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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1705, Sat Dec 16 12:37:25 2006 UTC
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1    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
4            align with proper position of "0", i.e., right for integers.
5            argument 'align' by default is "fancy".
6    
7    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
10            * R/Csparse.R: and fix "Compare" for more cases.
11            * tests/Class+Meth.R: test some of these (m == m, m != m)
12    
13    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/lsparseMatrix.R: all() and any() methods
16            * R/ldenseMatrix.R:      ditto
17            * NAMESPACE, R/Matrix.R: ditto
18    
19            * man/all-methods.Rd: document them minimally
20    
21            * tests/simple.R: add a few examples for these
22    
23    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([): fix long standing typo in symmetric case
26            * man/dsCMatrix-class.Rd: add example exhibiting the above case
27    
28    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
31            to LL before converting to a sparse matrix. (The LDL form can be
32            converted to a sparse matrix but it is implicitly a unit
33            triangular matrix and a diagonal matrix overwritten on the diagonal.)
34    
35    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
38    
39    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * DESCRIPTION (Version): updated -> release 0.9975-7
42            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
43    
44    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
47    
48    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
49    
50            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
51            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
52            is exactly singular.
53    
54    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Date): updated -> release 0.9975-6
57    
58    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
61            now returns symmetric.
62    
63            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
64    
65            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
66            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
67    
68            * R/Auxiliaries.R (.type.kind): added
69    
70    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
73            running src/CSparse_install.sh
74    
75            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
76    
77    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
80            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
81    
82            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
83    
84            * tests/Class+Meth.R (tstMatrixClass): now assure
85            the (important in method programming) property :
86    
87                    ###>>  Every "Matrix" is either
88                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
89    
90                    (where "*" stands for "Matrix")
91    
92            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
93    
94            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
95            * tests/validObj.R: checks for "comparison"
96    
97            * R/sparseMatrix.R ([): improved indexing for sparse;
98                    trying to keep <symmetric>[ n, n] symmmetric
99    
100            * tests/indexing.R: indexing for logical sparse now ok
101    
102    
103    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/Tsparse.c: use xTsparse_validate() , and hence remove
106    
107            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
108    
109    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
112    
113            * tests/simple.R: validObject() checking the above.
114    
115            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
116            replacing both dgCMatrix_validate and lgCM*.
117    
118            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
119            fix dimnames setting in other places.
120            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
121    
122    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
125    
126            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
127            symmetry test, via
128            * R/Auxiliaries.R (.as.dgC.0.factors):
129    
130    2006-11-01  Douglas Bates  <bates@r-project.org>
131    
132            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
133            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
134            <CsparseMatrix>) added
135    
136    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/matprod.R: add a variation of Harri's example
139    
140            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
141            recursive infinitely.
142    
143            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
144    
145            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
146    
147    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
150            matrix if possible; test m+m == 2*m; now test dgRMatrix.
151            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
152            satisfy the above test.
153    
154    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
157    
158            * R/dgCMatrix.R: solve(a, b="missing") based on
159            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
160            RHS = NULL.
161    
162            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
163            add more (needed) [t]crossprod() methods.
164    
165            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
166    
167            * R/Auxiliaries.R (as_CspClass): cleanup
168            (drop0): internal utility for "Csparse_drop(*, 0)"
169            (.bail.out.2): encourage active feedback
170    
171    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R(Compare): new(), then slots [no validity check]
174    
175            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
176            non-valid or 'sorted' case).
177    
178            * R/dsparseMatrix.R: add "chol" method.
179            * R/ddenseMatrix.R: ditto
180    
181            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
182            * NAMESPACE (Ops)
183            * R/diagMatrix.R (diag2T): simple utility used "higher level"
184            coercion; deprecating direct lower level coercions.
185    
186            * R/*.R (seq): use seq_len() and seq_along() where possible.
187    
188    
189    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * DESCRIPTION (Version): 0.9975-5 ready for release
192    
193    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
196    
197    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllClass.R (corMatrix): add 'validity' check;
200                    comment out unused "LDL" class definition
201            * NAMESPACE: mention, but do not export "LDL" class
202            * R/corMatrix.R: new (simple), needed for R-devel with
203            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
204              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
205    
206    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
209            use Rprintf and R's error handling.
210    
211    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
214            * tests/matprod.R: add tests for the bug fixed.
215    
216    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
219            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
220    
221    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
224    
225    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.9975-3
228    
229            * R/diagMatrix.R (bdiag): new function constructing block diagonal
230            (sparse) matrices.
231            * man/bdiag.Rd: docu + examples
232    
233            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
234    
235            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
236            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
237    
238            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
239            that result is sparse or diagonal (and not dense).
240    
241            * man/Subassign-methods.Rd: fix examples
242    
243            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
244            should always return a sparse (and not sometimes a diagonal) matrix.
245    
246    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
249    
250    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * DESCRIPTION (Version): 0.9975-2
253    
254            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
255    
256    2006-10-02  Douglas Bates  <bates@R-project.org>
257    
258            * tests/dg_Matrix.R: Simplify test taking into account new code.
259    
260    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
263    
264            * R/lsTMatrix.R: new files w/ missing methods
265            * R/nsTMatrix.R:  "  'for completeness'
266    
267            * tests/Class+Meth.R: a bit less 'not.ok.classes'
268    
269            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
270    
271    
272    2006-09-28  Douglas Bates  <bates@R-project.org>
273    
274            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
275            included.
276    
277            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
278            Export C-callable functions used in Zt_create in lme4.
279    
280    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version): 0.9975-1
283    
284            * tests/simple.R: less checks fail; using NA, found that our
285                    kronecker() is not base-compatible with NA's.
286    
287            * R/dMatrix.R: "Compare" method now implemented for all cases
288    
289            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
290    
291            * man/dtpMatrix-class.Rd: mention length of 'x' slot
292    
293            * src/dtpMatrix.c (dtpMatrix_validate): fix check
294            * src/dspMatrix.c (dspMatrix_validate): ditto
295    
296            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
297              including coercion to [nl]tTMatrix.
298    
299            * R/diagMatrix.R (show): print a header line as for other classes.
300    
301    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Makefile.win (SUBDIRS): fix typo
304    
305    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
308    
309    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
312            symmetric and y missing in R code using %*% (cholmod_aat doesn't
313            accept a symmetric matrix).
314            * tests/group-methods.R: Uncomment test of crossprod applied to
315            lsCMatrix objects.
316    
317    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R (symmetricMatrix): add validity method (available
320            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
321    
322            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
323    
324            * tests/indexing.Rout.save:
325            * tests/indexing.R: additions, mainly for 'lsparse'
326    
327            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
328            case.
329    
330            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
331    
332    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
335                    as 'N' (1-letter - Ok?)
336    
337            * tests/group-methods.R: add test for logical + NAs
338    
339            * R/dMatrix.R ("Compare"): fix to work with NA's
340    
341            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
342    
343            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
344                    which is implemented.
345    
346    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * src/chm_common.c: coerce logical <-> double instead of
349            typecasting;  needed for "l" matrix handling in cholmod.
350    
351            * tests/other-pkgs.R (graph): small extension in "graph" checks.
352    
353            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
354            (Tsp2grNEL): other fixes needed
355    
356    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
359                    Matrices, since "lMatrix", also "lsparseM" can have NA
360            * R/ndenseMatrix.R, etc: new source files
361            * man/nsparseMatrix-classes.Rd, etc: new help files
362            * tests/: adaptions
363            * src/chm_common.c (chm_dense_to_SEXP): and others:
364                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
365            * src/Csparse.c, etc: ditto
366    
367    2006-09-11  Douglas Bates  <bates@R-project.org>
368    
369            * src/Mutils.[ch],init.c inst/include/*.h: Move the
370            alloc_d**Matrix functions to the lme4 package.
371    
372    2006-09-09  Douglas Bates  <bates@R-project.org>
373    
374            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
375            fixed
376    
377    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/lMatrix.R: new
380    
381            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
382    
383            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
384            * man/tcrossprod.Rd: ditto
385    
386    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
389            for exported functions
390            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
391            Remove partitioning algorithms for sparse matrix reordering.  The
392            copyright on the Metis code was problematic and the methods were
393            rarely used.
394            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
395            operations are now done entirely in CHOLMOD code.
396    
397    2006-09-06  Douglas Bates  <bates@R-project.org>
398    
399            * src/Mutils.h: Remove functions that are no longer used.
400    
401    2006-09-04  Douglas Bates  <bates@R-project.org>
402    
403            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
404            * src/DEPS.mkf: update
405    
406    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * created branches/Matrix-for-R-2.3.x;  on trunk: do
409            * DESCRIPTION (Version): 0.9975-0
410            (Depends): R (>= 2.4.0)
411    
412    2006-09-01  Douglas Bates  <bates@R-project.org>
413    
414            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
415    
416    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
419            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
420    
421            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
422    
423    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
426            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
427            * R/dsparseMatrix.R: ditto
428            * R/Csparse.R: ditto
429    
430    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/dMatrix.R (Compare): improve availability of "<", etc
433            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
434    
435    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
438            of a 0-index which was used as 1-index (..hmm)
439    
440            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
441    
442            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
443            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
444            (.is.diagonal): ditto
445    
446            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
447    
448            * R/Matrix.R (Matrix): also work for NA data
449    
450  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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