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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1829, Thu Apr 26 06:35:20 2007 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (intI): new utility, used for "[" :
4                    Cleanup up there, and fixes for duplicated indices - more TODO!
5    
6            * tests/indexing.R(out): more tests
7    
8    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
9    
10            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
11            code that is now part of the R Lapack library.
12    
13            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
14            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
15    
16    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
19    
20    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
23            up with extraneous names '0'...'<n-1>'
24    
25    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/dgTMatrix.R (mat2dgT): care about NAs
28    
29    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/kronecker.R: triangularity preserving methods
32    
33    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/kronecker.R: new file collecting kronecker() methods in one
36                    place.  Goal: become much faster!
37    
38    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
41            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
42            can be much faster.
43    
44            * tests/matprod.R: add regression tests for these (upper & lower).
45    
46    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (diff): method for our Matrices.
49    
50            * R/sparseMatrix.R (isDiagonal): check dim()!
51    
52    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Matrix.R (dim<-): new method for "reshape()" built on a
55            proposal from Tamas Papp.
56    
57    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
60    
61            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
62            rather define and export  cBind() and rBind() only.
63            --> useRs *must* change code that used to have cbind()/rbind() !!
64    
65            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
66            * R/bind.Rout.save: ditto
67    
68    2007-02-16  Douglas Bates  <bates@r-project.org>
69    
70            * DESCRIPTION (Date, Version): 0.9975-11 with new date
71            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
72            const modifier on declaration of the array 'valid'
73    
74    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
75    
76            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
77    
78    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
81    
82            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
83            * tests/simple.R: test the above and some of these coercions:
84    
85            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
86                    be careful to avoid infinite recursion, using new coercions in
87            * R/ngCMatrix.R and nsC... and ntC...
88            * R/lsparseMatrix.R: ditto
89    
90            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
91    
92            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
93            * R/Rsparse.R: reactivate .Call()s
94    
95            * tests/Class+Meth.R: a bit more on actual classes
96    
97    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
100    
101    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * DESCRIPTION (Version): 0.9975-10 to upload
104    
105            * tests/Class+Meth.R (tstMatrixClass): require coercions to
106            specific classes less unconditionally.
107    
108            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
109    
110            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
111    
112            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
113            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
114            R_to_CMatrix segfaults on one platform.
115            Eliminate most coercion method to *specific* classes, and replace
116            with virtual classes coercions.
117    
118    
119    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
120    
121            * src/init.c: export the CHM...._validate() placeholders, since
122            they *are* called.
123    
124            * tests/Class+Meth.R (classCanCoerce): and starting to test
125            all as(<from>, <to>)
126    
127    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
130            * tests/indexing.R: tested now
131            * tests/indexing.Rout.save: updated
132    
133            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
134            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
135            appropriate.
136    
137            * NAMESPACE: export a trivial
138            * R/Matrix.R: drop() Matrix-method
139    
140            * R/AllClass.R: moved all prototypes to virtual super classes.
141    
142            * R/Rsparse.R: many more coercions to have less exceptions in
143            * tests/Class+Meth.R:
144    
145            * R/Ops.R (Compare): tweak for case with NA
146            * tests/simpl.R: hence another 'FIXME' eliminated
147    
148    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
151            objects.
152    
153            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
154              and more of "!", "&", "|", all, any; coercions
155    
156            * R/Rsparse.R: many coercions (which enable quite a few other
157            methods), thanks to enhancements in
158            * src/dgCMatrix.c (R_to_CMatrix): new, and
159            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
160            symmetric & triangular and ..RMatrix objects.
161    
162            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
163            renamed file from src/dsTMatrix.c;
164            now dealing with symmetric and triangular Tsparse coercions, both
165            to dense and general.
166    
167    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
170    
171            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
172            where sensible when the <numeric> is of length > 1.
173    
174    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Matrix.R ([<-): for M[] <- value: fix length
177    
178    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
181            * R/ndenseMatrix.R: new coercions n* -> l*
182    
183    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
186    
187            * R/Ops.R ("Logic"): and other "Ops", many updates
188    
189    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/Mutils.h (SET_DimNames): new utility
192    
193            * R/Auxiliaries.R (nnzero): improved and now exported via
194    
195            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
196    
197    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/diagMatrix.R (!): fix typo.
200    
201    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Auxiliaries.R (as_Csparse): and quite a few others:
204                    allow to pass class definition --> speedup
205            * R/sparseMatrix.R: apply the above
206    
207            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
208    
209            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
210            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
211            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
212    
213            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
214    
215            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
216            and use it for "sparse*" as well, since it's faster than the
217            as_Csparse(.) way.
218    
219    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
222    
223    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
226            as method for   M[ ij ] <- v
227            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
228    
229            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
230            FALSE answer
231    
232            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
233            * tests/indexing.R: test it, and some of the above
234    
235    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (is_duplicatedT): new utility
238    
239    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * src/init.c (R_init_Matrix): export cholmod_scale
242    
243    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
246            base::as.matrix to (x, ...)
247    
248    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
251            file; start using "Logic", hence
252    
253            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
254            * NAMESPACE: import and export "Logic"
255    
256    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
259            only needed previously to R version 2.5.0.
260    
261    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
264    
265            * R/Tsparse.R (replTmat): fix subassignment of triangular
266            * R/Csparse.R (replCmat): ditto
267            * tests/indexing.R: more tests, incl the above fix
268    
269    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Auxiliaries.R (drop0): extend for non CSparse
272            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
273    
274            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
275                    use uplo correctly (!); other places: use uplo_P() macro
276    
277            * R/Csparse.R (replCmat): call diagU2N() when needed
278            * R/Tsparse.R (replTmat): ditto
279    
280            * src/dtCMatrix.c (tCMatrix_validate): new
281            * src/dtTMatrix.c (tTMatrix_validate): new, used in
282            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
283    
284            * R/diagMatrix.R (replDiag): to use in [<-
285    
286    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
289                    also more general diagU2N().
290    
291    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
294            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
295    
296    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * tests/bind.R: a few more cases
299            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
300    
301            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
302            * R/ddenseMatrix.R (cbind2/rbind2)
303            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
304            * tests/indexing.R
305            * tests/indexing.Rout.save: updated
306    
307    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
310            * tests/indexing.R
311    
312    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
315            align with proper position of "0", i.e., right for integers.
316            argument 'align' by default is "fancy".
317    
318    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
321            * R/Csparse.R: and fix "Compare" for more cases.
322            * tests/Class+Meth.R: test some of these (m == m, m != m)
323    
324    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/lsparseMatrix.R: all() and any() methods
327            * R/ldenseMatrix.R:      ditto
328            * NAMESPACE, R/Matrix.R: ditto
329    
330            * man/all-methods.Rd: document them minimally
331    
332            * tests/simple.R: add a few examples for these
333    
334    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Tsparse.R ([): fix long standing typo in symmetric case
337            * man/dsCMatrix-class.Rd: add example exhibiting the above case
338    
339    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
342            to LL before converting to a sparse matrix. (The LDL form can be
343            converted to a sparse matrix but it is implicitly a unit
344            triangular matrix and a diagonal matrix overwritten on the diagonal.)
345    
346    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
349    
350    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * DESCRIPTION (Version): updated -> release 0.9975-7
353            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
354    
355    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
358    
359    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
362            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
363            is exactly singular.
364    
365    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * DESCRIPTION (Date): updated -> release 0.9975-6
368    
369    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
372            now returns symmetric.
373    
374            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
375    
376            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
377            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
378    
379            * R/Auxiliaries.R (.type.kind): added
380    
381    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
384            running src/CSparse_install.sh
385    
386            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
387    
388    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
391            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
392    
393            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
394    
395            * tests/Class+Meth.R (tstMatrixClass): now assure
396            the (important in method programming) property :
397    
398                    ###>>  Every "Matrix" is either
399                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
400    
401                    (where "*" stands for "Matrix")
402    
403            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
404    
405            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
406            * tests/validObj.R: checks for "comparison"
407    
408            * R/sparseMatrix.R ([): improved indexing for sparse;
409                    trying to keep <symmetric>[ n, n] symmmetric
410    
411            * tests/indexing.R: indexing for logical sparse now ok
412    
413    
414    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/Tsparse.c: use xTsparse_validate() , and hence remove
417    
418            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
419    
420    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
423    
424            * tests/simple.R: validObject() checking the above.
425    
426            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
427            replacing both dgCMatrix_validate and lgCM*.
428    
429            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
430            fix dimnames setting in other places.
431            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
432    
433    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
436    
437            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
438            symmetry test, via
439            * R/Auxiliaries.R (.as.dgC.0.factors):
440    
441    2006-11-01  Douglas Bates  <bates@r-project.org>
442    
443            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
444            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
445            <CsparseMatrix>) added
446    
447    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/matprod.R: add a variation of Harri's example
450    
451            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
452            recursive infinitely.
453    
454            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
455    
456            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
457    
458    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
461            matrix if possible; test m+m == 2*m; now test dgRMatrix.
462            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
463            satisfy the above test.
464    
465    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
468    
469            * R/dgCMatrix.R: solve(a, b="missing") based on
470            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
471            RHS = NULL.
472    
473            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
474            add more (needed) [t]crossprod() methods.
475    
476            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
477    
478            * R/Auxiliaries.R (as_CspClass): cleanup
479            (drop0): internal utility for "Csparse_drop(*, 0)"
480            (.bail.out.2): encourage active feedback
481    
482    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/dMatrix.R(Compare): new(), then slots [no validity check]
485    
486            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
487            non-valid or 'sorted' case).
488    
489            * R/dsparseMatrix.R: add "chol" method.
490            * R/ddenseMatrix.R: ditto
491    
492            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
493            * NAMESPACE (Ops)
494            * R/diagMatrix.R (diag2T): simple utility used "higher level"
495            coercion; deprecating direct lower level coercions.
496    
497            * R/*.R (seq): use seq_len() and seq_along() where possible.
498    
499    
500    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * DESCRIPTION (Version): 0.9975-5 ready for release
503    
504    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
507    
508    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/AllClass.R (corMatrix): add 'validity' check;
511                    comment out unused "LDL" class definition
512            * NAMESPACE: mention, but do not export "LDL" class
513            * R/corMatrix.R: new (simple), needed for R-devel with
514            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
515              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
516    
517    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
520            use Rprintf and R's error handling.
521    
522    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
525            * tests/matprod.R: add tests for the bug fixed.
526    
527    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
528    
529            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
530            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
531    
532    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
533    
534            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
535    
536    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Version): 0.9975-3
539    
540            * R/diagMatrix.R (bdiag): new function constructing block diagonal
541            (sparse) matrices.
542            * man/bdiag.Rd: docu + examples
543    
544            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
545    
546            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
547            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
548    
549            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
550            that result is sparse or diagonal (and not dense).
551    
552            * man/Subassign-methods.Rd: fix examples
553    
554            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
555            should always return a sparse (and not sometimes a diagonal) matrix.
556    
557    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
560    
561    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * DESCRIPTION (Version): 0.9975-2
564    
565            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
566    
567    2006-10-02  Douglas Bates  <bates@R-project.org>
568    
569            * tests/dg_Matrix.R: Simplify test taking into account new code.
570    
571    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
574    
575            * R/lsTMatrix.R: new files w/ missing methods
576            * R/nsTMatrix.R:  "  'for completeness'
577    
578            * tests/Class+Meth.R: a bit less 'not.ok.classes'
579    
580            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
581    
582    
583    2006-09-28  Douglas Bates  <bates@R-project.org>
584    
585            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
586            included.
587    
588            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
589            Export C-callable functions used in Zt_create in lme4.
590    
591    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * DESCRIPTION (Version): 0.9975-1
594    
595            * tests/simple.R: less checks fail; using NA, found that our
596                    kronecker() is not base-compatible with NA's.
597    
598            * R/dMatrix.R: "Compare" method now implemented for all cases
599    
600            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
601    
602            * man/dtpMatrix-class.Rd: mention length of 'x' slot
603    
604            * src/dtpMatrix.c (dtpMatrix_validate): fix check
605            * src/dspMatrix.c (dspMatrix_validate): ditto
606    
607            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
608              including coercion to [nl]tTMatrix.
609    
610            * R/diagMatrix.R (show): print a header line as for other classes.
611    
612    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * src/Makefile.win (SUBDIRS): fix typo
615    
616    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
619    
620    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
623            symmetric and y missing in R code using %*% (cholmod_aat doesn't
624            accept a symmetric matrix).
625            * tests/group-methods.R: Uncomment test of crossprod applied to
626            lsCMatrix objects.
627    
628    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/AllClass.R (symmetricMatrix): add validity method (available
631            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
632    
633            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
634    
635            * tests/indexing.Rout.save:
636            * tests/indexing.R: additions, mainly for 'lsparse'
637    
638            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
639            case.
640    
641            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
642    
643    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
646                    as 'N' (1-letter - Ok?)
647    
648            * tests/group-methods.R: add test for logical + NAs
649    
650            * R/dMatrix.R ("Compare"): fix to work with NA's
651    
652            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
653    
654            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
655                    which is implemented.
656    
657    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * src/chm_common.c: coerce logical <-> double instead of
660            typecasting;  needed for "l" matrix handling in cholmod.
661    
662            * tests/other-pkgs.R (graph): small extension in "graph" checks.
663    
664            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
665            (Tsp2grNEL): other fixes needed
666    
667    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
670                    Matrices, since "lMatrix", also "lsparseM" can have NA
671            * R/ndenseMatrix.R, etc: new source files
672            * man/nsparseMatrix-classes.Rd, etc: new help files
673            * tests/: adaptions
674            * src/chm_common.c (chm_dense_to_SEXP): and others:
675                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
676            * src/Csparse.c, etc: ditto
677    
678    2006-09-11  Douglas Bates  <bates@R-project.org>
679    
680            * src/Mutils.[ch],init.c inst/include/*.h: Move the
681            alloc_d**Matrix functions to the lme4 package.
682    
683    2006-09-09  Douglas Bates  <bates@R-project.org>
684    
685            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
686            fixed
687    
688    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/lMatrix.R: new
691    
692            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
693    
694            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
695            * man/tcrossprod.Rd: ditto
696    
697    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
698    
699            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
700            for exported functions
701            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
702            Remove partitioning algorithms for sparse matrix reordering.  The
703            copyright on the Metis code was problematic and the methods were
704            rarely used.
705            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
706            operations are now done entirely in CHOLMOD code.
707    
708    2006-09-06  Douglas Bates  <bates@R-project.org>
709    
710            * src/Mutils.h: Remove functions that are no longer used.
711    
712    2006-09-04  Douglas Bates  <bates@R-project.org>
713    
714            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
715            * src/DEPS.mkf: update
716    
717    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * created branches/Matrix-for-R-2.3.x;  on trunk: do
720            * DESCRIPTION (Version): 0.9975-0
721            (Depends): R (>= 2.4.0)
722    
723    2006-09-01  Douglas Bates  <bates@R-project.org>
724    
725            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
726    
727    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
730            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
731    
732            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
733    
734    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
737            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
738            * R/dsparseMatrix.R: ditto
739            * R/Csparse.R: ditto
740    
741    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/dMatrix.R (Compare): improve availability of "<", etc
744            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
745    
746    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
749            of a 0-index which was used as 1-index (..hmm)
750    
751            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
752    
753            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
754            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
755            (.is.diagonal): ditto
756    
757            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
758    
759            * R/Matrix.R (Matrix): also work for NA data
760    
761    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
764            in all cases.
765    
766    2006-08-27  Douglas Bates  <bates@R-project.org>
767    
768            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
769            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
770    
771    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
774            subclasses of "ddenseMatrix"
775            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
776            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
777            instead of half dozen specialized ones.
778    
779    2006-08-25  Douglas Bates  <bates@R-project.org>
780    
781            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
782            <tillard@cirad.fr> - ordering standard errors to match effects.
783    
784    2006-08-24  Douglas Bates  <bates@R-project.org>
785    
786            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
787            on R_ldl.
788            * R/lCholCMatrix.R,
789            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
790            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
791            * many files in ./R and ./src: Use more general version of
792            dup_mMatrix_as_dgeMatrix to simplify method definitions.
793            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
794            dtpMatrix, dspMatrix and dppMatrix conversions.
795    
796    
797    2006-08-23  Douglas Bates  <bates@R-project.org>
798    
799            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
800            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
801            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
802            dgeMatrix_crossprod (may need to do this in other places).
803            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
804            generic and method for dsCMatrix.  Use CHOLMOD for chol().
805    
806    2006-08-22  Douglas Bates  <bates@R-project.org>
807    
808            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
809            types of classed Matrices, matrices or numeric or logical vectors.
810            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
811            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
812            to Mutils.h (as an inline) and change name to Matrix_check_class;
813            fixes in as_cholmod_factor and chm_factor_to_SEXP.
814            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
815            dsCMatrix_matrix_solve.  Comment out vestigial functions.
816            * src/Csparse.c: use diag_P and uplo_P macros.
817    
818    2006-08-21  Douglas Bates  <bates@R-project.org>
819    
820            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
821            valgrind.
822            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
823            inverses.
824            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
825            -Wall warnings.
826            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
827            Use dup_mMatrix_as_dgeMatrix.
828    
829    2006-08-20  Douglas Bates  <bates@R-project.org>
830    
831            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
832            * tests/sparseQR.R: Added
833            * man/sparseQR-class.Rd: Document methods for qr.* generics
834            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
835    
836    2006-08-19  Douglas Bates  <bates@R-project.org>
837    
838            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
839            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
840            and qr.fitted.
841            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
842            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
843    
844    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
847            the base version has no "..." argument.
848    
849            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
850    
851            * R/Matrix.R: define and
852            * NAMESPACE: export as.numeric() and as.logical() methods.
853                    Let's hope these do not badly slow down something...
854            Finally export the zapsmall() method.
855    
856    2006-08-17  Douglas Bates  <bates@R-project.org>
857    
858            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
859            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
860            * src/dtCMatrix.c :Remove code that is no longer used
861            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
862    
863    2006-08-14  Douglas Bates  <bates@R-project.org>
864    
865            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
866            Csparse_to_logical and Csparse_symmetric_to_general.
867            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
868            coercion methods between CsparseMatrix and TsparseMatrix.
869    
870    2006-08-14  Douglas Bates  <bates@R-project.org>
871    
872            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
873            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
874            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
875            possible.
876    
877    2006-08-12  Douglas Bates  <bates@R-project.org>
878    
879            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
880              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
881              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
882              generalize conversions between TsparseMatrix, CsparseMatrix,
883              denseMatrix and matrix.  Preserve triangularity property and
884              propagate Dimnames in the easy cases.
885    
886    2006-08-10  Douglas Bates  <bates@R-project.org>
887    
888            * src/lmer.c: adjust checks in glmer_init for S4SXP
889            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
890            before S4SXP but for the wrong reasons.
891    
892    2006-08-08  Douglas Bates  <bates@R-project.org>
893    
894            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
895            Later modified to return the upper triangle only.
896            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
897    
898    2006-08-07  Douglas Bates  <bates@R-project.org>
899    
900            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
901            R-level conversion to a sparse symmetric class.
902            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
903            Remove conversion to sparse symmetric classes (now done in C code).
904    
905    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
908            * man/band.Rd:  adapt the \dontshow{} unit test.
909    
910    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * DESCRIPTION (Version): 0.995-14  for CRAN
913    
914            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
915    
916            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
917            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
918    
919            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
920            * R/Tsparse.R (tril, triu, band): methods
921            * R/dgRMatrix.R (tril, ...):    ditto
922            * man/band.Rd:                  ditto
923    
924    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/Matrix.R (head, tail): directly use utils:::head.matrix
927                    to be up-to-date automatically.
928    
929    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
932    
933            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
934            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
935            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
936            such that the S4 objects are always created by the current version
937            of R and 'Matrix' class definitions.
938    
939    2006-08-01  Douglas Bates  <bates@R-project.org>
940    
941            * R/lmer.R (LMEoptimize method), tests/lmer.R,
942            inst/external/test3comp.rda: Added warnings for convergence on
943            boundary and test cases.
944    
945            * src/lmer.c (mer_postVar): Modified to return the variances that
946            are marginal to the fixed effects, not conditional on them (which
947            is what the bVar slot contents represent).
948    
949    2006-07-31  Douglas Bates  <bates@R-project.org>
950    
951            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
952            function which calls the C function mer_hat_trace2.
953    
954            * man/ranef.Rd: Include description of "postVar" argument and
955            producing a caterpillar plot.
956    
957    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * NAMESPACE:    change  "correlation" to "corMatrix"
960            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
961            * R/dpoMatrix.R: ditto
962            * R/lmer.R:      ditto
963    
964    2006-07-28  Douglas Bates  <bates@R-project.org>
965    
966            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
967            RZXinv slot's contents into a separate internal function that can
968            be used in mer_hat_trace.
969    
970    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
973            via new smart
974            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
975            utility functions.
976    
977    
978    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * R/Csparse.R (tril, triu, band): do return *triangular* classed
981            matrices when appropriate; band() even symmetric ones.
982            (replCmat): extend to potentially all "CsparseMatrix"
983            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
984            allow subassignment for special sparse matrices.
985    
986            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
987    
988            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
989            argument; in glmer_*(): print only if(verbose).
990    
991            speed-optimize a few places by moving REAL(.) out of loops.
992    
993            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
994    
995    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
998                    since that wrongly triggers also for M[ logi , ]
999    
1000            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1001            a symmetric matrix that results in a non-symmetric one.
1002            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1003    
1004            * R/dMatrix.R: make round(M) work as round(M, 0)
1005    
1006            * R/dgTMatrix.R (image): coordinate system and axis now use
1007            1-based indices, not 0-based ones.
1008    
1009            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1010            * tests/indexing.R: test it.
1011    
1012            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1013            * man/isSymmetric-methods.Rd: and document it.
1014    
1015            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1016            * man/SparseM-conv.Rd: docu them
1017    
1018            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1019                    for 'SparseM' conversions
1020    
1021    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1022    
1023            * R/Matrix.R (head): added head() and tail() methods.
1024    
1025    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * DESCRIPTION (Version): 0.995-12 released to CRAN
1028    
1029    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * tests/simple.R: add check for correct dsT -> dgT coercion;
1032                    add check for correct printing of symmetric sparse matrices.
1033    
1034            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1035            for sparse symmetric matrices.
1036    
1037            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1038            diagonal twice.
1039    
1040    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1041    
1042            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1043            being applied to the x slot (detected by Brian Ripley).
1044    
1045    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1048    
1049            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1050    
1051    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * src/lgCMatrix.c (lgCMatrix_diag): new function
1054            * R/lgCMatrix.R (diag): for new method
1055    
1056            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1057                 ==> construction of illegal "*gTMatrix" via new() should
1058                 now be much less easy:
1059            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1060    
1061            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1062                    directly.
1063            * man/Matrix.Rd: documents it.
1064    
1065    2006-07-06  Douglas Bates  <bates@R-project.org>
1066    
1067            * src/pedigree.c (pedigree_inbreeding): Correction in
1068            initialization.  This function is not currently being used and is
1069            not fully tested.
1070    
1071            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1072            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1073            objects.  Modified validity check on pedigree objects to account
1074            for nonparallel patterns of missingness of parents.
1075    
1076            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1077            class.
1078    
1079    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/pMatrix.R: coercion pMatrix -> Tsparse
1082    
1083    2006-06-12  Douglas Bates  <bates@R-project.org>
1084    
1085            * DESCRIPTION (Version): 0.995-11 released to CRAN
1086    
1087            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1088            the output from mcmcsamp.
1089    
1090    2006-06-10  Douglas Bates  <bates@R-project.org>
1091    
1092            * R/lmer.R (simulestimate): added C code for calculating the trace
1093            of the hat matrix.
1094    
1095    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1098            classes.
1099            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1100    
1101    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/dgTMatrix.R (colSums): etc. All four of
1104            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1105            all "Matrices".
1106    
1107    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1108    
1109            * R/lmer.R (panel.ci): Add a reference line at zero and a
1110            background grid to the qqmath plot of ranef.lmer.
1111    
1112    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1113    
1114            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1115            grouping factors to be specified in the formula as (1|foo/bar).
1116    
1117    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1118    
1119            * R/lmer.R (findbars and others): Change check of is.numeric to
1120            !is.language to resolve the bug reported by Jacob Wegelin.
1121    
1122            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1123            code to evaluate inbreeding coefficients without calculating T,
1124            based on code in Sargolzaei and Iwaisaki's paper.
1125    
1126    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1127    
1128            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1129            generic and mer methods for isNested and denomDF. This denomDF was
1130            an attempt to emulate that in lme but I don't think that makes
1131            sense.  Use the trace of the hat matrix instead.
1132    
1133    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1136            the C code depending on a slot structure that's no longer valid.
1137            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1138    
1139    
1140    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1141    
1142            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1143            of lowerTriMatrix generic and methods to tril (also upper to triu)
1144            and added a general band extractor.
1145    
1146    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1147    
1148            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1149            allowable range with NAs. Added a corresponding check in the
1150            validity check for the pedigree class.
1151    
1152            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1153            crossprod methods now inherits from symmetricMatrix.
1154    
1155    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1156    
1157            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1158            generics lowerTriMatrix and upperTriMatrix along with methods for
1159            the Csparse virtual class.  Also added a C function Csparse_band
1160            that implements these methods by calling cholmod_band.
1161    
1162    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1165            erased when it was NULL.  This led to invalid subselections!
1166    
1167    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1168    
1169            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1170            in method for "t" so as not to lose the unit diagonal property.
1171    
1172    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1173    
1174            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1175            and methods.  This is now an option to the ranef method for the
1176            mer class.
1177    
1178            * src/cs_utils.c: Ensure that the nz component is -1 for a
1179            compressed column-oriented matrix.  Minor formatting cleanup.
1180    
1181            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1182            objects.
1183    
1184    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1187            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1188    
1189    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1190    
1191            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1192            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1193    
1194            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1195            for the dtCMatrix class.
1196    
1197    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1198    
1199            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1200            and methods for it.
1201    
1202    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1205            arguments, such that M %*% 1:6 now works
1206            * Tests/matprod.R: test the above
1207    
1208    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1209    
1210            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1211            the ranef.lmer class.
1212    
1213            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1214            methods to extract the posterior variances from the bVar slot.
1215    
1216    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1219            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1220    
1221            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1222            * tests/simple: (extended)
1223    
1224            * R/sparseMatrix.R (isTriangular): now using much improved
1225            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1226    
1227    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1228    
1229            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1230            (problem report from Franklin Parlamis).  This should be done
1231            generally.
1232    
1233    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1234    
1235            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1236            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1237            update the plot methods.
1238    
1239    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1240    
1241            * R/lmer.R (resid and ranef methods):  Added methods for the
1242            "residuals" and "resid" generic but only for linear mixed model
1243            fits.  Changed the ranef method to return a list of data frames so
1244            that the plot methods now work.
1245    
1246    2006-03-16  Douglas Bates  <bates@bates2>
1247    
1248            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1249            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1250    
1251            * DESCRIPTION (Date): New release
1252    
1253    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1256    
1257            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1258            * man/KNex.Rd: and other help files
1259            * tests/*.R: several ones needed adaption
1260            * inst/doc/Comparisons.Rnw: ditto
1261    
1262    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1263    
1264            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1265    
1266            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1267    
1268    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1269    
1270            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1271    
1272            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1273    
1274    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * R/dMatrix.R: enable things like  M [ M < 10 ]
1277            * R/dgeMatrix.R: implement it
1278    
1279    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * R/AllClass.R: define "summary.mer" and "*.lmer"
1282            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1283            * R/lmer.R (show): now works with summary()
1284    
1285    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1288            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1289                    support the above
1290    
1291    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1292    
1293            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1294            Use glmFit$prior.weights for weights in a glmm.
1295            Allow an option usePQL = FALSE to skip the PQL steps for the
1296            Laplace method (and, in time, the AGQ method).
1297    
1298            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1299            into a separate function internal_mer_Xfactor to be able to call
1300            it from internal_bhat.
1301    
1302    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * tests/Class+Meth.R (tstMatrixClass): function for much better
1305            testing; now again of all actual classes.
1306    
1307            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1308                    use macros and define make_d_matrix_* and make_i_matrix_*
1309                    where _i_ is for the ldense routines:
1310    
1311            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1312            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1313    
1314            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1315    
1316    
1317    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1320                    many different kinds of matrices.
1321            * R/*.R: quite a few new methods were needed for R CMD check with
1322                    new Matrix().  Very good for users playing around.
1323    
1324    
1325    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1326    
1327            * src/dgeMatrix.c (dMatrix_validate): new
1328            * src/Mutils.c (dense_nonpacked_validate): new
1329    
1330            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1331    
1332    
1333    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1334    
1335            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1336    
1337    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1338    
1339            * DESCRIPTION (Version): 0.99-6 released to CRAN
1340    
1341            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1342            segfault in cases with multiple non-nested grouping factors.
1343    
1344    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1345    
1346            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1347                    (Depends): also on 'utils'
1348    
1349            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1350            * R/diagMatrix.R (Diagonal): constructor and methods for
1351            diagonal matrices
1352    
1353            * R/ltTMatrix.R: new "minimal methods"
1354    
1355    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1356    
1357            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1358            all methods (and help files).
1359    
1360    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1361    
1362            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1363                    for case (dimn.  op  no_dimn.)
1364    
1365    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1366    
1367            * DESCRIPTION (Version): 0.99-2  released to CRAN
1368    
1369    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1370    
1371            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1372            by Julian Faraway.
1373    
1374    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1375    
1376            * R/Auxiliaries.R (try_as): new utility
1377            * R/sparseMatrix.R: use try_as() in coercion to original class
1378    
1379    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1380    
1381            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1382    
1383    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1384    
1385            * R/Auxiliaries.R (dimNamesCheck): added
1386    
1387            * R/Matrix.R (as.array), (as.vector): new
1388    
1389    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1390    
1391            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1392                    default.
1393            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1394                    "pMatrix" now contains "sparseMatrix"
1395    
1396    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1397    
1398            * tests/Class+Meth.R: new tests; t(t(m)) == m
1399    
1400            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1401    
1402            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1403            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1404    
1405            * R/dspMatrix.R: typo in "t" method
1406    
1407    2005-09-18  Douglas Bates  <bates@wisc.edu>
1408    
1409            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1410            * R/Tsparse.R: instead of R/gTMatrix.R
1411            * R/Csparse.R: new
1412            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1413            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1414            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1415                            via cholmod
1416    
1417    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * R/Auxiliaries.R (non0ind): new function using new C code
1420            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1421    
1422    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1423    
1424            * src/chm_common.h: header file required by all C sources that
1425            call CHOLMOD functions.  It defines a cholmod_common structure
1426            called 'c' whose address is passed as the last argument to
1427            (virtually) every CHOLMOD function.
1428    
1429            * src/Pattern.c: Simple example of the use of CHOLMOD.
1430    
1431            * src/init.c: initialize and finalize the cholmod_common structure.
1432    
1433            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1434            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1435    
1436    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1437    
1438            * inst/test-tools.R: new file collecting the utility functions used
1439                    in ./tests/*.R
1440    
1441            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1442            * R/Matrix.R (cbind2): methods for NULL and missing
1443    
1444    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1445    
1446            * R/AllClass.R: new "index" class for "[" and "[<-":
1447                    First cut at "symmetricMatrix" and "triangularMatrix"
1448            * R/gTMatrix.R (.ind.prep): new function;
1449                    Logical and character indexing now work too.
1450            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1451            * tests/indexing.R: new, including *.Rout.save
1452            * tests/dgTMatrix.R: new
1453    
1454    2005-08-29  Douglas Bates  <bates@wisc.edu>
1455    
1456            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1457            indicator pos not being updated.  Also enforced upper triangular
1458            for symmetric case.  Need to coerce edges component of elements of
1459            edge list - grr! (Why don't they define their classes cleanly?)
1460    
1461    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1462    
1463            * R/Matrix.R:  added first "[<-" methods; not yet functional
1464            * R/denseMatrix.R: ditto
1465            * man/Subassign-methods.Rd: new help file for these
1466    
1467    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1468    
1469            * DESCRIPTION (Version): 0.98-6
1470    
1471            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1472            matrices.
1473    
1474    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1475    
1476            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1477                    as( <logical>, "matrix")
1478    
1479            * R/pMatrix.R: coercion to "lgTMatrix"
1480    
1481            * R/gTMatrix.R: new virtual class to define "[" methods for.
1482            * man/gTMatrix-class.Rd:
1483            * General slight re-organization of where "[" methods are defined.
1484              more to come.
1485    
1486    2005-08-18  Douglas Bates  <bates@wisc.edu>
1487    
1488            * DESCRIPTION (Version): 0.98-5  released to CRAN
1489    
1490            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1491            * .....
1492    
1493    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1494    
1495            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1496            or glmer objects.
1497    
1498    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1499    
1500            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1501    
1502    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1503    
1504            * R/HBMM.R: finish re-writing R-only code.
1505    
1506    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1507    
1508            * man/externalFormats.Rd: move documentation for writeHB and
1509            writeMM here.
1510    
1511            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1512            (suggested by Paul Roecker).
1513    
1514            * tests/validObj.R (assertError): Comment out test that is failing
1515            after recent changes in r-devel.
1516    
1517    
1518    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1519    
1520            * R/AllClass.R: intermediate virtual class "denseMatrix"
1521            * man/denseMatrix-class.Rd
1522            * NAMESPACE: export it, and also export
1523            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1524    
1525    2005-08-10  Douglas Bates  <bates@wisc.edu>
1526    
1527            * DESCRIPTION (Version): 0.98-3 to CRAN
1528    
1529            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1530            matrix_solve code (which was really, really wrong).
1531    
1532    2005-08-07  Douglas Bates  <bates@wisc.edu>
1533    
1534            * DESCRIPTION (Version): 0.98-2
1535    
1536            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1537    
1538            * R/lmer.R (abbrvNms): new
1539            * R/lmer.R (mcmcsamp): allow transformed parameters
1540            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1541            for the Harwell-Boeing and the MatrixMarket formats.
1542    
1543    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * man/dtrMatrix-class.Rd: add examples
1546            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1547    
1548            * TODO: note the dtpMatrix (docu) bug
1549    
1550            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1551            in order to ensure that new as.matrix() is used by old functions,
1552            e.g., svd(), qr(), eigen(), dist(),..;
1553                  apply(), also matplot() or pairs().
1554    
1555    
1556    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1557    
1558            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1559              add comments about 'control' / lmerControl() arguments
1560    
1561    2005-07-27  Douglas Bates  <bates@wisc.edu>
1562    
1563            * man/sleepstudy.Rd: Added the sleep data set.
1564            * DESCRIPTION (Version): 0.98-1  released to CRAN
1565    
1566    2005-07-12  Douglas Bates  <bates@wisc.edu>
1567            * man/sleepstudy.Rd: Added the sleep data set.
1568    
1569            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1570            .Call calls that were producing spurious output.
1571    
1572    2005-07-05  Douglas Bates  <bates@wisc.edu>
1573    
1574            * R/lmer.R (lmer): stored updated variance component estimates in
1575            mer object for the generalized model.  (Bug reported by Renaud
1576            Lancelot).
1577    
1578    2005-07-03  Douglas Bates  <bates@wisc.edu>
1579    
1580            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1581            unidimensional case.
1582    
1583    2005-06-08  Douglas Bates  <bates@wisc.edu>
1584    
1585            * DESCRIPTION (Version): 0.96-1
1586    
1587            * moved  lmer-class' R and C code moved from lme4 to here
1588    
1589    2005-06-04  Douglas Bates  <bates@wisc.edu>
1590    
1591            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1592            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1593    
1594    2005-06-02  Douglas Bates  <bates@wisc.edu>
1595    
1596            * src/Makefile.win: Forgot to update this when Makefile changed.
1597    
1598    2005-05-11  Douglas Bates  <bates@wisc.edu>
1599    
1600            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1601            bug reported by Kurt Hornik and Michael Hahsler.
1602    
1603    2005-05-10  Douglas Bates  <bates@wisc.edu>
1604    
1605            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1606            logical sparse matrices.  These will also be used in the symbolic
1607            analysis for lmer objects.
1608    
1609            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1610            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1611    
1612    2005-05-06  Douglas Bates  <bates@wisc.edu>
1613    
1614            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1615            colMeans, colSums, rowMeans and rowSums.
1616    
1617    2005-04-18  Douglas Bates  <bates@wisc.edu>
1618    
1619            * src/lgCMatrix.[ch]: code for _validate method and stub for
1620            multiplication operation.
1621    
1622            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1623            to dgetrs.
1624    
1625            * src/init.c: Fix cut-and-paste error in definition of
1626            dgeMatrix_matrix_solve
1627    
1628            * src/{many files}: Tighten code by using ALLOC_SLOT.
1629    
1630    2005-04-15  Douglas Bates  <bates@wisc.edu>
1631    
1632            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1633    
1634            * DESCRIPTION: Eliminate import of stats.
1635    
1636    
1637    2005-04-06  Douglas Bates  <bates@wisc.edu>
1638    
1639            * R/AllClass.R : add logical sparse matrix classes
1640    
1641    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1642    
1643            * R/dgTMatrix.R: add "[" method for triplet matrices
1644            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1645    
1646    2005-03-31  Douglas Bates  <bates@wisc.edu>
1647    
1648            * DESCRIPTION (Version): release 0.95-5 to CRAN
1649    
1650            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1651            * R/sparseMatrix.R: %*%, crossprod()
1652            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1653            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1654            * src/lmer.c (lmer_fitted): fix thinko
1655    
1656    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1657    
1658            * R/AllClass.R: add two virtual sparse classes ``on top''
1659    
1660    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1661    
1662            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1663                    correspondingly fix examples and tests/ since new()
1664                    doesn't work for virtual classes.
1665    
1666    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1667    
1668            * R/Matrix.R (as.matrix): method and one for unname()
1669            * tests/dpoMatrix.R: tests should now be less platform dependent;
1670              also run for R 2.1.0; using as.matrix()
1671    
1672    2005-03-15  Douglas Bates  <bates@wisc.edu>
1673    
1674            * R/pMatrix.R: "pMatrix" class added
1675            * ....
1676    
1677    2005-03-14  Douglas Bates  <bates@wisc.edu>
1678    
1679            * R/dtpMatrix.R: Add unpack method and an example.
1680    
1681            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1682            of general symmetric matrices and associated S4 methods.
1683    
1684    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1685            +
1686    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1687    
1688            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1689              crossprod() and "%*%" methods added; tests, too.
1690            * tests/matprod.R: new, for testing these
1691    
1692    2005-03-03  Douglas Bates  <bates@wisc.edu>
1693    
1694            * src/lmer.c (lmer_fitted): Added.
1695    
1696    2005-03-02  Douglas Bates  <bates@wisc.edu>
1697    
1698            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1699    
1700    2005-02-28  Douglas Bates  <bates@wisc.edu>
1701    
1702            * src/*.c,po/,inst/po: Internationalization and localization of
1703            the package.
1704    
1705            * src/ldl.[ch]: Removed these as their contents are referenced in the
1706            R_ldl.c file.
1707    
1708            * src/flame.[ch]: Removed these source files.
1709    
1710            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1711    
1712            * src/LU.[ch],src/init.c: absorb in factorizations
1713    
1714            * src/Mutils.h: prepare for internationalization
1715    
1716            * src/cblas.h: move the enum definitions to Mutils.h and remove
1717            this file
1718    
1719    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1720    
1721            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1722    
1723            * R/dtrMatrix.R: fix t() method
1724    
1725            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1726            * NAMESPACE: export them (and import generics from "methods")
1727            * tests/group-methods.R : and test them.
1728    
1729            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1730            border case
1731    
1732    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1733    
1734            * DESCRIPTION (Version): 0.95-2  released to CRAN
1735    
1736            * src/dgBCMatrix.c:
1737            * src/lmer.c: many changes
1738            * ...
1739    
1740    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1741    
1742            * R/Matrix.R: add more sophisticated show() method.
1743    
1744    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1745    
1746            * */* : almost complete reorganization of classes.
1747    
1748    2005-01-26  Douglas Bates  <bates@wisc.edu>
1749    
1750            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1751            for the geMatrix class.
1752    
1753    2005-01-24  Douglas Bates  <bates@wisc.edu>
1754    
1755            * src/Makefile (clean): Remove *.a and *.so
1756    
1757            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1758    
1759    2005-01-23  Douglas Bates  <bates@wisc.edu>
1760    
1761            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1762            had an effect in cases with more than 2 grouping factors.
1763    
1764    2005-01-03  Douglas Bates  <bates@wisc.edu>
1765    
1766            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1767    
1768    2004-12-23  Douglas Bates  <bates@wisc.edu>
1769    
1770            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1771            and R_useDynamicSymbols (suggested by B.D.Ripley).
1772    
1773    2004-12-14  Douglas Bates  <bates@wisc.edu>
1774    
1775          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1776    
1777          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1778          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1779    
1780  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1781    
1782          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1783          no longer used.          no longer used.
# Line 17  Line 1789 
1789          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1790          Fixes part but not all of #15.          Fixes part but not all of #15.
1791    
1792  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1793    
1794          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1795          scalar grouping factors corrected.          scalar grouping factors corrected.
1796    
1797  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1798    
1799          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1800    
1801  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1802    
1803          * 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
1804          .h file can be included.          .h file can be included.
1805    
1806  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1807    
1808          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1809          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1810    
1811          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1812    
1813  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1814    
1815          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1816    
1817  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1818    
1819          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1820    
1821  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1822    
1823          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1824    
1825  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1826    
1827          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1828    
1829  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1830    
1831          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1832          routines.          routines.
1833    
1834  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1835    
1836          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1837    
1838  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1839    
1840          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1841    

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