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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1571, Sat Sep 16 21:03:12 2006 UTC
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1    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/group-methods.R: add test for logical + NAs
4    
5            * R/dMatrix.R ("Compare"): fix to work with NA's
6    
7            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
8    
9            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
10                    which is implemented.
11    
12    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/chm_common.c: coerce logical <-> double instead of
15            typecasting;  needed for "l" matrix handling in cholmod.
16    
17            * tests/other-pkgs.R (graph): small extension in "graph" checks.
18    
19            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
20            (Tsp2grNEL): other fixes needed
21    
22    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
25                    Matrices, since "lMatrix", also "lsparseM" can have NA
26            * R/ndenseMatrix.R, etc: new source files
27            * man/nsparseMatrix-classes.Rd, etc: new help files
28            * tests/: adaptions
29            * src/chm_common.c (chm_dense_to_SEXP): and others:
30                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
31            * src/Csparse.c, etc: dito
32    
33    2006-09-11  Douglas Bates  <bates@R-project.org>
34    
35            * src/Mutils.[ch],init.c inst/include/*.h: Move the
36            alloc_d**Matrix functions to the lme4 package.
37    
38    2006-09-09  Douglas Bates  <bates@R-project.org>
39    
40            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
41            fixed
42    
43    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/lMatrix.R: new
46    
47            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
48    
49            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
50            * man/tcrossprod.Rd: dito
51    
52    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
55            for exported functions
56            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
57            Remove partitioning algorithms for sparse matrix reordering.  The
58            copyright on the Metis code was problematic and the methods were
59            rarely used.
60            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
61            operations are now done entirely in CHOLMOD code.
62    
63    2006-09-06  Douglas Bates  <bates@R-project.org>
64    
65            * src/Mutils.h: Remove functions that are no longer used.
66    
67    2006-09-04  Douglas Bates  <bates@R-project.org>
68    
69            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
70            * src/DEPS.mkf: update
71    
72    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * created branches/Matrix-for-R-2.3.x;  on trunk: do
75            * DESCRIPTION (Version): 0.9975-0
76            (Depends): R (>= 2.4.0)
77    
78    2006-09-01  Douglas Bates  <bates@R-project.org>
79    
80            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
81    
82    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
85            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
86    
87            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
88    
89    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
92            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
93            * R/dsparseMatrix.R: dito
94            * R/Csparse.R: dito
95    
96    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R (Compare): improve availability of "<", etc
99            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
100    
101    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
104            of a 0-index which was used as 1-index (..hmm)
105    
106            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
107    
108            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
109            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
110            (.is.diagonal): dito
111    
112            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
113    
114            * R/Matrix.R (Matrix): also work for NA data
115    
116    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
119            in all cases.
120    
121    2006-08-27  Douglas Bates  <bates@R-project.org>
122    
123            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
124            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
125    
126    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
129            subclasses of "ddenseMatrix"
130            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
131            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
132            instead of half dozen specialized ones.
133    
134    2006-08-25  Douglas Bates  <bates@R-project.org>
135    
136            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
137            <tillard@cirad.fr> - ordering standard errors to match effects.
138    
139    2006-08-24  Douglas Bates  <bates@R-project.org>
140    
141            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
142            on R_ldl.
143            * R/lCholCMatrix.R,
144            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
145            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
146            * many files in ./R and ./src: Use more general version of
147            dup_mMatrix_as_dgeMatrix to simplify method definitions.
148            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
149            dtpMatrix, dspMatrix and dppMatrix conversions.
150    
151    
152    2006-08-23  Douglas Bates  <bates@R-project.org>
153    
154            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
155            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
156            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
157            dgeMatrix_crossprod (may need to do this in other places).
158            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
159            generic and method for dsCMatrix.  Use CHOLMOD for chol().
160    
161    2006-08-22  Douglas Bates  <bates@R-project.org>
162    
163            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
164            types of classed Matrices, matrices or numeric or logical vectors.
165            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
166            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
167            to Mutils.h (as an inline) and change name to Matrix_check_class;
168            fixes in as_cholmod_factor and chm_factor_to_SEXP.
169            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
170            dsCMatrix_matrix_solve.  Comment out vestigial functions.
171            * src/Csparse.c: use diag_P and uplo_P macros.
172    
173    2006-08-21  Douglas Bates  <bates@R-project.org>
174    
175            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
176            valgrind.
177            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
178            inverses.
179            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
180            -Wall warnings.
181            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
182            Use dup_mMatrix_as_dgeMatrix.
183    
184    2006-08-20  Douglas Bates  <bates@R-project.org>
185    
186            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
187            * tests/sparseQR.R: Added
188            * man/sparseQR-class.Rd: Document methods for qr.* generics
189            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
190    
191    2006-08-19  Douglas Bates  <bates@R-project.org>
192    
193            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
194            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
195            and qr.fitted.
196            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
197            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
198    
199    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
202            the base version has no "..." argument.
203    
204            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
205    
206            * R/Matrix.R: define and
207            * NAMESPACE: export as.numeric() and as.logical() methods.
208                    Let's hope these do not badly slow down something...
209            Finally export the zapsmall() method.
210    
211    2006-08-17  Douglas Bates  <bates@R-project.org>
212    
213            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
214            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
215            * src/dtCMatrix.c :Remove code that is no longer used
216            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
217    
218    2006-08-14  Douglas Bates  <bates@R-project.org>
219    
220            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
221            Csparse_to_logical and Csparse_symmetric_to_general.
222            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
223            coercion methods between CsparseMatrix and TsparseMatrix.
224    
225    2006-08-14  Douglas Bates  <bates@R-project.org>
226    
227            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
228            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
229            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
230            possible.
231    
232  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
233    
234          * 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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