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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1787, Fri Feb 16 20:02:19 2007 UTC
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1    2007-02-16  Douglas Bates  <bates@r-project.org>
2    
3            * DESCRIPTION (Date, Version): 0.9975-11 with new date
4            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
5            const modifier on declaration of the array 'valid'
6    
7    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
10    
11    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
14    
15            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
16            * tests/simple.R: test the above and some of these coercions:
17    
18            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
19                    be careful to avoid infinite recursion, using new coercions in
20            * R/ngCMatrix.R and nsC... and ntC...
21            * R/lsparseMatrix.R: ditto
22    
23            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
24    
25            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
26            * R/Rsparse.R: reactivate .Call()s
27    
28            * tests/Class+Meth.R: a bit more on actual classes
29    
30    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
33    
34    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.9975-10 to upload
37    
38            * tests/Class+Meth.R (tstMatrixClass): require coercions to
39            specific classes less unconditionally.
40    
41            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
42    
43            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
44    
45            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
46            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
47            R_to_CMatrix segfaults on one platform.
48            Eliminate most coercion method to *specific* classes, and replace
49            with virtual classes coercions.
50    
51    
52    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
53    
54            * src/init.c: export the CHM...._validate() placeholders, since
55            they *are* called.
56    
57            * tests/Class+Meth.R (classCanCoerce): and starting to test
58            all as(<from>, <to>)
59    
60    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
63            * tests/indexing.R: tested now
64            * tests/indexing.Rout.save: updated
65    
66            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
67            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
68            appropriate.
69    
70            * NAMESPACE: export a trivial
71            * R/Matrix.R: drop() Matrix-method
72    
73            * R/AllClass.R: moved all prototypes to virtual super classes.
74    
75            * R/Rsparse.R: many more coercions to have less exceptions in
76            * tests/Class+Meth.R:
77    
78            * R/Ops.R (Compare): tweak for case with NA
79            * tests/simpl.R: hence another 'FIXME' eliminated
80    
81    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
84            objects.
85    
86            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
87              and more of "!", "&", "|", all, any; coercions
88    
89            * R/Rsparse.R: many coercions (which enable quite a few other
90            methods), thanks to enhancements in
91            * src/dgCMatrix.c (R_to_CMatrix): new, and
92            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
93            symmetric & triangular and ..RMatrix objects.
94    
95            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
96            renamed file from src/dsTMatrix.c;
97            now dealing with symmetric and triangular Tsparse coercions, both
98            to dense and general.
99    
100    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
103    
104            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
105            where sensible when the <numeric> is of length > 1.
106    
107    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R ([<-): for M[] <- value: fix length
110    
111    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
114            * R/ndenseMatrix.R: new coercions n* -> l*
115    
116    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
119    
120            * R/Ops.R ("Logic"): and other "Ops", many updates
121    
122    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/Mutils.h (SET_DimNames): new utility
125    
126            * R/Auxiliaries.R (nnzero): improved and now exported via
127    
128            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
129    
130    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/diagMatrix.R (!): fix typo.
133    
134    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (as_Csparse): and quite a few others:
137                    allow to pass class definition --> speedup
138            * R/sparseMatrix.R: apply the above
139    
140            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
141    
142            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
143            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
144            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
145    
146            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
147    
148            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
149            and use it for "sparse*" as well, since it's faster than the
150            as_Csparse(.) way.
151    
152    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
155    
156    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
159            as method for   M[ ij ] <- v
160            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
161    
162            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
163            FALSE answer
164    
165            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
166            * tests/indexing.R: test it, and some of the above
167    
168    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (is_duplicatedT): new utility
171    
172    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
173    
174            * src/init.c (R_init_Matrix): export cholmod_scale
175    
176    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
179            base::as.matrix to (x, ...)
180    
181    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
184            file; start using "Logic", hence
185    
186            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
187            * NAMESPACE: import and export "Logic"
188    
189    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
192            only needed previously to R version 2.5.0.
193    
194    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
197    
198            * R/Tsparse.R (replTmat): fix subassignment of triangular
199            * R/Csparse.R (replCmat): ditto
200            * tests/indexing.R: more tests, incl the above fix
201    
202    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Auxiliaries.R (drop0): extend for non CSparse
205            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
206    
207            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
208                    use uplo correctly (!); other places: use uplo_P() macro
209    
210            * R/Csparse.R (replCmat): call diagU2N() when needed
211            * R/Tsparse.R (replTmat): ditto
212    
213            * src/dtCMatrix.c (tCMatrix_validate): new
214            * src/dtTMatrix.c (tTMatrix_validate): new, used in
215            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
216    
217            * R/diagMatrix.R (replDiag): to use in [<-
218    
219    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
222                    also more general diagU2N().
223    
224    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
227            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
228    
229    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * tests/bind.R: a few more cases
232            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
233    
234            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
235            * R/ddenseMatrix.R (cbind2/rbind2)
236            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
237            * tests/indexing.R
238            * tests/indexing.Rout.save: updated
239    
240    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
243            * tests/indexing.R
244    
245    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
248            align with proper position of "0", i.e., right for integers.
249            argument 'align' by default is "fancy".
250    
251    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
254            * R/Csparse.R: and fix "Compare" for more cases.
255            * tests/Class+Meth.R: test some of these (m == m, m != m)
256    
257    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/lsparseMatrix.R: all() and any() methods
260            * R/ldenseMatrix.R:      ditto
261            * NAMESPACE, R/Matrix.R: ditto
262    
263            * man/all-methods.Rd: document them minimally
264    
265            * tests/simple.R: add a few examples for these
266    
267    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R ([): fix long standing typo in symmetric case
270            * man/dsCMatrix-class.Rd: add example exhibiting the above case
271    
272    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
275            to LL before converting to a sparse matrix. (The LDL form can be
276            converted to a sparse matrix but it is implicitly a unit
277            triangular matrix and a diagonal matrix overwritten on the diagonal.)
278    
279    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
282    
283    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION (Version): updated -> release 0.9975-7
286            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
287    
288    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
291    
292    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
293    
294            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
295            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
296            is exactly singular.
297    
298    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Date): updated -> release 0.9975-6
301    
302    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
305            now returns symmetric.
306    
307            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
308    
309            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
310            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
311    
312            * R/Auxiliaries.R (.type.kind): added
313    
314    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
317            running src/CSparse_install.sh
318    
319            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
320    
321    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
324            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
325    
326            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
327    
328            * tests/Class+Meth.R (tstMatrixClass): now assure
329            the (important in method programming) property :
330    
331                    ###>>  Every "Matrix" is either
332                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
333    
334                    (where "*" stands for "Matrix")
335    
336            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
337    
338            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
339            * tests/validObj.R: checks for "comparison"
340    
341            * R/sparseMatrix.R ([): improved indexing for sparse;
342                    trying to keep <symmetric>[ n, n] symmmetric
343    
344            * tests/indexing.R: indexing for logical sparse now ok
345    
346    
347    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * src/Tsparse.c: use xTsparse_validate() , and hence remove
350    
351            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
352    
353    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
356    
357            * tests/simple.R: validObject() checking the above.
358    
359            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
360            replacing both dgCMatrix_validate and lgCM*.
361    
362            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
363            fix dimnames setting in other places.
364            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
365    
366    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
369    
370            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
371            symmetry test, via
372            * R/Auxiliaries.R (.as.dgC.0.factors):
373    
374    2006-11-01  Douglas Bates  <bates@r-project.org>
375    
376            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
377            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
378            <CsparseMatrix>) added
379    
380    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * tests/matprod.R: add a variation of Harri's example
383    
384            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
385            recursive infinitely.
386    
387            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
388    
389            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
390    
391    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
394            matrix if possible; test m+m == 2*m; now test dgRMatrix.
395            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
396            satisfy the above test.
397    
398    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
401    
402            * R/dgCMatrix.R: solve(a, b="missing") based on
403            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
404            RHS = NULL.
405    
406            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
407            add more (needed) [t]crossprod() methods.
408    
409            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
410    
411            * R/Auxiliaries.R (as_CspClass): cleanup
412            (drop0): internal utility for "Csparse_drop(*, 0)"
413            (.bail.out.2): encourage active feedback
414    
415    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/dMatrix.R(Compare): new(), then slots [no validity check]
418    
419            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
420            non-valid or 'sorted' case).
421    
422            * R/dsparseMatrix.R: add "chol" method.
423            * R/ddenseMatrix.R: ditto
424    
425            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
426            * NAMESPACE (Ops)
427            * R/diagMatrix.R (diag2T): simple utility used "higher level"
428            coercion; deprecating direct lower level coercions.
429    
430            * R/*.R (seq): use seq_len() and seq_along() where possible.
431    
432    
433    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * DESCRIPTION (Version): 0.9975-5 ready for release
436    
437    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
440    
441    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/AllClass.R (corMatrix): add 'validity' check;
444                    comment out unused "LDL" class definition
445            * NAMESPACE: mention, but do not export "LDL" class
446            * R/corMatrix.R: new (simple), needed for R-devel with
447            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
448              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
449    
450    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
453            use Rprintf and R's error handling.
454    
455    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
458            * tests/matprod.R: add tests for the bug fixed.
459    
460    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
461    
462            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
463            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
464    
465    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
468    
469    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Version): 0.9975-3
472    
473            * R/diagMatrix.R (bdiag): new function constructing block diagonal
474            (sparse) matrices.
475            * man/bdiag.Rd: docu + examples
476    
477            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
478    
479            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
480            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
481    
482            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
483            that result is sparse or diagonal (and not dense).
484    
485            * man/Subassign-methods.Rd: fix examples
486    
487            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
488            should always return a sparse (and not sometimes a diagonal) matrix.
489    
490    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
493    
494    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
495    
496            * DESCRIPTION (Version): 0.9975-2
497    
498            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
499    
500    2006-10-02  Douglas Bates  <bates@R-project.org>
501    
502            * tests/dg_Matrix.R: Simplify test taking into account new code.
503    
504    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
507    
508            * R/lsTMatrix.R: new files w/ missing methods
509            * R/nsTMatrix.R:  "  'for completeness'
510    
511            * tests/Class+Meth.R: a bit less 'not.ok.classes'
512    
513            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
514    
515    
516    2006-09-28  Douglas Bates  <bates@R-project.org>
517    
518            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
519            included.
520    
521            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
522            Export C-callable functions used in Zt_create in lme4.
523    
524    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Version): 0.9975-1
527    
528            * tests/simple.R: less checks fail; using NA, found that our
529                    kronecker() is not base-compatible with NA's.
530    
531            * R/dMatrix.R: "Compare" method now implemented for all cases
532    
533            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
534    
535            * man/dtpMatrix-class.Rd: mention length of 'x' slot
536    
537            * src/dtpMatrix.c (dtpMatrix_validate): fix check
538            * src/dspMatrix.c (dspMatrix_validate): ditto
539    
540            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
541              including coercion to [nl]tTMatrix.
542    
543            * R/diagMatrix.R (show): print a header line as for other classes.
544    
545    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * src/Makefile.win (SUBDIRS): fix typo
548    
549    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
552    
553    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
556            symmetric and y missing in R code using %*% (cholmod_aat doesn't
557            accept a symmetric matrix).
558            * tests/group-methods.R: Uncomment test of crossprod applied to
559            lsCMatrix objects.
560    
561    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/AllClass.R (symmetricMatrix): add validity method (available
564            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
565    
566            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
567    
568            * tests/indexing.Rout.save:
569            * tests/indexing.R: additions, mainly for 'lsparse'
570    
571            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
572            case.
573    
574            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
575    
576    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
579                    as 'N' (1-letter - Ok?)
580    
581            * tests/group-methods.R: add test for logical + NAs
582    
583            * R/dMatrix.R ("Compare"): fix to work with NA's
584    
585            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
586    
587            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
588                    which is implemented.
589    
590    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * src/chm_common.c: coerce logical <-> double instead of
593            typecasting;  needed for "l" matrix handling in cholmod.
594    
595            * tests/other-pkgs.R (graph): small extension in "graph" checks.
596    
597            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
598            (Tsp2grNEL): other fixes needed
599    
600    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
603                    Matrices, since "lMatrix", also "lsparseM" can have NA
604            * R/ndenseMatrix.R, etc: new source files
605            * man/nsparseMatrix-classes.Rd, etc: new help files
606            * tests/: adaptions
607            * src/chm_common.c (chm_dense_to_SEXP): and others:
608                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
609            * src/Csparse.c, etc: ditto
610    
611    2006-09-11  Douglas Bates  <bates@R-project.org>
612    
613            * src/Mutils.[ch],init.c inst/include/*.h: Move the
614            alloc_d**Matrix functions to the lme4 package.
615    
616    2006-09-09  Douglas Bates  <bates@R-project.org>
617    
618            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
619            fixed
620    
621    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/lMatrix.R: new
624    
625            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
626    
627            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
628            * man/tcrossprod.Rd: ditto
629    
630    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
631    
632            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
633            for exported functions
634            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
635            Remove partitioning algorithms for sparse matrix reordering.  The
636            copyright on the Metis code was problematic and the methods were
637            rarely used.
638            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
639            operations are now done entirely in CHOLMOD code.
640    
641    2006-09-06  Douglas Bates  <bates@R-project.org>
642    
643            * src/Mutils.h: Remove functions that are no longer used.
644    
645    2006-09-04  Douglas Bates  <bates@R-project.org>
646    
647            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
648            * src/DEPS.mkf: update
649    
650    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * created branches/Matrix-for-R-2.3.x;  on trunk: do
653            * DESCRIPTION (Version): 0.9975-0
654            (Depends): R (>= 2.4.0)
655    
656    2006-09-01  Douglas Bates  <bates@R-project.org>
657    
658            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
659    
660    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
663            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
664    
665            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
666    
667    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
670            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
671            * R/dsparseMatrix.R: ditto
672            * R/Csparse.R: ditto
673    
674    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/dMatrix.R (Compare): improve availability of "<", etc
677            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
678    
679    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
682            of a 0-index which was used as 1-index (..hmm)
683    
684            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
685    
686            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
687            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
688            (.is.diagonal): ditto
689    
690            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
691    
692            * R/Matrix.R (Matrix): also work for NA data
693    
694    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
697            in all cases.
698    
699    2006-08-27  Douglas Bates  <bates@R-project.org>
700    
701            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
702            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
703    
704    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
707            subclasses of "ddenseMatrix"
708            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
709            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
710            instead of half dozen specialized ones.
711    
712    2006-08-25  Douglas Bates  <bates@R-project.org>
713    
714            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
715            <tillard@cirad.fr> - ordering standard errors to match effects.
716    
717    2006-08-24  Douglas Bates  <bates@R-project.org>
718    
719            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
720            on R_ldl.
721            * R/lCholCMatrix.R,
722            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
723            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
724            * many files in ./R and ./src: Use more general version of
725            dup_mMatrix_as_dgeMatrix to simplify method definitions.
726            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
727            dtpMatrix, dspMatrix and dppMatrix conversions.
728    
729    
730    2006-08-23  Douglas Bates  <bates@R-project.org>
731    
732            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
733            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
734            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
735            dgeMatrix_crossprod (may need to do this in other places).
736            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
737            generic and method for dsCMatrix.  Use CHOLMOD for chol().
738    
739    2006-08-22  Douglas Bates  <bates@R-project.org>
740    
741            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
742            types of classed Matrices, matrices or numeric or logical vectors.
743            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
744            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
745            to Mutils.h (as an inline) and change name to Matrix_check_class;
746            fixes in as_cholmod_factor and chm_factor_to_SEXP.
747            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
748            dsCMatrix_matrix_solve.  Comment out vestigial functions.
749            * src/Csparse.c: use diag_P and uplo_P macros.
750    
751    2006-08-21  Douglas Bates  <bates@R-project.org>
752    
753            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
754            valgrind.
755            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
756            inverses.
757            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
758            -Wall warnings.
759            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
760            Use dup_mMatrix_as_dgeMatrix.
761    
762    2006-08-20  Douglas Bates  <bates@R-project.org>
763    
764            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
765            * tests/sparseQR.R: Added
766            * man/sparseQR-class.Rd: Document methods for qr.* generics
767            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
768    
769    2006-08-19  Douglas Bates  <bates@R-project.org>
770    
771            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
772            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
773            and qr.fitted.
774            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
775            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
776    
777    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
780            the base version has no "..." argument.
781    
782            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
783    
784            * R/Matrix.R: define and
785            * NAMESPACE: export as.numeric() and as.logical() methods.
786                    Let's hope these do not badly slow down something...
787            Finally export the zapsmall() method.
788    
789    2006-08-17  Douglas Bates  <bates@R-project.org>
790    
791            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
792            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
793            * src/dtCMatrix.c :Remove code that is no longer used
794            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
795    
796    2006-08-14  Douglas Bates  <bates@R-project.org>
797    
798            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
799            Csparse_to_logical and Csparse_symmetric_to_general.
800            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
801            coercion methods between CsparseMatrix and TsparseMatrix.
802    
803    2006-08-14  Douglas Bates  <bates@R-project.org>
804    
805            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
806            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
807            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
808            possible.
809    
810    2006-08-12  Douglas Bates  <bates@R-project.org>
811    
812            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
813              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
814              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
815              generalize conversions between TsparseMatrix, CsparseMatrix,
816              denseMatrix and matrix.  Preserve triangularity property and
817              propagate Dimnames in the easy cases.
818    
819    2006-08-10  Douglas Bates  <bates@R-project.org>
820    
821            * src/lmer.c: adjust checks in glmer_init for S4SXP
822            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
823            before S4SXP but for the wrong reasons.
824    
825    2006-08-08  Douglas Bates  <bates@R-project.org>
826    
827            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
828            Later modified to return the upper triangle only.
829            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
830    
831    2006-08-07  Douglas Bates  <bates@R-project.org>
832    
833            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
834            R-level conversion to a sparse symmetric class.
835            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
836            Remove conversion to sparse symmetric classes (now done in C code).
837    
838    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
841            * man/band.Rd:  adapt the \dontshow{} unit test.
842    
843    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * DESCRIPTION (Version): 0.995-14  for CRAN
846    
847            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
848    
849            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
850            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
851    
852            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
853            * R/Tsparse.R (tril, triu, band): methods
854            * R/dgRMatrix.R (tril, ...):    ditto
855            * man/band.Rd:                  ditto
856    
857    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Matrix.R (head, tail): directly use utils:::head.matrix
860                    to be up-to-date automatically.
861    
862    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
865    
866            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
867            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
868            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
869            such that the S4 objects are always created by the current version
870            of R and 'Matrix' class definitions.
871    
872    2006-08-01  Douglas Bates  <bates@R-project.org>
873    
874            * R/lmer.R (LMEoptimize method), tests/lmer.R,
875            inst/external/test3comp.rda: Added warnings for convergence on
876            boundary and test cases.
877    
878            * src/lmer.c (mer_postVar): Modified to return the variances that
879            are marginal to the fixed effects, not conditional on them (which
880            is what the bVar slot contents represent).
881    
882    2006-07-31  Douglas Bates  <bates@R-project.org>
883    
884            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
885            function which calls the C function mer_hat_trace2.
886    
887            * man/ranef.Rd: Include description of "postVar" argument and
888            producing a caterpillar plot.
889    
890    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * NAMESPACE:    change  "correlation" to "corMatrix"
893            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
894            * R/dpoMatrix.R: ditto
895            * R/lmer.R:      ditto
896    
897    2006-07-28  Douglas Bates  <bates@R-project.org>
898    
899            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
900            RZXinv slot's contents into a separate internal function that can
901            be used in mer_hat_trace.
902    
903    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
906            via new smart
907            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
908            utility functions.
909    
910    
911    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/Csparse.R (tril, triu, band): do return *triangular* classed
914            matrices when appropriate; band() even symmetric ones.
915            (replCmat): extend to potentially all "CsparseMatrix"
916            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
917            allow subassignment for special sparse matrices.
918    
919            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
920    
921            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
922            argument; in glmer_*(): print only if(verbose).
923    
924            speed-optimize a few places by moving REAL(.) out of loops.
925    
926            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
927    
928    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
931                    since that wrongly triggers also for M[ logi , ]
932    
933            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
934            a symmetric matrix that results in a non-symmetric one.
935            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
936    
937            * R/dMatrix.R: make round(M) work as round(M, 0)
938    
939            * R/dgTMatrix.R (image): coordinate system and axis now use
940            1-based indices, not 0-based ones.
941    
942            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
943            * tests/indexing.R: test it.
944    
945            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
946            * man/isSymmetric-methods.Rd: and document it.
947    
948            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
949            * man/SparseM-conv.Rd: docu them
950    
951            * tests/other-pkgs.R: renamed from tests/graph.R and add example
952                    for 'SparseM' conversions
953    
954    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
955    
956            * R/Matrix.R (head): added head() and tail() methods.
957    
958    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * DESCRIPTION (Version): 0.995-12 released to CRAN
961    
962    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * tests/simple.R: add check for correct dsT -> dgT coercion;
965                    add check for correct printing of symmetric sparse matrices.
966    
967            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
968            for sparse symmetric matrices.
969    
970            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
971            diagonal twice.
972    
973    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
974    
975            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
976            being applied to the x slot (detected by Brian Ripley).
977    
978    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
981    
982            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
983    
984    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * src/lgCMatrix.c (lgCMatrix_diag): new function
987            * R/lgCMatrix.R (diag): for new method
988    
989            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
990                 ==> construction of illegal "*gTMatrix" via new() should
991                 now be much less easy:
992            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
993    
994            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
995                    directly.
996            * man/Matrix.Rd: documents it.
997    
998    2006-07-06  Douglas Bates  <bates@R-project.org>
999    
1000            * src/pedigree.c (pedigree_inbreeding): Correction in
1001            initialization.  This function is not currently being used and is
1002            not fully tested.
1003    
1004            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1005            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1006            objects.  Modified validity check on pedigree objects to account
1007            for nonparallel patterns of missingness of parents.
1008    
1009            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1010            class.
1011    
1012    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/pMatrix.R: coercion pMatrix -> Tsparse
1015    
1016    2006-06-12  Douglas Bates  <bates@R-project.org>
1017    
1018            * DESCRIPTION (Version): 0.995-11 released to CRAN
1019    
1020            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1021            the output from mcmcsamp.
1022    
1023    2006-06-10  Douglas Bates  <bates@R-project.org>
1024    
1025            * R/lmer.R (simulestimate): added C code for calculating the trace
1026            of the hat matrix.
1027    
1028    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1031            classes.
1032            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1033    
1034    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/dgTMatrix.R (colSums): etc. All four of
1037            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1038            all "Matrices".
1039    
1040    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1041    
1042            * R/lmer.R (panel.ci): Add a reference line at zero and a
1043            background grid to the qqmath plot of ranef.lmer.
1044    
1045    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1046    
1047            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1048            grouping factors to be specified in the formula as (1|foo/bar).
1049    
1050    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1051    
1052            * R/lmer.R (findbars and others): Change check of is.numeric to
1053            !is.language to resolve the bug reported by Jacob Wegelin.
1054    
1055            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1056            code to evaluate inbreeding coefficients without calculating T,
1057            based on code in Sargolzaei and Iwaisaki's paper.
1058    
1059    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1060    
1061            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1062            generic and mer methods for isNested and denomDF. This denomDF was
1063            an attempt to emulate that in lme but I don't think that makes
1064            sense.  Use the trace of the hat matrix instead.
1065    
1066    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1069            the C code depending on a slot structure that's no longer valid.
1070            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1071    
1072    
1073    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1074    
1075            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1076            of lowerTriMatrix generic and methods to tril (also upper to triu)
1077            and added a general band extractor.
1078    
1079    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1080    
1081            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1082            allowable range with NAs. Added a corresponding check in the
1083            validity check for the pedigree class.
1084    
1085            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1086            crossprod methods now inherits from symmetricMatrix.
1087    
1088    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1089    
1090            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1091            generics lowerTriMatrix and upperTriMatrix along with methods for
1092            the Csparse virtual class.  Also added a C function Csparse_band
1093            that implements these methods by calling cholmod_band.
1094    
1095    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1098            erased when it was NULL.  This led to invalid subselections!
1099    
1100    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1101    
1102            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1103            in method for "t" so as not to lose the unit diagonal property.
1104    
1105    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1106    
1107            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1108            and methods.  This is now an option to the ranef method for the
1109            mer class.
1110    
1111            * src/cs_utils.c: Ensure that the nz component is -1 for a
1112            compressed column-oriented matrix.  Minor formatting cleanup.
1113    
1114            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1115            objects.
1116    
1117    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1120            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1121    
1122    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1123    
1124            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1125            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1126    
1127            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1128            for the dtCMatrix class.
1129    
1130    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1131    
1132            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1133            and methods for it.
1134    
1135    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1138            arguments, such that M %*% 1:6 now works
1139            * Tests/matprod.R: test the above
1140    
1141    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1142    
1143            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1144            the ranef.lmer class.
1145    
1146            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1147            methods to extract the posterior variances from the bVar slot.
1148    
1149    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1152            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1153    
1154            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1155            * tests/simple: (extended)
1156    
1157            * R/sparseMatrix.R (isTriangular): now using much improved
1158            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1159    
1160    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1161    
1162            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1163            (problem report from Franklin Parlamis).  This should be done
1164            generally.
1165    
1166    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1167    
1168            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1169            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1170            update the plot methods.
1171    
1172    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1173    
1174            * R/lmer.R (resid and ranef methods):  Added methods for the
1175            "residuals" and "resid" generic but only for linear mixed model
1176            fits.  Changed the ranef method to return a list of data frames so
1177            that the plot methods now work.
1178    
1179    2006-03-16  Douglas Bates  <bates@bates2>
1180    
1181            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1182            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1183    
1184            * DESCRIPTION (Date): New release
1185    
1186    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1189    
1190            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1191            * man/KNex.Rd: and other help files
1192            * tests/*.R: several ones needed adaption
1193            * inst/doc/Comparisons.Rnw: ditto
1194    
1195    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1198    
1199            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1200    
1201    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1204    
1205            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1206    
1207    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/dMatrix.R: enable things like  M [ M < 10 ]
1210            * R/dgeMatrix.R: implement it
1211    
1212    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1213    
1214            * R/AllClass.R: define "summary.mer" and "*.lmer"
1215            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1216            * R/lmer.R (show): now works with summary()
1217    
1218    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1221            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1222                    support the above
1223    
1224  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1225    
1226          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 1394 
1394  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1395    
1396          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1397          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1398          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1399    
1400  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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