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revision 1360, Tue Aug 8 17:29:03 2006 UTC revision 1548, Mon Sep 11 22:13:07 2006 UTC
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1    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
4                    Matrices, since "lMatrix", also "lsparseM" can have NA
5            * R/ndenseMatrix.R, etc: new source files
6            * man/nsparseMatrix-classes.Rd, etc: new help files
7            * tests/: adaptions
8            * src/chm_common.c (chm_dense_to_SEXP): and others:
9                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
10            * src/Csparse.c, etc: dito
11    
12    2006-09-11  Douglas Bates  <bates@R-project.org>
13    
14            * src/Mutils.[ch],init.c inst/include/*.h: Move the
15            alloc_d**Matrix functions to the lme4 package.
16    
17    2006-09-09  Douglas Bates  <bates@R-project.org>
18    
19            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
20            fixed
21    
22    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/lMatrix.R: new
25    
26            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
27    
28            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
29            * man/tcrossprod.Rd: dito
30    
31    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
34            for exported functions
35            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
36            Remove partitioning algorithms for sparse matrix reordering.  The
37            copyright on the Metis code was problematic and the methods were
38            rarely used.
39            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
40            operations are now done entirely in CHOLMOD code.
41    
42    2006-09-06  Douglas Bates  <bates@R-project.org>
43    
44            * src/Mutils.h: Remove functions that are no longer used.
45    
46    2006-09-04  Douglas Bates  <bates@R-project.org>
47    
48            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
49            * src/DEPS.mkf: update
50    
51    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * created branches/Matrix-for-R-2.3.x;  on trunk: do
54            * DESCRIPTION (Version): 0.9975-0
55            (Depends): R (>= 2.4.0)
56    
57    2006-09-01  Douglas Bates  <bates@R-project.org>
58    
59            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
60    
61    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
64            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
65    
66            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
67    
68    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
71            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
72            * R/dsparseMatrix.R: dito
73            * R/Csparse.R: dito
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R (Compare): improve availability of "<", etc
78            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
79    
80    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
83            of a 0-index which was used as 1-index (..hmm)
84    
85            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
86    
87            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
88            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
89            (.is.diagonal): dito
90    
91            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
92    
93            * R/Matrix.R (Matrix): also work for NA data
94    
95    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
98            in all cases.
99    
100    2006-08-27  Douglas Bates  <bates@R-project.org>
101    
102            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
103            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
104    
105    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
108            subclasses of "ddenseMatrix"
109            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
110            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
111            instead of half dozen specialized ones.
112    
113    2006-08-25  Douglas Bates  <bates@R-project.org>
114    
115            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
116            <tillard@cirad.fr> - ordering standard errors to match effects.
117    
118    2006-08-24  Douglas Bates  <bates@R-project.org>
119    
120            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
121            on R_ldl.
122            * R/lCholCMatrix.R,
123            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
124            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
125            * many files in ./R and ./src: Use more general version of
126            dup_mMatrix_as_dgeMatrix to simplify method definitions.
127            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
128            dtpMatrix, dspMatrix and dppMatrix conversions.
129    
130    
131    2006-08-23  Douglas Bates  <bates@R-project.org>
132    
133            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
134            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
135            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
136            dgeMatrix_crossprod (may need to do this in other places).
137            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
138            generic and method for dsCMatrix.  Use CHOLMOD for chol().
139    
140    2006-08-22  Douglas Bates  <bates@R-project.org>
141    
142            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
143            types of classed Matrices, matrices or numeric or logical vectors.
144            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
145            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
146            to Mutils.h (as an inline) and change name to Matrix_check_class;
147            fixes in as_cholmod_factor and chm_factor_to_SEXP.
148            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
149            dsCMatrix_matrix_solve.  Comment out vestigial functions.
150            * src/Csparse.c: use diag_P and uplo_P macros.
151    
152    2006-08-21  Douglas Bates  <bates@R-project.org>
153    
154            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
155            valgrind.
156            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
157            inverses.
158            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
159            -Wall warnings.
160            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
161            Use dup_mMatrix_as_dgeMatrix.
162    
163    2006-08-20  Douglas Bates  <bates@R-project.org>
164    
165            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
166            * tests/sparseQR.R: Added
167            * man/sparseQR-class.Rd: Document methods for qr.* generics
168            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
169    
170    2006-08-19  Douglas Bates  <bates@R-project.org>
171    
172            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
173            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
174            and qr.fitted.
175            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
176            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
177    
178    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
181            the base version has no "..." argument.
182    
183            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
184    
185            * R/Matrix.R: define and
186            * NAMESPACE: export as.numeric() and as.logical() methods.
187                    Let's hope these do not badly slow down something...
188            Finally export the zapsmall() method.
189    
190    2006-08-17  Douglas Bates  <bates@R-project.org>
191    
192            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
193            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
194            * src/dtCMatrix.c :Remove code that is no longer used
195            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
196    
197    2006-08-14  Douglas Bates  <bates@R-project.org>
198    
199            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
200            Csparse_to_logical and Csparse_symmetric_to_general.
201            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
202            coercion methods between CsparseMatrix and TsparseMatrix.
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
207            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
208            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
209            possible.
210    
211    2006-08-12  Douglas Bates  <bates@R-project.org>
212    
213            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
214              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
215              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
216              generalize conversions between TsparseMatrix, CsparseMatrix,
217              denseMatrix and matrix.  Preserve triangularity property and
218              propagate Dimnames in the easy cases.
219    
220    2006-08-10  Douglas Bates  <bates@R-project.org>
221    
222            * src/lmer.c: adjust checks in glmer_init for S4SXP
223            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
224            before S4SXP but for the wrong reasons.
225    
226  2006-08-08  Douglas Bates  <bates@R-project.org>  2006-08-08  Douglas Bates  <bates@R-project.org>
227    
228          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.

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