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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1660, Thu Nov 2 11:05:35 2006 UTC
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1    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
4    
5            * tests/simple.R: validObject() checking the above.
6    
7            * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,
8            replacing both dgCMatrix_validate and lgCM*.
9    
10            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
11            fix dimnames setting in other places.
12            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
13    
14    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
17    
18            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
19            symmetry test, via
20            * R/Auxiliaries.R (.as.dgC.0.factors):
21    
22    2006-11-01  Douglas Bates  <bates@r-project.org>
23    
24            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
25            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
26            <CsparseMatrix>) added
27    
28    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * tests/matprod.R: add a variation of Harri's example
31    
32            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
33            recursive infinitely.
34    
35            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
36    
37            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
38    
39    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
42            matrix if possible; test m+m == 2*m; now test dgRMatrix.
43            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
44            satisfy the above test.
45    
46    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
49    
50            * R/dgCMatrix.R: solve(a, b="missing") based on
51            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
52            RHS = NULL.
53    
54            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
55            add more (needed) [t]crossprod() methods.
56    
57            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
58    
59            * R/Auxiliaries.R (as_CspClass): cleanup
60            (drop0): internal utility for "Csparse_drop(*, 0)"
61            (.bail.out.2): encourage active feedback
62    
63    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/dMatrix.R(Compare): new(), then slots [no validity check]
66    
67            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
68            non-valid or 'sorted' case).
69    
70            * R/dsparseMatrix.R: add "chol" method.
71            * R/ddenseMatrix.R: ditto
72    
73            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
74            * NAMESPACE (Ops)
75            * R/diagMatrix.R (diag2T): simple utility used "higher level"
76            coercion; deprecating direct lower level coercions.
77    
78            * R/*.R (seq): use seq_len() and seq_along() where possible.
79    
80    
81    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Version): 0.9975-5 ready for release
84    
85    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
88    
89    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/AllClass.R (corMatrix): add 'validity' check;
92                    comment out unused "LDL" class definition
93            * NAMESPACE: mention, but do not export "LDL" class
94            * R/corMatrix.R: new (simple), needed for R-devel with
95            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
96              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
97    
98    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
101            use Rprintf and R's error handling.
102    
103    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
106            * tests/matprod.R: add tests for the bug fixed.
107    
108    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
111            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
112    
113    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
116    
117    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Version): 0.9975-3
120    
121            * R/diagMatrix.R (bdiag): new function constructing block diagonal
122            (sparse) matrices.
123            * man/bdiag.Rd: docu + examples
124    
125            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
126    
127            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
128            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
129    
130            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
131            that result is sparse or diagonal (and not dense).
132    
133            * man/Subassign-methods.Rd: fix examples
134    
135            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
136            should always return a sparse (and not sometimes a diagonal) matrix.
137    
138    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
141    
142    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * DESCRIPTION (Version): 0.9975-2
145    
146            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
147    
148    2006-10-02  Douglas Bates  <bates@R-project.org>
149    
150            * tests/dg_Matrix.R: Simplify test taking into account new code.
151    
152    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
155    
156            * R/lsTMatrix.R: new files w/ missing methods
157            * R/nsTMatrix.R:  "  'for completeness'
158    
159            * tests/Class+Meth.R: a bit less 'not.ok.classes'
160    
161            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
162    
163    
164    2006-09-28  Douglas Bates  <bates@R-project.org>
165    
166            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
167            included.
168    
169            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
170            Export C-callable functions used in Zt_create in lme4.
171    
172    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-1
175    
176            * tests/simple.R: less checks fail; using NA, found that our
177                    kronecker() is not base-compatible with NA's.
178    
179            * R/dMatrix.R: "Compare" method now implemented for all cases
180    
181            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
182    
183            * man/dtpMatrix-class.Rd: mention length of 'x' slot
184    
185            * src/dtpMatrix.c (dtpMatrix_validate): fix check
186            * src/dspMatrix.c (dspMatrix_validate): ditto
187    
188            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
189              including coercion to [nl]tTMatrix.
190    
191            * R/diagMatrix.R (show): print a header line as for other classes.
192    
193    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/Makefile.win (SUBDIRS): fix typo
196    
197    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
200    
201    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
202    
203            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
204            symmetric and y missing in R code using %*% (cholmod_aat doesn't
205            accept a symmetric matrix).
206            * tests/group-methods.R: Uncomment test of crossprod applied to
207            lsCMatrix objects.
208    
209    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/AllClass.R (symmetricMatrix): add validity method (available
212            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
213    
214            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
215    
216            * tests/indexing.Rout.save:
217            * tests/indexing.R: additions, mainly for 'lsparse'
218    
219            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
220            case.
221    
222            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
223    
224    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
227                    as 'N' (1-letter - Ok?)
228    
229            * tests/group-methods.R: add test for logical + NAs
230    
231            * R/dMatrix.R ("Compare"): fix to work with NA's
232    
233            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
234    
235            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
236                    which is implemented.
237    
238    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * src/chm_common.c: coerce logical <-> double instead of
241            typecasting;  needed for "l" matrix handling in cholmod.
242    
243            * tests/other-pkgs.R (graph): small extension in "graph" checks.
244    
245            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
246            (Tsp2grNEL): other fixes needed
247    
248    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
251                    Matrices, since "lMatrix", also "lsparseM" can have NA
252            * R/ndenseMatrix.R, etc: new source files
253            * man/nsparseMatrix-classes.Rd, etc: new help files
254            * tests/: adaptions
255            * src/chm_common.c (chm_dense_to_SEXP): and others:
256                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
257            * src/Csparse.c, etc: ditto
258    
259    2006-09-11  Douglas Bates  <bates@R-project.org>
260    
261            * src/Mutils.[ch],init.c inst/include/*.h: Move the
262            alloc_d**Matrix functions to the lme4 package.
263    
264    2006-09-09  Douglas Bates  <bates@R-project.org>
265    
266            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
267            fixed
268    
269    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/lMatrix.R: new
272    
273            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
274    
275            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
276            * man/tcrossprod.Rd: ditto
277    
278    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
281            for exported functions
282            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
283            Remove partitioning algorithms for sparse matrix reordering.  The
284            copyright on the Metis code was problematic and the methods were
285            rarely used.
286            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
287            operations are now done entirely in CHOLMOD code.
288    
289    2006-09-06  Douglas Bates  <bates@R-project.org>
290    
291            * src/Mutils.h: Remove functions that are no longer used.
292    
293    2006-09-04  Douglas Bates  <bates@R-project.org>
294    
295            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
296            * src/DEPS.mkf: update
297    
298    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * created branches/Matrix-for-R-2.3.x;  on trunk: do
301            * DESCRIPTION (Version): 0.9975-0
302            (Depends): R (>= 2.4.0)
303    
304    2006-09-01  Douglas Bates  <bates@R-project.org>
305    
306            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
307    
308    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
311            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
312    
313            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
314    
315    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
318            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
319            * R/dsparseMatrix.R: ditto
320            * R/Csparse.R: ditto
321    
322    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/dMatrix.R (Compare): improve availability of "<", etc
325            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
326    
327    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
330            of a 0-index which was used as 1-index (..hmm)
331    
332            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
333    
334            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
335            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
336            (.is.diagonal): ditto
337    
338            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
339    
340            * R/Matrix.R (Matrix): also work for NA data
341    
342    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
345            in all cases.
346    
347    2006-08-27  Douglas Bates  <bates@R-project.org>
348    
349            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
350            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
351    
352    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
355            subclasses of "ddenseMatrix"
356            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
357            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
358            instead of half dozen specialized ones.
359    
360    2006-08-25  Douglas Bates  <bates@R-project.org>
361    
362            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
363            <tillard@cirad.fr> - ordering standard errors to match effects.
364    
365    2006-08-24  Douglas Bates  <bates@R-project.org>
366    
367            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
368            on R_ldl.
369            * R/lCholCMatrix.R,
370            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
371            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
372            * many files in ./R and ./src: Use more general version of
373            dup_mMatrix_as_dgeMatrix to simplify method definitions.
374            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
375            dtpMatrix, dspMatrix and dppMatrix conversions.
376    
377    
378    2006-08-23  Douglas Bates  <bates@R-project.org>
379    
380            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
381            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
382            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
383            dgeMatrix_crossprod (may need to do this in other places).
384            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
385            generic and method for dsCMatrix.  Use CHOLMOD for chol().
386    
387    2006-08-22  Douglas Bates  <bates@R-project.org>
388    
389            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
390            types of classed Matrices, matrices or numeric or logical vectors.
391            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
392            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
393            to Mutils.h (as an inline) and change name to Matrix_check_class;
394            fixes in as_cholmod_factor and chm_factor_to_SEXP.
395            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
396            dsCMatrix_matrix_solve.  Comment out vestigial functions.
397            * src/Csparse.c: use diag_P and uplo_P macros.
398    
399    2006-08-21  Douglas Bates  <bates@R-project.org>
400    
401            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
402            valgrind.
403            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
404            inverses.
405            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
406            -Wall warnings.
407            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
408            Use dup_mMatrix_as_dgeMatrix.
409    
410    2006-08-20  Douglas Bates  <bates@R-project.org>
411    
412            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
413            * tests/sparseQR.R: Added
414            * man/sparseQR-class.Rd: Document methods for qr.* generics
415            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
416    
417    2006-08-19  Douglas Bates  <bates@R-project.org>
418    
419            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
420            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
421            and qr.fitted.
422            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
423            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
424    
425    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
428            the base version has no "..." argument.
429    
430            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
431    
432            * R/Matrix.R: define and
433            * NAMESPACE: export as.numeric() and as.logical() methods.
434                    Let's hope these do not badly slow down something...
435            Finally export the zapsmall() method.
436    
437    2006-08-17  Douglas Bates  <bates@R-project.org>
438    
439            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
440            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
441            * src/dtCMatrix.c :Remove code that is no longer used
442            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
443    
444    2006-08-14  Douglas Bates  <bates@R-project.org>
445    
446            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
447            Csparse_to_logical and Csparse_symmetric_to_general.
448            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
449            coercion methods between CsparseMatrix and TsparseMatrix.
450    
451    2006-08-14  Douglas Bates  <bates@R-project.org>
452    
453            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
454            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
455            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
456            possible.
457    
458  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
459    
460          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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