SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

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

Legend:
Removed from v.388  
changed lines
  Added in v.1760

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge