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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1655, Mon Oct 30 17:16:27 2006 UTC
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1    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/matprod.R: add a variation of Harri's example
4    
5            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
6            recursive infinitely.
7    
8            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
9    
10            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
11    
12    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
15            matrix if possible; test m+m == 2*m; now test dgRMatrix.
16            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
17            satisfy the above test.
18    
19    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
22    
23            * R/dgCMatrix.R: solve(a, b="missing") based on
24            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
25            RHS = NULL.
26    
27            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
28            add more (needed) [t]crossprod() methods.
29    
30            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
31    
32            * R/Auxiliaries.R (as_CspClass): cleanup
33            (drop0): internal utility for "Csparse_drop(*, 0)"
34            (.bail.out.2): encourage active feedback
35    
36    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dMatrix.R(Compare): new(), then slots [no validity check]
39    
40            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
41            non-valid or 'sorted' case).
42    
43            * R/dsparseMatrix.R: add "chol" method.
44            * R/ddenseMatrix.R: ditto
45    
46            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
47            * NAMESPACE (Ops)
48            * R/diagMatrix.R (diag2T): simple utility used "higher level"
49            coercion; deprecating direct lower level coercions.
50    
51            * R/*.R (seq): use seq_len() and seq_along() where possible.
52    
53    
54    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-5 ready for release
57    
58    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
61    
62    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (corMatrix): add 'validity' check;
65                    comment out unused "LDL" class definition
66            * NAMESPACE: mention, but do not export "LDL" class
67            * R/corMatrix.R: new (simple), needed for R-devel with
68            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
69              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
70    
71    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
74            use Rprintf and R's error handling.
75    
76    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
79            * tests/matprod.R: add tests for the bug fixed.
80    
81    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
84            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
85    
86    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
89    
90    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Version): 0.9975-3
93    
94            * R/diagMatrix.R (bdiag): new function constructing block diagonal
95            (sparse) matrices.
96            * man/bdiag.Rd: docu + examples
97    
98            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
99    
100            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
101            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
102    
103            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
104            that result is sparse or diagonal (and not dense).
105    
106            * man/Subassign-methods.Rd: fix examples
107    
108            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
109            should always return a sparse (and not sometimes a diagonal) matrix.
110    
111    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
114    
115    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * DESCRIPTION (Version): 0.9975-2
118    
119            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
120    
121    2006-10-02  Douglas Bates  <bates@R-project.org>
122    
123            * tests/dg_Matrix.R: Simplify test taking into account new code.
124    
125    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
128    
129            * R/lsTMatrix.R: new files w/ missing methods
130            * R/nsTMatrix.R:  "  'for completeness'
131    
132            * tests/Class+Meth.R: a bit less 'not.ok.classes'
133    
134            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
135    
136    
137    2006-09-28  Douglas Bates  <bates@R-project.org>
138    
139            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
140            included.
141    
142            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
143            Export C-callable functions used in Zt_create in lme4.
144    
145    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.9975-1
148    
149            * tests/simple.R: less checks fail; using NA, found that our
150                    kronecker() is not base-compatible with NA's.
151    
152            * R/dMatrix.R: "Compare" method now implemented for all cases
153    
154            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
155    
156            * man/dtpMatrix-class.Rd: mention length of 'x' slot
157    
158            * src/dtpMatrix.c (dtpMatrix_validate): fix check
159            * src/dspMatrix.c (dspMatrix_validate): ditto
160    
161            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
162              including coercion to [nl]tTMatrix.
163    
164            * R/diagMatrix.R (show): print a header line as for other classes.
165    
166    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Makefile.win (SUBDIRS): fix typo
169    
170    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
173    
174    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
177            symmetric and y missing in R code using %*% (cholmod_aat doesn't
178            accept a symmetric matrix).
179            * tests/group-methods.R: Uncomment test of crossprod applied to
180            lsCMatrix objects.
181    
182    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/AllClass.R (symmetricMatrix): add validity method (available
185            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
186    
187            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
188    
189            * tests/indexing.Rout.save:
190            * tests/indexing.R: additions, mainly for 'lsparse'
191    
192            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
193            case.
194    
195            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
196    
197    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
200                    as 'N' (1-letter - Ok?)
201    
202            * tests/group-methods.R: add test for logical + NAs
203    
204            * R/dMatrix.R ("Compare"): fix to work with NA's
205    
206            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
207    
208            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
209                    which is implemented.
210    
211    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/chm_common.c: coerce logical <-> double instead of
214            typecasting;  needed for "l" matrix handling in cholmod.
215    
216            * tests/other-pkgs.R (graph): small extension in "graph" checks.
217    
218            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
219            (Tsp2grNEL): other fixes needed
220    
221    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
224                    Matrices, since "lMatrix", also "lsparseM" can have NA
225            * R/ndenseMatrix.R, etc: new source files
226            * man/nsparseMatrix-classes.Rd, etc: new help files
227            * tests/: adaptions
228            * src/chm_common.c (chm_dense_to_SEXP): and others:
229                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
230            * src/Csparse.c, etc: ditto
231    
232    2006-09-11  Douglas Bates  <bates@R-project.org>
233    
234            * src/Mutils.[ch],init.c inst/include/*.h: Move the
235            alloc_d**Matrix functions to the lme4 package.
236    
237    2006-09-09  Douglas Bates  <bates@R-project.org>
238    
239            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
240            fixed
241    
242    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/lMatrix.R: new
245    
246            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
247    
248            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
249            * man/tcrossprod.Rd: ditto
250    
251    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
254            for exported functions
255            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
256            Remove partitioning algorithms for sparse matrix reordering.  The
257            copyright on the Metis code was problematic and the methods were
258            rarely used.
259            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
260            operations are now done entirely in CHOLMOD code.
261    
262    2006-09-06  Douglas Bates  <bates@R-project.org>
263    
264            * src/Mutils.h: Remove functions that are no longer used.
265    
266    2006-09-04  Douglas Bates  <bates@R-project.org>
267    
268            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
269            * src/DEPS.mkf: update
270    
271    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * created branches/Matrix-for-R-2.3.x;  on trunk: do
274            * DESCRIPTION (Version): 0.9975-0
275            (Depends): R (>= 2.4.0)
276    
277    2006-09-01  Douglas Bates  <bates@R-project.org>
278    
279            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
280    
281    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
284            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
285    
286            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
287    
288    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
291            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
292            * R/dsparseMatrix.R: ditto
293            * R/Csparse.R: ditto
294    
295    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/dMatrix.R (Compare): improve availability of "<", etc
298            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
299    
300    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
303            of a 0-index which was used as 1-index (..hmm)
304    
305            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
306    
307            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
308            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
309            (.is.diagonal): ditto
310    
311            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
312    
313            * R/Matrix.R (Matrix): also work for NA data
314    
315    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
318            in all cases.
319    
320    2006-08-27  Douglas Bates  <bates@R-project.org>
321    
322            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
323            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
324    
325    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
328            subclasses of "ddenseMatrix"
329            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
330            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
331            instead of half dozen specialized ones.
332    
333    2006-08-25  Douglas Bates  <bates@R-project.org>
334    
335            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
336            <tillard@cirad.fr> - ordering standard errors to match effects.
337    
338    2006-08-24  Douglas Bates  <bates@R-project.org>
339    
340            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
341            on R_ldl.
342            * R/lCholCMatrix.R,
343            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
344            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
345            * many files in ./R and ./src: Use more general version of
346            dup_mMatrix_as_dgeMatrix to simplify method definitions.
347            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
348            dtpMatrix, dspMatrix and dppMatrix conversions.
349    
350    
351    2006-08-23  Douglas Bates  <bates@R-project.org>
352    
353            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
354            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
355            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
356            dgeMatrix_crossprod (may need to do this in other places).
357            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
358            generic and method for dsCMatrix.  Use CHOLMOD for chol().
359    
360    2006-08-22  Douglas Bates  <bates@R-project.org>
361    
362            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
363            types of classed Matrices, matrices or numeric or logical vectors.
364            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
365            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
366            to Mutils.h (as an inline) and change name to Matrix_check_class;
367            fixes in as_cholmod_factor and chm_factor_to_SEXP.
368            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
369            dsCMatrix_matrix_solve.  Comment out vestigial functions.
370            * src/Csparse.c: use diag_P and uplo_P macros.
371    
372    2006-08-21  Douglas Bates  <bates@R-project.org>
373    
374            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
375            valgrind.
376            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
377            inverses.
378            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
379            -Wall warnings.
380            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
381            Use dup_mMatrix_as_dgeMatrix.
382    
383    2006-08-20  Douglas Bates  <bates@R-project.org>
384    
385            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
386            * tests/sparseQR.R: Added
387            * man/sparseQR-class.Rd: Document methods for qr.* generics
388            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
389    
390    2006-08-19  Douglas Bates  <bates@R-project.org>
391    
392            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
393            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
394            and qr.fitted.
395            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
396            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
397    
398    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
401            the base version has no "..." argument.
402    
403            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
404    
405            * R/Matrix.R: define and
406            * NAMESPACE: export as.numeric() and as.logical() methods.
407                    Let's hope these do not badly slow down something...
408            Finally export the zapsmall() method.
409    
410    2006-08-17  Douglas Bates  <bates@R-project.org>
411    
412            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
413            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
414            * src/dtCMatrix.c :Remove code that is no longer used
415            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
416    
417    2006-08-14  Douglas Bates  <bates@R-project.org>
418    
419            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
420            Csparse_to_logical and Csparse_symmetric_to_general.
421            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
422            coercion methods between CsparseMatrix and TsparseMatrix.
423    
424    2006-08-14  Douglas Bates  <bates@R-project.org>
425    
426            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
427            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
428            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
429            possible.
430    
431  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
432    
433          * 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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