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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1475, Fri Sep 1 22:35:59 2006 UTC
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1    2006-09-01  Douglas Bates  <bates@R-project.org>
2    
3            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
4    
5    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
8            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
9    
10            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
11    
12    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
15            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
16            * R/dsparseMatrix.R: dito
17            * R/Csparse.R: dito
18    
19    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dMatrix.R (Compare): improve availability of "<", etc
22            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
23    
24    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
27            of a 0-index which was used as 1-index (..hmm)
28    
29            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
30    
31            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
32            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
33            (.is.diagonal): dito
34    
35            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
36    
37            * R/Matrix.R (Matrix): also work for NA data
38    
39    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
42            in all cases.
43    
44    2006-08-27  Douglas Bates  <bates@R-project.org>
45    
46            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
47            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
48    
49    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
52            subclasses of "ddenseMatrix"
53            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
54            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
55            instead of half dozen specialized ones.
56    
57    2006-08-25  Douglas Bates  <bates@R-project.org>
58    
59            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
60            <tillard@cirad.fr> - ordering standard errors to match effects.
61    
62    2006-08-24  Douglas Bates  <bates@R-project.org>
63    
64            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
65            on R_ldl.
66            * R/lCholCMatrix.R,
67            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
68            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
69            * many files in ./R and ./src: Use more general version of
70            dup_mMatrix_as_dgeMatrix to simplify method definitions.
71            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
72            dtpMatrix, dspMatrix and dppMatrix conversions.
73    
74    
75    2006-08-23  Douglas Bates  <bates@R-project.org>
76    
77            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
78            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
79            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
80            dgeMatrix_crossprod (may need to do this in other places).
81            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
82            generic and method for dsCMatrix.  Use CHOLMOD for chol().
83    
84    2006-08-22  Douglas Bates  <bates@R-project.org>
85    
86            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
87            types of classed Matrices, matrices or numeric or logical vectors.
88            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
89            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
90            to Mutils.h (as an inline) and change name to Matrix_check_class;
91            fixes in as_cholmod_factor and chm_factor_to_SEXP.
92            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
93            dsCMatrix_matrix_solve.  Comment out vestigial functions.
94            * src/Csparse.c: use diag_P and uplo_P macros.
95    
96    2006-08-21  Douglas Bates  <bates@R-project.org>
97    
98            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
99            valgrind.
100            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
101            inverses.
102            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
103            -Wall warnings.
104            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
105            Use dup_mMatrix_as_dgeMatrix.
106    
107    2006-08-20  Douglas Bates  <bates@R-project.org>
108    
109            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
110            * tests/sparseQR.R: Added
111            * man/sparseQR-class.Rd: Document methods for qr.* generics
112            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
113    
114    2006-08-19  Douglas Bates  <bates@R-project.org>
115    
116            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
117            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
118            and qr.fitted.
119            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
120            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
121    
122    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
125            the base version has no "..." argument.
126    
127            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
128    
129            * R/Matrix.R: define and
130            * NAMESPACE: export as.numeric() and as.logical() methods.
131                    Let's hope these do not badly slow down something...
132            Finally export the zapsmall() method.
133    
134    2006-08-17  Douglas Bates  <bates@R-project.org>
135    
136            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
137            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
138            * src/dtCMatrix.c :Remove code that is no longer used
139            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
140    
141    2006-08-14  Douglas Bates  <bates@R-project.org>
142    
143            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
144            Csparse_to_logical and Csparse_symmetric_to_general.
145            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
146            coercion methods between CsparseMatrix and TsparseMatrix.
147    
148    2006-08-14  Douglas Bates  <bates@R-project.org>
149    
150            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
151            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
152            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
153            possible.
154    
155  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
156    
157          * 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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