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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1613, Wed Oct 4 22:41:49 2006 UTC
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1    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): 0.9975-2
4    
5            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
6    
7    2006-10-02  Douglas Bates  <bates@R-project.org>
8    
9            * tests/dg_Matrix.R: Simplify test taking into account new code.
10    
11    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
14    
15            * R/lsTMatrix.R: new files w/ missing methods
16            * R/nsTMatrix.R:  "  'for completeness'
17    
18            * tests/Class+Meth.R: a bit less 'not.ok.classes'
19    
20            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
21    
22    
23    2006-09-28  Douglas Bates  <bates@R-project.org>
24    
25            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
26            included.
27    
28            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
29            Export C-callable functions used in Zt_create in lme4.
30    
31    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.9975-1
34    
35            * tests/simple.R: less checks fail; using NA, found that our
36                    kronecker() is not base-compatible with NA's.
37    
38            * R/dMatrix.R: "Compare" method now implemented for all cases
39    
40            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
41    
42            * man/dtpMatrix-class.Rd: mention length of 'x' slot
43    
44            * src/dtpMatrix.c (dtpMatrix_validate): fix check
45            * src/dspMatrix.c (dspMatrix_validate): ditto
46    
47            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
48              including coercion to [nl]tTMatrix.
49    
50            * R/diagMatrix.R (show): print a header line as for other classes.
51    
52    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/Makefile.win (SUBDIRS): fix typo
55    
56    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
59    
60    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
63            symmetric and y missing in R code using %*% (cholmod_aat doesn't
64            accept a symmetric matrix).
65            * tests/group-methods.R: Uncomment test of crossprod applied to
66            lsCMatrix objects.
67    
68    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllClass.R (symmetricMatrix): add validity method (available
71            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
72    
73            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
74    
75            * tests/indexing.Rout.save:
76            * tests/indexing.R: additions, mainly for 'lsparse'
77    
78            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
79            case.
80    
81            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
82    
83    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
86                    as 'N' (1-letter - Ok?)
87    
88            * tests/group-methods.R: add test for logical + NAs
89    
90            * R/dMatrix.R ("Compare"): fix to work with NA's
91    
92            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
93    
94            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
95                    which is implemented.
96    
97    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * src/chm_common.c: coerce logical <-> double instead of
100            typecasting;  needed for "l" matrix handling in cholmod.
101    
102            * tests/other-pkgs.R (graph): small extension in "graph" checks.
103    
104            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
105            (Tsp2grNEL): other fixes needed
106    
107    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
110                    Matrices, since "lMatrix", also "lsparseM" can have NA
111            * R/ndenseMatrix.R, etc: new source files
112            * man/nsparseMatrix-classes.Rd, etc: new help files
113            * tests/: adaptions
114            * src/chm_common.c (chm_dense_to_SEXP): and others:
115                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
116            * src/Csparse.c, etc: ditto
117    
118    2006-09-11  Douglas Bates  <bates@R-project.org>
119    
120            * src/Mutils.[ch],init.c inst/include/*.h: Move the
121            alloc_d**Matrix functions to the lme4 package.
122    
123    2006-09-09  Douglas Bates  <bates@R-project.org>
124    
125            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
126            fixed
127    
128    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/lMatrix.R: new
131    
132            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
133    
134            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
135            * man/tcrossprod.Rd: ditto
136    
137    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
140            for exported functions
141            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
142            Remove partitioning algorithms for sparse matrix reordering.  The
143            copyright on the Metis code was problematic and the methods were
144            rarely used.
145            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
146            operations are now done entirely in CHOLMOD code.
147    
148    2006-09-06  Douglas Bates  <bates@R-project.org>
149    
150            * src/Mutils.h: Remove functions that are no longer used.
151    
152    2006-09-04  Douglas Bates  <bates@R-project.org>
153    
154            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
155            * src/DEPS.mkf: update
156    
157    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * created branches/Matrix-for-R-2.3.x;  on trunk: do
160            * DESCRIPTION (Version): 0.9975-0
161            (Depends): R (>= 2.4.0)
162    
163    2006-09-01  Douglas Bates  <bates@R-project.org>
164    
165            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
166    
167    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
170            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
171    
172            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
173    
174    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
177            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
178            * R/dsparseMatrix.R: ditto
179            * R/Csparse.R: ditto
180    
181    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/dMatrix.R (Compare): improve availability of "<", etc
184            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
185    
186    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
189            of a 0-index which was used as 1-index (..hmm)
190    
191            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
192    
193            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
194            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
195            (.is.diagonal): ditto
196    
197            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
198    
199            * R/Matrix.R (Matrix): also work for NA data
200    
201    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
204            in all cases.
205    
206    2006-08-27  Douglas Bates  <bates@R-project.org>
207    
208            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
209            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
210    
211    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
214            subclasses of "ddenseMatrix"
215            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
216            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
217            instead of half dozen specialized ones.
218    
219    2006-08-25  Douglas Bates  <bates@R-project.org>
220    
221            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
222            <tillard@cirad.fr> - ordering standard errors to match effects.
223    
224    2006-08-24  Douglas Bates  <bates@R-project.org>
225    
226            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
227            on R_ldl.
228            * R/lCholCMatrix.R,
229            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
230            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
231            * many files in ./R and ./src: Use more general version of
232            dup_mMatrix_as_dgeMatrix to simplify method definitions.
233            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
234            dtpMatrix, dspMatrix and dppMatrix conversions.
235    
236    
237    2006-08-23  Douglas Bates  <bates@R-project.org>
238    
239            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
240            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
241            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
242            dgeMatrix_crossprod (may need to do this in other places).
243            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
244            generic and method for dsCMatrix.  Use CHOLMOD for chol().
245    
246    2006-08-22  Douglas Bates  <bates@R-project.org>
247    
248            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
249            types of classed Matrices, matrices or numeric or logical vectors.
250            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
251            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
252            to Mutils.h (as an inline) and change name to Matrix_check_class;
253            fixes in as_cholmod_factor and chm_factor_to_SEXP.
254            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
255            dsCMatrix_matrix_solve.  Comment out vestigial functions.
256            * src/Csparse.c: use diag_P and uplo_P macros.
257    
258  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
259    
260          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
261          valgrind.          valgrind.
262            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
263            inverses.
264            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
265            -Wall warnings.
266            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
267            Use dup_mMatrix_as_dgeMatrix.
268    
269  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
270    

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