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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1592, Thu Sep 28 15:31:17 2006 UTC
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1    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-1
4    
5            * tests/simple.R: less checks fail; using NA, found that our
6                    kronecker() is not base-compatible with NA's.
7    
8            * R/dMatrix.R: "Compare" method now implemented for all cases
9    
10            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
11    
12            * man/dtpMatrix-class.Rd: mention length of 'x' slot
13    
14            * src/dtpMatrix.c (dtpMatrix_validate): fix check
15            * src/dspMatrix.c (dspMatrix_validate): ditto
16    
17            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
18              including coercion to [nl]tTMatrix.
19    
20            * R/diagMatrix.R (show): print a header line as for other classes.
21    
22    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/Makefile.win (SUBDIRS): fix typo
25    
26    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
29    
30    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
33            symmetric and y missing in R code using %*% (cholmod_aat doesn't
34            accept a symmetric matrix).
35            * tests/group-methods.R: Uncomment test of crossprod applied to
36            lsCMatrix objects.
37    
38    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/AllClass.R (symmetricMatrix): add validity method (available
41            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
42    
43            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
44    
45            * tests/indexing.Rout.save:
46            * tests/indexing.R: additions, mainly for 'lsparse'
47    
48            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
49            case.
50    
51            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
52    
53    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
56                    as 'N' (1-letter - Ok?)
57    
58            * tests/group-methods.R: add test for logical + NAs
59    
60            * R/dMatrix.R ("Compare"): fix to work with NA's
61    
62            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
63    
64            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
65                    which is implemented.
66    
67    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * src/chm_common.c: coerce logical <-> double instead of
70            typecasting;  needed for "l" matrix handling in cholmod.
71    
72            * tests/other-pkgs.R (graph): small extension in "graph" checks.
73    
74            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
75            (Tsp2grNEL): other fixes needed
76    
77    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
80                    Matrices, since "lMatrix", also "lsparseM" can have NA
81            * R/ndenseMatrix.R, etc: new source files
82            * man/nsparseMatrix-classes.Rd, etc: new help files
83            * tests/: adaptions
84            * src/chm_common.c (chm_dense_to_SEXP): and others:
85                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
86            * src/Csparse.c, etc: ditto
87    
88    2006-09-11  Douglas Bates  <bates@R-project.org>
89    
90            * src/Mutils.[ch],init.c inst/include/*.h: Move the
91            alloc_d**Matrix functions to the lme4 package.
92    
93    2006-09-09  Douglas Bates  <bates@R-project.org>
94    
95            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
96            fixed
97    
98    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/lMatrix.R: new
101    
102            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
103    
104            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
105            * man/tcrossprod.Rd: ditto
106    
107    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
110            for exported functions
111            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
112            Remove partitioning algorithms for sparse matrix reordering.  The
113            copyright on the Metis code was problematic and the methods were
114            rarely used.
115            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
116            operations are now done entirely in CHOLMOD code.
117    
118    2006-09-06  Douglas Bates  <bates@R-project.org>
119    
120            * src/Mutils.h: Remove functions that are no longer used.
121    
122    2006-09-04  Douglas Bates  <bates@R-project.org>
123    
124            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
125            * src/DEPS.mkf: update
126    
127    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * created branches/Matrix-for-R-2.3.x;  on trunk: do
130            * DESCRIPTION (Version): 0.9975-0
131            (Depends): R (>= 2.4.0)
132    
133    2006-09-01  Douglas Bates  <bates@R-project.org>
134    
135            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
136    
137    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
140            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
141    
142            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
143    
144    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
147            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
148            * R/dsparseMatrix.R: ditto
149            * R/Csparse.R: ditto
150    
151    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dMatrix.R (Compare): improve availability of "<", etc
154            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
155    
156    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
159            of a 0-index which was used as 1-index (..hmm)
160    
161            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
162    
163            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
164            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
165            (.is.diagonal): ditto
166    
167            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
168    
169            * R/Matrix.R (Matrix): also work for NA data
170    
171    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
174            in all cases.
175    
176    2006-08-27  Douglas Bates  <bates@R-project.org>
177    
178            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
179            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
180    
181    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
184            subclasses of "ddenseMatrix"
185            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
186            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
187            instead of half dozen specialized ones.
188    
189    2006-08-25  Douglas Bates  <bates@R-project.org>
190    
191            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
192            <tillard@cirad.fr> - ordering standard errors to match effects.
193    
194    2006-08-24  Douglas Bates  <bates@R-project.org>
195    
196            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
197            on R_ldl.
198            * R/lCholCMatrix.R,
199            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
200            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
201            * many files in ./R and ./src: Use more general version of
202            dup_mMatrix_as_dgeMatrix to simplify method definitions.
203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
204            dtpMatrix, dspMatrix and dppMatrix conversions.
205    
206    
207    2006-08-23  Douglas Bates  <bates@R-project.org>
208    
209            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
210            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
211            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
212            dgeMatrix_crossprod (may need to do this in other places).
213            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
214            generic and method for dsCMatrix.  Use CHOLMOD for chol().
215    
216    2006-08-22  Douglas Bates  <bates@R-project.org>
217    
218            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
219            types of classed Matrices, matrices or numeric or logical vectors.
220            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
221            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
222            to Mutils.h (as an inline) and change name to Matrix_check_class;
223            fixes in as_cholmod_factor and chm_factor_to_SEXP.
224            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
225            dsCMatrix_matrix_solve.  Comment out vestigial functions.
226            * src/Csparse.c: use diag_P and uplo_P macros.
227    
228    2006-08-21  Douglas Bates  <bates@R-project.org>
229    
230            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
231            valgrind.
232            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
233            inverses.
234            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
235            -Wall warnings.
236            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
237            Use dup_mMatrix_as_dgeMatrix.
238    
239    2006-08-20  Douglas Bates  <bates@R-project.org>
240    
241            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
242            * tests/sparseQR.R: Added
243            * man/sparseQR-class.Rd: Document methods for qr.* generics
244            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
245    
246    2006-08-19  Douglas Bates  <bates@R-project.org>
247    
248            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
249            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
250            and qr.fitted.
251            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
252            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
253    
254    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
257            the base version has no "..." argument.
258    
259            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
260    
261            * R/Matrix.R: define and
262            * NAMESPACE: export as.numeric() and as.logical() methods.
263                    Let's hope these do not badly slow down something...
264            Finally export the zapsmall() method.
265    
266    2006-08-17  Douglas Bates  <bates@R-project.org>
267    
268            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
269            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
270            * src/dtCMatrix.c :Remove code that is no longer used
271            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
272    
273    2006-08-14  Douglas Bates  <bates@R-project.org>
274    
275            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
276            Csparse_to_logical and Csparse_symmetric_to_general.
277            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
278            coercion methods between CsparseMatrix and TsparseMatrix.
279    
280    2006-08-14  Douglas Bates  <bates@R-project.org>
281    
282            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
283            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
284            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
285            possible.
286    
287  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
288    
289          * 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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