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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1799, Sat Mar 24 14:54:00 2007 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
4            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
5            can be much faster.
6    
7            * tests/matprod.R: add regression tests for these (upper & lower).
8    
9    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/Matrix.R (diff): method for our Matrices.
12    
13            * R/sparseMatrix.R (isDiagonal): check dim()!
14    
15    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (dim<-): new method for "reshape()" built on a
18            proposal from Tamas Papp.
19    
20    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
23    
24            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
25            rather define cBind() and rBind();
26            and also cbind()/rbind {in Matrix, but exported}.
27    
28    
29    2007-02-16  Douglas Bates  <bates@r-project.org>
30    
31            * DESCRIPTION (Date, Version): 0.9975-11 with new date
32            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
33            const modifier on declaration of the array 'valid'
34    
35    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
38    
39    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
42    
43            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
44            * tests/simple.R: test the above and some of these coercions:
45    
46            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
47                    be careful to avoid infinite recursion, using new coercions in
48            * R/ngCMatrix.R and nsC... and ntC...
49            * R/lsparseMatrix.R: ditto
50    
51            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
52    
53            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
54            * R/Rsparse.R: reactivate .Call()s
55    
56            * tests/Class+Meth.R: a bit more on actual classes
57    
58    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
61    
62    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * DESCRIPTION (Version): 0.9975-10 to upload
65    
66            * tests/Class+Meth.R (tstMatrixClass): require coercions to
67            specific classes less unconditionally.
68    
69            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
70    
71            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
72    
73            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
74            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
75            R_to_CMatrix segfaults on one platform.
76            Eliminate most coercion method to *specific* classes, and replace
77            with virtual classes coercions.
78    
79    
80    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
81    
82            * src/init.c: export the CHM...._validate() placeholders, since
83            they *are* called.
84    
85            * tests/Class+Meth.R (classCanCoerce): and starting to test
86            all as(<from>, <to>)
87    
88    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
91            * tests/indexing.R: tested now
92            * tests/indexing.Rout.save: updated
93    
94            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
95            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
96            appropriate.
97    
98            * NAMESPACE: export a trivial
99            * R/Matrix.R: drop() Matrix-method
100    
101            * R/AllClass.R: moved all prototypes to virtual super classes.
102    
103            * R/Rsparse.R: many more coercions to have less exceptions in
104            * tests/Class+Meth.R:
105    
106            * R/Ops.R (Compare): tweak for case with NA
107            * tests/simpl.R: hence another 'FIXME' eliminated
108    
109    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
112            objects.
113    
114            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
115              and more of "!", "&", "|", all, any; coercions
116    
117            * R/Rsparse.R: many coercions (which enable quite a few other
118            methods), thanks to enhancements in
119            * src/dgCMatrix.c (R_to_CMatrix): new, and
120            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
121            symmetric & triangular and ..RMatrix objects.
122    
123            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
124            renamed file from src/dsTMatrix.c;
125            now dealing with symmetric and triangular Tsparse coercions, both
126            to dense and general.
127    
128    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
131    
132            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
133            where sensible when the <numeric> is of length > 1.
134    
135    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R ([<-): for M[] <- value: fix length
138    
139    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
142            * R/ndenseMatrix.R: new coercions n* -> l*
143    
144    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
147    
148            * R/Ops.R ("Logic"): and other "Ops", many updates
149    
150    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/Mutils.h (SET_DimNames): new utility
153    
154            * R/Auxiliaries.R (nnzero): improved and now exported via
155    
156            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
157    
158    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (!): fix typo.
161    
162    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Auxiliaries.R (as_Csparse): and quite a few others:
165                    allow to pass class definition --> speedup
166            * R/sparseMatrix.R: apply the above
167    
168            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
169    
170            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
171            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
172            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
173    
174            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
175    
176            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
177            and use it for "sparse*" as well, since it's faster than the
178            as_Csparse(.) way.
179    
180    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
183    
184    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
187            as method for   M[ ij ] <- v
188            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
189    
190            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
191            FALSE answer
192    
193            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
194            * tests/indexing.R: test it, and some of the above
195    
196    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/Auxiliaries.R (is_duplicatedT): new utility
199    
200    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
201    
202            * src/init.c (R_init_Matrix): export cholmod_scale
203    
204    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
207            base::as.matrix to (x, ...)
208    
209    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
212            file; start using "Logic", hence
213    
214            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
215            * NAMESPACE: import and export "Logic"
216    
217    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
220            only needed previously to R version 2.5.0.
221    
222    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
225    
226            * R/Tsparse.R (replTmat): fix subassignment of triangular
227            * R/Csparse.R (replCmat): ditto
228            * tests/indexing.R: more tests, incl the above fix
229    
230    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Auxiliaries.R (drop0): extend for non CSparse
233            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
234    
235            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
236                    use uplo correctly (!); other places: use uplo_P() macro
237    
238            * R/Csparse.R (replCmat): call diagU2N() when needed
239            * R/Tsparse.R (replTmat): ditto
240    
241            * src/dtCMatrix.c (tCMatrix_validate): new
242            * src/dtTMatrix.c (tTMatrix_validate): new, used in
243            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
244    
245            * R/diagMatrix.R (replDiag): to use in [<-
246    
247    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
250                    also more general diagU2N().
251    
252    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
255            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
256    
257    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * tests/bind.R: a few more cases
260            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
261    
262            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
263            * R/ddenseMatrix.R (cbind2/rbind2)
264            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
265            * tests/indexing.R
266            * tests/indexing.Rout.save: updated
267    
268    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
271            * tests/indexing.R
272    
273    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
276            align with proper position of "0", i.e., right for integers.
277            argument 'align' by default is "fancy".
278    
279    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
282            * R/Csparse.R: and fix "Compare" for more cases.
283            * tests/Class+Meth.R: test some of these (m == m, m != m)
284    
285    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/lsparseMatrix.R: all() and any() methods
288            * R/ldenseMatrix.R:      ditto
289            * NAMESPACE, R/Matrix.R: ditto
290    
291            * man/all-methods.Rd: document them minimally
292    
293            * tests/simple.R: add a few examples for these
294    
295    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Tsparse.R ([): fix long standing typo in symmetric case
298            * man/dsCMatrix-class.Rd: add example exhibiting the above case
299    
300    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
303            to LL before converting to a sparse matrix. (The LDL form can be
304            converted to a sparse matrix but it is implicitly a unit
305            triangular matrix and a diagonal matrix overwritten on the diagonal.)
306    
307    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
310    
311    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * DESCRIPTION (Version): updated -> release 0.9975-7
314            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
315    
316    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
319    
320    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
321    
322            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
323            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
324            is exactly singular.
325    
326    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * DESCRIPTION (Date): updated -> release 0.9975-6
329    
330    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
333            now returns symmetric.
334    
335            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
336    
337            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
338            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
339    
340            * R/Auxiliaries.R (.type.kind): added
341    
342    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
345            running src/CSparse_install.sh
346    
347            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
348    
349    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
352            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
353    
354            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
355    
356            * tests/Class+Meth.R (tstMatrixClass): now assure
357            the (important in method programming) property :
358    
359                    ###>>  Every "Matrix" is either
360                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
361    
362                    (where "*" stands for "Matrix")
363    
364            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
365    
366            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
367            * tests/validObj.R: checks for "comparison"
368    
369            * R/sparseMatrix.R ([): improved indexing for sparse;
370                    trying to keep <symmetric>[ n, n] symmmetric
371    
372            * tests/indexing.R: indexing for logical sparse now ok
373    
374    
375    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * src/Tsparse.c: use xTsparse_validate() , and hence remove
378    
379            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
380    
381    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
384    
385            * tests/simple.R: validObject() checking the above.
386    
387            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
388            replacing both dgCMatrix_validate and lgCM*.
389    
390            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
391            fix dimnames setting in other places.
392            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
393    
394    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
397    
398            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
399            symmetry test, via
400            * R/Auxiliaries.R (.as.dgC.0.factors):
401    
402    2006-11-01  Douglas Bates  <bates@r-project.org>
403    
404            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
405            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
406            <CsparseMatrix>) added
407    
408    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * tests/matprod.R: add a variation of Harri's example
411    
412            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
413            recursive infinitely.
414    
415            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
416    
417            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
418    
419    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
422            matrix if possible; test m+m == 2*m; now test dgRMatrix.
423            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
424            satisfy the above test.
425    
426    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
429    
430            * R/dgCMatrix.R: solve(a, b="missing") based on
431            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
432            RHS = NULL.
433    
434            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
435            add more (needed) [t]crossprod() methods.
436    
437            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
438    
439            * R/Auxiliaries.R (as_CspClass): cleanup
440            (drop0): internal utility for "Csparse_drop(*, 0)"
441            (.bail.out.2): encourage active feedback
442    
443    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/dMatrix.R(Compare): new(), then slots [no validity check]
446    
447            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
448            non-valid or 'sorted' case).
449    
450            * R/dsparseMatrix.R: add "chol" method.
451            * R/ddenseMatrix.R: ditto
452    
453            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
454            * NAMESPACE (Ops)
455            * R/diagMatrix.R (diag2T): simple utility used "higher level"
456            coercion; deprecating direct lower level coercions.
457    
458            * R/*.R (seq): use seq_len() and seq_along() where possible.
459    
460    
461    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * DESCRIPTION (Version): 0.9975-5 ready for release
464    
465    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
468    
469    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/AllClass.R (corMatrix): add 'validity' check;
472                    comment out unused "LDL" class definition
473            * NAMESPACE: mention, but do not export "LDL" class
474            * R/corMatrix.R: new (simple), needed for R-devel with
475            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
476              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
477    
478    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
481            use Rprintf and R's error handling.
482    
483    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
486            * tests/matprod.R: add tests for the bug fixed.
487    
488    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
491            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
492    
493    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
496    
497    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * DESCRIPTION (Version): 0.9975-3
500    
501            * R/diagMatrix.R (bdiag): new function constructing block diagonal
502            (sparse) matrices.
503            * man/bdiag.Rd: docu + examples
504    
505            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
506    
507            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
508            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
509    
510            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
511            that result is sparse or diagonal (and not dense).
512    
513            * man/Subassign-methods.Rd: fix examples
514    
515            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
516            should always return a sparse (and not sometimes a diagonal) matrix.
517    
518    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
521    
522    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * DESCRIPTION (Version): 0.9975-2
525    
526            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
527    
528    2006-10-02  Douglas Bates  <bates@R-project.org>
529    
530            * tests/dg_Matrix.R: Simplify test taking into account new code.
531    
532    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
535    
536            * R/lsTMatrix.R: new files w/ missing methods
537            * R/nsTMatrix.R:  "  'for completeness'
538    
539            * tests/Class+Meth.R: a bit less 'not.ok.classes'
540    
541            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
542    
543    
544    2006-09-28  Douglas Bates  <bates@R-project.org>
545    
546            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
547            included.
548    
549            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
550            Export C-callable functions used in Zt_create in lme4.
551    
552    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * DESCRIPTION (Version): 0.9975-1
555    
556            * tests/simple.R: less checks fail; using NA, found that our
557                    kronecker() is not base-compatible with NA's.
558    
559            * R/dMatrix.R: "Compare" method now implemented for all cases
560    
561            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
562    
563            * man/dtpMatrix-class.Rd: mention length of 'x' slot
564    
565            * src/dtpMatrix.c (dtpMatrix_validate): fix check
566            * src/dspMatrix.c (dspMatrix_validate): ditto
567    
568            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
569              including coercion to [nl]tTMatrix.
570    
571            * R/diagMatrix.R (show): print a header line as for other classes.
572    
573    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * src/Makefile.win (SUBDIRS): fix typo
576    
577    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
580    
581    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
582    
583            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
584            symmetric and y missing in R code using %*% (cholmod_aat doesn't
585            accept a symmetric matrix).
586            * tests/group-methods.R: Uncomment test of crossprod applied to
587            lsCMatrix objects.
588    
589    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/AllClass.R (symmetricMatrix): add validity method (available
592            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
593    
594            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
595    
596            * tests/indexing.Rout.save:
597            * tests/indexing.R: additions, mainly for 'lsparse'
598    
599            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
600            case.
601    
602            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
603    
604    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
607                    as 'N' (1-letter - Ok?)
608    
609            * tests/group-methods.R: add test for logical + NAs
610    
611            * R/dMatrix.R ("Compare"): fix to work with NA's
612    
613            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
614    
615            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
616                    which is implemented.
617    
618    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * src/chm_common.c: coerce logical <-> double instead of
621            typecasting;  needed for "l" matrix handling in cholmod.
622    
623            * tests/other-pkgs.R (graph): small extension in "graph" checks.
624    
625            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
626            (Tsp2grNEL): other fixes needed
627    
628    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
631                    Matrices, since "lMatrix", also "lsparseM" can have NA
632            * R/ndenseMatrix.R, etc: new source files
633            * man/nsparseMatrix-classes.Rd, etc: new help files
634            * tests/: adaptions
635            * src/chm_common.c (chm_dense_to_SEXP): and others:
636                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
637            * src/Csparse.c, etc: ditto
638    
639    2006-09-11  Douglas Bates  <bates@R-project.org>
640    
641            * src/Mutils.[ch],init.c inst/include/*.h: Move the
642            alloc_d**Matrix functions to the lme4 package.
643    
644    2006-09-09  Douglas Bates  <bates@R-project.org>
645    
646            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
647            fixed
648    
649    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/lMatrix.R: new
652    
653            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
654    
655            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
656            * man/tcrossprod.Rd: ditto
657    
658    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
659    
660            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
661            for exported functions
662            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
663            Remove partitioning algorithms for sparse matrix reordering.  The
664            copyright on the Metis code was problematic and the methods were
665            rarely used.
666            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
667            operations are now done entirely in CHOLMOD code.
668    
669    2006-09-06  Douglas Bates  <bates@R-project.org>
670    
671            * src/Mutils.h: Remove functions that are no longer used.
672    
673    2006-09-04  Douglas Bates  <bates@R-project.org>
674    
675            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
676            * src/DEPS.mkf: update
677    
678    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * created branches/Matrix-for-R-2.3.x;  on trunk: do
681            * DESCRIPTION (Version): 0.9975-0
682            (Depends): R (>= 2.4.0)
683    
684    2006-09-01  Douglas Bates  <bates@R-project.org>
685    
686            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
687    
688    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
691            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
692    
693            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
694    
695    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
698            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
699            * R/dsparseMatrix.R: ditto
700            * R/Csparse.R: ditto
701    
702    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/dMatrix.R (Compare): improve availability of "<", etc
705            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
706    
707    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
710            of a 0-index which was used as 1-index (..hmm)
711    
712            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
713    
714            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
715            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
716            (.is.diagonal): ditto
717    
718            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
719    
720            * R/Matrix.R (Matrix): also work for NA data
721    
722    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
725            in all cases.
726    
727    2006-08-27  Douglas Bates  <bates@R-project.org>
728    
729            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
730            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
731    
732    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
735            subclasses of "ddenseMatrix"
736            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
737            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
738            instead of half dozen specialized ones.
739    
740    2006-08-25  Douglas Bates  <bates@R-project.org>
741    
742            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
743            <tillard@cirad.fr> - ordering standard errors to match effects.
744    
745    2006-08-24  Douglas Bates  <bates@R-project.org>
746    
747            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
748            on R_ldl.
749            * R/lCholCMatrix.R,
750            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
751            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
752            * many files in ./R and ./src: Use more general version of
753            dup_mMatrix_as_dgeMatrix to simplify method definitions.
754            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
755            dtpMatrix, dspMatrix and dppMatrix conversions.
756    
757    
758    2006-08-23  Douglas Bates  <bates@R-project.org>
759    
760            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
761            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
762            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
763            dgeMatrix_crossprod (may need to do this in other places).
764            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
765            generic and method for dsCMatrix.  Use CHOLMOD for chol().
766    
767    2006-08-22  Douglas Bates  <bates@R-project.org>
768    
769            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
770            types of classed Matrices, matrices or numeric or logical vectors.
771            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
772            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
773            to Mutils.h (as an inline) and change name to Matrix_check_class;
774            fixes in as_cholmod_factor and chm_factor_to_SEXP.
775            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
776            dsCMatrix_matrix_solve.  Comment out vestigial functions.
777            * src/Csparse.c: use diag_P and uplo_P macros.
778    
779    2006-08-21  Douglas Bates  <bates@R-project.org>
780    
781            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
782            valgrind.
783            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
784            inverses.
785            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
786            -Wall warnings.
787            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
788            Use dup_mMatrix_as_dgeMatrix.
789    
790    2006-08-20  Douglas Bates  <bates@R-project.org>
791    
792            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
793            * tests/sparseQR.R: Added
794            * man/sparseQR-class.Rd: Document methods for qr.* generics
795            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
796    
797    2006-08-19  Douglas Bates  <bates@R-project.org>
798    
799            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
800            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
801            and qr.fitted.
802            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
803            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
804    
805    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
808            the base version has no "..." argument.
809    
810            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
811    
812            * R/Matrix.R: define and
813            * NAMESPACE: export as.numeric() and as.logical() methods.
814                    Let's hope these do not badly slow down something...
815            Finally export the zapsmall() method.
816    
817    2006-08-17  Douglas Bates  <bates@R-project.org>
818    
819            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
820            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
821            * src/dtCMatrix.c :Remove code that is no longer used
822            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
823    
824    2006-08-14  Douglas Bates  <bates@R-project.org>
825    
826            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
827            Csparse_to_logical and Csparse_symmetric_to_general.
828            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
829            coercion methods between CsparseMatrix and TsparseMatrix.
830    
831    2006-08-14  Douglas Bates  <bates@R-project.org>
832    
833            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
834            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
835            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
836            possible.
837    
838    2006-08-12  Douglas Bates  <bates@R-project.org>
839    
840            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
841              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
842              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
843              generalize conversions between TsparseMatrix, CsparseMatrix,
844              denseMatrix and matrix.  Preserve triangularity property and
845              propagate Dimnames in the easy cases.
846    
847    2006-08-10  Douglas Bates  <bates@R-project.org>
848    
849            * src/lmer.c: adjust checks in glmer_init for S4SXP
850            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
851            before S4SXP but for the wrong reasons.
852    
853    2006-08-08  Douglas Bates  <bates@R-project.org>
854    
855            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
856            Later modified to return the upper triangle only.
857            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
858    
859    2006-08-07  Douglas Bates  <bates@R-project.org>
860    
861            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
862            R-level conversion to a sparse symmetric class.
863            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
864            Remove conversion to sparse symmetric classes (now done in C code).
865    
866    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
869            * man/band.Rd:  adapt the \dontshow{} unit test.
870    
871    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * DESCRIPTION (Version): 0.995-14  for CRAN
874    
875            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
876    
877            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
878            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
879    
880            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
881            * R/Tsparse.R (tril, triu, band): methods
882            * R/dgRMatrix.R (tril, ...):    ditto
883            * man/band.Rd:                  ditto
884    
885    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/Matrix.R (head, tail): directly use utils:::head.matrix
888                    to be up-to-date automatically.
889    
890    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
893    
894            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
895            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
896            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
897            such that the S4 objects are always created by the current version
898            of R and 'Matrix' class definitions.
899    
900    2006-08-01  Douglas Bates  <bates@R-project.org>
901    
902            * R/lmer.R (LMEoptimize method), tests/lmer.R,
903            inst/external/test3comp.rda: Added warnings for convergence on
904            boundary and test cases.
905    
906            * src/lmer.c (mer_postVar): Modified to return the variances that
907            are marginal to the fixed effects, not conditional on them (which
908            is what the bVar slot contents represent).
909    
910    2006-07-31  Douglas Bates  <bates@R-project.org>
911    
912            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
913            function which calls the C function mer_hat_trace2.
914    
915            * man/ranef.Rd: Include description of "postVar" argument and
916            producing a caterpillar plot.
917    
918    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * NAMESPACE:    change  "correlation" to "corMatrix"
921            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
922            * R/dpoMatrix.R: ditto
923            * R/lmer.R:      ditto
924    
925    2006-07-28  Douglas Bates  <bates@R-project.org>
926    
927            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
928            RZXinv slot's contents into a separate internal function that can
929            be used in mer_hat_trace.
930    
931    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
934            via new smart
935            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
936            utility functions.
937    
938    
939    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/Csparse.R (tril, triu, band): do return *triangular* classed
942            matrices when appropriate; band() even symmetric ones.
943            (replCmat): extend to potentially all "CsparseMatrix"
944            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
945            allow subassignment for special sparse matrices.
946    
947            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
948    
949            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
950            argument; in glmer_*(): print only if(verbose).
951    
952            speed-optimize a few places by moving REAL(.) out of loops.
953    
954            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
955    
956    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
959                    since that wrongly triggers also for M[ logi , ]
960    
961            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
962            a symmetric matrix that results in a non-symmetric one.
963            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
964    
965            * R/dMatrix.R: make round(M) work as round(M, 0)
966    
967            * R/dgTMatrix.R (image): coordinate system and axis now use
968            1-based indices, not 0-based ones.
969    
970            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
971            * tests/indexing.R: test it.
972    
973            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
974            * man/isSymmetric-methods.Rd: and document it.
975    
976            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
977            * man/SparseM-conv.Rd: docu them
978    
979            * tests/other-pkgs.R: renamed from tests/graph.R and add example
980                    for 'SparseM' conversions
981    
982    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
983    
984            * R/Matrix.R (head): added head() and tail() methods.
985    
986    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * DESCRIPTION (Version): 0.995-12 released to CRAN
989    
990    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * tests/simple.R: add check for correct dsT -> dgT coercion;
993                    add check for correct printing of symmetric sparse matrices.
994    
995            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
996            for sparse symmetric matrices.
997    
998            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
999            diagonal twice.
1000    
1001    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1002    
1003            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1004            being applied to the x slot (detected by Brian Ripley).
1005    
1006    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1009    
1010            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1011    
1012    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * src/lgCMatrix.c (lgCMatrix_diag): new function
1015            * R/lgCMatrix.R (diag): for new method
1016    
1017            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1018                 ==> construction of illegal "*gTMatrix" via new() should
1019                 now be much less easy:
1020            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1021    
1022            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1023                    directly.
1024            * man/Matrix.Rd: documents it.
1025    
1026    2006-07-06  Douglas Bates  <bates@R-project.org>
1027    
1028            * src/pedigree.c (pedigree_inbreeding): Correction in
1029            initialization.  This function is not currently being used and is
1030            not fully tested.
1031    
1032            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1033            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1034            objects.  Modified validity check on pedigree objects to account
1035            for nonparallel patterns of missingness of parents.
1036    
1037            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1038            class.
1039    
1040    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * R/pMatrix.R: coercion pMatrix -> Tsparse
1043    
1044    2006-06-12  Douglas Bates  <bates@R-project.org>
1045    
1046            * DESCRIPTION (Version): 0.995-11 released to CRAN
1047    
1048            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1049            the output from mcmcsamp.
1050    
1051    2006-06-10  Douglas Bates  <bates@R-project.org>
1052    
1053            * R/lmer.R (simulestimate): added C code for calculating the trace
1054            of the hat matrix.
1055    
1056    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1059            classes.
1060            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1061    
1062    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * R/dgTMatrix.R (colSums): etc. All four of
1065            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1066            all "Matrices".
1067    
1068    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1069    
1070            * R/lmer.R (panel.ci): Add a reference line at zero and a
1071            background grid to the qqmath plot of ranef.lmer.
1072    
1073    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1074    
1075            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1076            grouping factors to be specified in the formula as (1|foo/bar).
1077    
1078    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1079    
1080            * R/lmer.R (findbars and others): Change check of is.numeric to
1081            !is.language to resolve the bug reported by Jacob Wegelin.
1082    
1083            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1084            code to evaluate inbreeding coefficients without calculating T,
1085            based on code in Sargolzaei and Iwaisaki's paper.
1086    
1087    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1088    
1089            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1090            generic and mer methods for isNested and denomDF. This denomDF was
1091            an attempt to emulate that in lme but I don't think that makes
1092            sense.  Use the trace of the hat matrix instead.
1093    
1094    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1097            the C code depending on a slot structure that's no longer valid.
1098            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1099    
1100    
1101    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1102    
1103            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1104            of lowerTriMatrix generic and methods to tril (also upper to triu)
1105            and added a general band extractor.
1106    
1107    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1108    
1109            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1110            allowable range with NAs. Added a corresponding check in the
1111            validity check for the pedigree class.
1112    
1113            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1114            crossprod methods now inherits from symmetricMatrix.
1115    
1116    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1117    
1118            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1119            generics lowerTriMatrix and upperTriMatrix along with methods for
1120            the Csparse virtual class.  Also added a C function Csparse_band
1121            that implements these methods by calling cholmod_band.
1122    
1123    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1126            erased when it was NULL.  This led to invalid subselections!
1127    
1128    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1129    
1130            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1131            in method for "t" so as not to lose the unit diagonal property.
1132    
1133    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1134    
1135            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1136            and methods.  This is now an option to the ranef method for the
1137            mer class.
1138    
1139            * src/cs_utils.c: Ensure that the nz component is -1 for a
1140            compressed column-oriented matrix.  Minor formatting cleanup.
1141    
1142            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1143            objects.
1144    
1145    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1146    
1147            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1148            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1149    
1150    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1151    
1152            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1153            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1154    
1155            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1156            for the dtCMatrix class.
1157    
1158    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1159    
1160            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1161            and methods for it.
1162    
1163    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1166            arguments, such that M %*% 1:6 now works
1167            * Tests/matprod.R: test the above
1168    
1169    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1170    
1171            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1172            the ranef.lmer class.
1173    
1174            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1175            methods to extract the posterior variances from the bVar slot.
1176    
1177    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1180            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1181    
1182            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1183            * tests/simple: (extended)
1184    
1185            * R/sparseMatrix.R (isTriangular): now using much improved
1186            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1187    
1188    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1189    
1190            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1191            (problem report from Franklin Parlamis).  This should be done
1192            generally.
1193    
1194    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1195    
1196            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1197            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1198            update the plot methods.
1199    
1200    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1201    
1202            * R/lmer.R (resid and ranef methods):  Added methods for the
1203            "residuals" and "resid" generic but only for linear mixed model
1204            fits.  Changed the ranef method to return a list of data frames so
1205            that the plot methods now work.
1206    
1207    2006-03-16  Douglas Bates  <bates@bates2>
1208    
1209            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1210            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1211    
1212            * DESCRIPTION (Date): New release
1213    
1214    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1215    
1216            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1217    
1218            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1219            * man/KNex.Rd: and other help files
1220            * tests/*.R: several ones needed adaption
1221            * inst/doc/Comparisons.Rnw: ditto
1222    
1223    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1226    
1227            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1228    
1229    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1232    
1233            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1234    
1235    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1236    
1237            * R/dMatrix.R: enable things like  M [ M < 10 ]
1238            * R/dgeMatrix.R: implement it
1239    
1240    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * R/AllClass.R: define "summary.mer" and "*.lmer"
1243            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1244            * R/lmer.R (show): now works with summary()
1245    
1246    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1249            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1250                    support the above
1251    
1252    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1253    
1254            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1255            Use glmFit$prior.weights for weights in a glmm.
1256            Allow an option usePQL = FALSE to skip the PQL steps for the
1257            Laplace method (and, in time, the AGQ method).
1258    
1259            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1260            into a separate function internal_mer_Xfactor to be able to call
1261            it from internal_bhat.
1262    
1263    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1264    
1265            * tests/Class+Meth.R (tstMatrixClass): function for much better
1266            testing; now again of all actual classes.
1267    
1268            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1269                    use macros and define make_d_matrix_* and make_i_matrix_*
1270                    where _i_ is for the ldense routines:
1271    
1272            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1273            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1274    
1275            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1276    
1277    
1278    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1279    
1280            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1281                    many different kinds of matrices.
1282            * R/*.R: quite a few new methods were needed for R CMD check with
1283                    new Matrix().  Very good for users playing around.
1284    
1285    
1286    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1287    
1288            * src/dgeMatrix.c (dMatrix_validate): new
1289            * src/Mutils.c (dense_nonpacked_validate): new
1290    
1291            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1292    
1293    
1294    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1295    
1296            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1297    
1298    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1299    
1300            * DESCRIPTION (Version): 0.99-6 released to CRAN
1301    
1302            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1303            segfault in cases with multiple non-nested grouping factors.
1304    
1305    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1308                    (Depends): also on 'utils'
1309    
1310            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1311            * R/diagMatrix.R (Diagonal): constructor and methods for
1312            diagonal matrices
1313    
1314            * R/ltTMatrix.R: new "minimal methods"
1315    
1316    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1319            all methods (and help files).
1320    
1321    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1322    
1323            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1324                    for case (dimn.  op  no_dimn.)
1325    
1326    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1327    
1328            * DESCRIPTION (Version): 0.99-2  released to CRAN
1329    
1330    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1331    
1332            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1333            by Julian Faraway.
1334    
1335    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1336    
1337            * R/Auxiliaries.R (try_as): new utility
1338            * R/sparseMatrix.R: use try_as() in coercion to original class
1339    
1340    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1341    
1342            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1343    
1344    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1345    
1346            * R/Auxiliaries.R (dimNamesCheck): added
1347    
1348            * R/Matrix.R (as.array), (as.vector): new
1349    
1350    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1351    
1352            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1353                    default.
1354            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1355                    "pMatrix" now contains "sparseMatrix"
1356    
1357    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * tests/Class+Meth.R: new tests; t(t(m)) == m
1360    
1361            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1362    
1363            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1364            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1365    
1366            * R/dspMatrix.R: typo in "t" method
1367    
1368    2005-09-18  Douglas Bates  <bates@wisc.edu>
1369    
1370            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1371            * R/Tsparse.R: instead of R/gTMatrix.R
1372            * R/Csparse.R: new
1373            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1374            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1375            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1376                            via cholmod
1377    
1378    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1379    
1380            * R/Auxiliaries.R (non0ind): new function using new C code
1381            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1382    
1383    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1384    
1385            * src/chm_common.h: header file required by all C sources that
1386            call CHOLMOD functions.  It defines a cholmod_common structure
1387            called 'c' whose address is passed as the last argument to
1388            (virtually) every CHOLMOD function.
1389    
1390            * src/Pattern.c: Simple example of the use of CHOLMOD.
1391    
1392            * src/init.c: initialize and finalize the cholmod_common structure.
1393    
1394            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1395            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1396    
1397    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1398    
1399            * inst/test-tools.R: new file collecting the utility functions used
1400                    in ./tests/*.R
1401    
1402            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1403            * R/Matrix.R (cbind2): methods for NULL and missing
1404    
1405    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1406    
1407            * R/AllClass.R: new "index" class for "[" and "[<-":
1408                    First cut at "symmetricMatrix" and "triangularMatrix"
1409            * R/gTMatrix.R (.ind.prep): new function;
1410                    Logical and character indexing now work too.
1411            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1412            * tests/indexing.R: new, including *.Rout.save
1413            * tests/dgTMatrix.R: new
1414    
1415    2005-08-29  Douglas Bates  <bates@wisc.edu>
1416    
1417            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1418            indicator pos not being updated.  Also enforced upper triangular
1419            for symmetric case.  Need to coerce edges component of elements of
1420            edge list - grr! (Why don't they define their classes cleanly?)
1421    
1422    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/Matrix.R:  added first "[<-" methods; not yet functional
1425            * R/denseMatrix.R: ditto
1426            * man/Subassign-methods.Rd: new help file for these
1427    
1428    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * DESCRIPTION (Version): 0.98-6
1431    
1432            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1433            matrices.
1434    
1435    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1438                    as( <logical>, "matrix")
1439    
1440            * R/pMatrix.R: coercion to "lgTMatrix"
1441    
1442            * R/gTMatrix.R: new virtual class to define "[" methods for.
1443            * man/gTMatrix-class.Rd:
1444            * General slight re-organization of where "[" methods are defined.
1445              more to come.
1446    
1447    2005-08-18  Douglas Bates  <bates@wisc.edu>
1448    
1449            * DESCRIPTION (Version): 0.98-5  released to CRAN
1450    
1451            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1452            * .....
1453    
1454    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1455    
1456            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1457            or glmer objects.
1458    
1459    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1460    
1461            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1462    
1463    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1464    
1465            * R/HBMM.R: finish re-writing R-only code.
1466    
1467    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1468    
1469            * man/externalFormats.Rd: move documentation for writeHB and
1470            writeMM here.
1471    
1472            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1473            (suggested by Paul Roecker).
1474    
1475            * tests/validObj.R (assertError): Comment out test that is failing
1476            after recent changes in r-devel.
1477    
1478    
1479    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/AllClass.R: intermediate virtual class "denseMatrix"
1482            * man/denseMatrix-class.Rd
1483            * NAMESPACE: export it, and also export
1484            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1485    
1486    2005-08-10  Douglas Bates  <bates@wisc.edu>
1487    
1488            * DESCRIPTION (Version): 0.98-3 to CRAN
1489    
1490            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1491            matrix_solve code (which was really, really wrong).
1492    
1493    2005-08-07  Douglas Bates  <bates@wisc.edu>
1494    
1495            * DESCRIPTION (Version): 0.98-2
1496    
1497            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1498    
1499            * R/lmer.R (abbrvNms): new
1500            * R/lmer.R (mcmcsamp): allow transformed parameters
1501            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1502            for the Harwell-Boeing and the MatrixMarket formats.
1503    
1504    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1505    
1506            * man/dtrMatrix-class.Rd: add examples
1507            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1508    
1509            * TODO: note the dtpMatrix (docu) bug
1510    
1511            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1512            in order to ensure that new as.matrix() is used by old functions,
1513            e.g., svd(), qr(), eigen(), dist(),..;
1514                  apply(), also matplot() or pairs().
1515    
1516    
1517    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1520              add comments about 'control' / lmerControl() arguments
1521    
1522    2005-07-27  Douglas Bates  <bates@wisc.edu>
1523    
1524            * man/sleepstudy.Rd: Added the sleep data set.
1525            * DESCRIPTION (Version): 0.98-1  released to CRAN
1526    
1527    2005-07-12  Douglas Bates  <bates@wisc.edu>
1528            * man/sleepstudy.Rd: Added the sleep data set.
1529    
1530            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1531            .Call calls that were producing spurious output.
1532    
1533    2005-07-05  Douglas Bates  <bates@wisc.edu>
1534    
1535            * R/lmer.R (lmer): stored updated variance component estimates in
1536            mer object for the generalized model.  (Bug reported by Renaud
1537            Lancelot).
1538    
1539    2005-07-03  Douglas Bates  <bates@wisc.edu>
1540    
1541            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1542            unidimensional case.
1543    
1544    2005-06-08  Douglas Bates  <bates@wisc.edu>
1545    
1546            * DESCRIPTION (Version): 0.96-1
1547    
1548            * moved  lmer-class' R and C code moved from lme4 to here
1549    
1550    2005-06-04  Douglas Bates  <bates@wisc.edu>
1551    
1552            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1553            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1554    
1555    2005-06-02  Douglas Bates  <bates@wisc.edu>
1556    
1557            * src/Makefile.win: Forgot to update this when Makefile changed.
1558    
1559    2005-05-11  Douglas Bates  <bates@wisc.edu>
1560    
1561            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1562            bug reported by Kurt Hornik and Michael Hahsler.
1563    
1564    2005-05-10  Douglas Bates  <bates@wisc.edu>
1565    
1566            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1567            logical sparse matrices.  These will also be used in the symbolic
1568            analysis for lmer objects.
1569    
1570            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1571            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1572    
1573    2005-05-06  Douglas Bates  <bates@wisc.edu>
1574    
1575            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1576            colMeans, colSums, rowMeans and rowSums.
1577    
1578    2005-04-18  Douglas Bates  <bates@wisc.edu>
1579    
1580            * src/lgCMatrix.[ch]: code for _validate method and stub for
1581            multiplication operation.
1582    
1583            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1584            to dgetrs.
1585    
1586            * src/init.c: Fix cut-and-paste error in definition of
1587            dgeMatrix_matrix_solve
1588    
1589            * src/{many files}: Tighten code by using ALLOC_SLOT.
1590    
1591    2005-04-15  Douglas Bates  <bates@wisc.edu>
1592    
1593            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1594    
1595            * DESCRIPTION: Eliminate import of stats.
1596    
1597    
1598    2005-04-06  Douglas Bates  <bates@wisc.edu>
1599    
1600            * R/AllClass.R : add logical sparse matrix classes
1601    
1602    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1603    
1604            * R/dgTMatrix.R: add "[" method for triplet matrices
1605            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1606    
1607    2005-03-31  Douglas Bates  <bates@wisc.edu>
1608    
1609            * DESCRIPTION (Version): release 0.95-5 to CRAN
1610    
1611            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1612            * R/sparseMatrix.R: %*%, crossprod()
1613            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1614            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1615            * src/lmer.c (lmer_fitted): fix thinko
1616    
1617    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1618    
1619            * R/AllClass.R: add two virtual sparse classes ``on top''
1620    
1621    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1622    
1623            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1624                    correspondingly fix examples and tests/ since new()
1625                    doesn't work for virtual classes.
1626    
1627    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1628    
1629            * R/Matrix.R (as.matrix): method and one for unname()
1630            * tests/dpoMatrix.R: tests should now be less platform dependent;
1631              also run for R 2.1.0; using as.matrix()
1632    
1633    2005-03-15  Douglas Bates  <bates@wisc.edu>
1634    
1635            * R/pMatrix.R: "pMatrix" class added
1636            * ....
1637    
1638    2005-03-14  Douglas Bates  <bates@wisc.edu>
1639    
1640            * R/dtpMatrix.R: Add unpack method and an example.
1641    
1642            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1643            of general symmetric matrices and associated S4 methods.
1644    
1645    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1646            +
1647    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1648    
1649            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1650              crossprod() and "%*%" methods added; tests, too.
1651            * tests/matprod.R: new, for testing these
1652    
1653    2005-03-03  Douglas Bates  <bates@wisc.edu>
1654    
1655            * src/lmer.c (lmer_fitted): Added.
1656    
1657    2005-03-02  Douglas Bates  <bates@wisc.edu>
1658    
1659            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1660    
1661    2005-02-28  Douglas Bates  <bates@wisc.edu>
1662    
1663            * src/*.c,po/,inst/po: Internationalization and localization of
1664            the package.
1665    
1666            * src/ldl.[ch]: Removed these as their contents are referenced in the
1667            R_ldl.c file.
1668    
1669            * src/flame.[ch]: Removed these source files.
1670    
1671            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1672    
1673            * src/LU.[ch],src/init.c: absorb in factorizations
1674    
1675            * src/Mutils.h: prepare for internationalization
1676    
1677            * src/cblas.h: move the enum definitions to Mutils.h and remove
1678            this file
1679    
1680    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1681    
1682            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1683    
1684            * R/dtrMatrix.R: fix t() method
1685    
1686            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1687            * NAMESPACE: export them (and import generics from "methods")
1688            * tests/group-methods.R : and test them.
1689    
1690            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1691            border case
1692    
1693    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1694    
1695            * DESCRIPTION (Version): 0.95-2  released to CRAN
1696    
1697            * src/dgBCMatrix.c:
1698            * src/lmer.c: many changes
1699            * ...
1700    
1701    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1702    
1703            * R/Matrix.R: add more sophisticated show() method.
1704    
1705    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1706    
1707            * */* : almost complete reorganization of classes.
1708    
1709    2005-01-26  Douglas Bates  <bates@wisc.edu>
1710    
1711            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1712            for the geMatrix class.
1713    
1714    2005-01-24  Douglas Bates  <bates@wisc.edu>
1715    
1716            * src/Makefile (clean): Remove *.a and *.so
1717    
1718            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1719    
1720    2005-01-23  Douglas Bates  <bates@wisc.edu>
1721    
1722            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1723            had an effect in cases with more than 2 grouping factors.
1724    
1725    2005-01-03  Douglas Bates  <bates@wisc.edu>
1726    
1727            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1728    
1729    2004-12-23  Douglas Bates  <bates@wisc.edu>
1730    
1731            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1732            and R_useDynamicSymbols (suggested by B.D.Ripley).
1733    
1734    2004-12-14  Douglas Bates  <bates@wisc.edu>
1735    
1736            * R/sscMatrix.R: Add determinant methods
1737    
1738            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1739            for tripletMatrix to matrix.
1740    
1741    2004-12-13  Douglas Bates  <bates@wisc.edu>
1742    
1743            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1744            no longer used.
1745    
1746          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1747          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1750 
1750          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1751          Fixes part but not all of #15.          Fixes part but not all of #15.
1752    
1753  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1754    
1755          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1756          scalar grouping factors corrected.          scalar grouping factors corrected.
1757    
1758  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1759    
1760          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1761    
1762  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1763    
1764          * 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
1765          .h file can be included.          .h file can be included.
1766    
1767  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1768    
1769          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1770          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1771    
1772          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1773    
1774  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1775    
1776          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1777    
1778  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1779    
1780          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1781    
1782  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1783    
1784          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1785    
1786  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1787    
1788          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1789    
1790  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1791    
1792          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1793          routines.          routines.
1794    
1795  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1796    
1797          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1798    
1799  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1800    
1801          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1802    

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