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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1845, Wed May 16 21:24:41 2007 UTC
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1  2004-11-16  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    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (sparsapply): new utility, much faster than
8            tapply1() for large sparse matrices.
9    
10    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R (dim<-): reshape now via sparseVector.
13    
14            * R/sparseVector.R: methods and function for
15            * R/AllClass.R: new "sparseVector" class and daughters.
16            * NAMESPACE: export new classes
17    
18    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Version): 0.99875-1
21            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
22    
23    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
26            indexing
27            * tests/indexing.R: test set for that.
28    
29    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
32            entries.
33            * tests/indexing.R(out): add regression test for it
34    
35    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
38            name for "!" method definitions.
39    
40    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Tsparse.R (intI): new utility, used for "[" :
43                    Cleanup up there, and fixes for duplicated indices - more TODO!
44    
45            * tests/indexing.R(out): more tests
46    
47    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
50            code that is now part of the R Lapack library.
51    
52            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
53            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
54    
55    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
58    
59    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
62            up with extraneous names '0'...'<n-1>'
63    
64    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/dgTMatrix.R (mat2dgT): care about NAs
67    
68    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/kronecker.R: triangularity preserving methods
71    
72    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/kronecker.R: new file collecting kronecker() methods in one
75                    place.  Goal: become much faster!
76    
77    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
80            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
81            can be much faster.
82    
83            * tests/matprod.R: add regression tests for these (upper & lower).
84    
85    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R (diff): method for our Matrices.
88    
89            * R/sparseMatrix.R (isDiagonal): check dim()!
90    
91    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (dim<-): new method for "reshape()" built on a
94            proposal from Tamas Papp.
95    
96    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
99    
100            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
101            rather define and export  cBind() and rBind() only.
102            --> useRs *must* change code that used to have cbind()/rbind() !!
103    
104            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
105            * R/bind.Rout.save: ditto
106    
107    2007-02-16  Douglas Bates  <bates@r-project.org>
108    
109            * DESCRIPTION (Date, Version): 0.9975-11 with new date
110            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
111            const modifier on declaration of the array 'valid'
112    
113    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
116    
117    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
120    
121            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
122            * tests/simple.R: test the above and some of these coercions:
123    
124            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
125                    be careful to avoid infinite recursion, using new coercions in
126            * R/ngCMatrix.R and nsC... and ntC...
127            * R/lsparseMatrix.R: ditto
128    
129            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
130    
131            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
132            * R/Rsparse.R: reactivate .Call()s
133    
134            * tests/Class+Meth.R: a bit more on actual classes
135    
136    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
139    
140    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.9975-10 to upload
143    
144            * tests/Class+Meth.R (tstMatrixClass): require coercions to
145            specific classes less unconditionally.
146    
147            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
148    
149            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
150    
151            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
152            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
153            R_to_CMatrix segfaults on one platform.
154            Eliminate most coercion method to *specific* classes, and replace
155            with virtual classes coercions.
156    
157    
158    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
159    
160            * src/init.c: export the CHM...._validate() placeholders, since
161            they *are* called.
162    
163            * tests/Class+Meth.R (classCanCoerce): and starting to test
164            all as(<from>, <to>)
165    
166    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
169            * tests/indexing.R: tested now
170            * tests/indexing.Rout.save: updated
171    
172            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
173            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
174            appropriate.
175    
176            * NAMESPACE: export a trivial
177            * R/Matrix.R: drop() Matrix-method
178    
179            * R/AllClass.R: moved all prototypes to virtual super classes.
180    
181            * R/Rsparse.R: many more coercions to have less exceptions in
182            * tests/Class+Meth.R:
183    
184            * R/Ops.R (Compare): tweak for case with NA
185            * tests/simpl.R: hence another 'FIXME' eliminated
186    
187    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
190            objects.
191    
192            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
193              and more of "!", "&", "|", all, any; coercions
194    
195            * R/Rsparse.R: many coercions (which enable quite a few other
196            methods), thanks to enhancements in
197            * src/dgCMatrix.c (R_to_CMatrix): new, and
198            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
199            symmetric & triangular and ..RMatrix objects.
200    
201            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
202            renamed file from src/dsTMatrix.c;
203            now dealing with symmetric and triangular Tsparse coercions, both
204            to dense and general.
205    
206    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
209    
210            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
211            where sensible when the <numeric> is of length > 1.
212    
213    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R ([<-): for M[] <- value: fix length
216    
217    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
220            * R/ndenseMatrix.R: new coercions n* -> l*
221    
222    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
225    
226            * R/Ops.R ("Logic"): and other "Ops", many updates
227    
228    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/Mutils.h (SET_DimNames): new utility
231    
232            * R/Auxiliaries.R (nnzero): improved and now exported via
233    
234            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
235    
236    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/diagMatrix.R (!): fix typo.
239    
240    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Auxiliaries.R (as_Csparse): and quite a few others:
243                    allow to pass class definition --> speedup
244            * R/sparseMatrix.R: apply the above
245    
246            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
247    
248            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
249            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
250            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
251    
252            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
253    
254            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
255            and use it for "sparse*" as well, since it's faster than the
256            as_Csparse(.) way.
257    
258    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
261    
262    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
265            as method for   M[ ij ] <- v
266            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
267    
268            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
269            FALSE answer
270    
271            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
272            * tests/indexing.R: test it, and some of the above
273    
274    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Auxiliaries.R (is_duplicatedT): new utility
277    
278    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * src/init.c (R_init_Matrix): export cholmod_scale
281    
282    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
285            base::as.matrix to (x, ...)
286    
287    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
290            file; start using "Logic", hence
291    
292            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
293            * NAMESPACE: import and export "Logic"
294    
295    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
298            only needed previously to R version 2.5.0.
299    
300    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
303    
304            * R/Tsparse.R (replTmat): fix subassignment of triangular
305            * R/Csparse.R (replCmat): ditto
306            * tests/indexing.R: more tests, incl the above fix
307    
308    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (drop0): extend for non CSparse
311            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
312    
313            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
314                    use uplo correctly (!); other places: use uplo_P() macro
315    
316            * R/Csparse.R (replCmat): call diagU2N() when needed
317            * R/Tsparse.R (replTmat): ditto
318    
319            * src/dtCMatrix.c (tCMatrix_validate): new
320            * src/dtTMatrix.c (tTMatrix_validate): new, used in
321            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
322    
323            * R/diagMatrix.R (replDiag): to use in [<-
324    
325    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
328                    also more general diagU2N().
329    
330    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
333            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
334    
335    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * tests/bind.R: a few more cases
338            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
339    
340            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
341            * R/ddenseMatrix.R (cbind2/rbind2)
342            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
343            * tests/indexing.R
344            * tests/indexing.Rout.save: updated
345    
346    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
349            * tests/indexing.R
350    
351    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
354            align with proper position of "0", i.e., right for integers.
355            argument 'align' by default is "fancy".
356    
357    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
360            * R/Csparse.R: and fix "Compare" for more cases.
361            * tests/Class+Meth.R: test some of these (m == m, m != m)
362    
363    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/lsparseMatrix.R: all() and any() methods
366            * R/ldenseMatrix.R:      ditto
367            * NAMESPACE, R/Matrix.R: ditto
368    
369            * man/all-methods.Rd: document them minimally
370    
371            * tests/simple.R: add a few examples for these
372    
373    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Tsparse.R ([): fix long standing typo in symmetric case
376            * man/dsCMatrix-class.Rd: add example exhibiting the above case
377    
378    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
379    
380            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
381            to LL before converting to a sparse matrix. (The LDL form can be
382            converted to a sparse matrix but it is implicitly a unit
383            triangular matrix and a diagonal matrix overwritten on the diagonal.)
384    
385    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
388    
389    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
390    
391            * DESCRIPTION (Version): updated -> release 0.9975-7
392            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
393    
394    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
397    
398    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
401            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
402            is exactly singular.
403    
404    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * DESCRIPTION (Date): updated -> release 0.9975-6
407    
408    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
411            now returns symmetric.
412    
413            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
414    
415            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
416            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
417    
418            * R/Auxiliaries.R (.type.kind): added
419    
420    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
423            running src/CSparse_install.sh
424    
425            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
426    
427    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
430            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
431    
432            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
433    
434            * tests/Class+Meth.R (tstMatrixClass): now assure
435            the (important in method programming) property :
436    
437                    ###>>  Every "Matrix" is either
438                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
439    
440                    (where "*" stands for "Matrix")
441    
442            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
443    
444            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
445            * tests/validObj.R: checks for "comparison"
446    
447            * R/sparseMatrix.R ([): improved indexing for sparse;
448                    trying to keep <symmetric>[ n, n] symmmetric
449    
450            * tests/indexing.R: indexing for logical sparse now ok
451    
452    
453    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * src/Tsparse.c: use xTsparse_validate() , and hence remove
456    
457            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
458    
459    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
462    
463            * tests/simple.R: validObject() checking the above.
464    
465            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
466            replacing both dgCMatrix_validate and lgCM*.
467    
468            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
469            fix dimnames setting in other places.
470            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
471    
472    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
475    
476            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
477            symmetry test, via
478            * R/Auxiliaries.R (.as.dgC.0.factors):
479    
480    2006-11-01  Douglas Bates  <bates@r-project.org>
481    
482            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
483            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
484            <CsparseMatrix>) added
485    
486    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * tests/matprod.R: add a variation of Harri's example
489    
490            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
491            recursive infinitely.
492    
493            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
494    
495            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
496    
497    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
500            matrix if possible; test m+m == 2*m; now test dgRMatrix.
501            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
502            satisfy the above test.
503    
504    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
507    
508            * R/dgCMatrix.R: solve(a, b="missing") based on
509            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
510            RHS = NULL.
511    
512            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
513            add more (needed) [t]crossprod() methods.
514    
515            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
516    
517            * R/Auxiliaries.R (as_CspClass): cleanup
518            (drop0): internal utility for "Csparse_drop(*, 0)"
519            (.bail.out.2): encourage active feedback
520    
521    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/dMatrix.R(Compare): new(), then slots [no validity check]
524    
525            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
526            non-valid or 'sorted' case).
527    
528            * R/dsparseMatrix.R: add "chol" method.
529            * R/ddenseMatrix.R: ditto
530    
531            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
532            * NAMESPACE (Ops)
533            * R/diagMatrix.R (diag2T): simple utility used "higher level"
534            coercion; deprecating direct lower level coercions.
535    
536            * R/*.R (seq): use seq_len() and seq_along() where possible.
537    
538    
539    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Version): 0.9975-5 ready for release
542    
543    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
546    
547    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/AllClass.R (corMatrix): add 'validity' check;
550                    comment out unused "LDL" class definition
551            * NAMESPACE: mention, but do not export "LDL" class
552            * R/corMatrix.R: new (simple), needed for R-devel with
553            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
554              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
555    
556    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
559            use Rprintf and R's error handling.
560    
561    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
564            * tests/matprod.R: add tests for the bug fixed.
565    
566    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
567    
568            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
569            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
570    
571    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
572    
573            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
574    
575    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.9975-3
578    
579            * R/diagMatrix.R (bdiag): new function constructing block diagonal
580            (sparse) matrices.
581            * man/bdiag.Rd: docu + examples
582    
583            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
584    
585            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
586            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
587    
588            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
589            that result is sparse or diagonal (and not dense).
590    
591            * man/Subassign-methods.Rd: fix examples
592    
593            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
594            should always return a sparse (and not sometimes a diagonal) matrix.
595    
596    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
599    
600    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * DESCRIPTION (Version): 0.9975-2
603    
604            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
605    
606    2006-10-02  Douglas Bates  <bates@R-project.org>
607    
608            * tests/dg_Matrix.R: Simplify test taking into account new code.
609    
610    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
613    
614            * R/lsTMatrix.R: new files w/ missing methods
615            * R/nsTMatrix.R:  "  'for completeness'
616    
617            * tests/Class+Meth.R: a bit less 'not.ok.classes'
618    
619            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
620    
621    
622    2006-09-28  Douglas Bates  <bates@R-project.org>
623    
624            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
625            included.
626    
627            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
628            Export C-callable functions used in Zt_create in lme4.
629    
630    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * DESCRIPTION (Version): 0.9975-1
633    
634            * tests/simple.R: less checks fail; using NA, found that our
635                    kronecker() is not base-compatible with NA's.
636    
637            * R/dMatrix.R: "Compare" method now implemented for all cases
638    
639            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
640    
641            * man/dtpMatrix-class.Rd: mention length of 'x' slot
642    
643            * src/dtpMatrix.c (dtpMatrix_validate): fix check
644            * src/dspMatrix.c (dspMatrix_validate): ditto
645    
646            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
647              including coercion to [nl]tTMatrix.
648    
649            * R/diagMatrix.R (show): print a header line as for other classes.
650    
651    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * src/Makefile.win (SUBDIRS): fix typo
654    
655    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
658    
659    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
660    
661            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
662            symmetric and y missing in R code using %*% (cholmod_aat doesn't
663            accept a symmetric matrix).
664            * tests/group-methods.R: Uncomment test of crossprod applied to
665            lsCMatrix objects.
666    
667    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/AllClass.R (symmetricMatrix): add validity method (available
670            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
671    
672            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
673    
674            * tests/indexing.Rout.save:
675            * tests/indexing.R: additions, mainly for 'lsparse'
676    
677            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
678            case.
679    
680            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
681    
682    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
685                    as 'N' (1-letter - Ok?)
686    
687            * tests/group-methods.R: add test for logical + NAs
688    
689            * R/dMatrix.R ("Compare"): fix to work with NA's
690    
691            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
692    
693            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
694                    which is implemented.
695    
696    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * src/chm_common.c: coerce logical <-> double instead of
699            typecasting;  needed for "l" matrix handling in cholmod.
700    
701            * tests/other-pkgs.R (graph): small extension in "graph" checks.
702    
703            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
704            (Tsp2grNEL): other fixes needed
705    
706    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
709                    Matrices, since "lMatrix", also "lsparseM" can have NA
710            * R/ndenseMatrix.R, etc: new source files
711            * man/nsparseMatrix-classes.Rd, etc: new help files
712            * tests/: adaptions
713            * src/chm_common.c (chm_dense_to_SEXP): and others:
714                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
715            * src/Csparse.c, etc: ditto
716    
717    2006-09-11  Douglas Bates  <bates@R-project.org>
718    
719            * src/Mutils.[ch],init.c inst/include/*.h: Move the
720            alloc_d**Matrix functions to the lme4 package.
721    
722    2006-09-09  Douglas Bates  <bates@R-project.org>
723    
724            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
725            fixed
726    
727    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/lMatrix.R: new
730    
731            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
732    
733            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
734            * man/tcrossprod.Rd: ditto
735    
736    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
739            for exported functions
740            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
741            Remove partitioning algorithms for sparse matrix reordering.  The
742            copyright on the Metis code was problematic and the methods were
743            rarely used.
744            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
745            operations are now done entirely in CHOLMOD code.
746    
747    2006-09-06  Douglas Bates  <bates@R-project.org>
748    
749            * src/Mutils.h: Remove functions that are no longer used.
750    
751    2006-09-04  Douglas Bates  <bates@R-project.org>
752    
753            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
754            * src/DEPS.mkf: update
755    
756    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * created branches/Matrix-for-R-2.3.x;  on trunk: do
759            * DESCRIPTION (Version): 0.9975-0
760            (Depends): R (>= 2.4.0)
761    
762    2006-09-01  Douglas Bates  <bates@R-project.org>
763    
764            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
765    
766    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
769            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
770    
771            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
772    
773    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
776            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
777            * R/dsparseMatrix.R: ditto
778            * R/Csparse.R: ditto
779    
780    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/dMatrix.R (Compare): improve availability of "<", etc
783            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
784    
785    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
788            of a 0-index which was used as 1-index (..hmm)
789    
790            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
791    
792            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
793            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
794            (.is.diagonal): ditto
795    
796            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
797    
798            * R/Matrix.R (Matrix): also work for NA data
799    
800    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
803            in all cases.
804    
805    2006-08-27  Douglas Bates  <bates@R-project.org>
806    
807            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
808            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
809    
810    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
813            subclasses of "ddenseMatrix"
814            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
815            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
816            instead of half dozen specialized ones.
817    
818    2006-08-25  Douglas Bates  <bates@R-project.org>
819    
820            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
821            <tillard@cirad.fr> - ordering standard errors to match effects.
822    
823    2006-08-24  Douglas Bates  <bates@R-project.org>
824    
825            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
826            on R_ldl.
827            * R/lCholCMatrix.R,
828            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
829            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
830            * many files in ./R and ./src: Use more general version of
831            dup_mMatrix_as_dgeMatrix to simplify method definitions.
832            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
833            dtpMatrix, dspMatrix and dppMatrix conversions.
834    
835    
836    2006-08-23  Douglas Bates  <bates@R-project.org>
837    
838            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
839            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
840            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
841            dgeMatrix_crossprod (may need to do this in other places).
842            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
843            generic and method for dsCMatrix.  Use CHOLMOD for chol().
844    
845    2006-08-22  Douglas Bates  <bates@R-project.org>
846    
847            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
848            types of classed Matrices, matrices or numeric or logical vectors.
849            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
850            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
851            to Mutils.h (as an inline) and change name to Matrix_check_class;
852            fixes in as_cholmod_factor and chm_factor_to_SEXP.
853            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
854            dsCMatrix_matrix_solve.  Comment out vestigial functions.
855            * src/Csparse.c: use diag_P and uplo_P macros.
856    
857    2006-08-21  Douglas Bates  <bates@R-project.org>
858    
859            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
860            valgrind.
861            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
862            inverses.
863            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
864            -Wall warnings.
865            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
866            Use dup_mMatrix_as_dgeMatrix.
867    
868    2006-08-20  Douglas Bates  <bates@R-project.org>
869    
870            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
871            * tests/sparseQR.R: Added
872            * man/sparseQR-class.Rd: Document methods for qr.* generics
873            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
874    
875    2006-08-19  Douglas Bates  <bates@R-project.org>
876    
877            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
878            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
879            and qr.fitted.
880            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
881            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
882    
883    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
886            the base version has no "..." argument.
887    
888            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
889    
890            * R/Matrix.R: define and
891            * NAMESPACE: export as.numeric() and as.logical() methods.
892                    Let's hope these do not badly slow down something...
893            Finally export the zapsmall() method.
894    
895    2006-08-17  Douglas Bates  <bates@R-project.org>
896    
897            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
898            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
899            * src/dtCMatrix.c :Remove code that is no longer used
900            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
901    
902    2006-08-14  Douglas Bates  <bates@R-project.org>
903    
904            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
905            Csparse_to_logical and Csparse_symmetric_to_general.
906            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
907            coercion methods between CsparseMatrix and TsparseMatrix.
908    
909    2006-08-14  Douglas Bates  <bates@R-project.org>
910    
911            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
912            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
913            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
914            possible.
915    
916    2006-08-12  Douglas Bates  <bates@R-project.org>
917    
918            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
919              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
920              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
921              generalize conversions between TsparseMatrix, CsparseMatrix,
922              denseMatrix and matrix.  Preserve triangularity property and
923              propagate Dimnames in the easy cases.
924    
925    2006-08-10  Douglas Bates  <bates@R-project.org>
926    
927            * src/lmer.c: adjust checks in glmer_init for S4SXP
928            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
929            before S4SXP but for the wrong reasons.
930    
931    2006-08-08  Douglas Bates  <bates@R-project.org>
932    
933            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
934            Later modified to return the upper triangle only.
935            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
936    
937    2006-08-07  Douglas Bates  <bates@R-project.org>
938    
939            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
940            R-level conversion to a sparse symmetric class.
941            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
942            Remove conversion to sparse symmetric classes (now done in C code).
943    
944    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
947            * man/band.Rd:  adapt the \dontshow{} unit test.
948    
949    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * DESCRIPTION (Version): 0.995-14  for CRAN
952    
953            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
954    
955            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
956            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
957    
958            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
959            * R/Tsparse.R (tril, triu, band): methods
960            * R/dgRMatrix.R (tril, ...):    ditto
961            * man/band.Rd:                  ditto
962    
963    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Matrix.R (head, tail): directly use utils:::head.matrix
966                    to be up-to-date automatically.
967    
968    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
971    
972            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
973            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
974            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
975            such that the S4 objects are always created by the current version
976            of R and 'Matrix' class definitions.
977    
978    2006-08-01  Douglas Bates  <bates@R-project.org>
979    
980            * R/lmer.R (LMEoptimize method), tests/lmer.R,
981            inst/external/test3comp.rda: Added warnings for convergence on
982            boundary and test cases.
983    
984            * src/lmer.c (mer_postVar): Modified to return the variances that
985            are marginal to the fixed effects, not conditional on them (which
986            is what the bVar slot contents represent).
987    
988    2006-07-31  Douglas Bates  <bates@R-project.org>
989    
990            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
991            function which calls the C function mer_hat_trace2.
992    
993            * man/ranef.Rd: Include description of "postVar" argument and
994            producing a caterpillar plot.
995    
996    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * NAMESPACE:    change  "correlation" to "corMatrix"
999            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1000            * R/dpoMatrix.R: ditto
1001            * R/lmer.R:      ditto
1002    
1003    2006-07-28  Douglas Bates  <bates@R-project.org>
1004    
1005            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1006            RZXinv slot's contents into a separate internal function that can
1007            be used in mer_hat_trace.
1008    
1009    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1012            via new smart
1013            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1014            utility functions.
1015    
1016    
1017    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1020            matrices when appropriate; band() even symmetric ones.
1021            (replCmat): extend to potentially all "CsparseMatrix"
1022            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1023            allow subassignment for special sparse matrices.
1024    
1025            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1026    
1027            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1028            argument; in glmer_*(): print only if(verbose).
1029    
1030            speed-optimize a few places by moving REAL(.) out of loops.
1031    
1032            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1033    
1034    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1037                    since that wrongly triggers also for M[ logi , ]
1038    
1039            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1040            a symmetric matrix that results in a non-symmetric one.
1041            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1042    
1043            * R/dMatrix.R: make round(M) work as round(M, 0)
1044    
1045            * R/dgTMatrix.R (image): coordinate system and axis now use
1046            1-based indices, not 0-based ones.
1047    
1048            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1049            * tests/indexing.R: test it.
1050    
1051            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1052            * man/isSymmetric-methods.Rd: and document it.
1053    
1054            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1055            * man/SparseM-conv.Rd: docu them
1056    
1057            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1058                    for 'SparseM' conversions
1059    
1060    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1061    
1062            * R/Matrix.R (head): added head() and tail() methods.
1063    
1064    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * DESCRIPTION (Version): 0.995-12 released to CRAN
1067    
1068    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * tests/simple.R: add check for correct dsT -> dgT coercion;
1071                    add check for correct printing of symmetric sparse matrices.
1072    
1073            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1074            for sparse symmetric matrices.
1075    
1076            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1077            diagonal twice.
1078    
1079    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1080    
1081            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1082            being applied to the x slot (detected by Brian Ripley).
1083    
1084    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1087    
1088            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1089    
1090    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1091    
1092            * src/lgCMatrix.c (lgCMatrix_diag): new function
1093            * R/lgCMatrix.R (diag): for new method
1094    
1095            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1096                 ==> construction of illegal "*gTMatrix" via new() should
1097                 now be much less easy:
1098            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1099    
1100            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1101                    directly.
1102            * man/Matrix.Rd: documents it.
1103    
1104    2006-07-06  Douglas Bates  <bates@R-project.org>
1105    
1106            * src/pedigree.c (pedigree_inbreeding): Correction in
1107            initialization.  This function is not currently being used and is
1108            not fully tested.
1109    
1110            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1111            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1112            objects.  Modified validity check on pedigree objects to account
1113            for nonparallel patterns of missingness of parents.
1114    
1115            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1116            class.
1117    
1118    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1119    
1120            * R/pMatrix.R: coercion pMatrix -> Tsparse
1121    
1122    2006-06-12  Douglas Bates  <bates@R-project.org>
1123    
1124            * DESCRIPTION (Version): 0.995-11 released to CRAN
1125    
1126            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1127            the output from mcmcsamp.
1128    
1129    2006-06-10  Douglas Bates  <bates@R-project.org>
1130    
1131            * R/lmer.R (simulestimate): added C code for calculating the trace
1132            of the hat matrix.
1133    
1134    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1137            classes.
1138            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1139    
1140    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/dgTMatrix.R (colSums): etc. All four of
1143            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1144            all "Matrices".
1145    
1146    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1147    
1148            * R/lmer.R (panel.ci): Add a reference line at zero and a
1149            background grid to the qqmath plot of ranef.lmer.
1150    
1151    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1152    
1153            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1154            grouping factors to be specified in the formula as (1|foo/bar).
1155    
1156    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1157    
1158            * R/lmer.R (findbars and others): Change check of is.numeric to
1159            !is.language to resolve the bug reported by Jacob Wegelin.
1160    
1161            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1162            code to evaluate inbreeding coefficients without calculating T,
1163            based on code in Sargolzaei and Iwaisaki's paper.
1164    
1165    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1166    
1167            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1168            generic and mer methods for isNested and denomDF. This denomDF was
1169            an attempt to emulate that in lme but I don't think that makes
1170            sense.  Use the trace of the hat matrix instead.
1171    
1172    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1175            the C code depending on a slot structure that's no longer valid.
1176            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1177    
1178    
1179    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1180    
1181            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1182            of lowerTriMatrix generic and methods to tril (also upper to triu)
1183            and added a general band extractor.
1184    
1185    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1186    
1187            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1188            allowable range with NAs. Added a corresponding check in the
1189            validity check for the pedigree class.
1190    
1191            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1192            crossprod methods now inherits from symmetricMatrix.
1193    
1194    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1195    
1196            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1197            generics lowerTriMatrix and upperTriMatrix along with methods for
1198            the Csparse virtual class.  Also added a C function Csparse_band
1199            that implements these methods by calling cholmod_band.
1200    
1201    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1204            erased when it was NULL.  This led to invalid subselections!
1205    
1206    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1207    
1208            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1209            in method for "t" so as not to lose the unit diagonal property.
1210    
1211    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1212    
1213            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1214            and methods.  This is now an option to the ranef method for the
1215            mer class.
1216    
1217            * src/cs_utils.c: Ensure that the nz component is -1 for a
1218            compressed column-oriented matrix.  Minor formatting cleanup.
1219    
1220            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1221            objects.
1222    
1223    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1226            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1227    
1228    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1229    
1230            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1231            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1232    
1233            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1234            for the dtCMatrix class.
1235    
1236    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1237    
1238            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1239            and methods for it.
1240    
1241    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1242    
1243            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1244            arguments, such that M %*% 1:6 now works
1245            * Tests/matprod.R: test the above
1246    
1247    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1248    
1249            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1250            the ranef.lmer class.
1251    
1252            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1253            methods to extract the posterior variances from the bVar slot.
1254    
1255    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1258            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1259    
1260            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1261            * tests/simple: (extended)
1262    
1263            * R/sparseMatrix.R (isTriangular): now using much improved
1264            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1265    
1266    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1267    
1268            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1269            (problem report from Franklin Parlamis).  This should be done
1270            generally.
1271    
1272    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1273    
1274            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1275            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1276            update the plot methods.
1277    
1278    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1279    
1280            * R/lmer.R (resid and ranef methods):  Added methods for the
1281            "residuals" and "resid" generic but only for linear mixed model
1282            fits.  Changed the ranef method to return a list of data frames so
1283            that the plot methods now work.
1284    
1285    2006-03-16  Douglas Bates  <bates@bates2>
1286    
1287            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1288            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1289    
1290            * DESCRIPTION (Date): New release
1291    
1292    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1295    
1296            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1297            * man/KNex.Rd: and other help files
1298            * tests/*.R: several ones needed adaption
1299            * inst/doc/Comparisons.Rnw: ditto
1300    
1301    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1302    
1303            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1304    
1305            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1306    
1307    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1310    
1311            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1312    
1313    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1314    
1315            * R/dMatrix.R: enable things like  M [ M < 10 ]
1316            * R/dgeMatrix.R: implement it
1317    
1318    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/AllClass.R: define "summary.mer" and "*.lmer"
1321            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1322            * R/lmer.R (show): now works with summary()
1323    
1324    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1325    
1326            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1327            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1328                    support the above
1329    
1330    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1331    
1332            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1333            Use glmFit$prior.weights for weights in a glmm.
1334            Allow an option usePQL = FALSE to skip the PQL steps for the
1335            Laplace method (and, in time, the AGQ method).
1336    
1337            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1338            into a separate function internal_mer_Xfactor to be able to call
1339            it from internal_bhat.
1340    
1341    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1342    
1343            * tests/Class+Meth.R (tstMatrixClass): function for much better
1344            testing; now again of all actual classes.
1345    
1346            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1347                    use macros and define make_d_matrix_* and make_i_matrix_*
1348                    where _i_ is for the ldense routines:
1349    
1350            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1351            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1352    
1353            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1354    
1355    
1356    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1357    
1358            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1359                    many different kinds of matrices.
1360            * R/*.R: quite a few new methods were needed for R CMD check with
1361                    new Matrix().  Very good for users playing around.
1362    
1363    
1364    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1365    
1366            * src/dgeMatrix.c (dMatrix_validate): new
1367            * src/Mutils.c (dense_nonpacked_validate): new
1368    
1369            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1370    
1371    
1372    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1373    
1374            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1375    
1376    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1377    
1378            * DESCRIPTION (Version): 0.99-6 released to CRAN
1379    
1380            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1381            segfault in cases with multiple non-nested grouping factors.
1382    
1383    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1384    
1385            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1386                    (Depends): also on 'utils'
1387    
1388            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1389            * R/diagMatrix.R (Diagonal): constructor and methods for
1390            diagonal matrices
1391    
1392            * R/ltTMatrix.R: new "minimal methods"
1393    
1394    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1395    
1396            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1397            all methods (and help files).
1398    
1399    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1400    
1401            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1402                    for case (dimn.  op  no_dimn.)
1403    
1404    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1405    
1406            * DESCRIPTION (Version): 0.99-2  released to CRAN
1407    
1408    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1409    
1410            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1411            by Julian Faraway.
1412    
1413    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * R/Auxiliaries.R (try_as): new utility
1416            * R/sparseMatrix.R: use try_as() in coercion to original class
1417    
1418    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1419    
1420            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1421    
1422    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/Auxiliaries.R (dimNamesCheck): added
1425    
1426            * R/Matrix.R (as.array), (as.vector): new
1427    
1428    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1431                    default.
1432            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1433                    "pMatrix" now contains "sparseMatrix"
1434    
1435    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * tests/Class+Meth.R: new tests; t(t(m)) == m
1438    
1439            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1440    
1441            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1442            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1443    
1444            * R/dspMatrix.R: typo in "t" method
1445    
1446    2005-09-18  Douglas Bates  <bates@wisc.edu>
1447    
1448            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1449            * R/Tsparse.R: instead of R/gTMatrix.R
1450            * R/Csparse.R: new
1451            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1452            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1453            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1454                            via cholmod
1455    
1456    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1457    
1458            * R/Auxiliaries.R (non0ind): new function using new C code
1459            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1460    
1461    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1462    
1463            * src/chm_common.h: header file required by all C sources that
1464            call CHOLMOD functions.  It defines a cholmod_common structure
1465            called 'c' whose address is passed as the last argument to
1466            (virtually) every CHOLMOD function.
1467    
1468            * src/Pattern.c: Simple example of the use of CHOLMOD.
1469    
1470            * src/init.c: initialize and finalize the cholmod_common structure.
1471    
1472            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1473            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1474    
1475    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1476    
1477            * inst/test-tools.R: new file collecting the utility functions used
1478                    in ./tests/*.R
1479    
1480            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1481            * R/Matrix.R (cbind2): methods for NULL and missing
1482    
1483    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1484    
1485            * R/AllClass.R: new "index" class for "[" and "[<-":
1486                    First cut at "symmetricMatrix" and "triangularMatrix"
1487            * R/gTMatrix.R (.ind.prep): new function;
1488                    Logical and character indexing now work too.
1489            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1490            * tests/indexing.R: new, including *.Rout.save
1491            * tests/dgTMatrix.R: new
1492    
1493    2005-08-29  Douglas Bates  <bates@wisc.edu>
1494    
1495            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1496            indicator pos not being updated.  Also enforced upper triangular
1497            for symmetric case.  Need to coerce edges component of elements of
1498            edge list - grr! (Why don't they define their classes cleanly?)
1499    
1500    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1501    
1502            * R/Matrix.R:  added first "[<-" methods; not yet functional
1503            * R/denseMatrix.R: ditto
1504            * man/Subassign-methods.Rd: new help file for these
1505    
1506    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * DESCRIPTION (Version): 0.98-6
1509    
1510            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1511            matrices.
1512    
1513    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1514    
1515            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1516                    as( <logical>, "matrix")
1517    
1518            * R/pMatrix.R: coercion to "lgTMatrix"
1519    
1520            * R/gTMatrix.R: new virtual class to define "[" methods for.
1521            * man/gTMatrix-class.Rd:
1522            * General slight re-organization of where "[" methods are defined.
1523              more to come.
1524    
1525    2005-08-18  Douglas Bates  <bates@wisc.edu>
1526    
1527            * DESCRIPTION (Version): 0.98-5  released to CRAN
1528    
1529            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1530            * .....
1531    
1532    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1533    
1534            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1535            or glmer objects.
1536    
1537    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1538    
1539            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1540    
1541    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1542    
1543            * R/HBMM.R: finish re-writing R-only code.
1544    
1545    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1546    
1547            * man/externalFormats.Rd: move documentation for writeHB and
1548            writeMM here.
1549    
1550            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1551            (suggested by Paul Roecker).
1552    
1553            * tests/validObj.R (assertError): Comment out test that is failing
1554            after recent changes in r-devel.
1555    
1556    
1557    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
1559            * R/AllClass.R: intermediate virtual class "denseMatrix"
1560            * man/denseMatrix-class.Rd
1561            * NAMESPACE: export it, and also export
1562            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1563    
1564    2005-08-10  Douglas Bates  <bates@wisc.edu>
1565    
1566            * DESCRIPTION (Version): 0.98-3 to CRAN
1567    
1568            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1569            matrix_solve code (which was really, really wrong).
1570    
1571    2005-08-07  Douglas Bates  <bates@wisc.edu>
1572    
1573            * DESCRIPTION (Version): 0.98-2
1574    
1575            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1576    
1577            * R/lmer.R (abbrvNms): new
1578            * R/lmer.R (mcmcsamp): allow transformed parameters
1579            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1580            for the Harwell-Boeing and the MatrixMarket formats.
1581    
1582    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1583    
1584            * man/dtrMatrix-class.Rd: add examples
1585            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1586    
1587            * TODO: note the dtpMatrix (docu) bug
1588    
1589            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1590            in order to ensure that new as.matrix() is used by old functions,
1591            e.g., svd(), qr(), eigen(), dist(),..;
1592                  apply(), also matplot() or pairs().
1593    
1594    
1595    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1596    
1597            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1598              add comments about 'control' / lmerControl() arguments
1599    
1600    2005-07-27  Douglas Bates  <bates@wisc.edu>
1601    
1602            * man/sleepstudy.Rd: Added the sleep data set.
1603            * DESCRIPTION (Version): 0.98-1  released to CRAN
1604    
1605    2005-07-12  Douglas Bates  <bates@wisc.edu>
1606            * man/sleepstudy.Rd: Added the sleep data set.
1607    
1608            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1609            .Call calls that were producing spurious output.
1610    
1611    2005-07-05  Douglas Bates  <bates@wisc.edu>
1612    
1613            * R/lmer.R (lmer): stored updated variance component estimates in
1614            mer object for the generalized model.  (Bug reported by Renaud
1615            Lancelot).
1616    
1617    2005-07-03  Douglas Bates  <bates@wisc.edu>
1618    
1619            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1620            unidimensional case.
1621    
1622    2005-06-08  Douglas Bates  <bates@wisc.edu>
1623    
1624            * DESCRIPTION (Version): 0.96-1
1625    
1626            * moved  lmer-class' R and C code moved from lme4 to here
1627    
1628    2005-06-04  Douglas Bates  <bates@wisc.edu>
1629    
1630            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1631            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1632    
1633    2005-06-02  Douglas Bates  <bates@wisc.edu>
1634    
1635            * src/Makefile.win: Forgot to update this when Makefile changed.
1636    
1637    2005-05-11  Douglas Bates  <bates@wisc.edu>
1638    
1639            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1640            bug reported by Kurt Hornik and Michael Hahsler.
1641    
1642    2005-05-10  Douglas Bates  <bates@wisc.edu>
1643    
1644            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1645            logical sparse matrices.  These will also be used in the symbolic
1646            analysis for lmer objects.
1647    
1648            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1649            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1650    
1651    2005-05-06  Douglas Bates  <bates@wisc.edu>
1652    
1653            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1654            colMeans, colSums, rowMeans and rowSums.
1655    
1656    2005-04-18  Douglas Bates  <bates@wisc.edu>
1657    
1658            * src/lgCMatrix.[ch]: code for _validate method and stub for
1659            multiplication operation.
1660    
1661            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1662            to dgetrs.
1663    
1664            * src/init.c: Fix cut-and-paste error in definition of
1665            dgeMatrix_matrix_solve
1666    
1667            * src/{many files}: Tighten code by using ALLOC_SLOT.
1668    
1669    2005-04-15  Douglas Bates  <bates@wisc.edu>
1670    
1671            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1672    
1673            * DESCRIPTION: Eliminate import of stats.
1674    
1675    
1676    2005-04-06  Douglas Bates  <bates@wisc.edu>
1677    
1678            * R/AllClass.R : add logical sparse matrix classes
1679    
1680    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1681    
1682            * R/dgTMatrix.R: add "[" method for triplet matrices
1683            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1684    
1685    2005-03-31  Douglas Bates  <bates@wisc.edu>
1686    
1687            * DESCRIPTION (Version): release 0.95-5 to CRAN
1688    
1689            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1690            * R/sparseMatrix.R: %*%, crossprod()
1691            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1692            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1693            * src/lmer.c (lmer_fitted): fix thinko
1694    
1695    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1696    
1697            * R/AllClass.R: add two virtual sparse classes ``on top''
1698    
1699    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1700    
1701            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1702                    correspondingly fix examples and tests/ since new()
1703                    doesn't work for virtual classes.
1704    
1705    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1706    
1707            * R/Matrix.R (as.matrix): method and one for unname()
1708            * tests/dpoMatrix.R: tests should now be less platform dependent;
1709              also run for R 2.1.0; using as.matrix()
1710    
1711    2005-03-15  Douglas Bates  <bates@wisc.edu>
1712    
1713            * R/pMatrix.R: "pMatrix" class added
1714            * ....
1715    
1716    2005-03-14  Douglas Bates  <bates@wisc.edu>
1717    
1718            * R/dtpMatrix.R: Add unpack method and an example.
1719    
1720            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1721            of general symmetric matrices and associated S4 methods.
1722    
1723    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1724            +
1725    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1726    
1727            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1728              crossprod() and "%*%" methods added; tests, too.
1729            * tests/matprod.R: new, for testing these
1730    
1731    2005-03-03  Douglas Bates  <bates@wisc.edu>
1732    
1733            * src/lmer.c (lmer_fitted): Added.
1734    
1735    2005-03-02  Douglas Bates  <bates@wisc.edu>
1736    
1737            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1738    
1739    2005-02-28  Douglas Bates  <bates@wisc.edu>
1740    
1741            * src/*.c,po/,inst/po: Internationalization and localization of
1742            the package.
1743    
1744            * src/ldl.[ch]: Removed these as their contents are referenced in the
1745            R_ldl.c file.
1746    
1747            * src/flame.[ch]: Removed these source files.
1748    
1749            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1750    
1751            * src/LU.[ch],src/init.c: absorb in factorizations
1752    
1753            * src/Mutils.h: prepare for internationalization
1754    
1755            * src/cblas.h: move the enum definitions to Mutils.h and remove
1756            this file
1757    
1758    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1759    
1760            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1761    
1762            * R/dtrMatrix.R: fix t() method
1763    
1764            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1765            * NAMESPACE: export them (and import generics from "methods")
1766            * tests/group-methods.R : and test them.
1767    
1768            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1769            border case
1770    
1771    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1772    
1773            * DESCRIPTION (Version): 0.95-2  released to CRAN
1774    
1775            * src/dgBCMatrix.c:
1776            * src/lmer.c: many changes
1777            * ...
1778    
1779    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1780    
1781            * R/Matrix.R: add more sophisticated show() method.
1782    
1783    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1784    
1785            * */* : almost complete reorganization of classes.
1786    
1787    2005-01-26  Douglas Bates  <bates@wisc.edu>
1788    
1789            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1790            for the geMatrix class.
1791    
1792    2005-01-24  Douglas Bates  <bates@wisc.edu>
1793    
1794            * src/Makefile (clean): Remove *.a and *.so
1795    
1796            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1797    
1798    2005-01-23  Douglas Bates  <bates@wisc.edu>
1799    
1800            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1801            had an effect in cases with more than 2 grouping factors.
1802    
1803    2005-01-03  Douglas Bates  <bates@wisc.edu>
1804    
1805            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1806    
1807    2004-12-23  Douglas Bates  <bates@wisc.edu>
1808    
1809            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1810            and R_useDynamicSymbols (suggested by B.D.Ripley).
1811    
1812    2004-12-14  Douglas Bates  <bates@wisc.edu>
1813    
1814            * R/sscMatrix.R: Add determinant methods
1815    
1816            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1817            for tripletMatrix to matrix.
1818    
1819    2004-12-13  Douglas Bates  <bates@wisc.edu>
1820    
1821            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1822            no longer used.
1823    
1824            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1825            with dynamic allocation of scratch arrays.
1826    
1827            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1828            for multivariate random effects with multiple grouping factors.
1829            Fixes part but not all of #15.
1830    
1831    2004-12-03  Douglas Bates  <bates@wisc.edu>
1832    
1833            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1834            scalar grouping factors corrected.
1835    
1836    2004-11-29  Douglas Bates  <bates@wisc.edu>
1837    
1838            * src/bCrosstab.c: remove diag_update which is no longer used
1839    
1840    2004-11-16  Douglas Bates  <bates@wisc.edu>
1841    
1842          * 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
1843          .h file can be included.          .h file can be included.
1844    
1845  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1846    
1847          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1848          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1849    
1850          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1851    
1852  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1853    
1854          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1855    
1856  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1857    
1858          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1859    
1860  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1861    
1862          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1863    
1864  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1865    
1866          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1867    
1868  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1869    
1870          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1871          routines.          routines.
1872    
1873  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1874    
1875          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1876    
1877  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1878    
1879          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1880    

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