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revision 10, Mon Mar 22 20:20:05 2004 UTC revision 1827, Wed Apr 25 22:22:41 2007 UTC
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1    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
4            code that is now part of the R Lapack library.
5    
6            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
7            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
8    
9    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/dgTMatrix.R (mat2dgT): care about NAs
12    
13    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/kronecker.R: triangularity preserving methods
16    
17    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/kronecker.R: new file collecting kronecker() methods in one
20                    place.  Goal: become much faster!
21    
22    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
25            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
26            can be much faster.
27    
28            * tests/matprod.R: add regression tests for these (upper & lower).
29    
30    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (diff): method for our Matrices.
33    
34            * R/sparseMatrix.R (isDiagonal): check dim()!
35    
36    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R (dim<-): new method for "reshape()" built on a
39            proposal from Tamas Papp.
40    
41    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
44    
45            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
46            rather define and export  cBind() and rBind() only.
47            --> useRs *must* change code that used to have cbind()/rbind() !!
48    
49            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
50            * R/bind.Rout.save: ditto
51    
52    2007-02-16  Douglas Bates  <bates@r-project.org>
53    
54            * DESCRIPTION (Date, Version): 0.9975-11 with new date
55            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
56            const modifier on declaration of the array 'valid'
57    
58    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
61    
62    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
65    
66            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
67            * tests/simple.R: test the above and some of these coercions:
68    
69            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
70                    be careful to avoid infinite recursion, using new coercions in
71            * R/ngCMatrix.R and nsC... and ntC...
72            * R/lsparseMatrix.R: ditto
73    
74            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
75    
76            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
77            * R/Rsparse.R: reactivate .Call()s
78    
79            * tests/Class+Meth.R: a bit more on actual classes
80    
81    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
84    
85    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * DESCRIPTION (Version): 0.9975-10 to upload
88    
89            * tests/Class+Meth.R (tstMatrixClass): require coercions to
90            specific classes less unconditionally.
91    
92            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
93    
94            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
95    
96            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
97            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
98            R_to_CMatrix segfaults on one platform.
99            Eliminate most coercion method to *specific* classes, and replace
100            with virtual classes coercions.
101    
102    
103    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
104    
105            * src/init.c: export the CHM...._validate() placeholders, since
106            they *are* called.
107    
108            * tests/Class+Meth.R (classCanCoerce): and starting to test
109            all as(<from>, <to>)
110    
111    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
114            * tests/indexing.R: tested now
115            * tests/indexing.Rout.save: updated
116    
117            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
118            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
119            appropriate.
120    
121            * NAMESPACE: export a trivial
122            * R/Matrix.R: drop() Matrix-method
123    
124            * R/AllClass.R: moved all prototypes to virtual super classes.
125    
126            * R/Rsparse.R: many more coercions to have less exceptions in
127            * tests/Class+Meth.R:
128    
129            * R/Ops.R (Compare): tweak for case with NA
130            * tests/simpl.R: hence another 'FIXME' eliminated
131    
132    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
135            objects.
136    
137            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
138              and more of "!", "&", "|", all, any; coercions
139    
140            * R/Rsparse.R: many coercions (which enable quite a few other
141            methods), thanks to enhancements in
142            * src/dgCMatrix.c (R_to_CMatrix): new, and
143            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
144            symmetric & triangular and ..RMatrix objects.
145    
146            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
147            renamed file from src/dsTMatrix.c;
148            now dealing with symmetric and triangular Tsparse coercions, both
149            to dense and general.
150    
151    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
154    
155            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
156            where sensible when the <numeric> is of length > 1.
157    
158    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Matrix.R ([<-): for M[] <- value: fix length
161    
162    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
165            * R/ndenseMatrix.R: new coercions n* -> l*
166    
167    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
170    
171            * R/Ops.R ("Logic"): and other "Ops", many updates
172    
173    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * src/Mutils.h (SET_DimNames): new utility
176    
177            * R/Auxiliaries.R (nnzero): improved and now exported via
178    
179            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
180    
181    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/diagMatrix.R (!): fix typo.
184    
185    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Auxiliaries.R (as_Csparse): and quite a few others:
188                    allow to pass class definition --> speedup
189            * R/sparseMatrix.R: apply the above
190    
191            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
192    
193            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
194            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
195            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
196    
197            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
198    
199            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
200            and use it for "sparse*" as well, since it's faster than the
201            as_Csparse(.) way.
202    
203    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
206    
207    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
210            as method for   M[ ij ] <- v
211            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
212    
213            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
214            FALSE answer
215    
216            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
217            * tests/indexing.R: test it, and some of the above
218    
219    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Auxiliaries.R (is_duplicatedT): new utility
222    
223    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * src/init.c (R_init_Matrix): export cholmod_scale
226    
227    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
230            base::as.matrix to (x, ...)
231    
232    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
235            file; start using "Logic", hence
236    
237            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
238            * NAMESPACE: import and export "Logic"
239    
240    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
243            only needed previously to R version 2.5.0.
244    
245    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
248    
249            * R/Tsparse.R (replTmat): fix subassignment of triangular
250            * R/Csparse.R (replCmat): ditto
251            * tests/indexing.R: more tests, incl the above fix
252    
253    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Auxiliaries.R (drop0): extend for non CSparse
256            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
257    
258            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
259                    use uplo correctly (!); other places: use uplo_P() macro
260    
261            * R/Csparse.R (replCmat): call diagU2N() when needed
262            * R/Tsparse.R (replTmat): ditto
263    
264            * src/dtCMatrix.c (tCMatrix_validate): new
265            * src/dtTMatrix.c (tTMatrix_validate): new, used in
266            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
267    
268            * R/diagMatrix.R (replDiag): to use in [<-
269    
270    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
273                    also more general diagU2N().
274    
275    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
278            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
279    
280    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * tests/bind.R: a few more cases
283            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
284    
285            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
286            * R/ddenseMatrix.R (cbind2/rbind2)
287            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
288            * tests/indexing.R
289            * tests/indexing.Rout.save: updated
290    
291    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
294            * tests/indexing.R
295    
296    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
299            align with proper position of "0", i.e., right for integers.
300            argument 'align' by default is "fancy".
301    
302    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
305            * R/Csparse.R: and fix "Compare" for more cases.
306            * tests/Class+Meth.R: test some of these (m == m, m != m)
307    
308    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/lsparseMatrix.R: all() and any() methods
311            * R/ldenseMatrix.R:      ditto
312            * NAMESPACE, R/Matrix.R: ditto
313    
314            * man/all-methods.Rd: document them minimally
315    
316            * tests/simple.R: add a few examples for these
317    
318    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R ([): fix long standing typo in symmetric case
321            * man/dsCMatrix-class.Rd: add example exhibiting the above case
322    
323    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
326            to LL before converting to a sparse matrix. (The LDL form can be
327            converted to a sparse matrix but it is implicitly a unit
328            triangular matrix and a diagonal matrix overwritten on the diagonal.)
329    
330    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
333    
334    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * DESCRIPTION (Version): updated -> release 0.9975-7
337            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
338    
339    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
342    
343    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
346            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
347            is exactly singular.
348    
349    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Date): updated -> release 0.9975-6
352    
353    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
356            now returns symmetric.
357    
358            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
359    
360            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
361            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
362    
363            * R/Auxiliaries.R (.type.kind): added
364    
365    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
368            running src/CSparse_install.sh
369    
370            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
371    
372    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
375            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
376    
377            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
378    
379            * tests/Class+Meth.R (tstMatrixClass): now assure
380            the (important in method programming) property :
381    
382                    ###>>  Every "Matrix" is either
383                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
384    
385                    (where "*" stands for "Matrix")
386    
387            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
388    
389            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
390            * tests/validObj.R: checks for "comparison"
391    
392            * R/sparseMatrix.R ([): improved indexing for sparse;
393                    trying to keep <symmetric>[ n, n] symmmetric
394    
395            * tests/indexing.R: indexing for logical sparse now ok
396    
397    
398    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/Tsparse.c: use xTsparse_validate() , and hence remove
401    
402            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
403    
404    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
407    
408            * tests/simple.R: validObject() checking the above.
409    
410            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
411            replacing both dgCMatrix_validate and lgCM*.
412    
413            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
414            fix dimnames setting in other places.
415            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
416    
417    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
420    
421            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
422            symmetry test, via
423            * R/Auxiliaries.R (.as.dgC.0.factors):
424    
425    2006-11-01  Douglas Bates  <bates@r-project.org>
426    
427            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
428            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
429            <CsparseMatrix>) added
430    
431    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * tests/matprod.R: add a variation of Harri's example
434    
435            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
436            recursive infinitely.
437    
438            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
439    
440            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
441    
442    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
445            matrix if possible; test m+m == 2*m; now test dgRMatrix.
446            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
447            satisfy the above test.
448    
449    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
452    
453            * R/dgCMatrix.R: solve(a, b="missing") based on
454            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
455            RHS = NULL.
456    
457            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
458            add more (needed) [t]crossprod() methods.
459    
460            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
461    
462            * R/Auxiliaries.R (as_CspClass): cleanup
463            (drop0): internal utility for "Csparse_drop(*, 0)"
464            (.bail.out.2): encourage active feedback
465    
466    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/dMatrix.R(Compare): new(), then slots [no validity check]
469    
470            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
471            non-valid or 'sorted' case).
472    
473            * R/dsparseMatrix.R: add "chol" method.
474            * R/ddenseMatrix.R: ditto
475    
476            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
477            * NAMESPACE (Ops)
478            * R/diagMatrix.R (diag2T): simple utility used "higher level"
479            coercion; deprecating direct lower level coercions.
480    
481            * R/*.R (seq): use seq_len() and seq_along() where possible.
482    
483    
484    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * DESCRIPTION (Version): 0.9975-5 ready for release
487    
488    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
491    
492    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/AllClass.R (corMatrix): add 'validity' check;
495                    comment out unused "LDL" class definition
496            * NAMESPACE: mention, but do not export "LDL" class
497            * R/corMatrix.R: new (simple), needed for R-devel with
498            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
499              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
500    
501    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
504            use Rprintf and R's error handling.
505    
506    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
509            * tests/matprod.R: add tests for the bug fixed.
510    
511    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
512    
513            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
514            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
515    
516    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
517    
518            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
519    
520    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * DESCRIPTION (Version): 0.9975-3
523    
524            * R/diagMatrix.R (bdiag): new function constructing block diagonal
525            (sparse) matrices.
526            * man/bdiag.Rd: docu + examples
527    
528            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
529    
530            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
531            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
532    
533            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
534            that result is sparse or diagonal (and not dense).
535    
536            * man/Subassign-methods.Rd: fix examples
537    
538            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
539            should always return a sparse (and not sometimes a diagonal) matrix.
540    
541    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
544    
545    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
546    
547            * DESCRIPTION (Version): 0.9975-2
548    
549            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
550    
551    2006-10-02  Douglas Bates  <bates@R-project.org>
552    
553            * tests/dg_Matrix.R: Simplify test taking into account new code.
554    
555    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
558    
559            * R/lsTMatrix.R: new files w/ missing methods
560            * R/nsTMatrix.R:  "  'for completeness'
561    
562            * tests/Class+Meth.R: a bit less 'not.ok.classes'
563    
564            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
565    
566    
567    2006-09-28  Douglas Bates  <bates@R-project.org>
568    
569            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
570            included.
571    
572            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
573            Export C-callable functions used in Zt_create in lme4.
574    
575    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.9975-1
578    
579            * tests/simple.R: less checks fail; using NA, found that our
580                    kronecker() is not base-compatible with NA's.
581    
582            * R/dMatrix.R: "Compare" method now implemented for all cases
583    
584            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
585    
586            * man/dtpMatrix-class.Rd: mention length of 'x' slot
587    
588            * src/dtpMatrix.c (dtpMatrix_validate): fix check
589            * src/dspMatrix.c (dspMatrix_validate): ditto
590    
591            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
592              including coercion to [nl]tTMatrix.
593    
594            * R/diagMatrix.R (show): print a header line as for other classes.
595    
596    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/Makefile.win (SUBDIRS): fix typo
599    
600    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
603    
604    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
605    
606            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
607            symmetric and y missing in R code using %*% (cholmod_aat doesn't
608            accept a symmetric matrix).
609            * tests/group-methods.R: Uncomment test of crossprod applied to
610            lsCMatrix objects.
611    
612    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/AllClass.R (symmetricMatrix): add validity method (available
615            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
616    
617            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
618    
619            * tests/indexing.Rout.save:
620            * tests/indexing.R: additions, mainly for 'lsparse'
621    
622            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
623            case.
624    
625            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
626    
627    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
630                    as 'N' (1-letter - Ok?)
631    
632            * tests/group-methods.R: add test for logical + NAs
633    
634            * R/dMatrix.R ("Compare"): fix to work with NA's
635    
636            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
637    
638            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
639                    which is implemented.
640    
641    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * src/chm_common.c: coerce logical <-> double instead of
644            typecasting;  needed for "l" matrix handling in cholmod.
645    
646            * tests/other-pkgs.R (graph): small extension in "graph" checks.
647    
648            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
649            (Tsp2grNEL): other fixes needed
650    
651    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
654                    Matrices, since "lMatrix", also "lsparseM" can have NA
655            * R/ndenseMatrix.R, etc: new source files
656            * man/nsparseMatrix-classes.Rd, etc: new help files
657            * tests/: adaptions
658            * src/chm_common.c (chm_dense_to_SEXP): and others:
659                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
660            * src/Csparse.c, etc: ditto
661    
662    2006-09-11  Douglas Bates  <bates@R-project.org>
663    
664            * src/Mutils.[ch],init.c inst/include/*.h: Move the
665            alloc_d**Matrix functions to the lme4 package.
666    
667    2006-09-09  Douglas Bates  <bates@R-project.org>
668    
669            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
670            fixed
671    
672    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/lMatrix.R: new
675    
676            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
677    
678            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
679            * man/tcrossprod.Rd: ditto
680    
681    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
684            for exported functions
685            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
686            Remove partitioning algorithms for sparse matrix reordering.  The
687            copyright on the Metis code was problematic and the methods were
688            rarely used.
689            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
690            operations are now done entirely in CHOLMOD code.
691    
692    2006-09-06  Douglas Bates  <bates@R-project.org>
693    
694            * src/Mutils.h: Remove functions that are no longer used.
695    
696    2006-09-04  Douglas Bates  <bates@R-project.org>
697    
698            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
699            * src/DEPS.mkf: update
700    
701    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * created branches/Matrix-for-R-2.3.x;  on trunk: do
704            * DESCRIPTION (Version): 0.9975-0
705            (Depends): R (>= 2.4.0)
706    
707    2006-09-01  Douglas Bates  <bates@R-project.org>
708    
709            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
710    
711    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
714            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
715    
716            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
717    
718    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
721            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
722            * R/dsparseMatrix.R: ditto
723            * R/Csparse.R: ditto
724    
725    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dMatrix.R (Compare): improve availability of "<", etc
728            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
729    
730    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
733            of a 0-index which was used as 1-index (..hmm)
734    
735            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
736    
737            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
738            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
739            (.is.diagonal): ditto
740    
741            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
742    
743            * R/Matrix.R (Matrix): also work for NA data
744    
745    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
748            in all cases.
749    
750    2006-08-27  Douglas Bates  <bates@R-project.org>
751    
752            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
753            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
754    
755    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
758            subclasses of "ddenseMatrix"
759            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
760            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
761            instead of half dozen specialized ones.
762    
763    2006-08-25  Douglas Bates  <bates@R-project.org>
764    
765            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
766            <tillard@cirad.fr> - ordering standard errors to match effects.
767    
768    2006-08-24  Douglas Bates  <bates@R-project.org>
769    
770            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
771            on R_ldl.
772            * R/lCholCMatrix.R,
773            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
774            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
775            * many files in ./R and ./src: Use more general version of
776            dup_mMatrix_as_dgeMatrix to simplify method definitions.
777            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
778            dtpMatrix, dspMatrix and dppMatrix conversions.
779    
780    
781    2006-08-23  Douglas Bates  <bates@R-project.org>
782    
783            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
784            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
785            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
786            dgeMatrix_crossprod (may need to do this in other places).
787            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
788            generic and method for dsCMatrix.  Use CHOLMOD for chol().
789    
790    2006-08-22  Douglas Bates  <bates@R-project.org>
791    
792            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
793            types of classed Matrices, matrices or numeric or logical vectors.
794            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
795            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
796            to Mutils.h (as an inline) and change name to Matrix_check_class;
797            fixes in as_cholmod_factor and chm_factor_to_SEXP.
798            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
799            dsCMatrix_matrix_solve.  Comment out vestigial functions.
800            * src/Csparse.c: use diag_P and uplo_P macros.
801    
802    2006-08-21  Douglas Bates  <bates@R-project.org>
803    
804            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
805            valgrind.
806            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
807            inverses.
808            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
809            -Wall warnings.
810            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
811            Use dup_mMatrix_as_dgeMatrix.
812    
813    2006-08-20  Douglas Bates  <bates@R-project.org>
814    
815            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
816            * tests/sparseQR.R: Added
817            * man/sparseQR-class.Rd: Document methods for qr.* generics
818            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
819    
820    2006-08-19  Douglas Bates  <bates@R-project.org>
821    
822            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
823            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
824            and qr.fitted.
825            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
826            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
827    
828    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
831            the base version has no "..." argument.
832    
833            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
834    
835            * R/Matrix.R: define and
836            * NAMESPACE: export as.numeric() and as.logical() methods.
837                    Let's hope these do not badly slow down something...
838            Finally export the zapsmall() method.
839    
840    2006-08-17  Douglas Bates  <bates@R-project.org>
841    
842            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
843            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
844            * src/dtCMatrix.c :Remove code that is no longer used
845            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
846    
847    2006-08-14  Douglas Bates  <bates@R-project.org>
848    
849            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
850            Csparse_to_logical and Csparse_symmetric_to_general.
851            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
852            coercion methods between CsparseMatrix and TsparseMatrix.
853    
854    2006-08-14  Douglas Bates  <bates@R-project.org>
855    
856            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
857            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
858            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
859            possible.
860    
861    2006-08-12  Douglas Bates  <bates@R-project.org>
862    
863            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
864              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
865              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
866              generalize conversions between TsparseMatrix, CsparseMatrix,
867              denseMatrix and matrix.  Preserve triangularity property and
868              propagate Dimnames in the easy cases.
869    
870    2006-08-10  Douglas Bates  <bates@R-project.org>
871    
872            * src/lmer.c: adjust checks in glmer_init for S4SXP
873            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
874            before S4SXP but for the wrong reasons.
875    
876    2006-08-08  Douglas Bates  <bates@R-project.org>
877    
878            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
879            Later modified to return the upper triangle only.
880            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
881    
882    2006-08-07  Douglas Bates  <bates@R-project.org>
883    
884            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
885            R-level conversion to a sparse symmetric class.
886            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
887            Remove conversion to sparse symmetric classes (now done in C code).
888    
889    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
892            * man/band.Rd:  adapt the \dontshow{} unit test.
893    
894    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * DESCRIPTION (Version): 0.995-14  for CRAN
897    
898            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
899    
900            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
901            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
902    
903            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
904            * R/Tsparse.R (tril, triu, band): methods
905            * R/dgRMatrix.R (tril, ...):    ditto
906            * man/band.Rd:                  ditto
907    
908    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * R/Matrix.R (head, tail): directly use utils:::head.matrix
911                    to be up-to-date automatically.
912    
913    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
916    
917            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
918            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
919            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
920            such that the S4 objects are always created by the current version
921            of R and 'Matrix' class definitions.
922    
923    2006-08-01  Douglas Bates  <bates@R-project.org>
924    
925            * R/lmer.R (LMEoptimize method), tests/lmer.R,
926            inst/external/test3comp.rda: Added warnings for convergence on
927            boundary and test cases.
928    
929            * src/lmer.c (mer_postVar): Modified to return the variances that
930            are marginal to the fixed effects, not conditional on them (which
931            is what the bVar slot contents represent).
932    
933    2006-07-31  Douglas Bates  <bates@R-project.org>
934    
935            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
936            function which calls the C function mer_hat_trace2.
937    
938            * man/ranef.Rd: Include description of "postVar" argument and
939            producing a caterpillar plot.
940    
941    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * NAMESPACE:    change  "correlation" to "corMatrix"
944            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
945            * R/dpoMatrix.R: ditto
946            * R/lmer.R:      ditto
947    
948    2006-07-28  Douglas Bates  <bates@R-project.org>
949    
950            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
951            RZXinv slot's contents into a separate internal function that can
952            be used in mer_hat_trace.
953    
954    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
957            via new smart
958            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
959            utility functions.
960    
961    
962    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * R/Csparse.R (tril, triu, band): do return *triangular* classed
965            matrices when appropriate; band() even symmetric ones.
966            (replCmat): extend to potentially all "CsparseMatrix"
967            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
968            allow subassignment for special sparse matrices.
969    
970            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
971    
972            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
973            argument; in glmer_*(): print only if(verbose).
974    
975            speed-optimize a few places by moving REAL(.) out of loops.
976    
977            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
978    
979    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
982                    since that wrongly triggers also for M[ logi , ]
983    
984            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
985            a symmetric matrix that results in a non-symmetric one.
986            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
987    
988            * R/dMatrix.R: make round(M) work as round(M, 0)
989    
990            * R/dgTMatrix.R (image): coordinate system and axis now use
991            1-based indices, not 0-based ones.
992    
993            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
994            * tests/indexing.R: test it.
995    
996            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
997            * man/isSymmetric-methods.Rd: and document it.
998    
999            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1000            * man/SparseM-conv.Rd: docu them
1001    
1002            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1003                    for 'SparseM' conversions
1004    
1005    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1006    
1007            * R/Matrix.R (head): added head() and tail() methods.
1008    
1009    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * DESCRIPTION (Version): 0.995-12 released to CRAN
1012    
1013    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * tests/simple.R: add check for correct dsT -> dgT coercion;
1016                    add check for correct printing of symmetric sparse matrices.
1017    
1018            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1019            for sparse symmetric matrices.
1020    
1021            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1022            diagonal twice.
1023    
1024    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1025    
1026            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1027            being applied to the x slot (detected by Brian Ripley).
1028    
1029    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1032    
1033            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1034    
1035    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * src/lgCMatrix.c (lgCMatrix_diag): new function
1038            * R/lgCMatrix.R (diag): for new method
1039    
1040            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1041                 ==> construction of illegal "*gTMatrix" via new() should
1042                 now be much less easy:
1043            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1044    
1045            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1046                    directly.
1047            * man/Matrix.Rd: documents it.
1048    
1049    2006-07-06  Douglas Bates  <bates@R-project.org>
1050    
1051            * src/pedigree.c (pedigree_inbreeding): Correction in
1052            initialization.  This function is not currently being used and is
1053            not fully tested.
1054    
1055            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1056            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1057            objects.  Modified validity check on pedigree objects to account
1058            for nonparallel patterns of missingness of parents.
1059    
1060            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1061            class.
1062    
1063    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/pMatrix.R: coercion pMatrix -> Tsparse
1066    
1067    2006-06-12  Douglas Bates  <bates@R-project.org>
1068    
1069            * DESCRIPTION (Version): 0.995-11 released to CRAN
1070    
1071            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1072            the output from mcmcsamp.
1073    
1074    2006-06-10  Douglas Bates  <bates@R-project.org>
1075    
1076            * R/lmer.R (simulestimate): added C code for calculating the trace
1077            of the hat matrix.
1078    
1079    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1082            classes.
1083            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1084    
1085    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/dgTMatrix.R (colSums): etc. All four of
1088            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1089            all "Matrices".
1090    
1091    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1092    
1093            * R/lmer.R (panel.ci): Add a reference line at zero and a
1094            background grid to the qqmath plot of ranef.lmer.
1095    
1096    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1097    
1098            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1099            grouping factors to be specified in the formula as (1|foo/bar).
1100    
1101    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1102    
1103            * R/lmer.R (findbars and others): Change check of is.numeric to
1104            !is.language to resolve the bug reported by Jacob Wegelin.
1105    
1106            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1107            code to evaluate inbreeding coefficients without calculating T,
1108            based on code in Sargolzaei and Iwaisaki's paper.
1109    
1110    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1111    
1112            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1113            generic and mer methods for isNested and denomDF. This denomDF was
1114            an attempt to emulate that in lme but I don't think that makes
1115            sense.  Use the trace of the hat matrix instead.
1116    
1117    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1120            the C code depending on a slot structure that's no longer valid.
1121            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1122    
1123    
1124    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1125    
1126            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1127            of lowerTriMatrix generic and methods to tril (also upper to triu)
1128            and added a general band extractor.
1129    
1130    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1131    
1132            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1133            allowable range with NAs. Added a corresponding check in the
1134            validity check for the pedigree class.
1135    
1136            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1137            crossprod methods now inherits from symmetricMatrix.
1138    
1139    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1140    
1141            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1142            generics lowerTriMatrix and upperTriMatrix along with methods for
1143            the Csparse virtual class.  Also added a C function Csparse_band
1144            that implements these methods by calling cholmod_band.
1145    
1146    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1149            erased when it was NULL.  This led to invalid subselections!
1150    
1151    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1152    
1153            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1154            in method for "t" so as not to lose the unit diagonal property.
1155    
1156    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1157    
1158            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1159            and methods.  This is now an option to the ranef method for the
1160            mer class.
1161    
1162            * src/cs_utils.c: Ensure that the nz component is -1 for a
1163            compressed column-oriented matrix.  Minor formatting cleanup.
1164    
1165            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1166            objects.
1167    
1168    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1171            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1172    
1173    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1174    
1175            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1176            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1177    
1178            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1179            for the dtCMatrix class.
1180    
1181    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1182    
1183            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1184            and methods for it.
1185    
1186    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1189            arguments, such that M %*% 1:6 now works
1190            * Tests/matprod.R: test the above
1191    
1192    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1193    
1194            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1195            the ranef.lmer class.
1196    
1197            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1198            methods to extract the posterior variances from the bVar slot.
1199    
1200    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1203            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1204    
1205            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1206            * tests/simple: (extended)
1207    
1208            * R/sparseMatrix.R (isTriangular): now using much improved
1209            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1210    
1211    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1212    
1213            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1214            (problem report from Franklin Parlamis).  This should be done
1215            generally.
1216    
1217    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1218    
1219            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1220            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1221            update the plot methods.
1222    
1223    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225            * R/lmer.R (resid and ranef methods):  Added methods for the
1226            "residuals" and "resid" generic but only for linear mixed model
1227            fits.  Changed the ranef method to return a list of data frames so
1228            that the plot methods now work.
1229    
1230    2006-03-16  Douglas Bates  <bates@bates2>
1231    
1232            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1233            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1234    
1235            * DESCRIPTION (Date): New release
1236    
1237    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1240    
1241            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1242            * man/KNex.Rd: and other help files
1243            * tests/*.R: several ones needed adaption
1244            * inst/doc/Comparisons.Rnw: ditto
1245    
1246    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1249    
1250            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1251    
1252    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1253    
1254            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1255    
1256            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1257    
1258    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1259    
1260            * R/dMatrix.R: enable things like  M [ M < 10 ]
1261            * R/dgeMatrix.R: implement it
1262    
1263    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1264    
1265            * R/AllClass.R: define "summary.mer" and "*.lmer"
1266            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1267            * R/lmer.R (show): now works with summary()
1268    
1269    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1272            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1273                    support the above
1274    
1275    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1276    
1277            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1278            Use glmFit$prior.weights for weights in a glmm.
1279            Allow an option usePQL = FALSE to skip the PQL steps for the
1280            Laplace method (and, in time, the AGQ method).
1281    
1282            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1283            into a separate function internal_mer_Xfactor to be able to call
1284            it from internal_bhat.
1285    
1286    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1287    
1288            * tests/Class+Meth.R (tstMatrixClass): function for much better
1289            testing; now again of all actual classes.
1290    
1291            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1292                    use macros and define make_d_matrix_* and make_i_matrix_*
1293                    where _i_ is for the ldense routines:
1294    
1295            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1296            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1297    
1298            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1299    
1300    
1301    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1302    
1303            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1304                    many different kinds of matrices.
1305            * R/*.R: quite a few new methods were needed for R CMD check with
1306                    new Matrix().  Very good for users playing around.
1307    
1308    
1309    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1310    
1311            * src/dgeMatrix.c (dMatrix_validate): new
1312            * src/Mutils.c (dense_nonpacked_validate): new
1313    
1314            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1315    
1316    
1317    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1318    
1319            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1320    
1321    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1322    
1323            * DESCRIPTION (Version): 0.99-6 released to CRAN
1324    
1325            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1326            segfault in cases with multiple non-nested grouping factors.
1327    
1328    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1331                    (Depends): also on 'utils'
1332    
1333            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1334            * R/diagMatrix.R (Diagonal): constructor and methods for
1335            diagonal matrices
1336    
1337            * R/ltTMatrix.R: new "minimal methods"
1338    
1339    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1340    
1341            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1342            all methods (and help files).
1343    
1344    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1345    
1346            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1347                    for case (dimn.  op  no_dimn.)
1348    
1349    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1350    
1351            * DESCRIPTION (Version): 0.99-2  released to CRAN
1352    
1353    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1354    
1355            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1356            by Julian Faraway.
1357    
1358    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360            * R/Auxiliaries.R (try_as): new utility
1361            * R/sparseMatrix.R: use try_as() in coercion to original class
1362    
1363    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1364    
1365            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1366    
1367    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
1369            * R/Auxiliaries.R (dimNamesCheck): added
1370    
1371            * R/Matrix.R (as.array), (as.vector): new
1372    
1373    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1376                    default.
1377            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1378                    "pMatrix" now contains "sparseMatrix"
1379    
1380    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
1382            * tests/Class+Meth.R: new tests; t(t(m)) == m
1383    
1384            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1385    
1386            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1387            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1388    
1389            * R/dspMatrix.R: typo in "t" method
1390    
1391    2005-09-18  Douglas Bates  <bates@wisc.edu>
1392    
1393            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1394            * R/Tsparse.R: instead of R/gTMatrix.R
1395            * R/Csparse.R: new
1396            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1397            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1398            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1399                            via cholmod
1400    
1401    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * R/Auxiliaries.R (non0ind): new function using new C code
1404            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1405    
1406    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1407    
1408            * src/chm_common.h: header file required by all C sources that
1409            call CHOLMOD functions.  It defines a cholmod_common structure
1410            called 'c' whose address is passed as the last argument to
1411            (virtually) every CHOLMOD function.
1412    
1413            * src/Pattern.c: Simple example of the use of CHOLMOD.
1414    
1415            * src/init.c: initialize and finalize the cholmod_common structure.
1416    
1417            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1418            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1419    
1420    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1421    
1422            * inst/test-tools.R: new file collecting the utility functions used
1423                    in ./tests/*.R
1424    
1425            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1426            * R/Matrix.R (cbind2): methods for NULL and missing
1427    
1428    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * R/AllClass.R: new "index" class for "[" and "[<-":
1431                    First cut at "symmetricMatrix" and "triangularMatrix"
1432            * R/gTMatrix.R (.ind.prep): new function;
1433                    Logical and character indexing now work too.
1434            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1435            * tests/indexing.R: new, including *.Rout.save
1436            * tests/dgTMatrix.R: new
1437    
1438    2005-08-29  Douglas Bates  <bates@wisc.edu>
1439    
1440            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1441            indicator pos not being updated.  Also enforced upper triangular
1442            for symmetric case.  Need to coerce edges component of elements of
1443            edge list - grr! (Why don't they define their classes cleanly?)
1444    
1445    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * R/Matrix.R:  added first "[<-" methods; not yet functional
1448            * R/denseMatrix.R: ditto
1449            * man/Subassign-methods.Rd: new help file for these
1450    
1451    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1452    
1453            * DESCRIPTION (Version): 0.98-6
1454    
1455            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1456            matrices.
1457    
1458    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1459    
1460            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1461                    as( <logical>, "matrix")
1462    
1463            * R/pMatrix.R: coercion to "lgTMatrix"
1464    
1465            * R/gTMatrix.R: new virtual class to define "[" methods for.
1466            * man/gTMatrix-class.Rd:
1467            * General slight re-organization of where "[" methods are defined.
1468              more to come.
1469    
1470    2005-08-18  Douglas Bates  <bates@wisc.edu>
1471    
1472            * DESCRIPTION (Version): 0.98-5  released to CRAN
1473    
1474            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1475            * .....
1476    
1477    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1478    
1479            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1480            or glmer objects.
1481    
1482    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1483    
1484            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1485    
1486    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1487    
1488            * R/HBMM.R: finish re-writing R-only code.
1489    
1490    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1491    
1492            * man/externalFormats.Rd: move documentation for writeHB and
1493            writeMM here.
1494    
1495            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1496            (suggested by Paul Roecker).
1497    
1498            * tests/validObj.R (assertError): Comment out test that is failing
1499            after recent changes in r-devel.
1500    
1501    
1502    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1503    
1504            * R/AllClass.R: intermediate virtual class "denseMatrix"
1505            * man/denseMatrix-class.Rd
1506            * NAMESPACE: export it, and also export
1507            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1508    
1509    2005-08-10  Douglas Bates  <bates@wisc.edu>
1510    
1511            * DESCRIPTION (Version): 0.98-3 to CRAN
1512    
1513            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1514            matrix_solve code (which was really, really wrong).
1515    
1516    2005-08-07  Douglas Bates  <bates@wisc.edu>
1517    
1518            * DESCRIPTION (Version): 0.98-2
1519    
1520            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1521    
1522            * R/lmer.R (abbrvNms): new
1523            * R/lmer.R (mcmcsamp): allow transformed parameters
1524            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1525            for the Harwell-Boeing and the MatrixMarket formats.
1526    
1527    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1528    
1529            * man/dtrMatrix-class.Rd: add examples
1530            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1531    
1532            * TODO: note the dtpMatrix (docu) bug
1533    
1534            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1535            in order to ensure that new as.matrix() is used by old functions,
1536            e.g., svd(), qr(), eigen(), dist(),..;
1537                  apply(), also matplot() or pairs().
1538    
1539    
1540    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1541    
1542            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1543              add comments about 'control' / lmerControl() arguments
1544    
1545    2005-07-27  Douglas Bates  <bates@wisc.edu>
1546    
1547            * man/sleepstudy.Rd: Added the sleep data set.
1548            * DESCRIPTION (Version): 0.98-1  released to CRAN
1549    
1550    2005-07-12  Douglas Bates  <bates@wisc.edu>
1551            * man/sleepstudy.Rd: Added the sleep data set.
1552    
1553            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1554            .Call calls that were producing spurious output.
1555    
1556    2005-07-05  Douglas Bates  <bates@wisc.edu>
1557    
1558            * R/lmer.R (lmer): stored updated variance component estimates in
1559            mer object for the generalized model.  (Bug reported by Renaud
1560            Lancelot).
1561    
1562    2005-07-03  Douglas Bates  <bates@wisc.edu>
1563    
1564            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1565            unidimensional case.
1566    
1567    2005-06-08  Douglas Bates  <bates@wisc.edu>
1568    
1569            * DESCRIPTION (Version): 0.96-1
1570    
1571            * moved  lmer-class' R and C code moved from lme4 to here
1572    
1573    2005-06-04  Douglas Bates  <bates@wisc.edu>
1574    
1575            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1576            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1577    
1578    2005-06-02  Douglas Bates  <bates@wisc.edu>
1579    
1580            * src/Makefile.win: Forgot to update this when Makefile changed.
1581    
1582    2005-05-11  Douglas Bates  <bates@wisc.edu>
1583    
1584            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1585            bug reported by Kurt Hornik and Michael Hahsler.
1586    
1587    2005-05-10  Douglas Bates  <bates@wisc.edu>
1588    
1589            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1590            logical sparse matrices.  These will also be used in the symbolic
1591            analysis for lmer objects.
1592    
1593            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1594            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1595    
1596    2005-05-06  Douglas Bates  <bates@wisc.edu>
1597    
1598            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1599            colMeans, colSums, rowMeans and rowSums.
1600    
1601    2005-04-18  Douglas Bates  <bates@wisc.edu>
1602    
1603            * src/lgCMatrix.[ch]: code for _validate method and stub for
1604            multiplication operation.
1605    
1606            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1607            to dgetrs.
1608    
1609            * src/init.c: Fix cut-and-paste error in definition of
1610            dgeMatrix_matrix_solve
1611    
1612            * src/{many files}: Tighten code by using ALLOC_SLOT.
1613    
1614    2005-04-15  Douglas Bates  <bates@wisc.edu>
1615    
1616            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1617    
1618            * DESCRIPTION: Eliminate import of stats.
1619    
1620    
1621    2005-04-06  Douglas Bates  <bates@wisc.edu>
1622    
1623            * R/AllClass.R : add logical sparse matrix classes
1624    
1625    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1626    
1627            * R/dgTMatrix.R: add "[" method for triplet matrices
1628            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1629    
1630    2005-03-31  Douglas Bates  <bates@wisc.edu>
1631    
1632            * DESCRIPTION (Version): release 0.95-5 to CRAN
1633    
1634            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1635            * R/sparseMatrix.R: %*%, crossprod()
1636            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1637            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1638            * src/lmer.c (lmer_fitted): fix thinko
1639    
1640    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1641    
1642            * R/AllClass.R: add two virtual sparse classes ``on top''
1643    
1644    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1645    
1646            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1647                    correspondingly fix examples and tests/ since new()
1648                    doesn't work for virtual classes.
1649    
1650    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1651    
1652            * R/Matrix.R (as.matrix): method and one for unname()
1653            * tests/dpoMatrix.R: tests should now be less platform dependent;
1654              also run for R 2.1.0; using as.matrix()
1655    
1656    2005-03-15  Douglas Bates  <bates@wisc.edu>
1657    
1658            * R/pMatrix.R: "pMatrix" class added
1659            * ....
1660    
1661    2005-03-14  Douglas Bates  <bates@wisc.edu>
1662    
1663            * R/dtpMatrix.R: Add unpack method and an example.
1664    
1665            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1666            of general symmetric matrices and associated S4 methods.
1667    
1668    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1669            +
1670    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1671    
1672            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1673              crossprod() and "%*%" methods added; tests, too.
1674            * tests/matprod.R: new, for testing these
1675    
1676    2005-03-03  Douglas Bates  <bates@wisc.edu>
1677    
1678            * src/lmer.c (lmer_fitted): Added.
1679    
1680    2005-03-02  Douglas Bates  <bates@wisc.edu>
1681    
1682            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1683    
1684    2005-02-28  Douglas Bates  <bates@wisc.edu>
1685    
1686            * src/*.c,po/,inst/po: Internationalization and localization of
1687            the package.
1688    
1689            * src/ldl.[ch]: Removed these as their contents are referenced in the
1690            R_ldl.c file.
1691    
1692            * src/flame.[ch]: Removed these source files.
1693    
1694            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1695    
1696            * src/LU.[ch],src/init.c: absorb in factorizations
1697    
1698            * src/Mutils.h: prepare for internationalization
1699    
1700            * src/cblas.h: move the enum definitions to Mutils.h and remove
1701            this file
1702    
1703    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1704    
1705            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1706    
1707            * R/dtrMatrix.R: fix t() method
1708    
1709            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1710            * NAMESPACE: export them (and import generics from "methods")
1711            * tests/group-methods.R : and test them.
1712    
1713            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1714            border case
1715    
1716    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1717    
1718            * DESCRIPTION (Version): 0.95-2  released to CRAN
1719    
1720            * src/dgBCMatrix.c:
1721            * src/lmer.c: many changes
1722            * ...
1723    
1724    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1725    
1726            * R/Matrix.R: add more sophisticated show() method.
1727    
1728    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1729    
1730            * */* : almost complete reorganization of classes.
1731    
1732    2005-01-26  Douglas Bates  <bates@wisc.edu>
1733    
1734            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1735            for the geMatrix class.
1736    
1737    2005-01-24  Douglas Bates  <bates@wisc.edu>
1738    
1739            * src/Makefile (clean): Remove *.a and *.so
1740    
1741            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1742    
1743    2005-01-23  Douglas Bates  <bates@wisc.edu>
1744    
1745            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1746            had an effect in cases with more than 2 grouping factors.
1747    
1748    2005-01-03  Douglas Bates  <bates@wisc.edu>
1749    
1750            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1751    
1752    2004-12-23  Douglas Bates  <bates@wisc.edu>
1753    
1754            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1755            and R_useDynamicSymbols (suggested by B.D.Ripley).
1756    
1757    2004-12-14  Douglas Bates  <bates@wisc.edu>
1758    
1759            * R/sscMatrix.R: Add determinant methods
1760    
1761            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1762            for tripletMatrix to matrix.
1763    
1764    2004-12-13  Douglas Bates  <bates@wisc.edu>
1765    
1766            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1767            no longer used.
1768    
1769            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1770            with dynamic allocation of scratch arrays.
1771    
1772            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1773            for multivariate random effects with multiple grouping factors.
1774            Fixes part but not all of #15.
1775    
1776    2004-12-03  Douglas Bates  <bates@wisc.edu>
1777    
1778            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1779            scalar grouping factors corrected.
1780    
1781    2004-11-29  Douglas Bates  <bates@wisc.edu>
1782    
1783            * src/bCrosstab.c: remove diag_update which is no longer used
1784    
1785    2004-11-16  Douglas Bates  <bates@wisc.edu>
1786    
1787            * src/Metis_utils.c: Move metis.h include to C sources so that the
1788            .h file can be included.
1789    
1790    2004-11-12  Douglas Bates  <bates@wisc.edu>
1791    
1792            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1793            Complete allocation of slots in NEW_OBJECT.
1794    
1795            * src/Mutils.h: Moved list of symbols to an include file
1796    
1797    2004-11-11  Douglas Bates  <bates@wisc.edu>
1798    
1799            * src/geMutils.c (Matrix_init): remove unused function
1800    
1801    2004-11-10  Douglas Bates  <bates@wisc.edu>
1802    
1803            * src/cscMatrix.c (csc_to_imagemat): removed unused function
1804    
1805    2004-11-05  Douglas Bates  <bates@wisc.edu>
1806    
1807            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1808    
1809    2004-10-27  Douglas Bates  <bates@wisc.edu>
1810    
1811            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1812    
1813    2004-10-04  Douglas Bates  <bates@wisc.edu>
1814    
1815            * src/init.c: Created R_init_Matrix and added registration of C
1816            routines.
1817    
1818    2004-10-02  Douglas Bates  <bates@wisc.edu>
1819    
1820            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1821    
1822    2004-06-15  Douglas Bates  <bates@wisc.edu>
1823    
1824            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1825    
1826    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
1827    
1828            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1829    
1830    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
1831    
1832            * src/ssclme.c (ssclme_update_mm): fix logic error in
1833            ssclme_update_mm
1834    
1835    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
1836    
1837            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1838            in the order of unconstrained and constrained parameters.
1839            (ssclme_gradient): Added the gradients (not yet correct for
1840            multidimensional, unconstrained case).
1841    
1842    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
1843    
1844            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1845    
1846            * src/Makefile.win: Remove unneeded ranlib call
1847    
1848    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
1849    
1850            * DESCRIPTION (Version): New release
1851    
1852            * src/Makefile.win: Update Makefile.win to umfpack removal.
1853    
1854    2004-04-05  Douglas Bates  <bates@bates2_home>
1855    
1856            * src/triplet_to_col.c: Create triplet_to_col as a native
1857            function, not the version from umfpack.  There were problems with
1858            the configuration of UMFPACK for 64-bit processors and there was
1859            only one umfpack routine being used so I moved it here.
1860    
1861    2004-04-04  Douglas Bates  <bates@bates2_home>
1862    
1863            * src/ssclme.c (ssclme_variances): New function.
1864    
1865    2004-03-28  Douglas Bates  <bates@bates2_home>
1866    
1867            * src/ssclme.c (ssclme_fitted): Added function.
1868    
1869    2004-03-27  Douglas Bates  <bates@bates2_home>
1870    
1871            * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1872            store the dimnames in the XtX and bVar slots
1873            (ssclme_update_mm): Change the dimensions of the bVar slot
1874            components and the returned value from ssclme_ranef.
1875    
1876  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>
1877    
1878          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},

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