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

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