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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1517, Wed Sep 6 13:34:03 2006 UTC
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1    2006-09-06  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.h: Remove functions that are no longer used.
4    
5    2006-09-04  Douglas Bates  <bates@R-project.org>
6    
7            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
8            * src/DEPS.mkf: update
9    
10    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * created branches/Matrix-for-R-2.3.x;  on trunk: do
13            * DESCRIPTION (Version): 0.9975-0
14            (Depends): R (>= 2.4.0)
15    
16    2006-09-01  Douglas Bates  <bates@R-project.org>
17    
18            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
19    
20    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
23            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
24    
25            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
26    
27    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
30            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
31            * R/dsparseMatrix.R: dito
32            * R/Csparse.R: dito
33    
34    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/dMatrix.R (Compare): improve availability of "<", etc
37            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
38    
39    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
42            of a 0-index which was used as 1-index (..hmm)
43    
44            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
45    
46            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
47            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
48            (.is.diagonal): dito
49    
50            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
51    
52            * R/Matrix.R (Matrix): also work for NA data
53    
54    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
57            in all cases.
58    
59    2006-08-27  Douglas Bates  <bates@R-project.org>
60    
61            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
62            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
63    
64    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
67            subclasses of "ddenseMatrix"
68            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
69            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
70            instead of half dozen specialized ones.
71    
72    2006-08-25  Douglas Bates  <bates@R-project.org>
73    
74            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
75            <tillard@cirad.fr> - ordering standard errors to match effects.
76    
77    2006-08-24  Douglas Bates  <bates@R-project.org>
78    
79            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
80            on R_ldl.
81            * R/lCholCMatrix.R,
82            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
83            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
84            * many files in ./R and ./src: Use more general version of
85            dup_mMatrix_as_dgeMatrix to simplify method definitions.
86            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
87            dtpMatrix, dspMatrix and dppMatrix conversions.
88    
89    
90    2006-08-23  Douglas Bates  <bates@R-project.org>
91    
92            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
93            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
94            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
95            dgeMatrix_crossprod (may need to do this in other places).
96            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
97            generic and method for dsCMatrix.  Use CHOLMOD for chol().
98    
99    2006-08-22  Douglas Bates  <bates@R-project.org>
100    
101            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
102            types of classed Matrices, matrices or numeric or logical vectors.
103            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
104            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
105            to Mutils.h (as an inline) and change name to Matrix_check_class;
106            fixes in as_cholmod_factor and chm_factor_to_SEXP.
107            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
108            dsCMatrix_matrix_solve.  Comment out vestigial functions.
109            * src/Csparse.c: use diag_P and uplo_P macros.
110    
111    2006-08-21  Douglas Bates  <bates@R-project.org>
112    
113            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
114            valgrind.
115            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
116            inverses.
117            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
118            -Wall warnings.
119            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
120            Use dup_mMatrix_as_dgeMatrix.
121    
122    2006-08-20  Douglas Bates  <bates@R-project.org>
123    
124            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
125            * tests/sparseQR.R: Added
126            * man/sparseQR-class.Rd: Document methods for qr.* generics
127            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
128    
129    2006-08-19  Douglas Bates  <bates@R-project.org>
130    
131            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
132            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
133            and qr.fitted.
134            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
135            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
136    
137    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
140            the base version has no "..." argument.
141    
142            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
143    
144            * R/Matrix.R: define and
145            * NAMESPACE: export as.numeric() and as.logical() methods.
146                    Let's hope these do not badly slow down something...
147            Finally export the zapsmall() method.
148    
149    2006-08-17  Douglas Bates  <bates@R-project.org>
150    
151            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
152            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
153            * src/dtCMatrix.c :Remove code that is no longer used
154            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
155    
156    2006-08-14  Douglas Bates  <bates@R-project.org>
157    
158            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
159            Csparse_to_logical and Csparse_symmetric_to_general.
160            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
161            coercion methods between CsparseMatrix and TsparseMatrix.
162    
163    2006-08-14  Douglas Bates  <bates@R-project.org>
164    
165            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
166            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
167            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
168            possible.
169    
170  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
171    
172          * 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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