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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1481, Sat Sep 2 16:43:22 2006 UTC
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1    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * created branches/Matrix-for-R-2.3.x;  on trunk: do
4            * DESCRIPTION (Version): 0.9975-0
5            (Depends): R (>= 2.4.0)
6    
7    2006-09-01  Douglas Bates  <bates@R-project.org>
8    
9            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
10    
11    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
14            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
15    
16            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
17    
18    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
21            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
22            * R/dsparseMatrix.R: dito
23            * R/Csparse.R: dito
24    
25    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/dMatrix.R (Compare): improve availability of "<", etc
28            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
29    
30    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
33            of a 0-index which was used as 1-index (..hmm)
34    
35            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
36    
37            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
38            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
39            (.is.diagonal): dito
40    
41            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
42    
43            * R/Matrix.R (Matrix): also work for NA data
44    
45    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
48            in all cases.
49    
50    2006-08-27  Douglas Bates  <bates@R-project.org>
51    
52            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
53            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
54    
55    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
58            subclasses of "ddenseMatrix"
59            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
60            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
61            instead of half dozen specialized ones.
62    
63    2006-08-25  Douglas Bates  <bates@R-project.org>
64    
65            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
66            <tillard@cirad.fr> - ordering standard errors to match effects.
67    
68    2006-08-24  Douglas Bates  <bates@R-project.org>
69    
70            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
71            on R_ldl.
72            * R/lCholCMatrix.R,
73            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
74            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
75            * many files in ./R and ./src: Use more general version of
76            dup_mMatrix_as_dgeMatrix to simplify method definitions.
77            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
78            dtpMatrix, dspMatrix and dppMatrix conversions.
79    
80    
81    2006-08-23  Douglas Bates  <bates@R-project.org>
82    
83            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
84            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
85            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
86            dgeMatrix_crossprod (may need to do this in other places).
87            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
88            generic and method for dsCMatrix.  Use CHOLMOD for chol().
89    
90    2006-08-22  Douglas Bates  <bates@R-project.org>
91    
92            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
93            types of classed Matrices, matrices or numeric or logical vectors.
94            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
95            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
96            to Mutils.h (as an inline) and change name to Matrix_check_class;
97            fixes in as_cholmod_factor and chm_factor_to_SEXP.
98            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
99            dsCMatrix_matrix_solve.  Comment out vestigial functions.
100            * src/Csparse.c: use diag_P and uplo_P macros.
101    
102    2006-08-21  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
105            valgrind.
106            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
107            inverses.
108            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
109            -Wall warnings.
110            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
111            Use dup_mMatrix_as_dgeMatrix.
112    
113    2006-08-20  Douglas Bates  <bates@R-project.org>
114    
115            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
116            * tests/sparseQR.R: Added
117            * man/sparseQR-class.Rd: Document methods for qr.* generics
118            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
119    
120    2006-08-19  Douglas Bates  <bates@R-project.org>
121    
122            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
123            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
124            and qr.fitted.
125            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
126            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
127    
128    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
131            the base version has no "..." argument.
132    
133            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
134    
135            * R/Matrix.R: define and
136            * NAMESPACE: export as.numeric() and as.logical() methods.
137                    Let's hope these do not badly slow down something...
138            Finally export the zapsmall() method.
139    
140    2006-08-17  Douglas Bates  <bates@R-project.org>
141    
142            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
143            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
144            * src/dtCMatrix.c :Remove code that is no longer used
145            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
146    
147    2006-08-14  Douglas Bates  <bates@R-project.org>
148    
149            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
150            Csparse_to_logical and Csparse_symmetric_to_general.
151            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
152            coercion methods between CsparseMatrix and TsparseMatrix.
153    
154    2006-08-14  Douglas Bates  <bates@R-project.org>
155    
156            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
157            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
158            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
159            possible.
160    
161  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
162    
163          * 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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