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Diff of /pkg/ChangeLog

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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1472, Fri Sep 1 15:31:04 2006 UTC
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1    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
4            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
5    
6            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
7    
8    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
11            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
12            * R/dsparseMatrix.R: dito
13            * R/Csparse.R: dito
14    
15    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/dMatrix.R (Compare): improve availability of "<", etc
18            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
19    
20    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
23            of a 0-index which was used as 1-index (..hmm)
24    
25            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
26    
27            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
28            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
29            (.is.diagonal): dito
30    
31            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
32    
33            * R/Matrix.R (Matrix): also work for NA data
34    
35    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
38            in all cases.
39    
40    2006-08-27  Douglas Bates  <bates@R-project.org>
41    
42            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
43            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
44    
45    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
48            subclasses of "ddenseMatrix"
49            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
50            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
51            instead of half dozen specialized ones.
52    
53    2006-08-25  Douglas Bates  <bates@R-project.org>
54    
55            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
56            <tillard@cirad.fr> - ordering standard errors to match effects.
57    
58    2006-08-24  Douglas Bates  <bates@R-project.org>
59    
60            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
61            on R_ldl.
62            * R/lCholCMatrix.R,
63            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
64            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
65            * many files in ./R and ./src: Use more general version of
66            dup_mMatrix_as_dgeMatrix to simplify method definitions.
67            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
68            dtpMatrix, dspMatrix and dppMatrix conversions.
69    
70    
71    2006-08-23  Douglas Bates  <bates@R-project.org>
72    
73            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
74            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
75            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
76            dgeMatrix_crossprod (may need to do this in other places).
77            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
78            generic and method for dsCMatrix.  Use CHOLMOD for chol().
79    
80    2006-08-22  Douglas Bates  <bates@R-project.org>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
83            types of classed Matrices, matrices or numeric or logical vectors.
84            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
85            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
86            to Mutils.h (as an inline) and change name to Matrix_check_class;
87            fixes in as_cholmod_factor and chm_factor_to_SEXP.
88            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
89            dsCMatrix_matrix_solve.  Comment out vestigial functions.
90            * src/Csparse.c: use diag_P and uplo_P macros.
91    
92    2006-08-21  Douglas Bates  <bates@R-project.org>
93    
94            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
95            valgrind.
96            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
97            inverses.
98            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
99            -Wall warnings.
100            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
101            Use dup_mMatrix_as_dgeMatrix.
102    
103    2006-08-20  Douglas Bates  <bates@R-project.org>
104    
105            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
106            * tests/sparseQR.R: Added
107            * man/sparseQR-class.Rd: Document methods for qr.* generics
108            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
109    
110    2006-08-19  Douglas Bates  <bates@R-project.org>
111    
112            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
113            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
114            and qr.fitted.
115            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
116            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
117    
118    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
121            the base version has no "..." argument.
122    
123            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
124    
125            * R/Matrix.R: define and
126            * NAMESPACE: export as.numeric() and as.logical() methods.
127                    Let's hope these do not badly slow down something...
128            Finally export the zapsmall() method.
129    
130    2006-08-17  Douglas Bates  <bates@R-project.org>
131    
132            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
133            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
134            * src/dtCMatrix.c :Remove code that is no longer used
135            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
136    
137    2006-08-14  Douglas Bates  <bates@R-project.org>
138    
139            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
140            Csparse_to_logical and Csparse_symmetric_to_general.
141            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
142            coercion methods between CsparseMatrix and TsparseMatrix.
143    
144    2006-08-14  Douglas Bates  <bates@R-project.org>
145    
146            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
147            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
148            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
149            possible.
150    
151  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
152    
153          * 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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