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revision 1398, Sun Aug 20 03:26:06 2006 UTC revision 1654, Fri Oct 27 16:58:15 2006 UTC
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1    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: solve(a, b="missing") based on
4            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
5            RHS = NULL.
6    
7            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
8            add more (needed) [t]crossprod() methods.
9    
10            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
11    
12            * R/Auxiliaries.R (as_CspClass): cleanup
13            (drop0): internal utility for "Csparse_drop(*, 0)"
14            (.bail.out.2): encourage active feedback
15    
16    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dMatrix.R(Compare): new(), then slots [no validity check]
19    
20            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
21            non-valid or 'sorted' case).
22    
23            * R/dsparseMatrix.R: add "chol" method.
24            * R/ddenseMatrix.R: ditto
25    
26            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
27            * NAMESPACE (Ops)
28            * R/diagMatrix.R (diag2T): simple utility used "higher level"
29            coercion; deprecating direct lower level coercions.
30    
31            * R/*.R (seq): use seq_len() and seq_along() where possible.
32    
33    
34    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.9975-5 ready for release
37    
38    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
41    
42    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/AllClass.R (corMatrix): add 'validity' check;
45                    comment out unused "LDL" class definition
46            * NAMESPACE: mention, but do not export "LDL" class
47            * R/corMatrix.R: new (simple), needed for R-devel with
48            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
49              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
50    
51    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
54            use Rprintf and R's error handling.
55    
56    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
59            * tests/matprod.R: add tests for the bug fixed.
60    
61    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
64            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
65    
66    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
69    
70    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.9975-3
73    
74            * R/diagMatrix.R (bdiag): new function constructing block diagonal
75            (sparse) matrices.
76            * man/bdiag.Rd: docu + examples
77    
78            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
79    
80            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
81            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
82    
83            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
84            that result is sparse or diagonal (and not dense).
85    
86            * man/Subassign-methods.Rd: fix examples
87    
88            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
89            should always return a sparse (and not sometimes a diagonal) matrix.
90    
91    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
94    
95    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
96    
97            * DESCRIPTION (Version): 0.9975-2
98    
99            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
100    
101    2006-10-02  Douglas Bates  <bates@R-project.org>
102    
103            * tests/dg_Matrix.R: Simplify test taking into account new code.
104    
105    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
108    
109            * R/lsTMatrix.R: new files w/ missing methods
110            * R/nsTMatrix.R:  "  'for completeness'
111    
112            * tests/Class+Meth.R: a bit less 'not.ok.classes'
113    
114            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
115    
116    
117    2006-09-28  Douglas Bates  <bates@R-project.org>
118    
119            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
120            included.
121    
122            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
123            Export C-callable functions used in Zt_create in lme4.
124    
125    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * DESCRIPTION (Version): 0.9975-1
128    
129            * tests/simple.R: less checks fail; using NA, found that our
130                    kronecker() is not base-compatible with NA's.
131    
132            * R/dMatrix.R: "Compare" method now implemented for all cases
133    
134            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
135    
136            * man/dtpMatrix-class.Rd: mention length of 'x' slot
137    
138            * src/dtpMatrix.c (dtpMatrix_validate): fix check
139            * src/dspMatrix.c (dspMatrix_validate): ditto
140    
141            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
142              including coercion to [nl]tTMatrix.
143    
144            * R/diagMatrix.R (show): print a header line as for other classes.
145    
146    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * src/Makefile.win (SUBDIRS): fix typo
149    
150    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
153    
154    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
157            symmetric and y missing in R code using %*% (cholmod_aat doesn't
158            accept a symmetric matrix).
159            * tests/group-methods.R: Uncomment test of crossprod applied to
160            lsCMatrix objects.
161    
162    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/AllClass.R (symmetricMatrix): add validity method (available
165            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
166    
167            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
168    
169            * tests/indexing.Rout.save:
170            * tests/indexing.R: additions, mainly for 'lsparse'
171    
172            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
173            case.
174    
175            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
176    
177    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
180                    as 'N' (1-letter - Ok?)
181    
182            * tests/group-methods.R: add test for logical + NAs
183    
184            * R/dMatrix.R ("Compare"): fix to work with NA's
185    
186            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
187    
188            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
189                    which is implemented.
190    
191    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * src/chm_common.c: coerce logical <-> double instead of
194            typecasting;  needed for "l" matrix handling in cholmod.
195    
196            * tests/other-pkgs.R (graph): small extension in "graph" checks.
197    
198            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
199            (Tsp2grNEL): other fixes needed
200    
201    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
204                    Matrices, since "lMatrix", also "lsparseM" can have NA
205            * R/ndenseMatrix.R, etc: new source files
206            * man/nsparseMatrix-classes.Rd, etc: new help files
207            * tests/: adaptions
208            * src/chm_common.c (chm_dense_to_SEXP): and others:
209                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
210            * src/Csparse.c, etc: ditto
211    
212    2006-09-11  Douglas Bates  <bates@R-project.org>
213    
214            * src/Mutils.[ch],init.c inst/include/*.h: Move the
215            alloc_d**Matrix functions to the lme4 package.
216    
217    2006-09-09  Douglas Bates  <bates@R-project.org>
218    
219            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
220            fixed
221    
222    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/lMatrix.R: new
225    
226            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
227    
228            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
229            * man/tcrossprod.Rd: ditto
230    
231    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
234            for exported functions
235            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
236            Remove partitioning algorithms for sparse matrix reordering.  The
237            copyright on the Metis code was problematic and the methods were
238            rarely used.
239            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
240            operations are now done entirely in CHOLMOD code.
241    
242    2006-09-06  Douglas Bates  <bates@R-project.org>
243    
244            * src/Mutils.h: Remove functions that are no longer used.
245    
246    2006-09-04  Douglas Bates  <bates@R-project.org>
247    
248            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
249            * src/DEPS.mkf: update
250    
251    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * created branches/Matrix-for-R-2.3.x;  on trunk: do
254            * DESCRIPTION (Version): 0.9975-0
255            (Depends): R (>= 2.4.0)
256    
257    2006-09-01  Douglas Bates  <bates@R-project.org>
258    
259            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
260    
261    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
264            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
265    
266            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
267    
268    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
271            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
272            * R/dsparseMatrix.R: ditto
273            * R/Csparse.R: ditto
274    
275    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/dMatrix.R (Compare): improve availability of "<", etc
278            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
279    
280    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
283            of a 0-index which was used as 1-index (..hmm)
284    
285            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
286    
287            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
288            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
289            (.is.diagonal): ditto
290    
291            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
292    
293            * R/Matrix.R (Matrix): also work for NA data
294    
295    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
298            in all cases.
299    
300    2006-08-27  Douglas Bates  <bates@R-project.org>
301    
302            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
303            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
304    
305    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
308            subclasses of "ddenseMatrix"
309            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
310            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
311            instead of half dozen specialized ones.
312    
313    2006-08-25  Douglas Bates  <bates@R-project.org>
314    
315            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
316            <tillard@cirad.fr> - ordering standard errors to match effects.
317    
318    2006-08-24  Douglas Bates  <bates@R-project.org>
319    
320            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
321            on R_ldl.
322            * R/lCholCMatrix.R,
323            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
324            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
325            * many files in ./R and ./src: Use more general version of
326            dup_mMatrix_as_dgeMatrix to simplify method definitions.
327            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
328            dtpMatrix, dspMatrix and dppMatrix conversions.
329    
330    
331    2006-08-23  Douglas Bates  <bates@R-project.org>
332    
333            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
334            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
335            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
336            dgeMatrix_crossprod (may need to do this in other places).
337            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
338            generic and method for dsCMatrix.  Use CHOLMOD for chol().
339    
340    2006-08-22  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
343            types of classed Matrices, matrices or numeric or logical vectors.
344            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
345            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
346            to Mutils.h (as an inline) and change name to Matrix_check_class;
347            fixes in as_cholmod_factor and chm_factor_to_SEXP.
348            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
349            dsCMatrix_matrix_solve.  Comment out vestigial functions.
350            * src/Csparse.c: use diag_P and uplo_P macros.
351    
352    2006-08-21  Douglas Bates  <bates@R-project.org>
353    
354            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
355            valgrind.
356            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
357            inverses.
358            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
359            -Wall warnings.
360            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
361            Use dup_mMatrix_as_dgeMatrix.
362    
363    2006-08-20  Douglas Bates  <bates@R-project.org>
364    
365            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
366            * tests/sparseQR.R: Added
367            * man/sparseQR-class.Rd: Document methods for qr.* generics
368            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
369    
370  2006-08-19  Douglas Bates  <bates@R-project.org>  2006-08-19  Douglas Bates  <bates@R-project.org>
371    
372          * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:          * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:

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