things like  M [ M < 10 ]
1198            * R/dgeMatrix.R: implement it
1199    
1200    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/AllClass.R: define "summary.mer" and "*.lmer"
1203            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1204            * R/lmer.R (show): now works with summary()
1205    
1206    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1209            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1210                    support the above
1211    
1212    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1213    
1214            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1215            Use glmFit$prior.weights for weights in a glmm.
1216            Allow an option usePQL = FALSE to skip the PQL steps for the
1217            Laplace method (and, in time, the AGQ method).
1218    
1219            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1220            into a separate function internal_mer_Xfactor to be able to call
1221            it from internal_bhat.
1222    
1223    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * tests/Class+Meth.R (tstMatrixClass): function for much better
1226            testing; now again of all actual classes.
1227    
1228            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1229                    use macros and define make_d_matrix_* and make_i_matrix_*
1230                    where _i_ is for the ldense routines:
1231    
1232            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1233            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1234    
1235            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1236    
1237    
1238    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1239    
1240            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1241                    many different kinds of matrices.
1242            * R/*.R: quite a few new methods were needed for R CMD check with
1243                    new Matrix().  Very good for users playing around.
1244    
1245    
1246    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * src/dgeMatrix.c (dMatrix_validate): new
1249            * src/Mutils.c (dense_nonpacked_validate): new
1250    
1251            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1252    
1253    
1254    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1255    
1256            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1257    
1258    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1259    
1260            * DESCRIPTION (Version): 0.99-6 released to CRAN
1261    
1262            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1263            segfault in cases with multiple non-nested grouping factors.
1264    
1265    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1266    
1267            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1268                    (Depends): also on 'utils'
1269    
1270            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1271            * R/diagMatrix.R (Diagonal): constructor and methods for
1272            diagonal matrices
1273    
1274            * R/ltTMatrix.R: new "minimal methods"
1275    
1276    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1277    
1278            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1279            all methods (and help files).
1280    
1281    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1284                    for case (dimn.  op  no_dimn.)
1285    
1286    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1287    
1288            * DESCRIPTION (Version): 0.99-2  released to CRAN
1289    
1290    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1291    
1292            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1293            by Julian Faraway.
1294    
1295    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1296    
1297            * R/Auxiliaries.R (try_as): new utility
1298            * R/sparseMatrix.R: use try_as() in coercion to original class
1299    
1300    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1303    
1304    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1305    
1306            * R/Auxiliaries.R (dimNamesCheck): added
1307    
1308            * R/Matrix.R (as.array), (as.vector): new
1309    
1310    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1311    
1312            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1313                    default.
1314            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1315                    "pMatrix" now contains "sparseMatrix"
1316    
1317    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * tests/Class+Meth.R: new tests; t(t(m)) == m
1320    
1321            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1322    
1323            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1324            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1325    
1326            * R/dspMatrix.R: typo in "t" method
1327    
1328    2005-09-18  Douglas Bates  <bates@wisc.edu>
1329    
1330            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1331            * R/Tsparse.R: instead of R/gTMatrix.R
1332            * R/Csparse.R: new
1333            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1334            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1335            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1336                            via cholmod
1337    
1338    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1339    
1340            * R/Auxiliaries.R (non0ind): new function using new C code
1341            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1342    
1343    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1344    
1345            * src/chm_common.h: header file required by all C sources that
1346            call CHOLMOD functions.  It defines a cholmod_common structure
1347            called 'c' whose address is passed as the last argument to
1348            (virtually) every CHOLMOD function.
1349    
1350            * src/Pattern.c: Simple example of the use of CHOLMOD.
1351    
1352            * src/init.c: initialize and finalize the cholmod_common structure.
1353    
1354            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1355            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1356    
1357    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * inst/test-tools.R: new file collecting the utility functions used
1360                    in ./tests/*.R
1361    
1362            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1363            * R/Matrix.R (cbind2): methods for NULL and missing
1364    
1365    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1366    
1367            * R/AllClass.R: new "index" class for "[" and "[<-":
1368                    First cut at "symmetricMatrix" and "triangularMatrix"
1369            * R/gTMatrix.R (.ind.prep): new function;
1370                    Logical and character indexing now work too.
1371            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1372            * tests/indexing.R: new, including *.Rout.save
1373            * tests/dgTMatrix.R: new
1374    
1375    2005-08-29  Douglas Bates  <bates@wisc.edu>
1376    
1377            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1378            indicator pos not being updated.  Also enforced upper triangular
1379            for symmetric case.  Need to coerce edges component of elements of
1380            edge list - grr! (Why don't they define their classes cleanly?)
1381    
1382    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1383    
1384            * R/Matrix.R:  added first "[<-" methods; not yet functional
1385            * R/denseMatrix.R: ditto
1386            * man/Subassign-methods.Rd: new help file for these
1387    
1388    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * DESCRIPTION (Version): 0.98-6
1391    
1392            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1393            matrices.
1394    
1395    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1396    
1397            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1398                    as( <logical>, "matrix")
1399    
1400            * R/pMatrix.R: coercion to "lgTMatrix"
1401    
1402            * R/gTMatrix.R: new virtual class to define "[" methods for.
1403            * man/gTMatrix-class.Rd:
1404            * General slight re-organization of where "[" methods are defined.
1405              more to come.
1406    
1407    2005-08-18  Douglas Bates  <bates@wisc.edu>
1408    
1409            * DESCRIPTION (Version): 0.98-5  released to CRAN
1410    
1411            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1412            * .....
1413    
1414    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1415    
1416            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1417            or glmer objects.
1418    
1419    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1420    
1421            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1422    
1423    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1424    
1425            * R/HBMM.R: finish re-writing R-only code.
1426    
1427    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1428    
1429            * man/externalFormats.Rd: move documentation for writeHB and
1430            writeMM here.
1431    
1432            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1433            (suggested by Paul Roecker).
1434    
1435            * tests/validObj.R (assertError): Comment out test that is failing
1436            after recent changes in r-devel.
1437    
1438    
1439    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1440    
1441            * R/AllClass.R: intermediate virtual class "denseMatrix"
1442            * man/denseMatrix-class.Rd
1443            * NAMESPACE: export it, and also export
1444            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1445    
1446    2005-08-10  Douglas Bates  <bates@wisc.edu>
1447    
1448            * DESCRIPTION (Version): 0.98-3 to CRAN
1449    
1450            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1451            matrix_solve code (which was really, really wrong).
1452    
1453    2005-08-07  Douglas Bates  <bates@wisc.edu>
1454    
1455            * DESCRIPTION (Version): 0.98-2
1456    
1457            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1458    
1459            * R/lmer.R (abbrvNms): new
1460            * R/lmer.R (mcmcsamp): allow transformed parameters
1461            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1462            for the Harwell-Boeing and the MatrixMarket formats.
1463    
1464    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1465    
1466            * man/dtrMatrix-class.Rd: add examples
1467            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1468    
1469            * TODO: note the dtpMatrix (docu) bug
1470    
1471            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1472            in order to ensure that new as.matrix() is used by old functions,
1473            e.g., svd(), qr(), eigen(), dist(),..;
1474                  apply(), also matplot() or pairs().
1475    
1476    
1477    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1478    
1479            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1480              add comments about 'control' / lmerControl() arguments
1481    
1482    2005-07-27  Douglas Bates  <bates@wisc.edu>
1483    
1484            * man/sleepstudy.Rd: Added the sleep data set.
1485            * DESCRIPTION (Version): 0.98-1  released to CRAN
1486    
1487    2005-07-12  Douglas Bates  <bates@wisc.edu>
1488            * man/sleepstudy.Rd: Added the sleep data set.
1489    
1490            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1491            .Call calls that were producing spurious output.
1492    
1493    2005-07-05  Douglas Bates  <bates@wisc.edu>
1494    
1495            * R/lmer.R (lmer): stored updated variance component estimates in
1496            mer object for the generalized model.  (Bug reported by Renaud
1497            Lancelot).
1498    
1499    2005-07-03  Douglas Bates  <bates@wisc.edu>
1500    
1501            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1502            unidimensional case.
1503    
1504    2005-06-08  Douglas Bates  <bates@wisc.edu>
1505    
1506            * DESCRIPTION (Version): 0.96-1
1507    
1508            * moved  lmer-class' R and C code moved from lme4 to here
1509    
1510    2005-06-04  Douglas Bates  <bates@wisc.edu>
1511    
1512            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1513            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1514    
1515    2005-06-02  Douglas Bates  <bates@wisc.edu>
1516    
1517            * src/Makefile.win: Forgot to update this when Makefile changed.
1518    
1519    2005-05-11  Douglas Bates  <bates@wisc.edu>
1520    
1521            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1522            bug reported by Kurt Hornik and Michael Hahsler.
1523    
1524    2005-05-10  Douglas Bates  <bates@wisc.edu>
1525    
1526            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1527            logical sparse matrices.  These will also be used in the symbolic
1528            analysis for lmer objects.
1529    
1530            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1531            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1532    
1533    2005-05-06  Douglas Bates  <bates@wisc.edu>
1534    
1535            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1536            colMeans, colSums, rowMeans and rowSums.
1537    
1538    2005-04-18  Douglas Bates  <bates@wisc.edu>
1539    
1540            * src/lgCMatrix.[ch]: code for _validate method and stub for
1541            multiplication operation.
1542    
1543            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1544            to dgetrs.
1545    
1546            * src/init.c: Fix cut-and-paste error in definition of
1547            dgeMatrix_matrix_solve
1548    
1549            * src/{many files}: Tighten code by using ALLOC_SLOT.
1550    
1551    2005-04-15  Douglas Bates  <bates@wisc.edu>
1552    
1553            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1554    
1555            * DESCRIPTION: Eliminate import of stats.
1556    
1557    
1558    2005-04-06  Douglas Bates  <bates@wisc.edu>
1559    
1560            * R/AllClass.R : add logical sparse matrix classes
1561    
1562    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1563    
1564            * R/dgTMatrix.R: add "[" method for triplet matrices
1565            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1566    
1567    2005-03-31  Douglas Bates  <bates@wisc.edu>
1568    
1569            * DESCRIPTION (Version): release 0.95-5 to CRAN
1570    
1571            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1572            * R/sparseMatrix.R: %*%, crossprod()
1573            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1574            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1575            * src/lmer.c (lmer_fitted): fix thinko
1576    
1577    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1578    
1579            * R/AllClass.R: add two virtual sparse classes ``on top''
1580    
1581    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1582    
1583            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1584                    correspondingly fix examples and tests/ since new()
1585                    doesn't work for virtual classes.
1586    
1587    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1588    
1589            * R/Matrix.R (as.matrix): method and one for unname()
1590            * tests/dpoMatrix.R: tests should now be less platform dependent;
1591              also run for R 2.1.0; using as.matrix()
1592    
1593    2005-03-15  Douglas Bates  <bates@wisc.edu>
1594    
1595            * R/pMatrix.R: "pMatrix" class added
1596            * ....
1597    
1598    2005-03-14  Douglas Bates  <bates@wisc.edu>
1599    
1600            * R/dtpMatrix.R: Add unpack method and an example.
1601    
1602            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1603            of general symmetric matrices and associated S4 methods.
1604    
1605    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1606            +
1607    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1608    
1609            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1610              crossprod() and "%*%" methods added; tests, too.
1611            * tests/matprod.R: new, for testing these
1612    
1613    2005-03-03  Douglas Bates  <bates@wisc.edu>
1614    
1615            * src/lmer.c (lmer_fitted): Added.
1616    
1617    2005-03-02  Douglas Bates  <bates@wisc.edu>
1618    
1619            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1620    
1621    2005-02-28  Douglas Bates  <bates@wisc.edu>
1622    
1623            * src/*.c,po/,inst/po: Internationalization and localization of
1624            the package.
1625    
1626            * src/ldl.[ch]: Removed these as their contents are referenced in the
1627            R_ldl.c file.
1628    
1629            * src/flame.[ch]: Removed these source files.
1630    
1631            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1632    
1633            * src/LU.[ch],src/init.c: absorb in factorizations
1634    
1635            * src/Mutils.h: prepare for internationalization
1636    
1637            * src/cblas.h: move the enum definitions to Mutils.h and remove
1638            this file
1639    
1640    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1641    
1642            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1643    
1644            * R/dtrMatrix.R: fix t() method
1645    
1646            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1647            * NAMESPACE: export them (and import generics from "methods")
1648            * tests/group-methods.R : and test them.
1649    
1650            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1651            border case
1652    
1653    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1654    
1655            * DESCRIPTION (Version): 0.95-2  released to CRAN
1656    
1657            * src/dgBCMatrix.c:
1658            * src/lmer.c: many changes
1659            * ...
1660    
1661    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1662    
1663            * R/Matrix.R: add more sophisticated show() method.
1664    
1665    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1666    
1667            * */* : almost complete reorganization of classes.
1668    
1669    2005-01-26  Douglas Bates  <bates@wisc.edu>
1670    
1671            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1672            for the geMatrix class.
1673    
1674    2005-01-24  Douglas Bates  <bates@wisc.edu>
1675    
1676            * src/Makefile (clean): Remove *.a and *.so
1677    
1678            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1679    
1680    2005-01-23  Douglas Bates  <bates@wisc.edu>
1681    
1682            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1683            had an effect in cases with more than 2 grouping factors.
1684    
1685    2005-01-03  Douglas Bates  <bates@wisc.edu>
1686    
1687            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1688    
1689    2004-12-23  Douglas Bates  <bates@wisc.edu>
1690    
1691            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1692            and R_useDynamicSymbols (suggested by B.D.Ripley).
1693    
1694    2004-12-14  Douglas Bates  <bates@wisc.edu>
1695    
1696            * R/sscMatrix.R: Add determinant methods
1697    
1698            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1699            for tripletMatrix to matrix.
1700    
1701    2004-12-13  Douglas Bates  <bates@wisc.edu>
1702    
1703            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1704            no longer used.
1705    
1706          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1707          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1710 
1710          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1711          Fixes part but not all of #15.          Fixes part but not all of #15.
1712    
1713  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1714    
1715          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1716          scalar grouping factors corrected.          scalar grouping factors corrected.
1717    
1718  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1719    
1720          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1721    
1722  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1723    
1724          * 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
1725          .h file can be included.          .h file can be included.
1726    
1727  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1728    
1729          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1730          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1731    
1732          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1733    
1734  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1735    
1736          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1737    
1738  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1739    
1740          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1741    
1742  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1743    
1744          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1745    
1746  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1747    
1748          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1749    
1750  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1751    
1752          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1753          routines.          routines.
1754    
1755  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1756    
1757          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1758    
1759  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1760    
1761          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1762    

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