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revision 1420, Tue Aug 22 22:49:40 2006 UTC revision 1682, Fri Dec 1 18:42:40 2006 UTC
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1    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
4    
5    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
8            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
9            is exactly singular.
10    
11    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date): updated -> release 0.9975-6
14    
15    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
18            now returns symmetric.
19    
20            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
21    
22            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
23            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
24    
25            * R/Auxiliaries.R (.type.kind): added
26    
27    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
30            running src/CSparse_install.sh
31    
32            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
33    
34    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
37            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
38    
39            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
40    
41            * tests/Class+Meth.R (tstMatrixClass): now assure
42            the (important in method programming) property :
43    
44                    ###>>  Every "Matrix" is either
45                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
46    
47                    (where "*" stands for "Matrix")
48    
49            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
50    
51            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
52            * tests/validObj.R: checks for "comparison"
53    
54            * R/sparseMatrix.R ([): improved indexing for sparse;
55                    trying to keep <symmetric>[ n, n] symmmetric
56    
57            * tests/indexing.R: indexing for logical sparse now ok
58    
59    
60    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/Tsparse.c: use xTsparse_validate() , and hence remove
63    
64            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
65    
66    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
69    
70            * tests/simple.R: validObject() checking the above.
71    
72            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
73            replacing both dgCMatrix_validate and lgCM*.
74    
75            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
76            fix dimnames setting in other places.
77            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
78    
79    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
82    
83            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
84            symmetry test, via
85            * R/Auxiliaries.R (.as.dgC.0.factors):
86    
87    2006-11-01  Douglas Bates  <bates@r-project.org>
88    
89            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
90            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
91            <CsparseMatrix>) added
92    
93    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * tests/matprod.R: add a variation of Harri's example
96    
97            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
98            recursive infinitely.
99    
100            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
101    
102            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
103    
104    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
107            matrix if possible; test m+m == 2*m; now test dgRMatrix.
108            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
109            satisfy the above test.
110    
111    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
114    
115            * R/dgCMatrix.R: solve(a, b="missing") based on
116            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
117            RHS = NULL.
118    
119            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
120            add more (needed) [t]crossprod() methods.
121    
122            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
123    
124            * R/Auxiliaries.R (as_CspClass): cleanup
125            (drop0): internal utility for "Csparse_drop(*, 0)"
126            (.bail.out.2): encourage active feedback
127    
128    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dMatrix.R(Compare): new(), then slots [no validity check]
131    
132            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
133            non-valid or 'sorted' case).
134    
135            * R/dsparseMatrix.R: add "chol" method.
136            * R/ddenseMatrix.R: ditto
137    
138            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
139            * NAMESPACE (Ops)
140            * R/diagMatrix.R (diag2T): simple utility used "higher level"
141            coercion; deprecating direct lower level coercions.
142    
143            * R/*.R (seq): use seq_len() and seq_along() where possible.
144    
145    
146    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Version): 0.9975-5 ready for release
149    
150    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
153    
154    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R (corMatrix): add 'validity' check;
157                    comment out unused "LDL" class definition
158            * NAMESPACE: mention, but do not export "LDL" class
159            * R/corMatrix.R: new (simple), needed for R-devel with
160            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
161              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
162    
163    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
166            use Rprintf and R's error handling.
167    
168    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
171            * tests/matprod.R: add tests for the bug fixed.
172    
173    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
176            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
177    
178    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
181    
182    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.9975-3
185    
186            * R/diagMatrix.R (bdiag): new function constructing block diagonal
187            (sparse) matrices.
188            * man/bdiag.Rd: docu + examples
189    
190            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
191    
192            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
193            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
194    
195            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
196            that result is sparse or diagonal (and not dense).
197    
198            * man/Subassign-methods.Rd: fix examples
199    
200            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
201            should always return a sparse (and not sometimes a diagonal) matrix.
202    
203    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
206    
207    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * DESCRIPTION (Version): 0.9975-2
210    
211            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
212    
213    2006-10-02  Douglas Bates  <bates@R-project.org>
214    
215            * tests/dg_Matrix.R: Simplify test taking into account new code.
216    
217    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
220    
221            * R/lsTMatrix.R: new files w/ missing methods
222            * R/nsTMatrix.R:  "  'for completeness'
223    
224            * tests/Class+Meth.R: a bit less 'not.ok.classes'
225    
226            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
227    
228    
229    2006-09-28  Douglas Bates  <bates@R-project.org>
230    
231            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
232            included.
233    
234            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
235            Export C-callable functions used in Zt_create in lme4.
236    
237    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * DESCRIPTION (Version): 0.9975-1
240    
241            * tests/simple.R: less checks fail; using NA, found that our
242                    kronecker() is not base-compatible with NA's.
243    
244            * R/dMatrix.R: "Compare" method now implemented for all cases
245    
246            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
247    
248            * man/dtpMatrix-class.Rd: mention length of 'x' slot
249    
250            * src/dtpMatrix.c (dtpMatrix_validate): fix check
251            * src/dspMatrix.c (dspMatrix_validate): ditto
252    
253            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
254              including coercion to [nl]tTMatrix.
255    
256            * R/diagMatrix.R (show): print a header line as for other classes.
257    
258    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/Makefile.win (SUBDIRS): fix typo
261    
262    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
265    
266    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
267    
268            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
269            symmetric and y missing in R code using %*% (cholmod_aat doesn't
270            accept a symmetric matrix).
271            * tests/group-methods.R: Uncomment test of crossprod applied to
272            lsCMatrix objects.
273    
274    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllClass.R (symmetricMatrix): add validity method (available
277            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
278    
279            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
280    
281            * tests/indexing.Rout.save:
282            * tests/indexing.R: additions, mainly for 'lsparse'
283    
284            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
285            case.
286    
287            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
288    
289    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
292                    as 'N' (1-letter - Ok?)
293    
294            * tests/group-methods.R: add test for logical + NAs
295    
296            * R/dMatrix.R ("Compare"): fix to work with NA's
297    
298            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
299    
300            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
301                    which is implemented.
302    
303    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * src/chm_common.c: coerce logical <-> double instead of
306            typecasting;  needed for "l" matrix handling in cholmod.
307    
308            * tests/other-pkgs.R (graph): small extension in "graph" checks.
309    
310            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
311            (Tsp2grNEL): other fixes needed
312    
313    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
316                    Matrices, since "lMatrix", also "lsparseM" can have NA
317            * R/ndenseMatrix.R, etc: new source files
318            * man/nsparseMatrix-classes.Rd, etc: new help files
319            * tests/: adaptions
320            * src/chm_common.c (chm_dense_to_SEXP): and others:
321                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
322            * src/Csparse.c, etc: ditto
323    
324    2006-09-11  Douglas Bates  <bates@R-project.org>
325    
326            * src/Mutils.[ch],init.c inst/include/*.h: Move the
327            alloc_d**Matrix functions to the lme4 package.
328    
329    2006-09-09  Douglas Bates  <bates@R-project.org>
330    
331            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
332            fixed
333    
334    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/lMatrix.R: new
337    
338            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
339    
340            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
341            * man/tcrossprod.Rd: ditto
342    
343    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
346            for exported functions
347            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
348            Remove partitioning algorithms for sparse matrix reordering.  The
349            copyright on the Metis code was problematic and the methods were
350            rarely used.
351            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
352            operations are now done entirely in CHOLMOD code.
353    
354    2006-09-06  Douglas Bates  <bates@R-project.org>
355    
356            * src/Mutils.h: Remove functions that are no longer used.
357    
358    2006-09-04  Douglas Bates  <bates@R-project.org>
359    
360            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
361            * src/DEPS.mkf: update
362    
363    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * created branches/Matrix-for-R-2.3.x;  on trunk: do
366            * DESCRIPTION (Version): 0.9975-0
367            (Depends): R (>= 2.4.0)
368    
369    2006-09-01  Douglas Bates  <bates@R-project.org>
370    
371            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
372    
373    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
376            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
377    
378            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
379    
380    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
383            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
384            * R/dsparseMatrix.R: ditto
385            * R/Csparse.R: ditto
386    
387    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R (Compare): improve availability of "<", etc
390            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
391    
392    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
395            of a 0-index which was used as 1-index (..hmm)
396    
397            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
398    
399            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
400            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
401            (.is.diagonal): ditto
402    
403            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
404    
405            * R/Matrix.R (Matrix): also work for NA data
406    
407    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
410            in all cases.
411    
412    2006-08-27  Douglas Bates  <bates@R-project.org>
413    
414            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
415            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
416    
417    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
420            subclasses of "ddenseMatrix"
421            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
422            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
423            instead of half dozen specialized ones.
424    
425    2006-08-25  Douglas Bates  <bates@R-project.org>
426    
427            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
428            <tillard@cirad.fr> - ordering standard errors to match effects.
429    
430    2006-08-24  Douglas Bates  <bates@R-project.org>
431    
432            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
433            on R_ldl.
434            * R/lCholCMatrix.R,
435            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
436            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
437            * many files in ./R and ./src: Use more general version of
438            dup_mMatrix_as_dgeMatrix to simplify method definitions.
439            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
440            dtpMatrix, dspMatrix and dppMatrix conversions.
441    
442    
443    2006-08-23  Douglas Bates  <bates@R-project.org>
444    
445            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
446            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
447            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
448            dgeMatrix_crossprod (may need to do this in other places).
449            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
450            generic and method for dsCMatrix.  Use CHOLMOD for chol().
451    
452  2006-08-22  Douglas Bates  <bates@R-project.org>  2006-08-22  Douglas Bates  <bates@R-project.org>
453    
454          * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general          * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
455          types of classed Matrices, matrices or numeric or logical vectors.          types of classed Matrices, matrices or numeric or logical vectors.
   
456          * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.          * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
457            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
458            to Mutils.h (as an inline) and change name to Matrix_check_class;
459            fixes in as_cholmod_factor and chm_factor_to_SEXP.
460            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
461            dsCMatrix_matrix_solve.  Comment out vestigial functions.
462            * src/Csparse.c: use diag_P and uplo_P macros.
463    
464  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
465    

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