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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1618, Fri Oct 6 15:44:01 2006 UTC
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1    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-3
4    
5            * R/diagMatrix.R (bdiag): new function constructing block diagonal
6            (sparse) matrices.
7            * man/bdiag.Rd: docu + examples
8    
9            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
10            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
11    
12            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
13            that result is sparse or diagonal (and not dense).
14    
15            * man/Subassign-methods.Rd: fix examples
16    
17            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
18            should always return a sparse (and not sometimes a diagonal) matrix.
19    
20    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
23    
24    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * DESCRIPTION (Version): 0.9975-2
27    
28            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
29    
30    2006-10-02  Douglas Bates  <bates@R-project.org>
31    
32            * tests/dg_Matrix.R: Simplify test taking into account new code.
33    
34    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
37    
38            * R/lsTMatrix.R: new files w/ missing methods
39            * R/nsTMatrix.R:  "  'for completeness'
40    
41            * tests/Class+Meth.R: a bit less 'not.ok.classes'
42    
43            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
44    
45    
46    2006-09-28  Douglas Bates  <bates@R-project.org>
47    
48            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
49            included.
50    
51            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
52            Export C-callable functions used in Zt_create in lme4.
53    
54    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-1
57    
58            * tests/simple.R: less checks fail; using NA, found that our
59                    kronecker() is not base-compatible with NA's.
60    
61            * R/dMatrix.R: "Compare" method now implemented for all cases
62    
63            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
64    
65            * man/dtpMatrix-class.Rd: mention length of 'x' slot
66    
67            * src/dtpMatrix.c (dtpMatrix_validate): fix check
68            * src/dspMatrix.c (dspMatrix_validate): ditto
69    
70            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
71              including coercion to [nl]tTMatrix.
72    
73            * R/diagMatrix.R (show): print a header line as for other classes.
74    
75    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/Makefile.win (SUBDIRS): fix typo
78    
79    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
82    
83    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
86            symmetric and y missing in R code using %*% (cholmod_aat doesn't
87            accept a symmetric matrix).
88            * tests/group-methods.R: Uncomment test of crossprod applied to
89            lsCMatrix objects.
90    
91    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/AllClass.R (symmetricMatrix): add validity method (available
94            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
95    
96            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
97    
98            * tests/indexing.Rout.save:
99            * tests/indexing.R: additions, mainly for 'lsparse'
100    
101            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
102            case.
103    
104            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
105    
106    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
109                    as 'N' (1-letter - Ok?)
110    
111            * tests/group-methods.R: add test for logical + NAs
112    
113            * R/dMatrix.R ("Compare"): fix to work with NA's
114    
115            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
116    
117            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
118                    which is implemented.
119    
120    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/chm_common.c: coerce logical <-> double instead of
123            typecasting;  needed for "l" matrix handling in cholmod.
124    
125            * tests/other-pkgs.R (graph): small extension in "graph" checks.
126    
127            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
128            (Tsp2grNEL): other fixes needed
129    
130    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
133                    Matrices, since "lMatrix", also "lsparseM" can have NA
134            * R/ndenseMatrix.R, etc: new source files
135            * man/nsparseMatrix-classes.Rd, etc: new help files
136            * tests/: adaptions
137            * src/chm_common.c (chm_dense_to_SEXP): and others:
138                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
139            * src/Csparse.c, etc: ditto
140    
141    2006-09-11  Douglas Bates  <bates@R-project.org>
142    
143            * src/Mutils.[ch],init.c inst/include/*.h: Move the
144            alloc_d**Matrix functions to the lme4 package.
145    
146    2006-09-09  Douglas Bates  <bates@R-project.org>
147    
148            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
149            fixed
150    
151    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/lMatrix.R: new
154    
155            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
156    
157            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
158            * man/tcrossprod.Rd: ditto
159    
160    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
161    
162            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
163            for exported functions
164            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
165            Remove partitioning algorithms for sparse matrix reordering.  The
166            copyright on the Metis code was problematic and the methods were
167            rarely used.
168            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
169            operations are now done entirely in CHOLMOD code.
170    
171    2006-09-06  Douglas Bates  <bates@R-project.org>
172    
173            * src/Mutils.h: Remove functions that are no longer used.
174    
175    2006-09-04  Douglas Bates  <bates@R-project.org>
176    
177            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
178            * src/DEPS.mkf: update
179    
180    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * created branches/Matrix-for-R-2.3.x;  on trunk: do
183            * DESCRIPTION (Version): 0.9975-0
184            (Depends): R (>= 2.4.0)
185    
186    2006-09-01  Douglas Bates  <bates@R-project.org>
187    
188            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
189    
190    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
193            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
194    
195            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
196    
197    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
200            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
201            * R/dsparseMatrix.R: ditto
202            * R/Csparse.R: ditto
203    
204    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dMatrix.R (Compare): improve availability of "<", etc
207            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
208    
209    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
212            of a 0-index which was used as 1-index (..hmm)
213    
214            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
215    
216            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
217            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
218            (.is.diagonal): ditto
219    
220            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
221    
222            * R/Matrix.R (Matrix): also work for NA data
223    
224    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
227            in all cases.
228    
229    2006-08-27  Douglas Bates  <bates@R-project.org>
230    
231            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
232            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
233    
234    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
237            subclasses of "ddenseMatrix"
238            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
239            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
240            instead of half dozen specialized ones.
241    
242    2006-08-25  Douglas Bates  <bates@R-project.org>
243    
244            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
245            <tillard@cirad.fr> - ordering standard errors to match effects.
246    
247    2006-08-24  Douglas Bates  <bates@R-project.org>
248    
249            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
250            on R_ldl.
251            * R/lCholCMatrix.R,
252            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
253            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
254            * many files in ./R and ./src: Use more general version of
255            dup_mMatrix_as_dgeMatrix to simplify method definitions.
256            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
257            dtpMatrix, dspMatrix and dppMatrix conversions.
258    
259    
260    2006-08-23  Douglas Bates  <bates@R-project.org>
261    
262            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
263            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
264            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
265            dgeMatrix_crossprod (may need to do this in other places).
266            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
267            generic and method for dsCMatrix.  Use CHOLMOD for chol().
268    
269    2006-08-22  Douglas Bates  <bates@R-project.org>
270    
271            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
272            types of classed Matrices, matrices or numeric or logical vectors.
273            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
274            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
275            to Mutils.h (as an inline) and change name to Matrix_check_class;
276            fixes in as_cholmod_factor and chm_factor_to_SEXP.
277            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
278            dsCMatrix_matrix_solve.  Comment out vestigial functions.
279            * src/Csparse.c: use diag_P and uplo_P macros.
280    
281  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
282    
283          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
284          valgrind.          valgrind.
285            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
286            inverses.
287            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
288            -Wall warnings.
289            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
290            Use dup_mMatrix_as_dgeMatrix.
291    
292  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
293    

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