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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1696, Mon Dec 11 21:41:37 2006 UTC
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1    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): fix long standing typo in symmetric case
4            * man/dsCMatrix-class.Rd: add example exhibiting the above case
5    
6    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
9            to LL before converting to a sparse matrix. (The LDL form can be
10            converted to a sparse matrix but it is implicitly a unit
11            triangular matrix and a diagonal matrix overwritten on the diagonal.)
12    
13    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
16    
17    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * DESCRIPTION (Version): updated -> release 0.9975-7
20            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
21    
22    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
25    
26    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
29            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
30            is exactly singular.
31    
32    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Date): updated -> release 0.9975-6
35    
36    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
39            now returns symmetric.
40    
41            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
42    
43            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
44            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
45    
46            * R/Auxiliaries.R (.type.kind): added
47    
48    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
51            running src/CSparse_install.sh
52    
53            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
54    
55    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
58            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
59    
60            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
61    
62            * tests/Class+Meth.R (tstMatrixClass): now assure
63            the (important in method programming) property :
64    
65                    ###>>  Every "Matrix" is either
66                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
67    
68                    (where "*" stands for "Matrix")
69    
70            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
71    
72            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
73            * tests/validObj.R: checks for "comparison"
74    
75            * R/sparseMatrix.R ([): improved indexing for sparse;
76                    trying to keep <symmetric>[ n, n] symmmetric
77    
78            * tests/indexing.R: indexing for logical sparse now ok
79    
80    
81    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * src/Tsparse.c: use xTsparse_validate() , and hence remove
84    
85            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
86    
87    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
90    
91            * tests/simple.R: validObject() checking the above.
92    
93            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
94            replacing both dgCMatrix_validate and lgCM*.
95    
96            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
97            fix dimnames setting in other places.
98            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
99    
100    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
103    
104            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
105            symmetry test, via
106            * R/Auxiliaries.R (.as.dgC.0.factors):
107    
108    2006-11-01  Douglas Bates  <bates@r-project.org>
109    
110            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
111            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
112            <CsparseMatrix>) added
113    
114    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * tests/matprod.R: add a variation of Harri's example
117    
118            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
119            recursive infinitely.
120    
121            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
122    
123            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
124    
125    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
128            matrix if possible; test m+m == 2*m; now test dgRMatrix.
129            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
130            satisfy the above test.
131    
132    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
135    
136            * R/dgCMatrix.R: solve(a, b="missing") based on
137            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
138            RHS = NULL.
139    
140            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
141            add more (needed) [t]crossprod() methods.
142    
143            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
144    
145            * R/Auxiliaries.R (as_CspClass): cleanup
146            (drop0): internal utility for "Csparse_drop(*, 0)"
147            (.bail.out.2): encourage active feedback
148    
149    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dMatrix.R(Compare): new(), then slots [no validity check]
152    
153            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
154            non-valid or 'sorted' case).
155    
156            * R/dsparseMatrix.R: add "chol" method.
157            * R/ddenseMatrix.R: ditto
158    
159            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
160            * NAMESPACE (Ops)
161            * R/diagMatrix.R (diag2T): simple utility used "higher level"
162            coercion; deprecating direct lower level coercions.
163    
164            * R/*.R (seq): use seq_len() and seq_along() where possible.
165    
166    
167    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * DESCRIPTION (Version): 0.9975-5 ready for release
170    
171    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
174    
175    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/AllClass.R (corMatrix): add 'validity' check;
178                    comment out unused "LDL" class definition
179            * NAMESPACE: mention, but do not export "LDL" class
180            * R/corMatrix.R: new (simple), needed for R-devel with
181            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
182              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
183    
184    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
187            use Rprintf and R's error handling.
188    
189    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
192            * tests/matprod.R: add tests for the bug fixed.
193    
194    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
197            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
198    
199    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
202    
203    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.9975-3
206    
207            * R/diagMatrix.R (bdiag): new function constructing block diagonal
208            (sparse) matrices.
209            * man/bdiag.Rd: docu + examples
210    
211            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
212    
213            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
214            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
215    
216            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
217            that result is sparse or diagonal (and not dense).
218    
219            * man/Subassign-methods.Rd: fix examples
220    
221            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
222            should always return a sparse (and not sometimes a diagonal) matrix.
223    
224    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
227    
228    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
229    
230            * DESCRIPTION (Version): 0.9975-2
231    
232            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
233    
234    2006-10-02  Douglas Bates  <bates@R-project.org>
235    
236            * tests/dg_Matrix.R: Simplify test taking into account new code.
237    
238    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
241    
242            * R/lsTMatrix.R: new files w/ missing methods
243            * R/nsTMatrix.R:  "  'for completeness'
244    
245            * tests/Class+Meth.R: a bit less 'not.ok.classes'
246    
247            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
248    
249    
250    2006-09-28  Douglas Bates  <bates@R-project.org>
251    
252            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
253            included.
254    
255            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
256            Export C-callable functions used in Zt_create in lme4.
257    
258    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Version): 0.9975-1
261    
262            * tests/simple.R: less checks fail; using NA, found that our
263                    kronecker() is not base-compatible with NA's.
264    
265            * R/dMatrix.R: "Compare" method now implemented for all cases
266    
267            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
268    
269            * man/dtpMatrix-class.Rd: mention length of 'x' slot
270    
271            * src/dtpMatrix.c (dtpMatrix_validate): fix check
272            * src/dspMatrix.c (dspMatrix_validate): ditto
273    
274            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
275              including coercion to [nl]tTMatrix.
276    
277            * R/diagMatrix.R (show): print a header line as for other classes.
278    
279    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/Makefile.win (SUBDIRS): fix typo
282    
283    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
286    
287    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
290            symmetric and y missing in R code using %*% (cholmod_aat doesn't
291            accept a symmetric matrix).
292            * tests/group-methods.R: Uncomment test of crossprod applied to
293            lsCMatrix objects.
294    
295    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/AllClass.R (symmetricMatrix): add validity method (available
298            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
299    
300            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
301    
302            * tests/indexing.Rout.save:
303            * tests/indexing.R: additions, mainly for 'lsparse'
304    
305            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
306            case.
307    
308            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
309    
310    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
313                    as 'N' (1-letter - Ok?)
314    
315            * tests/group-methods.R: add test for logical + NAs
316    
317            * R/dMatrix.R ("Compare"): fix to work with NA's
318    
319            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
320    
321            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
322                    which is implemented.
323    
324    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/chm_common.c: coerce logical <-> double instead of
327            typecasting;  needed for "l" matrix handling in cholmod.
328    
329            * tests/other-pkgs.R (graph): small extension in "graph" checks.
330    
331            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
332            (Tsp2grNEL): other fixes needed
333    
334    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
337                    Matrices, since "lMatrix", also "lsparseM" can have NA
338            * R/ndenseMatrix.R, etc: new source files
339            * man/nsparseMatrix-classes.Rd, etc: new help files
340            * tests/: adaptions
341            * src/chm_common.c (chm_dense_to_SEXP): and others:
342                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
343            * src/Csparse.c, etc: ditto
344    
345    2006-09-11  Douglas Bates  <bates@R-project.org>
346    
347            * src/Mutils.[ch],init.c inst/include/*.h: Move the
348            alloc_d**Matrix functions to the lme4 package.
349    
350    2006-09-09  Douglas Bates  <bates@R-project.org>
351    
352            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
353            fixed
354    
355    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/lMatrix.R: new
358    
359            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
360    
361            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
362            * man/tcrossprod.Rd: ditto
363    
364    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
367            for exported functions
368            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
369            Remove partitioning algorithms for sparse matrix reordering.  The
370            copyright on the Metis code was problematic and the methods were
371            rarely used.
372            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
373            operations are now done entirely in CHOLMOD code.
374    
375    2006-09-06  Douglas Bates  <bates@R-project.org>
376    
377            * src/Mutils.h: Remove functions that are no longer used.
378    
379    2006-09-04  Douglas Bates  <bates@R-project.org>
380    
381            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
382            * src/DEPS.mkf: update
383    
384    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * created branches/Matrix-for-R-2.3.x;  on trunk: do
387            * DESCRIPTION (Version): 0.9975-0
388            (Depends): R (>= 2.4.0)
389    
390    2006-09-01  Douglas Bates  <bates@R-project.org>
391    
392            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
393    
394    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
397            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
398    
399            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
400    
401    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
404            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
405            * R/dsparseMatrix.R: ditto
406            * R/Csparse.R: ditto
407    
408    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/dMatrix.R (Compare): improve availability of "<", etc
411            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
412    
413    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
416            of a 0-index which was used as 1-index (..hmm)
417    
418            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
419    
420            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
421            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
422            (.is.diagonal): ditto
423    
424            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
425    
426            * R/Matrix.R (Matrix): also work for NA data
427    
428    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
431            in all cases.
432    
433    2006-08-27  Douglas Bates  <bates@R-project.org>
434    
435            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
436            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
437    
438    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
441            subclasses of "ddenseMatrix"
442            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
443            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
444            instead of half dozen specialized ones.
445    
446    2006-08-25  Douglas Bates  <bates@R-project.org>
447    
448            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
449            <tillard@cirad.fr> - ordering standard errors to match effects.
450    
451    2006-08-24  Douglas Bates  <bates@R-project.org>
452    
453            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
454            on R_ldl.
455            * R/lCholCMatrix.R,
456            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
457            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
458            * many files in ./R and ./src: Use more general version of
459            dup_mMatrix_as_dgeMatrix to simplify method definitions.
460            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
461            dtpMatrix, dspMatrix and dppMatrix conversions.
462    
463    
464    2006-08-23  Douglas Bates  <bates@R-project.org>
465    
466            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
467            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
468            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
469            dgeMatrix_crossprod (may need to do this in other places).
470            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
471            generic and method for dsCMatrix.  Use CHOLMOD for chol().
472    
473    2006-08-22  Douglas Bates  <bates@R-project.org>
474    
475            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
476            types of classed Matrices, matrices or numeric or logical vectors.
477            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
478            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
479            to Mutils.h (as an inline) and change name to Matrix_check_class;
480            fixes in as_cholmod_factor and chm_factor_to_SEXP.
481            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
482            dsCMatrix_matrix_solve.  Comment out vestigial functions.
483            * src/Csparse.c: use diag_P and uplo_P macros.
484    
485  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
486    
487          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
488          valgrind.          valgrind.
489            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
490            inverses.
491            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
492            -Wall warnings.
493            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
494            Use dup_mMatrix_as_dgeMatrix.
495    
496  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
497    

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