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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1844, Wed May 16 20:40:34 2007 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
4    
5    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * DESCRIPTION (Version): 0.99875-1
8            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
9    
10    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
13            indexing
14            * tests/indexing.R: test set for that.
15    
16    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
19            entries.
20            * tests/indexing.R(out): add regression test for it
21    
22    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
25            name for "!" method definitions.
26    
27    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Tsparse.R (intI): new utility, used for "[" :
30                    Cleanup up there, and fixes for duplicated indices - more TODO!
31    
32            * tests/indexing.R(out): more tests
33    
34    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
35    
36            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
37            code that is now part of the R Lapack library.
38    
39            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
40            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
41    
42    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
45    
46    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
49            up with extraneous names '0'...'<n-1>'
50    
51    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/dgTMatrix.R (mat2dgT): care about NAs
54    
55    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/kronecker.R: triangularity preserving methods
58    
59    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/kronecker.R: new file collecting kronecker() methods in one
62                    place.  Goal: become much faster!
63    
64    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
67            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
68            can be much faster.
69    
70            * tests/matprod.R: add regression tests for these (upper & lower).
71    
72    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Matrix.R (diff): method for our Matrices.
75    
76            * R/sparseMatrix.R (isDiagonal): check dim()!
77    
78    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Matrix.R (dim<-): new method for "reshape()" built on a
81            proposal from Tamas Papp.
82    
83    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
86    
87            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
88            rather define and export  cBind() and rBind() only.
89            --> useRs *must* change code that used to have cbind()/rbind() !!
90    
91            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
92            * R/bind.Rout.save: ditto
93    
94    2007-02-16  Douglas Bates  <bates@r-project.org>
95    
96            * DESCRIPTION (Date, Version): 0.9975-11 with new date
97            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
98            const modifier on declaration of the array 'valid'
99    
100    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
101    
102            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
103    
104    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
107    
108            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
109            * tests/simple.R: test the above and some of these coercions:
110    
111            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
112                    be careful to avoid infinite recursion, using new coercions in
113            * R/ngCMatrix.R and nsC... and ntC...
114            * R/lsparseMatrix.R: ditto
115    
116            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
117    
118            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
119            * R/Rsparse.R: reactivate .Call()s
120    
121            * tests/Class+Meth.R: a bit more on actual classes
122    
123    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
126    
127    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.9975-10 to upload
130    
131            * tests/Class+Meth.R (tstMatrixClass): require coercions to
132            specific classes less unconditionally.
133    
134            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
135    
136            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
137    
138            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
139            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
140            R_to_CMatrix segfaults on one platform.
141            Eliminate most coercion method to *specific* classes, and replace
142            with virtual classes coercions.
143    
144    
145    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
146    
147            * src/init.c: export the CHM...._validate() placeholders, since
148            they *are* called.
149    
150            * tests/Class+Meth.R (classCanCoerce): and starting to test
151            all as(<from>, <to>)
152    
153    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
156            * tests/indexing.R: tested now
157            * tests/indexing.Rout.save: updated
158    
159            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
160            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
161            appropriate.
162    
163            * NAMESPACE: export a trivial
164            * R/Matrix.R: drop() Matrix-method
165    
166            * R/AllClass.R: moved all prototypes to virtual super classes.
167    
168            * R/Rsparse.R: many more coercions to have less exceptions in
169            * tests/Class+Meth.R:
170    
171            * R/Ops.R (Compare): tweak for case with NA
172            * tests/simpl.R: hence another 'FIXME' eliminated
173    
174    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
177            objects.
178    
179            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
180              and more of "!", "&", "|", all, any; coercions
181    
182            * R/Rsparse.R: many coercions (which enable quite a few other
183            methods), thanks to enhancements in
184            * src/dgCMatrix.c (R_to_CMatrix): new, and
185            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
186            symmetric & triangular and ..RMatrix objects.
187    
188            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
189            renamed file from src/dsTMatrix.c;
190            now dealing with symmetric and triangular Tsparse coercions, both
191            to dense and general.
192    
193    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
196    
197            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
198            where sensible when the <numeric> is of length > 1.
199    
200    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R ([<-): for M[] <- value: fix length
203    
204    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
207            * R/ndenseMatrix.R: new coercions n* -> l*
208    
209    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
212    
213            * R/Ops.R ("Logic"): and other "Ops", many updates
214    
215    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Mutils.h (SET_DimNames): new utility
218    
219            * R/Auxiliaries.R (nnzero): improved and now exported via
220    
221            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
222    
223    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/diagMatrix.R (!): fix typo.
226    
227    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/Auxiliaries.R (as_Csparse): and quite a few others:
230                    allow to pass class definition --> speedup
231            * R/sparseMatrix.R: apply the above
232    
233            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
234    
235            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
236            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
237            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
238    
239            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
240    
241            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
242            and use it for "sparse*" as well, since it's faster than the
243            as_Csparse(.) way.
244    
245    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
248    
249    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
252            as method for   M[ ij ] <- v
253            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
254    
255            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
256            FALSE answer
257    
258            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
259            * tests/indexing.R: test it, and some of the above
260    
261    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/Auxiliaries.R (is_duplicatedT): new utility
264    
265    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * src/init.c (R_init_Matrix): export cholmod_scale
268    
269    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
272            base::as.matrix to (x, ...)
273    
274    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
277            file; start using "Logic", hence
278    
279            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
280            * NAMESPACE: import and export "Logic"
281    
282    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
285            only needed previously to R version 2.5.0.
286    
287    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
290    
291            * R/Tsparse.R (replTmat): fix subassignment of triangular
292            * R/Csparse.R (replCmat): ditto
293            * tests/indexing.R: more tests, incl the above fix
294    
295    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (drop0): extend for non CSparse
298            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
299    
300            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
301                    use uplo correctly (!); other places: use uplo_P() macro
302    
303            * R/Csparse.R (replCmat): call diagU2N() when needed
304            * R/Tsparse.R (replTmat): ditto
305    
306            * src/dtCMatrix.c (tCMatrix_validate): new
307            * src/dtTMatrix.c (tTMatrix_validate): new, used in
308            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
309    
310            * R/diagMatrix.R (replDiag): to use in [<-
311    
312    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
315                    also more general diagU2N().
316    
317    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
320            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
321    
322    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * tests/bind.R: a few more cases
325            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
326    
327            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
328            * R/ddenseMatrix.R (cbind2/rbind2)
329            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
330            * tests/indexing.R
331            * tests/indexing.Rout.save: updated
332    
333    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
336            * tests/indexing.R
337    
338    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
341            align with proper position of "0", i.e., right for integers.
342            argument 'align' by default is "fancy".
343    
344    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
347            * R/Csparse.R: and fix "Compare" for more cases.
348            * tests/Class+Meth.R: test some of these (m == m, m != m)
349    
350    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/lsparseMatrix.R: all() and any() methods
353            * R/ldenseMatrix.R:      ditto
354            * NAMESPACE, R/Matrix.R: ditto
355    
356            * man/all-methods.Rd: document them minimally
357    
358            * tests/simple.R: add a few examples for these
359    
360    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/Tsparse.R ([): fix long standing typo in symmetric case
363            * man/dsCMatrix-class.Rd: add example exhibiting the above case
364    
365    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
368            to LL before converting to a sparse matrix. (The LDL form can be
369            converted to a sparse matrix but it is implicitly a unit
370            triangular matrix and a diagonal matrix overwritten on the diagonal.)
371    
372    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
375    
376    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * DESCRIPTION (Version): updated -> release 0.9975-7
379            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
380    
381    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
384    
385    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
388            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
389            is exactly singular.
390    
391    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * DESCRIPTION (Date): updated -> release 0.9975-6
394    
395    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
398            now returns symmetric.
399    
400            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
401    
402            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
403            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
404    
405            * R/Auxiliaries.R (.type.kind): added
406    
407    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
410            running src/CSparse_install.sh
411    
412            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
413    
414    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
417            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
418    
419            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
420    
421            * tests/Class+Meth.R (tstMatrixClass): now assure
422            the (important in method programming) property :
423    
424                    ###>>  Every "Matrix" is either
425                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
426    
427                    (where "*" stands for "Matrix")
428    
429            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
430    
431            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
432            * tests/validObj.R: checks for "comparison"
433    
434            * R/sparseMatrix.R ([): improved indexing for sparse;
435                    trying to keep <symmetric>[ n, n] symmmetric
436    
437            * tests/indexing.R: indexing for logical sparse now ok
438    
439    
440    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/Tsparse.c: use xTsparse_validate() , and hence remove
443    
444            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
445    
446    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
449    
450            * tests/simple.R: validObject() checking the above.
451    
452            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
453            replacing both dgCMatrix_validate and lgCM*.
454    
455            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
456            fix dimnames setting in other places.
457            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
458    
459    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
462    
463            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
464            symmetry test, via
465            * R/Auxiliaries.R (.as.dgC.0.factors):
466    
467    2006-11-01  Douglas Bates  <bates@r-project.org>
468    
469            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
470            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
471            <CsparseMatrix>) added
472    
473    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * tests/matprod.R: add a variation of Harri's example
476    
477            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
478            recursive infinitely.
479    
480            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
481    
482            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
483    
484    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
487            matrix if possible; test m+m == 2*m; now test dgRMatrix.
488            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
489            satisfy the above test.
490    
491    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
494    
495            * R/dgCMatrix.R: solve(a, b="missing") based on
496            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
497            RHS = NULL.
498    
499            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
500            add more (needed) [t]crossprod() methods.
501    
502            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
503    
504            * R/Auxiliaries.R (as_CspClass): cleanup
505            (drop0): internal utility for "Csparse_drop(*, 0)"
506            (.bail.out.2): encourage active feedback
507    
508    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/dMatrix.R(Compare): new(), then slots [no validity check]
511    
512            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
513            non-valid or 'sorted' case).
514    
515            * R/dsparseMatrix.R: add "chol" method.
516            * R/ddenseMatrix.R: ditto
517    
518            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
519            * NAMESPACE (Ops)
520            * R/diagMatrix.R (diag2T): simple utility used "higher level"
521            coercion; deprecating direct lower level coercions.
522    
523            * R/*.R (seq): use seq_len() and seq_along() where possible.
524    
525    
526    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * DESCRIPTION (Version): 0.9975-5 ready for release
529    
530    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
533    
534    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/AllClass.R (corMatrix): add 'validity' check;
537                    comment out unused "LDL" class definition
538            * NAMESPACE: mention, but do not export "LDL" class
539            * R/corMatrix.R: new (simple), needed for R-devel with
540            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
541              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
542    
543    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
546            use Rprintf and R's error handling.
547    
548    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
551            * tests/matprod.R: add tests for the bug fixed.
552    
553    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
556            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
557    
558    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
559    
560            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
561    
562    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * DESCRIPTION (Version): 0.9975-3
565    
566            * R/diagMatrix.R (bdiag): new function constructing block diagonal
567            (sparse) matrices.
568            * man/bdiag.Rd: docu + examples
569    
570            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
571    
572            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
573            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
574    
575            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
576            that result is sparse or diagonal (and not dense).
577    
578            * man/Subassign-methods.Rd: fix examples
579    
580            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
581            should always return a sparse (and not sometimes a diagonal) matrix.
582    
583    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
586    
587    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
588    
589            * DESCRIPTION (Version): 0.9975-2
590    
591            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
592    
593    2006-10-02  Douglas Bates  <bates@R-project.org>
594    
595            * tests/dg_Matrix.R: Simplify test taking into account new code.
596    
597    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
600    
601            * R/lsTMatrix.R: new files w/ missing methods
602            * R/nsTMatrix.R:  "  'for completeness'
603    
604            * tests/Class+Meth.R: a bit less 'not.ok.classes'
605    
606            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
607    
608    
609    2006-09-28  Douglas Bates  <bates@R-project.org>
610    
611            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
612            included.
613    
614            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
615            Export C-callable functions used in Zt_create in lme4.
616    
617    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * DESCRIPTION (Version): 0.9975-1
620    
621            * tests/simple.R: less checks fail; using NA, found that our
622                    kronecker() is not base-compatible with NA's.
623    
624            * R/dMatrix.R: "Compare" method now implemented for all cases
625    
626            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
627    
628            * man/dtpMatrix-class.Rd: mention length of 'x' slot
629    
630            * src/dtpMatrix.c (dtpMatrix_validate): fix check
631            * src/dspMatrix.c (dspMatrix_validate): ditto
632    
633            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
634              including coercion to [nl]tTMatrix.
635    
636            * R/diagMatrix.R (show): print a header line as for other classes.
637    
638    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * src/Makefile.win (SUBDIRS): fix typo
641    
642    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
645    
646    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
649            symmetric and y missing in R code using %*% (cholmod_aat doesn't
650            accept a symmetric matrix).
651            * tests/group-methods.R: Uncomment test of crossprod applied to
652            lsCMatrix objects.
653    
654    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/AllClass.R (symmetricMatrix): add validity method (available
657            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
658    
659            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
660    
661            * tests/indexing.Rout.save:
662            * tests/indexing.R: additions, mainly for 'lsparse'
663    
664            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
665            case.
666    
667            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
668    
669    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
672                    as 'N' (1-letter - Ok?)
673    
674            * tests/group-methods.R: add test for logical + NAs
675    
676            * R/dMatrix.R ("Compare"): fix to work with NA's
677    
678            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
679    
680            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
681                    which is implemented.
682    
683    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/chm_common.c: coerce logical <-> double instead of
686            typecasting;  needed for "l" matrix handling in cholmod.
687    
688            * tests/other-pkgs.R (graph): small extension in "graph" checks.
689    
690            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
691            (Tsp2grNEL): other fixes needed
692    
693    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
696                    Matrices, since "lMatrix", also "lsparseM" can have NA
697            * R/ndenseMatrix.R, etc: new source files
698            * man/nsparseMatrix-classes.Rd, etc: new help files
699            * tests/: adaptions
700            * src/chm_common.c (chm_dense_to_SEXP): and others:
701                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
702            * src/Csparse.c, etc: ditto
703    
704    2006-09-11  Douglas Bates  <bates@R-project.org>
705    
706            * src/Mutils.[ch],init.c inst/include/*.h: Move the
707            alloc_d**Matrix functions to the lme4 package.
708    
709    2006-09-09  Douglas Bates  <bates@R-project.org>
710    
711            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
712            fixed
713    
714    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/lMatrix.R: new
717    
718            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
719    
720            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
721            * man/tcrossprod.Rd: ditto
722    
723    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
726            for exported functions
727            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
728            Remove partitioning algorithms for sparse matrix reordering.  The
729            copyright on the Metis code was problematic and the methods were
730            rarely used.
731            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
732            operations are now done entirely in CHOLMOD code.
733    
734    2006-09-06  Douglas Bates  <bates@R-project.org>
735    
736            * src/Mutils.h: Remove functions that are no longer used.
737    
738    2006-09-04  Douglas Bates  <bates@R-project.org>
739    
740            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
741            * src/DEPS.mkf: update
742    
743    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * created branches/Matrix-for-R-2.3.x;  on trunk: do
746            * DESCRIPTION (Version): 0.9975-0
747            (Depends): R (>= 2.4.0)
748    
749    2006-09-01  Douglas Bates  <bates@R-project.org>
750    
751            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
752    
753    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
756            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
757    
758            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
759    
760    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
763            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
764            * R/dsparseMatrix.R: ditto
765            * R/Csparse.R: ditto
766    
767    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dMatrix.R (Compare): improve availability of "<", etc
770            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
771    
772    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
775            of a 0-index which was used as 1-index (..hmm)
776    
777            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
778    
779            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
780            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
781            (.is.diagonal): ditto
782    
783            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
784    
785            * R/Matrix.R (Matrix): also work for NA data
786    
787    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
790            in all cases.
791    
792    2006-08-27  Douglas Bates  <bates@R-project.org>
793    
794            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
795            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
796    
797    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
800            subclasses of "ddenseMatrix"
801            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
802            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
803            instead of half dozen specialized ones.
804    
805    2006-08-25  Douglas Bates  <bates@R-project.org>
806    
807            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
808            <tillard@cirad.fr> - ordering standard errors to match effects.
809    
810    2006-08-24  Douglas Bates  <bates@R-project.org>
811    
812            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
813            on R_ldl.
814            * R/lCholCMatrix.R,
815            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
816            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
817            * many files in ./R and ./src: Use more general version of
818            dup_mMatrix_as_dgeMatrix to simplify method definitions.
819            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
820            dtpMatrix, dspMatrix and dppMatrix conversions.
821    
822    
823    2006-08-23  Douglas Bates  <bates@R-project.org>
824    
825            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
826            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
827            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
828            dgeMatrix_crossprod (may need to do this in other places).
829            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
830            generic and method for dsCMatrix.  Use CHOLMOD for chol().
831    
832    2006-08-22  Douglas Bates  <bates@R-project.org>
833    
834            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
835            types of classed Matrices, matrices or numeric or logical vectors.
836            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
837            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
838            to Mutils.h (as an inline) and change name to Matrix_check_class;
839            fixes in as_cholmod_factor and chm_factor_to_SEXP.
840            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
841            dsCMatrix_matrix_solve.  Comment out vestigial functions.
842            * src/Csparse.c: use diag_P and uplo_P macros.
843    
844    2006-08-21  Douglas Bates  <bates@R-project.org>
845    
846            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
847            valgrind.
848            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
849            inverses.
850            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
851            -Wall warnings.
852            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
853            Use dup_mMatrix_as_dgeMatrix.
854    
855    2006-08-20  Douglas Bates  <bates@R-project.org>
856    
857            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
858            * tests/sparseQR.R: Added
859            * man/sparseQR-class.Rd: Document methods for qr.* generics
860            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
861    
862    2006-08-19  Douglas Bates  <bates@R-project.org>
863    
864            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
865            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
866            and qr.fitted.
867            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
868            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
869    
870    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
873            the base version has no "..." argument.
874    
875            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
876    
877            * R/Matrix.R: define and
878            * NAMESPACE: export as.numeric() and as.logical() methods.
879                    Let's hope these do not badly slow down something...
880            Finally export the zapsmall() method.
881    
882    2006-08-17  Douglas Bates  <bates@R-project.org>
883    
884            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
885            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
886            * src/dtCMatrix.c :Remove code that is no longer used
887            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
888    
889    2006-08-14  Douglas Bates  <bates@R-project.org>
890    
891            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
892            Csparse_to_logical and Csparse_symmetric_to_general.
893            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
894            coercion methods between CsparseMatrix and TsparseMatrix.
895    
896    2006-08-14  Douglas Bates  <bates@R-project.org>
897    
898            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
899            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
900            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
901            possible.
902    
903    2006-08-12  Douglas Bates  <bates@R-project.org>
904    
905            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
906              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
907              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
908              generalize conversions between TsparseMatrix, CsparseMatrix,
909              denseMatrix and matrix.  Preserve triangularity property and
910              propagate Dimnames in the easy cases.
911    
912    2006-08-10  Douglas Bates  <bates@R-project.org>
913    
914            * src/lmer.c: adjust checks in glmer_init for S4SXP
915            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
916            before S4SXP but for the wrong reasons.
917    
918    2006-08-08  Douglas Bates  <bates@R-project.org>
919    
920            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
921            Later modified to return the upper triangle only.
922            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
923    
924    2006-08-07  Douglas Bates  <bates@R-project.org>
925    
926            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
927            R-level conversion to a sparse symmetric class.
928            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
929            Remove conversion to sparse symmetric classes (now done in C code).
930    
931    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
934            * man/band.Rd:  adapt the \dontshow{} unit test.
935    
936    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * DESCRIPTION (Version): 0.995-14  for CRAN
939    
940            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
941    
942            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
943            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
944    
945            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
946            * R/Tsparse.R (tril, triu, band): methods
947            * R/dgRMatrix.R (tril, ...):    ditto
948            * man/band.Rd:                  ditto
949    
950    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/Matrix.R (head, tail): directly use utils:::head.matrix
953                    to be up-to-date automatically.
954    
955    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
958    
959            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
960            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
961            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
962            such that the S4 objects are always created by the current version
963            of R and 'Matrix' class definitions.
964    
965    2006-08-01  Douglas Bates  <bates@R-project.org>
966    
967            * R/lmer.R (LMEoptimize method), tests/lmer.R,
968            inst/external/test3comp.rda: Added warnings for convergence on
969            boundary and test cases.
970    
971            * src/lmer.c (mer_postVar): Modified to return the variances that
972            are marginal to the fixed effects, not conditional on them (which
973            is what the bVar slot contents represent).
974    
975    2006-07-31  Douglas Bates  <bates@R-project.org>
976    
977            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
978            function which calls the C function mer_hat_trace2.
979    
980            * man/ranef.Rd: Include description of "postVar" argument and
981            producing a caterpillar plot.
982    
983    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * NAMESPACE:    change  "correlation" to "corMatrix"
986            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
987            * R/dpoMatrix.R: ditto
988            * R/lmer.R:      ditto
989    
990    2006-07-28  Douglas Bates  <bates@R-project.org>
991    
992            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
993            RZXinv slot's contents into a separate internal function that can
994            be used in mer_hat_trace.
995    
996    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
999            via new smart
1000            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1001            utility functions.
1002    
1003    
1004    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1007            matrices when appropriate; band() even symmetric ones.
1008            (replCmat): extend to potentially all "CsparseMatrix"
1009            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1010            allow subassignment for special sparse matrices.
1011    
1012            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1013    
1014            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1015            argument; in glmer_*(): print only if(verbose).
1016    
1017            speed-optimize a few places by moving REAL(.) out of loops.
1018    
1019            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1020    
1021    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1024                    since that wrongly triggers also for M[ logi , ]
1025    
1026            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1027            a symmetric matrix that results in a non-symmetric one.
1028            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1029    
1030            * R/dMatrix.R: make round(M) work as round(M, 0)
1031    
1032            * R/dgTMatrix.R (image): coordinate system and axis now use
1033            1-based indices, not 0-based ones.
1034    
1035            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1036            * tests/indexing.R: test it.
1037    
1038            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1039            * man/isSymmetric-methods.Rd: and document it.
1040    
1041            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1042            * man/SparseM-conv.Rd: docu them
1043    
1044            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1045                    for 'SparseM' conversions
1046    
1047    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1048    
1049            * R/Matrix.R (head): added head() and tail() methods.
1050    
1051    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * DESCRIPTION (Version): 0.995-12 released to CRAN
1054    
1055    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * tests/simple.R: add check for correct dsT -> dgT coercion;
1058                    add check for correct printing of symmetric sparse matrices.
1059    
1060            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1061            for sparse symmetric matrices.
1062    
1063            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1064            diagonal twice.
1065    
1066    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1067    
1068            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1069            being applied to the x slot (detected by Brian Ripley).
1070    
1071    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1074    
1075            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1076    
1077    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1078    
1079            * src/lgCMatrix.c (lgCMatrix_diag): new function
1080            * R/lgCMatrix.R (diag): for new method
1081    
1082            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1083                 ==> construction of illegal "*gTMatrix" via new() should
1084                 now be much less easy:
1085            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1086    
1087            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1088                    directly.
1089            * man/Matrix.Rd: documents it.
1090    
1091    2006-07-06  Douglas Bates  <bates@R-project.org>
1092    
1093            * src/pedigree.c (pedigree_inbreeding): Correction in
1094            initialization.  This function is not currently being used and is
1095            not fully tested.
1096    
1097            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1098            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1099            objects.  Modified validity check on pedigree objects to account
1100            for nonparallel patterns of missingness of parents.
1101    
1102            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1103            class.
1104    
1105    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/pMatrix.R: coercion pMatrix -> Tsparse
1108    
1109    2006-06-12  Douglas Bates  <bates@R-project.org>
1110    
1111            * DESCRIPTION (Version): 0.995-11 released to CRAN
1112    
1113            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1114            the output from mcmcsamp.
1115    
1116    2006-06-10  Douglas Bates  <bates@R-project.org>
1117    
1118            * R/lmer.R (simulestimate): added C code for calculating the trace
1119            of the hat matrix.
1120    
1121    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1124            classes.
1125            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1126    
1127    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/dgTMatrix.R (colSums): etc. All four of
1130            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1131            all "Matrices".
1132    
1133    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1134    
1135            * R/lmer.R (panel.ci): Add a reference line at zero and a
1136            background grid to the qqmath plot of ranef.lmer.
1137    
1138    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1139    
1140            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1141            grouping factors to be specified in the formula as (1|foo/bar).
1142    
1143    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1144    
1145            * R/lmer.R (findbars and others): Change check of is.numeric to
1146            !is.language to resolve the bug reported by Jacob Wegelin.
1147    
1148            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1149            code to evaluate inbreeding coefficients without calculating T,
1150            based on code in Sargolzaei and Iwaisaki's paper.
1151    
1152    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1153    
1154            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1155            generic and mer methods for isNested and denomDF. This denomDF was
1156            an attempt to emulate that in lme but I don't think that makes
1157            sense.  Use the trace of the hat matrix instead.
1158    
1159    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1160    
1161            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1162            the C code depending on a slot structure that's no longer valid.
1163            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1164    
1165    
1166    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1167    
1168            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1169            of lowerTriMatrix generic and methods to tril (also upper to triu)
1170            and added a general band extractor.
1171    
1172    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1173    
1174            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1175            allowable range with NAs. Added a corresponding check in the
1176            validity check for the pedigree class.
1177    
1178            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1179            crossprod methods now inherits from symmetricMatrix.
1180    
1181    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1182    
1183            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1184            generics lowerTriMatrix and upperTriMatrix along with methods for
1185            the Csparse virtual class.  Also added a C function Csparse_band
1186            that implements these methods by calling cholmod_band.
1187    
1188    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1191            erased when it was NULL.  This led to invalid subselections!
1192    
1193    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1194    
1195            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1196            in method for "t" so as not to lose the unit diagonal property.
1197    
1198    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1199    
1200            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1201            and methods.  This is now an option to the ranef method for the
1202            mer class.
1203    
1204            * src/cs_utils.c: Ensure that the nz component is -1 for a
1205            compressed column-oriented matrix.  Minor formatting cleanup.
1206    
1207            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1208            objects.
1209    
1210    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1211    
1212            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1213            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1214    
1215    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1216    
1217            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1218            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1219    
1220            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1221            for the dtCMatrix class.
1222    
1223    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1226            and methods for it.
1227    
1228    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1229    
1230            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1231            arguments, such that M %*% 1:6 now works
1232            * Tests/matprod.R: test the above
1233    
1234    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1235    
1236            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1237            the ranef.lmer class.
1238    
1239            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1240            methods to extract the posterior variances from the bVar slot.
1241    
1242    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1245            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1246    
1247            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1248            * tests/simple: (extended)
1249    
1250            * R/sparseMatrix.R (isTriangular): now using much improved
1251            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1252    
1253    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1254    
1255            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1256            (problem report from Franklin Parlamis).  This should be done
1257            generally.
1258    
1259    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1260    
1261            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1262            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1263            update the plot methods.
1264    
1265    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1266    
1267            * R/lmer.R (resid and ranef methods):  Added methods for the
1268            "residuals" and "resid" generic but only for linear mixed model
1269            fits.  Changed the ranef method to return a list of data frames so
1270            that the plot methods now work.
1271    
1272    2006-03-16  Douglas Bates  <bates@bates2>
1273    
1274            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1275            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1276    
1277            * DESCRIPTION (Date): New release
1278    
1279    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1282    
1283            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1284            * man/KNex.Rd: and other help files
1285            * tests/*.R: several ones needed adaption
1286            * inst/doc/Comparisons.Rnw: ditto
1287    
1288    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1289    
1290            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1291    
1292            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1293    
1294    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1297    
1298            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1299    
1300    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * R/dMatrix.R: enable things like  M [ M < 10 ]
1303            * R/dgeMatrix.R: implement it
1304    
1305    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/AllClass.R: define "summary.mer" and "*.lmer"
1308            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1309            * R/lmer.R (show): now works with summary()
1310    
1311    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1312    
1313            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1314            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1315                    support the above
1316    
1317    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1318    
1319            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1320            Use glmFit$prior.weights for weights in a glmm.
1321            Allow an option usePQL = FALSE to skip the PQL steps for the
1322            Laplace method (and, in time, the AGQ method).
1323    
1324            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1325            into a separate function internal_mer_Xfactor to be able to call
1326            it from internal_bhat.
1327    
1328    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * tests/Class+Meth.R (tstMatrixClass): function for much better
1331            testing; now again of all actual classes.
1332    
1333            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1334                    use macros and define make_d_matrix_* and make_i_matrix_*
1335                    where _i_ is for the ldense routines:
1336    
1337            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1338            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1339    
1340            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1341    
1342    
1343    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1344    
1345            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1346                    many different kinds of matrices.
1347            * R/*.R: quite a few new methods were needed for R CMD check with
1348                    new Matrix().  Very good for users playing around.
1349    
1350    
1351    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1352    
1353            * src/dgeMatrix.c (dMatrix_validate): new
1354            * src/Mutils.c (dense_nonpacked_validate): new
1355    
1356            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1357    
1358    
1359    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1360    
1361            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1362    
1363    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1364    
1365            * DESCRIPTION (Version): 0.99-6 released to CRAN
1366    
1367            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1368            segfault in cases with multiple non-nested grouping factors.
1369    
1370    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1371    
1372            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1373                    (Depends): also on 'utils'
1374    
1375            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1376            * R/diagMatrix.R (Diagonal): constructor and methods for
1377            diagonal matrices
1378    
1379            * R/ltTMatrix.R: new "minimal methods"
1380    
1381    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1382    
1383            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1384            all methods (and help files).
1385    
1386    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1387    
1388            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1389                    for case (dimn.  op  no_dimn.)
1390    
1391    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1392    
1393            * DESCRIPTION (Version): 0.99-2  released to CRAN
1394    
1395    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1396    
1397            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1398            by Julian Faraway.
1399    
1400    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * R/Auxiliaries.R (try_as): new utility
1403            * R/sparseMatrix.R: use try_as() in coercion to original class
1404    
1405    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1406    
1407            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1408    
1409    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1410    
1411            * R/Auxiliaries.R (dimNamesCheck): added
1412    
1413            * R/Matrix.R (as.array), (as.vector): new
1414    
1415    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1416    
1417            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1418                    default.
1419            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1420                    "pMatrix" now contains "sparseMatrix"
1421    
1422    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * tests/Class+Meth.R: new tests; t(t(m)) == m
1425    
1426            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1427    
1428            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1429            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1430    
1431            * R/dspMatrix.R: typo in "t" method
1432    
1433    2005-09-18  Douglas Bates  <bates@wisc.edu>
1434    
1435            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1436            * R/Tsparse.R: instead of R/gTMatrix.R
1437            * R/Csparse.R: new
1438            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1439            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1440            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1441                            via cholmod
1442    
1443    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1444    
1445            * R/Auxiliaries.R (non0ind): new function using new C code
1446            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1447    
1448    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1449    
1450            * src/chm_common.h: header file required by all C sources that
1451            call CHOLMOD functions.  It defines a cholmod_common structure
1452            called 'c' whose address is passed as the last argument to
1453            (virtually) every CHOLMOD function.
1454    
1455            * src/Pattern.c: Simple example of the use of CHOLMOD.
1456    
1457            * src/init.c: initialize and finalize the cholmod_common structure.
1458    
1459            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1460            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1461    
1462    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1463    
1464            * inst/test-tools.R: new file collecting the utility functions used
1465                    in ./tests/*.R
1466    
1467            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1468            * R/Matrix.R (cbind2): methods for NULL and missing
1469    
1470    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1471    
1472            * R/AllClass.R: new "index" class for "[" and "[<-":
1473                    First cut at "symmetricMatrix" and "triangularMatrix"
1474            * R/gTMatrix.R (.ind.prep): new function;
1475                    Logical and character indexing now work too.
1476            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1477            * tests/indexing.R: new, including *.Rout.save
1478            * tests/dgTMatrix.R: new
1479    
1480    2005-08-29  Douglas Bates  <bates@wisc.edu>
1481    
1482            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1483            indicator pos not being updated.  Also enforced upper triangular
1484            for symmetric case.  Need to coerce edges component of elements of
1485            edge list - grr! (Why don't they define their classes cleanly?)
1486    
1487    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1488    
1489            * R/Matrix.R:  added first "[<-" methods; not yet functional
1490            * R/denseMatrix.R: ditto
1491            * man/Subassign-methods.Rd: new help file for these
1492    
1493    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1494    
1495            * DESCRIPTION (Version): 0.98-6
1496    
1497            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1498            matrices.
1499    
1500    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1501    
1502            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1503                    as( <logical>, "matrix")
1504    
1505            * R/pMatrix.R: coercion to "lgTMatrix"
1506    
1507            * R/gTMatrix.R: new virtual class to define "[" methods for.
1508            * man/gTMatrix-class.Rd:
1509            * General slight re-organization of where "[" methods are defined.
1510              more to come.
1511    
1512    2005-08-18  Douglas Bates  <bates@wisc.edu>
1513    
1514            * DESCRIPTION (Version): 0.98-5  released to CRAN
1515    
1516            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1517            * .....
1518    
1519    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1520    
1521            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1522            or glmer objects.
1523    
1524    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1527    
1528    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1529    
1530            * R/HBMM.R: finish re-writing R-only code.
1531    
1532    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1533    
1534            * man/externalFormats.Rd: move documentation for writeHB and
1535            writeMM here.
1536    
1537            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1538            (suggested by Paul Roecker).
1539    
1540            * tests/validObj.R (assertError): Comment out test that is failing
1541            after recent changes in r-devel.
1542    
1543    
1544    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1545    
1546            * R/AllClass.R: intermediate virtual class "denseMatrix"
1547            * man/denseMatrix-class.Rd
1548            * NAMESPACE: export it, and also export
1549            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1550    
1551    2005-08-10  Douglas Bates  <bates@wisc.edu>
1552    
1553            * DESCRIPTION (Version): 0.98-3 to CRAN
1554    
1555            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1556            matrix_solve code (which was really, really wrong).
1557    
1558    2005-08-07  Douglas Bates  <bates@wisc.edu>
1559    
1560            * DESCRIPTION (Version): 0.98-2
1561    
1562            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1563    
1564            * R/lmer.R (abbrvNms): new
1565            * R/lmer.R (mcmcsamp): allow transformed parameters
1566            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1567            for the Harwell-Boeing and the MatrixMarket formats.
1568    
1569    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1570    
1571            * man/dtrMatrix-class.Rd: add examples
1572            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1573    
1574            * TODO: note the dtpMatrix (docu) bug
1575    
1576            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1577            in order to ensure that new as.matrix() is used by old functions,
1578            e.g., svd(), qr(), eigen(), dist(),..;
1579                  apply(), also matplot() or pairs().
1580    
1581    
1582    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1583    
1584            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1585              add comments about 'control' / lmerControl() arguments
1586    
1587    2005-07-27  Douglas Bates  <bates@wisc.edu>
1588    
1589            * man/sleepstudy.Rd: Added the sleep data set.
1590            * DESCRIPTION (Version): 0.98-1  released to CRAN
1591    
1592    2005-07-12  Douglas Bates  <bates@wisc.edu>
1593            * man/sleepstudy.Rd: Added the sleep data set.
1594    
1595            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1596            .Call calls that were producing spurious output.
1597    
1598    2005-07-05  Douglas Bates  <bates@wisc.edu>
1599    
1600            * R/lmer.R (lmer): stored updated variance component estimates in
1601            mer object for the generalized model.  (Bug reported by Renaud
1602            Lancelot).
1603    
1604    2005-07-03  Douglas Bates  <bates@wisc.edu>
1605    
1606            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1607            unidimensional case.
1608    
1609    2005-06-08  Douglas Bates  <bates@wisc.edu>
1610    
1611            * DESCRIPTION (Version): 0.96-1
1612    
1613            * moved  lmer-class' R and C code moved from lme4 to here
1614    
1615    2005-06-04  Douglas Bates  <bates@wisc.edu>
1616    
1617            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1618            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1619    
1620    2005-06-02  Douglas Bates  <bates@wisc.edu>
1621    
1622            * src/Makefile.win: Forgot to update this when Makefile changed.
1623    
1624    2005-05-11  Douglas Bates  <bates@wisc.edu>
1625    
1626            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1627            bug reported by Kurt Hornik and Michael Hahsler.
1628    
1629    2005-05-10  Douglas Bates  <bates@wisc.edu>
1630    
1631            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1632            logical sparse matrices.  These will also be used in the symbolic
1633            analysis for lmer objects.
1634    
1635            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1636            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1637    
1638    2005-05-06  Douglas Bates  <bates@wisc.edu>
1639    
1640            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1641            colMeans, colSums, rowMeans and rowSums.
1642    
1643    2005-04-18  Douglas Bates  <bates@wisc.edu>
1644    
1645            * src/lgCMatrix.[ch]: code for _validate method and stub for
1646            multiplication operation.
1647    
1648            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1649            to dgetrs.
1650    
1651            * src/init.c: Fix cut-and-paste error in definition of
1652            dgeMatrix_matrix_solve
1653    
1654            * src/{many files}: Tighten code by using ALLOC_SLOT.
1655    
1656    2005-04-15  Douglas Bates  <bates@wisc.edu>
1657    
1658            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1659    
1660            * DESCRIPTION: Eliminate import of stats.
1661    
1662    
1663    2005-04-06  Douglas Bates  <bates@wisc.edu>
1664    
1665            * R/AllClass.R : add logical sparse matrix classes
1666    
1667    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1668    
1669            * R/dgTMatrix.R: add "[" method for triplet matrices
1670            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1671    
1672    2005-03-31  Douglas Bates  <bates@wisc.edu>
1673    
1674            * DESCRIPTION (Version): release 0.95-5 to CRAN
1675    
1676            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1677            * R/sparseMatrix.R: %*%, crossprod()
1678            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1679            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1680            * src/lmer.c (lmer_fitted): fix thinko
1681    
1682    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1683    
1684            * R/AllClass.R: add two virtual sparse classes ``on top''
1685    
1686    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1687    
1688            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1689                    correspondingly fix examples and tests/ since new()
1690                    doesn't work for virtual classes.
1691    
1692    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1693    
1694            * R/Matrix.R (as.matrix): method and one for unname()
1695            * tests/dpoMatrix.R: tests should now be less platform dependent;
1696              also run for R 2.1.0; using as.matrix()
1697    
1698    2005-03-15  Douglas Bates  <bates@wisc.edu>
1699    
1700            * R/pMatrix.R: "pMatrix" class added
1701            * ....
1702    
1703    2005-03-14  Douglas Bates  <bates@wisc.edu>
1704    
1705            * R/dtpMatrix.R: Add unpack method and an example.
1706    
1707            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1708            of general symmetric matrices and associated S4 methods.
1709    
1710    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1711            +
1712    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1713    
1714            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1715              crossprod() and "%*%" methods added; tests, too.
1716            * tests/matprod.R: new, for testing these
1717    
1718    2005-03-03  Douglas Bates  <bates@wisc.edu>
1719    
1720            * src/lmer.c (lmer_fitted): Added.
1721    
1722    2005-03-02  Douglas Bates  <bates@wisc.edu>
1723    
1724            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1725    
1726    2005-02-28  Douglas Bates  <bates@wisc.edu>
1727    
1728            * src/*.c,po/,inst/po: Internationalization and localization of
1729            the package.
1730    
1731            * src/ldl.[ch]: Removed these as their contents are referenced in the
1732            R_ldl.c file.
1733    
1734            * src/flame.[ch]: Removed these source files.
1735    
1736            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1737    
1738            * src/LU.[ch],src/init.c: absorb in factorizations
1739    
1740            * src/Mutils.h: prepare for internationalization
1741    
1742            * src/cblas.h: move the enum definitions to Mutils.h and remove
1743            this file
1744    
1745    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1746    
1747            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1748    
1749            * R/dtrMatrix.R: fix t() method
1750    
1751            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1752            * NAMESPACE: export them (and import generics from "methods")
1753            * tests/group-methods.R : and test them.
1754    
1755            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1756            border case
1757    
1758    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1759    
1760            * DESCRIPTION (Version): 0.95-2  released to CRAN
1761    
1762            * src/dgBCMatrix.c:
1763            * src/lmer.c: many changes
1764            * ...
1765    
1766    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1767    
1768            * R/Matrix.R: add more sophisticated show() method.
1769    
1770    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1771    
1772            * */* : almost complete reorganization of classes.
1773    
1774    2005-01-26  Douglas Bates  <bates@wisc.edu>
1775    
1776            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1777            for the geMatrix class.
1778    
1779    2005-01-24  Douglas Bates  <bates@wisc.edu>
1780    
1781            * src/Makefile (clean): Remove *.a and *.so
1782    
1783            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1784    
1785    2005-01-23  Douglas Bates  <bates@wisc.edu>
1786    
1787            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1788            had an effect in cases with more than 2 grouping factors.
1789    
1790    2005-01-03  Douglas Bates  <bates@wisc.edu>
1791    
1792            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1793    
1794    2004-12-23  Douglas Bates  <bates@wisc.edu>
1795    
1796            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1797            and R_useDynamicSymbols (suggested by B.D.Ripley).
1798    
1799    2004-12-14  Douglas Bates  <bates@wisc.edu>
1800    
1801          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1802    
1803          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1804          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1805    
1806  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1807    
1808          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1809          no longer used.          no longer used.
# Line 17  Line 1815 
1815          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1816          Fixes part but not all of #15.          Fixes part but not all of #15.
1817    
1818  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1819    
1820          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1821          scalar grouping factors corrected.          scalar grouping factors corrected.
1822    
1823  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1824    
1825          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1826    
1827  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1828    
1829          * 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
1830          .h file can be included.          .h file can be included.
1831    
1832  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1833    
1834          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1835          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1836    
1837          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1838    
1839  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1840    
1841          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1842    
1843  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1844    
1845          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1846    
1847  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1848    
1849          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1850    
1851  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1852    
1853          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1854    
1855  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1856    
1857          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1858          routines.          routines.
1859    
1860  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1861    
1862          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1863    
1864  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1865    
1866          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1867    

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