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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1611, Mon Oct 2 17:07:16 2006 UTC
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1    2006-10-02  Douglas Bates  <bates@R-project.org>
2    
3            * tests/dg_Matrix.R: Simplify test taking into account new code.
4    
5    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
8    
9            * R/lsTMatrix.R: new files w/ missing methods
10            * R/nsTMatrix.R:  "  'for completeness'
11    
12            * tests/Class+Meth.R: a bit less 'not.ok.classes'
13    
14            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
15    
16    
17    2006-09-28  Douglas Bates  <bates@R-project.org>
18    
19            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
20            included.
21    
22            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
23            Export C-callable functions used in Zt_create in lme4.
24    
25    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.9975-1
28    
29            * tests/simple.R: less checks fail; using NA, found that our
30                    kronecker() is not base-compatible with NA's.
31    
32            * R/dMatrix.R: "Compare" method now implemented for all cases
33    
34            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
35    
36            * man/dtpMatrix-class.Rd: mention length of 'x' slot
37    
38            * src/dtpMatrix.c (dtpMatrix_validate): fix check
39            * src/dspMatrix.c (dspMatrix_validate): ditto
40    
41            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
42              including coercion to [nl]tTMatrix.
43    
44            * R/diagMatrix.R (show): print a header line as for other classes.
45    
46    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Makefile.win (SUBDIRS): fix typo
49    
50    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
53    
54    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
57            symmetric and y missing in R code using %*% (cholmod_aat doesn't
58            accept a symmetric matrix).
59            * tests/group-methods.R: Uncomment test of crossprod applied to
60            lsCMatrix objects.
61    
62    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (symmetricMatrix): add validity method (available
65            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
66    
67            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
68    
69            * tests/indexing.Rout.save:
70            * tests/indexing.R: additions, mainly for 'lsparse'
71    
72            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
73            case.
74    
75            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
76    
77    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
80                    as 'N' (1-letter - Ok?)
81    
82            * tests/group-methods.R: add test for logical + NAs
83    
84            * R/dMatrix.R ("Compare"): fix to work with NA's
85    
86            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
87    
88            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
89                    which is implemented.
90    
91    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/chm_common.c: coerce logical <-> double instead of
94            typecasting;  needed for "l" matrix handling in cholmod.
95    
96            * tests/other-pkgs.R (graph): small extension in "graph" checks.
97    
98            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
99            (Tsp2grNEL): other fixes needed
100    
101    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
104                    Matrices, since "lMatrix", also "lsparseM" can have NA
105            * R/ndenseMatrix.R, etc: new source files
106            * man/nsparseMatrix-classes.Rd, etc: new help files
107            * tests/: adaptions
108            * src/chm_common.c (chm_dense_to_SEXP): and others:
109                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
110            * src/Csparse.c, etc: ditto
111    
112    2006-09-11  Douglas Bates  <bates@R-project.org>
113    
114            * src/Mutils.[ch],init.c inst/include/*.h: Move the
115            alloc_d**Matrix functions to the lme4 package.
116    
117    2006-09-09  Douglas Bates  <bates@R-project.org>
118    
119            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
120            fixed
121    
122    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/lMatrix.R: new
125    
126            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
127    
128            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
129            * man/tcrossprod.Rd: ditto
130    
131    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
134            for exported functions
135            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
136            Remove partitioning algorithms for sparse matrix reordering.  The
137            copyright on the Metis code was problematic and the methods were
138            rarely used.
139            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
140            operations are now done entirely in CHOLMOD code.
141    
142    2006-09-06  Douglas Bates  <bates@R-project.org>
143    
144            * src/Mutils.h: Remove functions that are no longer used.
145    
146    2006-09-04  Douglas Bates  <bates@R-project.org>
147    
148            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
149            * src/DEPS.mkf: update
150    
151    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * created branches/Matrix-for-R-2.3.x;  on trunk: do
154            * DESCRIPTION (Version): 0.9975-0
155            (Depends): R (>= 2.4.0)
156    
157    2006-09-01  Douglas Bates  <bates@R-project.org>
158    
159            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
160    
161    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
164            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
165    
166            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
167    
168    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
171            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
172            * R/dsparseMatrix.R: ditto
173            * R/Csparse.R: ditto
174    
175    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/dMatrix.R (Compare): improve availability of "<", etc
178            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
179    
180    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
183            of a 0-index which was used as 1-index (..hmm)
184    
185            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
186    
187            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
188            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
189            (.is.diagonal): ditto
190    
191            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
192    
193            * R/Matrix.R (Matrix): also work for NA data
194    
195    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
198            in all cases.
199    
200    2006-08-27  Douglas Bates  <bates@R-project.org>
201    
202            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
203            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
204    
205    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
208            subclasses of "ddenseMatrix"
209            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
210            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
211            instead of half dozen specialized ones.
212    
213    2006-08-25  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
216            <tillard@cirad.fr> - ordering standard errors to match effects.
217    
218    2006-08-24  Douglas Bates  <bates@R-project.org>
219    
220            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
221            on R_ldl.
222            * R/lCholCMatrix.R,
223            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
224            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
225            * many files in ./R and ./src: Use more general version of
226            dup_mMatrix_as_dgeMatrix to simplify method definitions.
227            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
228            dtpMatrix, dspMatrix and dppMatrix conversions.
229    
230    
231    2006-08-23  Douglas Bates  <bates@R-project.org>
232    
233            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
234            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
235            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
236            dgeMatrix_crossprod (may need to do this in other places).
237            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
238            generic and method for dsCMatrix.  Use CHOLMOD for chol().
239    
240    2006-08-22  Douglas Bates  <bates@R-project.org>
241    
242            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
243            types of classed Matrices, matrices or numeric or logical vectors.
244            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
245            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
246            to Mutils.h (as an inline) and change name to Matrix_check_class;
247            fixes in as_cholmod_factor and chm_factor_to_SEXP.
248            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
249            dsCMatrix_matrix_solve.  Comment out vestigial functions.
250            * src/Csparse.c: use diag_P and uplo_P macros.
251    
252  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
253    
254          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
255          valgrind.          valgrind.
256            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
257            inverses.
258            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
259            -Wall warnings.
260            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
261            Use dup_mMatrix_as_dgeMatrix.
262    
263  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
264    

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