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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1543, Sat Sep 9 13:44:15 2006 UTC
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1    2006-09-09  Douglas Bates  <bates@R-project.org>
2    
3            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
4            fixed
5    
6    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
9            for exported functions
10            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
11            Remove partitioning algorithms for sparse matrix reordering.  The
12            copyright on the Metis code was problematic and the methods were
13            rarely used.
14            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
15            operations are now done entirely in CHOLMOD code.
16    
17    2006-09-06  Douglas Bates  <bates@R-project.org>
18    
19            * src/Mutils.h: Remove functions that are no longer used.
20    
21    2006-09-04  Douglas Bates  <bates@R-project.org>
22    
23            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
24            * src/DEPS.mkf: update
25    
26    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * created branches/Matrix-for-R-2.3.x;  on trunk: do
29            * DESCRIPTION (Version): 0.9975-0
30            (Depends): R (>= 2.4.0)
31    
32    2006-09-01  Douglas Bates  <bates@R-project.org>
33    
34            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
35    
36    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
39            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
40    
41            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
42    
43    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
46            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
47            * R/dsparseMatrix.R: dito
48            * R/Csparse.R: dito
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dMatrix.R (Compare): improve availability of "<", etc
53            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
54    
55    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
58            of a 0-index which was used as 1-index (..hmm)
59    
60            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
61    
62            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
63            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
64            (.is.diagonal): dito
65    
66            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
67    
68            * R/Matrix.R (Matrix): also work for NA data
69    
70    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
73            in all cases.
74    
75    2006-08-27  Douglas Bates  <bates@R-project.org>
76    
77            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
78            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
79    
80    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
83            subclasses of "ddenseMatrix"
84            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
85            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
86            instead of half dozen specialized ones.
87    
88    2006-08-25  Douglas Bates  <bates@R-project.org>
89    
90            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
91            <tillard@cirad.fr> - ordering standard errors to match effects.
92    
93    2006-08-24  Douglas Bates  <bates@R-project.org>
94    
95            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
96            on R_ldl.
97            * R/lCholCMatrix.R,
98            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
99            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
100            * many files in ./R and ./src: Use more general version of
101            dup_mMatrix_as_dgeMatrix to simplify method definitions.
102            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
103            dtpMatrix, dspMatrix and dppMatrix conversions.
104    
105    
106    2006-08-23  Douglas Bates  <bates@R-project.org>
107    
108            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
109            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
110            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
111            dgeMatrix_crossprod (may need to do this in other places).
112            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
113            generic and method for dsCMatrix.  Use CHOLMOD for chol().
114    
115    2006-08-22  Douglas Bates  <bates@R-project.org>
116    
117            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
118            types of classed Matrices, matrices or numeric or logical vectors.
119            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
120            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
121            to Mutils.h (as an inline) and change name to Matrix_check_class;
122            fixes in as_cholmod_factor and chm_factor_to_SEXP.
123            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
124            dsCMatrix_matrix_solve.  Comment out vestigial functions.
125            * src/Csparse.c: use diag_P and uplo_P macros.
126    
127    2006-08-21  Douglas Bates  <bates@R-project.org>
128    
129            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
130            valgrind.
131            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
132            inverses.
133            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
134            -Wall warnings.
135            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
136            Use dup_mMatrix_as_dgeMatrix.
137    
138    2006-08-20  Douglas Bates  <bates@R-project.org>
139    
140            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
141            * tests/sparseQR.R: Added
142            * man/sparseQR-class.Rd: Document methods for qr.* generics
143            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
144    
145    2006-08-19  Douglas Bates  <bates@R-project.org>
146    
147            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
148            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
149            and qr.fitted.
150            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
151            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
152    
153    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
156            the base version has no "..." argument.
157    
158            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
159    
160            * R/Matrix.R: define and
161            * NAMESPACE: export as.numeric() and as.logical() methods.
162                    Let's hope these do not badly slow down something...
163            Finally export the zapsmall() method.
164    
165    2006-08-17  Douglas Bates  <bates@R-project.org>
166    
167            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
168            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
169            * src/dtCMatrix.c :Remove code that is no longer used
170            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
171    
172    2006-08-14  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
175            Csparse_to_logical and Csparse_symmetric_to_general.
176            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
177            coercion methods between CsparseMatrix and TsparseMatrix.
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
182            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
183            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
184            possible.
185    
186  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
187    
188          * 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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