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

Legend:
Removed from v.388  
changed lines
  Added in v.1837

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