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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1583, Tue Sep 19 08:33:54 2006 UTC
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1    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
4    
5    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
8            symmetric and y missing in R code using %*% (cholmod_aat doesn't
9            accept a symmetric matrix).
10            * tests/group-methods.R: Uncomment test of crossprod applied to
11            lsCMatrix objects.
12    
13    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/AllClass.R (symmetricMatrix): add validity method (available
16            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
17    
18            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
19    
20            * tests/indexing.Rout.save:
21            * tests/indexing.R: additions, mainly for 'lsparse'
22    
23            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
24            case.
25    
26            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
27    
28    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
31                    as 'N' (1-letter - Ok?)
32    
33            * tests/group-methods.R: add test for logical + NAs
34    
35            * R/dMatrix.R ("Compare"): fix to work with NA's
36    
37            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
38    
39            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
40                    which is implemented.
41    
42    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/chm_common.c: coerce logical <-> double instead of
45            typecasting;  needed for "l" matrix handling in cholmod.
46    
47            * tests/other-pkgs.R (graph): small extension in "graph" checks.
48    
49            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
50            (Tsp2grNEL): other fixes needed
51    
52    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
55                    Matrices, since "lMatrix", also "lsparseM" can have NA
56            * R/ndenseMatrix.R, etc: new source files
57            * man/nsparseMatrix-classes.Rd, etc: new help files
58            * tests/: adaptions
59            * src/chm_common.c (chm_dense_to_SEXP): and others:
60                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
61            * src/Csparse.c, etc: ditto
62    
63    2006-09-11  Douglas Bates  <bates@R-project.org>
64    
65            * src/Mutils.[ch],init.c inst/include/*.h: Move the
66            alloc_d**Matrix functions to the lme4 package.
67    
68    2006-09-09  Douglas Bates  <bates@R-project.org>
69    
70            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
71            fixed
72    
73    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/lMatrix.R: new
76    
77            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
78    
79            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
80            * man/tcrossprod.Rd: ditto
81    
82    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
85            for exported functions
86            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
87            Remove partitioning algorithms for sparse matrix reordering.  The
88            copyright on the Metis code was problematic and the methods were
89            rarely used.
90            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
91            operations are now done entirely in CHOLMOD code.
92    
93    2006-09-06  Douglas Bates  <bates@R-project.org>
94    
95            * src/Mutils.h: Remove functions that are no longer used.
96    
97    2006-09-04  Douglas Bates  <bates@R-project.org>
98    
99            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
100            * src/DEPS.mkf: update
101    
102    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * created branches/Matrix-for-R-2.3.x;  on trunk: do
105            * DESCRIPTION (Version): 0.9975-0
106            (Depends): R (>= 2.4.0)
107    
108    2006-09-01  Douglas Bates  <bates@R-project.org>
109    
110            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
111    
112    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
115            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
116    
117            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
118    
119    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
122            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
123            * R/dsparseMatrix.R: ditto
124            * R/Csparse.R: ditto
125    
126    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/dMatrix.R (Compare): improve availability of "<", etc
129            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
130    
131    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
134            of a 0-index which was used as 1-index (..hmm)
135    
136            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
137    
138            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
139            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
140            (.is.diagonal): ditto
141    
142            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
143    
144            * R/Matrix.R (Matrix): also work for NA data
145    
146    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
149            in all cases.
150    
151    2006-08-27  Douglas Bates  <bates@R-project.org>
152    
153            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
154            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
155    
156    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
159            subclasses of "ddenseMatrix"
160            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
161            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
162            instead of half dozen specialized ones.
163    
164    2006-08-25  Douglas Bates  <bates@R-project.org>
165    
166            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
167            <tillard@cirad.fr> - ordering standard errors to match effects.
168    
169    2006-08-24  Douglas Bates  <bates@R-project.org>
170    
171            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
172            on R_ldl.
173            * R/lCholCMatrix.R,
174            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
175            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
176            * many files in ./R and ./src: Use more general version of
177            dup_mMatrix_as_dgeMatrix to simplify method definitions.
178            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
179            dtpMatrix, dspMatrix and dppMatrix conversions.
180    
181    
182    2006-08-23  Douglas Bates  <bates@R-project.org>
183    
184            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
185            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
186            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
187            dgeMatrix_crossprod (may need to do this in other places).
188            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
189            generic and method for dsCMatrix.  Use CHOLMOD for chol().
190    
191    2006-08-22  Douglas Bates  <bates@R-project.org>
192    
193            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
194            types of classed Matrices, matrices or numeric or logical vectors.
195            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
196            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
197            to Mutils.h (as an inline) and change name to Matrix_check_class;
198            fixes in as_cholmod_factor and chm_factor_to_SEXP.
199            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
200            dsCMatrix_matrix_solve.  Comment out vestigial functions.
201            * src/Csparse.c: use diag_P and uplo_P macros.
202    
203    2006-08-21  Douglas Bates  <bates@R-project.org>
204    
205            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
206            valgrind.
207            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
208            inverses.
209            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
210            -Wall warnings.
211            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
212            Use dup_mMatrix_as_dgeMatrix.
213    
214    2006-08-20  Douglas Bates  <bates@R-project.org>
215    
216            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
217            * tests/sparseQR.R: Added
218            * man/sparseQR-class.Rd: Document methods for qr.* generics
219            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
220    
221    2006-08-19  Douglas Bates  <bates@R-project.org>
222    
223            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
224            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
225            and qr.fitted.
226            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
227            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
228    
229    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
232            the base version has no "..." argument.
233    
234            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
235    
236            * R/Matrix.R: define and
237            * NAMESPACE: export as.numeric() and as.logical() methods.
238                    Let's hope these do not badly slow down something...
239            Finally export the zapsmall() method.
240    
241    2006-08-17  Douglas Bates  <bates@R-project.org>
242    
243            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
244            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
245            * src/dtCMatrix.c :Remove code that is no longer used
246            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
247    
248    2006-08-14  Douglas Bates  <bates@R-project.org>
249    
250            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
251            Csparse_to_logical and Csparse_symmetric_to_general.
252            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
253            coercion methods between CsparseMatrix and TsparseMatrix.
254    
255    2006-08-14  Douglas Bates  <bates@R-project.org>
256    
257            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
258            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
259            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
260            possible.
261    
262  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
263    
264          * 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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