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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1708, Fri Dec 22 19:53:37 2006 UTC
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1    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
4                    also more general diagU2N().
5    
6    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
9            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
10    
11    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * tests/bind.R: a few more cases
14            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
15    
16            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
17            * R/ddenseMatrix.R (cbind2/rbind2)
18            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
19            * tests/indexing.R
20            * tests/indexing.Rout.save: updated
21    
22    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
25            * tests/indexing.R
26    
27    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
30            align with proper position of "0", i.e., right for integers.
31            argument 'align' by default is "fancy".
32    
33    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
36            * R/Csparse.R: and fix "Compare" for more cases.
37            * tests/Class+Meth.R: test some of these (m == m, m != m)
38    
39    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/lsparseMatrix.R: all() and any() methods
42            * R/ldenseMatrix.R:      ditto
43            * NAMESPACE, R/Matrix.R: ditto
44    
45            * man/all-methods.Rd: document them minimally
46    
47            * tests/simple.R: add a few examples for these
48    
49    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/Tsparse.R ([): fix long standing typo in symmetric case
52            * man/dsCMatrix-class.Rd: add example exhibiting the above case
53    
54    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
57            to LL before converting to a sparse matrix. (The LDL form can be
58            converted to a sparse matrix but it is implicitly a unit
59            triangular matrix and a diagonal matrix overwritten on the diagonal.)
60    
61    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
64    
65    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * DESCRIPTION (Version): updated -> release 0.9975-7
68            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
69    
70    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
73    
74    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
75    
76            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
77            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
78            is exactly singular.
79    
80    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * DESCRIPTION (Date): updated -> release 0.9975-6
83    
84    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
87            now returns symmetric.
88    
89            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
90    
91            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
92            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
93    
94            * R/Auxiliaries.R (.type.kind): added
95    
96    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
99            running src/CSparse_install.sh
100    
101            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
102    
103    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
106            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
107    
108            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
109    
110            * tests/Class+Meth.R (tstMatrixClass): now assure
111            the (important in method programming) property :
112    
113                    ###>>  Every "Matrix" is either
114                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
115    
116                    (where "*" stands for "Matrix")
117    
118            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
119    
120            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
121            * tests/validObj.R: checks for "comparison"
122    
123            * R/sparseMatrix.R ([): improved indexing for sparse;
124                    trying to keep <symmetric>[ n, n] symmmetric
125    
126            * tests/indexing.R: indexing for logical sparse now ok
127    
128    
129    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/Tsparse.c: use xTsparse_validate() , and hence remove
132    
133            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
134    
135    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
138    
139            * tests/simple.R: validObject() checking the above.
140    
141            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
142            replacing both dgCMatrix_validate and lgCM*.
143    
144            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
145            fix dimnames setting in other places.
146            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
147    
148    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
151    
152            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
153            symmetry test, via
154            * R/Auxiliaries.R (.as.dgC.0.factors):
155    
156    2006-11-01  Douglas Bates  <bates@r-project.org>
157    
158            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
159            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
160            <CsparseMatrix>) added
161    
162    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * tests/matprod.R: add a variation of Harri's example
165    
166            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
167            recursive infinitely.
168    
169            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
170    
171            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
172    
173    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
176            matrix if possible; test m+m == 2*m; now test dgRMatrix.
177            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
178            satisfy the above test.
179    
180    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
183    
184            * R/dgCMatrix.R: solve(a, b="missing") based on
185            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
186            RHS = NULL.
187    
188            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
189            add more (needed) [t]crossprod() methods.
190    
191            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
192    
193            * R/Auxiliaries.R (as_CspClass): cleanup
194            (drop0): internal utility for "Csparse_drop(*, 0)"
195            (.bail.out.2): encourage active feedback
196    
197    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/dMatrix.R(Compare): new(), then slots [no validity check]
200    
201            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
202            non-valid or 'sorted' case).
203    
204            * R/dsparseMatrix.R: add "chol" method.
205            * R/ddenseMatrix.R: ditto
206    
207            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
208            * NAMESPACE (Ops)
209            * R/diagMatrix.R (diag2T): simple utility used "higher level"
210            coercion; deprecating direct lower level coercions.
211    
212            * R/*.R (seq): use seq_len() and seq_along() where possible.
213    
214    
215    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * DESCRIPTION (Version): 0.9975-5 ready for release
218    
219    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
222    
223    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/AllClass.R (corMatrix): add 'validity' check;
226                    comment out unused "LDL" class definition
227            * NAMESPACE: mention, but do not export "LDL" class
228            * R/corMatrix.R: new (simple), needed for R-devel with
229            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
230              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
231    
232    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
235            use Rprintf and R's error handling.
236    
237    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
240            * tests/matprod.R: add tests for the bug fixed.
241    
242    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
245            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
246    
247    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
248    
249            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
250    
251    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * DESCRIPTION (Version): 0.9975-3
254    
255            * R/diagMatrix.R (bdiag): new function constructing block diagonal
256            (sparse) matrices.
257            * man/bdiag.Rd: docu + examples
258    
259            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
260    
261            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
262            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
263    
264            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
265            that result is sparse or diagonal (and not dense).
266    
267            * man/Subassign-methods.Rd: fix examples
268    
269            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
270            should always return a sparse (and not sometimes a diagonal) matrix.
271    
272    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
275    
276    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
277    
278            * DESCRIPTION (Version): 0.9975-2
279    
280            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
281    
282    2006-10-02  Douglas Bates  <bates@R-project.org>
283    
284            * tests/dg_Matrix.R: Simplify test taking into account new code.
285    
286    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
289    
290            * R/lsTMatrix.R: new files w/ missing methods
291            * R/nsTMatrix.R:  "  'for completeness'
292    
293            * tests/Class+Meth.R: a bit less 'not.ok.classes'
294    
295            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
296    
297    
298    2006-09-28  Douglas Bates  <bates@R-project.org>
299    
300            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
301            included.
302    
303            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
304            Export C-callable functions used in Zt_create in lme4.
305    
306    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * DESCRIPTION (Version): 0.9975-1
309    
310            * tests/simple.R: less checks fail; using NA, found that our
311                    kronecker() is not base-compatible with NA's.
312    
313            * R/dMatrix.R: "Compare" method now implemented for all cases
314    
315            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
316    
317            * man/dtpMatrix-class.Rd: mention length of 'x' slot
318    
319            * src/dtpMatrix.c (dtpMatrix_validate): fix check
320            * src/dspMatrix.c (dspMatrix_validate): ditto
321    
322            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
323              including coercion to [nl]tTMatrix.
324    
325            * R/diagMatrix.R (show): print a header line as for other classes.
326    
327    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/Makefile.win (SUBDIRS): fix typo
330    
331    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
334    
335    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
338            symmetric and y missing in R code using %*% (cholmod_aat doesn't
339            accept a symmetric matrix).
340            * tests/group-methods.R: Uncomment test of crossprod applied to
341            lsCMatrix objects.
342    
343    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/AllClass.R (symmetricMatrix): add validity method (available
346            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
347    
348            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
349    
350            * tests/indexing.Rout.save:
351            * tests/indexing.R: additions, mainly for 'lsparse'
352    
353            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
354            case.
355    
356            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
357    
358    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
361                    as 'N' (1-letter - Ok?)
362    
363            * tests/group-methods.R: add test for logical + NAs
364    
365            * R/dMatrix.R ("Compare"): fix to work with NA's
366    
367            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
368    
369            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
370                    which is implemented.
371    
372    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/chm_common.c: coerce logical <-> double instead of
375            typecasting;  needed for "l" matrix handling in cholmod.
376    
377            * tests/other-pkgs.R (graph): small extension in "graph" checks.
378    
379            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
380            (Tsp2grNEL): other fixes needed
381    
382    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
385                    Matrices, since "lMatrix", also "lsparseM" can have NA
386            * R/ndenseMatrix.R, etc: new source files
387            * man/nsparseMatrix-classes.Rd, etc: new help files
388            * tests/: adaptions
389            * src/chm_common.c (chm_dense_to_SEXP): and others:
390                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
391            * src/Csparse.c, etc: ditto
392    
393    2006-09-11  Douglas Bates  <bates@R-project.org>
394    
395            * src/Mutils.[ch],init.c inst/include/*.h: Move the
396            alloc_d**Matrix functions to the lme4 package.
397    
398    2006-09-09  Douglas Bates  <bates@R-project.org>
399    
400            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
401            fixed
402    
403    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/lMatrix.R: new
406    
407            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
408    
409            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
410            * man/tcrossprod.Rd: ditto
411    
412    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
415            for exported functions
416            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
417            Remove partitioning algorithms for sparse matrix reordering.  The
418            copyright on the Metis code was problematic and the methods were
419            rarely used.
420            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
421            operations are now done entirely in CHOLMOD code.
422    
423    2006-09-06  Douglas Bates  <bates@R-project.org>
424    
425            * src/Mutils.h: Remove functions that are no longer used.
426    
427    2006-09-04  Douglas Bates  <bates@R-project.org>
428    
429            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
430            * src/DEPS.mkf: update
431    
432    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * created branches/Matrix-for-R-2.3.x;  on trunk: do
435            * DESCRIPTION (Version): 0.9975-0
436            (Depends): R (>= 2.4.0)
437    
438    2006-09-01  Douglas Bates  <bates@R-project.org>
439    
440            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
441    
442    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
445            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
446    
447            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
448    
449    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
452            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
453            * R/dsparseMatrix.R: ditto
454            * R/Csparse.R: ditto
455    
456    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/dMatrix.R (Compare): improve availability of "<", etc
459            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
460    
461    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
464            of a 0-index which was used as 1-index (..hmm)
465    
466            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
467    
468            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
469            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
470            (.is.diagonal): ditto
471    
472            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
473    
474            * R/Matrix.R (Matrix): also work for NA data
475    
476  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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