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revision 1316, Tue Jul 11 22:00:41 2006 UTC revision 1716, Sat Jan 6 02:01:24 2007 UTC
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1    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/init.c (R_init_Matrix): export cholmod_scale
4    
5    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
8            file; start using "Logic", hence
9    
10            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
11            * NAMESPACE: import and export "Logic"
12    
13    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
16            only needed previously to R version 2.5.0.
17    
18    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
21    
22            * R/Tsparse.R (replTmat): fix subassignment of triangular
23            * R/Csparse.R (replCmat): ditto
24            * tests/indexing.R: more tests, incl the above fix
25    
26    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (drop0): extend for non CSparse
29            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
30    
31            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
32                    use uplo correctly (!); other places: use uplo_P() macro
33    
34            * R/Csparse.R (replCmat): call diagU2N() when needed
35            * R/Tsparse.R (replTmat): ditto
36    
37            * src/dtCMatrix.c (tCMatrix_validate): new
38            * src/dtTMatrix.c (tTMatrix_validate): new, used in
39            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
40    
41            * R/diagMatrix.R (replDiag): to use in [<-
42    
43    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
46                    also more general diagU2N().
47    
48    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
51            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
52    
53    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * tests/bind.R: a few more cases
56            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
57    
58            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
59            * R/ddenseMatrix.R (cbind2/rbind2)
60            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
61            * tests/indexing.R
62            * tests/indexing.Rout.save: updated
63    
64    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
67            * tests/indexing.R
68    
69    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
72            align with proper position of "0", i.e., right for integers.
73            argument 'align' by default is "fancy".
74    
75    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
78            * R/Csparse.R: and fix "Compare" for more cases.
79            * tests/Class+Meth.R: test some of these (m == m, m != m)
80    
81    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/lsparseMatrix.R: all() and any() methods
84            * R/ldenseMatrix.R:      ditto
85            * NAMESPACE, R/Matrix.R: ditto
86    
87            * man/all-methods.Rd: document them minimally
88    
89            * tests/simple.R: add a few examples for these
90    
91    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ([): fix long standing typo in symmetric case
94            * man/dsCMatrix-class.Rd: add example exhibiting the above case
95    
96    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
99            to LL before converting to a sparse matrix. (The LDL form can be
100            converted to a sparse matrix but it is implicitly a unit
101            triangular matrix and a diagonal matrix overwritten on the diagonal.)
102    
103    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
104    
105            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
106    
107    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * DESCRIPTION (Version): updated -> release 0.9975-7
110            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
111    
112    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
115    
116    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
119            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
120            is exactly singular.
121    
122    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * DESCRIPTION (Date): updated -> release 0.9975-6
125    
126    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
129            now returns symmetric.
130    
131            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
132    
133            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
134            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
135    
136            * R/Auxiliaries.R (.type.kind): added
137    
138    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
141            running src/CSparse_install.sh
142    
143            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
144    
145    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
148            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
149    
150            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
151    
152            * tests/Class+Meth.R (tstMatrixClass): now assure
153            the (important in method programming) property :
154    
155                    ###>>  Every "Matrix" is either
156                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
157    
158                    (where "*" stands for "Matrix")
159    
160            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
161    
162            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
163            * tests/validObj.R: checks for "comparison"
164    
165            * R/sparseMatrix.R ([): improved indexing for sparse;
166                    trying to keep <symmetric>[ n, n] symmmetric
167    
168            * tests/indexing.R: indexing for logical sparse now ok
169    
170    
171    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * src/Tsparse.c: use xTsparse_validate() , and hence remove
174    
175            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
176    
177    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
180    
181            * tests/simple.R: validObject() checking the above.
182    
183            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
184            replacing both dgCMatrix_validate and lgCM*.
185    
186            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
187            fix dimnames setting in other places.
188            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
189    
190    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
193    
194            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
195            symmetry test, via
196            * R/Auxiliaries.R (.as.dgC.0.factors):
197    
198    2006-11-01  Douglas Bates  <bates@r-project.org>
199    
200            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
201            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
202            <CsparseMatrix>) added
203    
204    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * tests/matprod.R: add a variation of Harri's example
207    
208            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
209            recursive infinitely.
210    
211            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
212    
213            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
214    
215    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
218            matrix if possible; test m+m == 2*m; now test dgRMatrix.
219            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
220            satisfy the above test.
221    
222    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
225    
226            * R/dgCMatrix.R: solve(a, b="missing") based on
227            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
228            RHS = NULL.
229    
230            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
231            add more (needed) [t]crossprod() methods.
232    
233            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
234    
235            * R/Auxiliaries.R (as_CspClass): cleanup
236            (drop0): internal utility for "Csparse_drop(*, 0)"
237            (.bail.out.2): encourage active feedback
238    
239    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dMatrix.R(Compare): new(), then slots [no validity check]
242    
243            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
244            non-valid or 'sorted' case).
245    
246            * R/dsparseMatrix.R: add "chol" method.
247            * R/ddenseMatrix.R: ditto
248    
249            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
250            * NAMESPACE (Ops)
251            * R/diagMatrix.R (diag2T): simple utility used "higher level"
252            coercion; deprecating direct lower level coercions.
253    
254            * R/*.R (seq): use seq_len() and seq_along() where possible.
255    
256    
257    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.9975-5 ready for release
260    
261    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
264    
265    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/AllClass.R (corMatrix): add 'validity' check;
268                    comment out unused "LDL" class definition
269            * NAMESPACE: mention, but do not export "LDL" class
270            * R/corMatrix.R: new (simple), needed for R-devel with
271            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
272              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
273    
274    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
277            use Rprintf and R's error handling.
278    
279    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
282            * tests/matprod.R: add tests for the bug fixed.
283    
284    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
287            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
288    
289    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
292    
293    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * DESCRIPTION (Version): 0.9975-3
296    
297            * R/diagMatrix.R (bdiag): new function constructing block diagonal
298            (sparse) matrices.
299            * man/bdiag.Rd: docu + examples
300    
301            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
302    
303            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
304            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
305    
306            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
307            that result is sparse or diagonal (and not dense).
308    
309            * man/Subassign-methods.Rd: fix examples
310    
311            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
312            should always return a sparse (and not sometimes a diagonal) matrix.
313    
314    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
317    
318    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): 0.9975-2
321    
322            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
323    
324    2006-10-02  Douglas Bates  <bates@R-project.org>
325    
326            * tests/dg_Matrix.R: Simplify test taking into account new code.
327    
328    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
331    
332            * R/lsTMatrix.R: new files w/ missing methods
333            * R/nsTMatrix.R:  "  'for completeness'
334    
335            * tests/Class+Meth.R: a bit less 'not.ok.classes'
336    
337            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
338    
339    
340    2006-09-28  Douglas Bates  <bates@R-project.org>
341    
342            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
343            included.
344    
345            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
346            Export C-callable functions used in Zt_create in lme4.
347    
348    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * DESCRIPTION (Version): 0.9975-1
351    
352            * tests/simple.R: less checks fail; using NA, found that our
353                    kronecker() is not base-compatible with NA's.
354    
355            * R/dMatrix.R: "Compare" method now implemented for all cases
356    
357            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
358    
359            * man/dtpMatrix-class.Rd: mention length of 'x' slot
360    
361            * src/dtpMatrix.c (dtpMatrix_validate): fix check
362            * src/dspMatrix.c (dspMatrix_validate): ditto
363    
364            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
365              including coercion to [nl]tTMatrix.
366    
367            * R/diagMatrix.R (show): print a header line as for other classes.
368    
369    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * src/Makefile.win (SUBDIRS): fix typo
372    
373    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
376    
377    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
380            symmetric and y missing in R code using %*% (cholmod_aat doesn't
381            accept a symmetric matrix).
382            * tests/group-methods.R: Uncomment test of crossprod applied to
383            lsCMatrix objects.
384    
385    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/AllClass.R (symmetricMatrix): add validity method (available
388            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
389    
390            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
391    
392            * tests/indexing.Rout.save:
393            * tests/indexing.R: additions, mainly for 'lsparse'
394    
395            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
396            case.
397    
398            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
399    
400    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
403                    as 'N' (1-letter - Ok?)
404    
405            * tests/group-methods.R: add test for logical + NAs
406    
407            * R/dMatrix.R ("Compare"): fix to work with NA's
408    
409            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
410    
411            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
412                    which is implemented.
413    
414    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/chm_common.c: coerce logical <-> double instead of
417            typecasting;  needed for "l" matrix handling in cholmod.
418    
419            * tests/other-pkgs.R (graph): small extension in "graph" checks.
420    
421            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
422            (Tsp2grNEL): other fixes needed
423    
424    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
427                    Matrices, since "lMatrix", also "lsparseM" can have NA
428            * R/ndenseMatrix.R, etc: new source files
429            * man/nsparseMatrix-classes.Rd, etc: new help files
430            * tests/: adaptions
431            * src/chm_common.c (chm_dense_to_SEXP): and others:
432                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
433            * src/Csparse.c, etc: ditto
434    
435    2006-09-11  Douglas Bates  <bates@R-project.org>
436    
437            * src/Mutils.[ch],init.c inst/include/*.h: Move the
438            alloc_d**Matrix functions to the lme4 package.
439    
440    2006-09-09  Douglas Bates  <bates@R-project.org>
441    
442            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
443            fixed
444    
445    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/lMatrix.R: new
448    
449            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
450    
451            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
452            * man/tcrossprod.Rd: ditto
453    
454    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
455    
456            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
457            for exported functions
458            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
459            Remove partitioning algorithms for sparse matrix reordering.  The
460            copyright on the Metis code was problematic and the methods were
461            rarely used.
462            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
463            operations are now done entirely in CHOLMOD code.
464    
465    2006-09-06  Douglas Bates  <bates@R-project.org>
466    
467            * src/Mutils.h: Remove functions that are no longer used.
468    
469    2006-09-04  Douglas Bates  <bates@R-project.org>
470    
471            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
472            * src/DEPS.mkf: update
473    
474    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * created branches/Matrix-for-R-2.3.x;  on trunk: do
477            * DESCRIPTION (Version): 0.9975-0
478            (Depends): R (>= 2.4.0)
479    
480    2006-09-01  Douglas Bates  <bates@R-project.org>
481    
482            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
483    
484    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
487            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
488    
489            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
490    
491    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
494            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
495            * R/dsparseMatrix.R: ditto
496            * R/Csparse.R: ditto
497    
498    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/dMatrix.R (Compare): improve availability of "<", etc
501            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
502    
503    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
506            of a 0-index which was used as 1-index (..hmm)
507    
508            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
509    
510            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
511            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
512            (.is.diagonal): ditto
513    
514            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
515    
516            * R/Matrix.R (Matrix): also work for NA data
517    
518    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
521            in all cases.
522    
523    2006-08-27  Douglas Bates  <bates@R-project.org>
524    
525            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
526            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
527    
528    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
531            subclasses of "ddenseMatrix"
532            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
533            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
534            instead of half dozen specialized ones.
535    
536    2006-08-25  Douglas Bates  <bates@R-project.org>
537    
538            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
539            <tillard@cirad.fr> - ordering standard errors to match effects.
540    
541    2006-08-24  Douglas Bates  <bates@R-project.org>
542    
543            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
544            on R_ldl.
545            * R/lCholCMatrix.R,
546            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
547            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
548            * many files in ./R and ./src: Use more general version of
549            dup_mMatrix_as_dgeMatrix to simplify method definitions.
550            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
551            dtpMatrix, dspMatrix and dppMatrix conversions.
552    
553    
554    2006-08-23  Douglas Bates  <bates@R-project.org>
555    
556            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
557            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
558            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
559            dgeMatrix_crossprod (may need to do this in other places).
560            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
561            generic and method for dsCMatrix.  Use CHOLMOD for chol().
562    
563    2006-08-22  Douglas Bates  <bates@R-project.org>
564    
565            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
566            types of classed Matrices, matrices or numeric or logical vectors.
567            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
568            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
569            to Mutils.h (as an inline) and change name to Matrix_check_class;
570            fixes in as_cholmod_factor and chm_factor_to_SEXP.
571            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
572            dsCMatrix_matrix_solve.  Comment out vestigial functions.
573            * src/Csparse.c: use diag_P and uplo_P macros.
574    
575    2006-08-21  Douglas Bates  <bates@R-project.org>
576    
577            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
578            valgrind.
579            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
580            inverses.
581            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
582            -Wall warnings.
583            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
584            Use dup_mMatrix_as_dgeMatrix.
585    
586    2006-08-20  Douglas Bates  <bates@R-project.org>
587    
588            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
589            * tests/sparseQR.R: Added
590            * man/sparseQR-class.Rd: Document methods for qr.* generics
591            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
592    
593    2006-08-19  Douglas Bates  <bates@R-project.org>
594    
595            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
596            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
597            and qr.fitted.
598            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
599            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
600    
601    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
604            the base version has no "..." argument.
605    
606            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
607    
608            * R/Matrix.R: define and
609            * NAMESPACE: export as.numeric() and as.logical() methods.
610                    Let's hope these do not badly slow down something...
611            Finally export the zapsmall() method.
612    
613    2006-08-17  Douglas Bates  <bates@R-project.org>
614    
615            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
616            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
617            * src/dtCMatrix.c :Remove code that is no longer used
618            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
619    
620    2006-08-14  Douglas Bates  <bates@R-project.org>
621    
622            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
623            Csparse_to_logical and Csparse_symmetric_to_general.
624            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
625            coercion methods between CsparseMatrix and TsparseMatrix.
626    
627    2006-08-14  Douglas Bates  <bates@R-project.org>
628    
629            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
630            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
631            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
632            possible.
633    
634    2006-08-12  Douglas Bates  <bates@R-project.org>
635    
636            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
637              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
638              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
639              generalize conversions between TsparseMatrix, CsparseMatrix,
640              denseMatrix and matrix.  Preserve triangularity property and
641              propagate Dimnames in the easy cases.
642    
643    2006-08-10  Douglas Bates  <bates@R-project.org>
644    
645            * src/lmer.c: adjust checks in glmer_init for S4SXP
646            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
647            before S4SXP but for the wrong reasons.
648    
649    2006-08-08  Douglas Bates  <bates@R-project.org>
650    
651            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
652            Later modified to return the upper triangle only.
653            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
654    
655    2006-08-07  Douglas Bates  <bates@R-project.org>
656    
657            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
658            R-level conversion to a sparse symmetric class.
659            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
660            Remove conversion to sparse symmetric classes (now done in C code).
661    
662    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
665            * man/band.Rd:  adapt the \dontshow{} unit test.
666    
667    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * DESCRIPTION (Version): 0.995-14  for CRAN
670    
671            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
672    
673            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
674            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
675    
676            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
677            * R/Tsparse.R (tril, triu, band): methods
678            * R/dgRMatrix.R (tril, ...):    ditto
679            * man/band.Rd:                  ditto
680    
681    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Matrix.R (head, tail): directly use utils:::head.matrix
684                    to be up-to-date automatically.
685    
686    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
689    
690            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
691            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
692            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
693            such that the S4 objects are always created by the current version
694            of R and 'Matrix' class definitions.
695    
696    2006-08-01  Douglas Bates  <bates@R-project.org>
697    
698            * R/lmer.R (LMEoptimize method), tests/lmer.R,
699            inst/external/test3comp.rda: Added warnings for convergence on
700            boundary and test cases.
701    
702            * src/lmer.c (mer_postVar): Modified to return the variances that
703            are marginal to the fixed effects, not conditional on them (which
704            is what the bVar slot contents represent).
705    
706    2006-07-31  Douglas Bates  <bates@R-project.org>
707    
708            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
709            function which calls the C function mer_hat_trace2.
710    
711            * man/ranef.Rd: Include description of "postVar" argument and
712            producing a caterpillar plot.
713    
714    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * NAMESPACE:    change  "correlation" to "corMatrix"
717            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
718            * R/dpoMatrix.R: ditto
719            * R/lmer.R:      ditto
720    
721    2006-07-28  Douglas Bates  <bates@R-project.org>
722    
723            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
724            RZXinv slot's contents into a separate internal function that can
725            be used in mer_hat_trace.
726    
727    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
730            via new smart
731            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
732            utility functions.
733    
734    
735    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Csparse.R (tril, triu, band): do return *triangular* classed
738            matrices when appropriate; band() even symmetric ones.
739            (replCmat): extend to potentially all "CsparseMatrix"
740            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
741            allow subassignment for special sparse matrices.
742    
743            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
744    
745            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
746            argument; in glmer_*(): print only if(verbose).
747    
748            speed-optimize a few places by moving REAL(.) out of loops.
749    
750            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
751    
752    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
755                    since that wrongly triggers also for M[ logi , ]
756    
757            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
758            a symmetric matrix that results in a non-symmetric one.
759            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
760    
761            * R/dMatrix.R: make round(M) work as round(M, 0)
762    
763            * R/dgTMatrix.R (image): coordinate system and axis now use
764            1-based indices, not 0-based ones.
765    
766            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
767            * tests/indexing.R: test it.
768    
769            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
770            * man/isSymmetric-methods.Rd: and document it.
771    
772            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
773            * man/SparseM-conv.Rd: docu them
774    
775            * tests/other-pkgs.R: renamed from tests/graph.R and add example
776                    for 'SparseM' conversions
777    
778    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
779    
780            * R/Matrix.R (head): added head() and tail() methods.
781    
782    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * DESCRIPTION (Version): 0.995-12 released to CRAN
785    
786    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * tests/simple.R: add check for correct dsT -> dgT coercion;
789                    add check for correct printing of symmetric sparse matrices.
790    
791            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
792            for sparse symmetric matrices.
793    
794            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
795            diagonal twice.
796    
797  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
798    
799          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
800          being applied to the x slot (detected by Brian Ripley).  Possible          being applied to the x slot (detected by Brian Ripley).
         problem with copying the diagonal elements twice?  
801    
802  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
# Line 44  Line 839 
839    
840  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
841    
842            * DESCRIPTION (Version): 0.995-11 released to CRAN
843    
844          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
845          the output from mcmcsamp.          the output from mcmcsamp.
846    
# Line 94  Line 891 
891    
892          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
893          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
894          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
895    
896    
897  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 217  Line 1014 
1014          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1015          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1016          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1017          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1018    
1019  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
# Line 421  Line 1218 
1218  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1221          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1222          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1223    
1224  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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