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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1565, Fri Sep 15 14:02:48 2006 UTC
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1    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/other-pkgs.R (graph): small extenion in "graph" checks.
4    
5            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
6            (Tsp2grNEL): other fixes needed
7    
8    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
11                    Matrices, since "lMatrix", also "lsparseM" can have NA
12            * R/ndenseMatrix.R, etc: new source files
13            * man/nsparseMatrix-classes.Rd, etc: new help files
14            * tests/: adaptions
15            * src/chm_common.c (chm_dense_to_SEXP): and others:
16                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
17            * src/Csparse.c, etc: dito
18    
19    2006-09-11  Douglas Bates  <bates@R-project.org>
20    
21            * src/Mutils.[ch],init.c inst/include/*.h: Move the
22            alloc_d**Matrix functions to the lme4 package.
23    
24    2006-09-09  Douglas Bates  <bates@R-project.org>
25    
26            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
27            fixed
28    
29    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lMatrix.R: new
32    
33            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
34    
35            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
36            * man/tcrossprod.Rd: dito
37    
38    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
41            for exported functions
42            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
43            Remove partitioning algorithms for sparse matrix reordering.  The
44            copyright on the Metis code was problematic and the methods were
45            rarely used.
46            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
47            operations are now done entirely in CHOLMOD code.
48    
49    2006-09-06  Douglas Bates  <bates@R-project.org>
50    
51            * src/Mutils.h: Remove functions that are no longer used.
52    
53    2006-09-04  Douglas Bates  <bates@R-project.org>
54    
55            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
56            * src/DEPS.mkf: update
57    
58    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * created branches/Matrix-for-R-2.3.x;  on trunk: do
61            * DESCRIPTION (Version): 0.9975-0
62            (Depends): R (>= 2.4.0)
63    
64    2006-09-01  Douglas Bates  <bates@R-project.org>
65    
66            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
67    
68    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
71            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
72    
73            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
78            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
79            * R/dsparseMatrix.R: dito
80            * R/Csparse.R: dito
81    
82    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Compare): improve availability of "<", etc
85            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
86    
87    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
90            of a 0-index which was used as 1-index (..hmm)
91    
92            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
93    
94            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
95            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
96            (.is.diagonal): dito
97    
98            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
99    
100            * R/Matrix.R (Matrix): also work for NA data
101    
102    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
105            in all cases.
106    
107    2006-08-27  Douglas Bates  <bates@R-project.org>
108    
109            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
110            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
111    
112    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
115            subclasses of "ddenseMatrix"
116            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
117            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
118            instead of half dozen specialized ones.
119    
120    2006-08-25  Douglas Bates  <bates@R-project.org>
121    
122            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
123            <tillard@cirad.fr> - ordering standard errors to match effects.
124    
125    2006-08-24  Douglas Bates  <bates@R-project.org>
126    
127            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
128            on R_ldl.
129            * R/lCholCMatrix.R,
130            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
131            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
132            * many files in ./R and ./src: Use more general version of
133            dup_mMatrix_as_dgeMatrix to simplify method definitions.
134            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
135            dtpMatrix, dspMatrix and dppMatrix conversions.
136    
137    
138    2006-08-23  Douglas Bates  <bates@R-project.org>
139    
140            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
141            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
142            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
143            dgeMatrix_crossprod (may need to do this in other places).
144            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
145            generic and method for dsCMatrix.  Use CHOLMOD for chol().
146    
147    2006-08-22  Douglas Bates  <bates@R-project.org>
148    
149            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
150            types of classed Matrices, matrices or numeric or logical vectors.
151            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
152            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
153            to Mutils.h (as an inline) and change name to Matrix_check_class;
154            fixes in as_cholmod_factor and chm_factor_to_SEXP.
155            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
156            dsCMatrix_matrix_solve.  Comment out vestigial functions.
157            * src/Csparse.c: use diag_P and uplo_P macros.
158    
159    2006-08-21  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
162            valgrind.
163            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
164            inverses.
165            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
166            -Wall warnings.
167            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
168            Use dup_mMatrix_as_dgeMatrix.
169    
170    2006-08-20  Douglas Bates  <bates@R-project.org>
171    
172            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
173            * tests/sparseQR.R: Added
174            * man/sparseQR-class.Rd: Document methods for qr.* generics
175            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
176    
177    2006-08-19  Douglas Bates  <bates@R-project.org>
178    
179            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
180            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
181            and qr.fitted.
182            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
183            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
184    
185    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
188            the base version has no "..." argument.
189    
190            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
191    
192            * R/Matrix.R: define and
193            * NAMESPACE: export as.numeric() and as.logical() methods.
194                    Let's hope these do not badly slow down something...
195            Finally export the zapsmall() method.
196    
197    2006-08-17  Douglas Bates  <bates@R-project.org>
198    
199            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
200            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
201            * src/dtCMatrix.c :Remove code that is no longer used
202            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
207            Csparse_to_logical and Csparse_symmetric_to_general.
208            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
209            coercion methods between CsparseMatrix and TsparseMatrix.
210    
211    2006-08-14  Douglas Bates  <bates@R-project.org>
212    
213            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
214            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
215            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
216            possible.
217    
218  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
219    
220          * 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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