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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1546, Mon Sep 11 14:49:05 2006 UTC
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1    2006-09-11  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.[ch],init.c inst/include/*.h: Move the
4            alloc_d**Matrix functions to the lme4 package.
5    
6    2006-09-09  Douglas Bates  <bates@R-project.org>
7    
8            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
9            fixed
10    
11    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
14    
15            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
16            * man/tcrossprod.Rd: dito
17    
18    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
21            for exported functions
22            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
23            Remove partitioning algorithms for sparse matrix reordering.  The
24            copyright on the Metis code was problematic and the methods were
25            rarely used.
26            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
27            operations are now done entirely in CHOLMOD code.
28    
29    2006-09-06  Douglas Bates  <bates@R-project.org>
30    
31            * src/Mutils.h: Remove functions that are no longer used.
32    
33    2006-09-04  Douglas Bates  <bates@R-project.org>
34    
35            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
36            * src/DEPS.mkf: update
37    
38    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * created branches/Matrix-for-R-2.3.x;  on trunk: do
41            * DESCRIPTION (Version): 0.9975-0
42            (Depends): R (>= 2.4.0)
43    
44    2006-09-01  Douglas Bates  <bates@R-project.org>
45    
46            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
47    
48    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
51            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
52    
53            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
54    
55    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
58            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
59            * R/dsparseMatrix.R: dito
60            * R/Csparse.R: dito
61    
62    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dMatrix.R (Compare): improve availability of "<", etc
65            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
66    
67    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
70            of a 0-index which was used as 1-index (..hmm)
71    
72            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
73    
74            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
75            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
76            (.is.diagonal): dito
77    
78            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
79    
80            * R/Matrix.R (Matrix): also work for NA data
81    
82    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
85            in all cases.
86    
87    2006-08-27  Douglas Bates  <bates@R-project.org>
88    
89            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
90            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
91    
92    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
95            subclasses of "ddenseMatrix"
96            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
97            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
98            instead of half dozen specialized ones.
99    
100    2006-08-25  Douglas Bates  <bates@R-project.org>
101    
102            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
103            <tillard@cirad.fr> - ordering standard errors to match effects.
104    
105    2006-08-24  Douglas Bates  <bates@R-project.org>
106    
107            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
108            on R_ldl.
109            * R/lCholCMatrix.R,
110            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
111            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
112            * many files in ./R and ./src: Use more general version of
113            dup_mMatrix_as_dgeMatrix to simplify method definitions.
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
115            dtpMatrix, dspMatrix and dppMatrix conversions.
116    
117    
118    2006-08-23  Douglas Bates  <bates@R-project.org>
119    
120            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
121            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
122            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
123            dgeMatrix_crossprod (may need to do this in other places).
124            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
125            generic and method for dsCMatrix.  Use CHOLMOD for chol().
126    
127    2006-08-22  Douglas Bates  <bates@R-project.org>
128    
129            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
130            types of classed Matrices, matrices or numeric or logical vectors.
131            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
132            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
133            to Mutils.h (as an inline) and change name to Matrix_check_class;
134            fixes in as_cholmod_factor and chm_factor_to_SEXP.
135            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
136            dsCMatrix_matrix_solve.  Comment out vestigial functions.
137            * src/Csparse.c: use diag_P and uplo_P macros.
138    
139    2006-08-21  Douglas Bates  <bates@R-project.org>
140    
141            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
142            valgrind.
143            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
144            inverses.
145            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
146            -Wall warnings.
147            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
148            Use dup_mMatrix_as_dgeMatrix.
149    
150    2006-08-20  Douglas Bates  <bates@R-project.org>
151    
152            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
153            * tests/sparseQR.R: Added
154            * man/sparseQR-class.Rd: Document methods for qr.* generics
155            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
156    
157    2006-08-19  Douglas Bates  <bates@R-project.org>
158    
159            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
160            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
161            and qr.fitted.
162            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
163            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
164    
165    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
168            the base version has no "..." argument.
169    
170            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
171    
172            * R/Matrix.R: define and
173            * NAMESPACE: export as.numeric() and as.logical() methods.
174                    Let's hope these do not badly slow down something...
175            Finally export the zapsmall() method.
176    
177    2006-08-17  Douglas Bates  <bates@R-project.org>
178    
179            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
180            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
181            * src/dtCMatrix.c :Remove code that is no longer used
182            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
183    
184    2006-08-14  Douglas Bates  <bates@R-project.org>
185    
186            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
187            Csparse_to_logical and Csparse_symmetric_to_general.
188            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
189            coercion methods between CsparseMatrix and TsparseMatrix.
190    
191    2006-08-14  Douglas Bates  <bates@R-project.org>
192    
193            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
194            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
195            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
196            possible.
197    
198  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
199    
200          * 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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