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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1575, Mon Sep 18 14:47:40 2006 UTC
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1    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (symmetricMatrix): add validity method (available
4            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
5    
6            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
7    
8            * tests/indexing.Rout.save:
9            * tests/indexing.R: additions, mainly for 'lsparse'
10    
11            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
12            case.
13    
14            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
15    
16    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
19                    as 'N' (1-letter - Ok?)
20    
21            * tests/group-methods.R: add test for logical + NAs
22    
23            * R/dMatrix.R ("Compare"): fix to work with NA's
24    
25            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
26    
27            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
28                    which is implemented.
29    
30    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/chm_common.c: coerce logical <-> double instead of
33            typecasting;  needed for "l" matrix handling in cholmod.
34    
35            * tests/other-pkgs.R (graph): small extension in "graph" checks.
36    
37            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
38            (Tsp2grNEL): other fixes needed
39    
40    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
43                    Matrices, since "lMatrix", also "lsparseM" can have NA
44            * R/ndenseMatrix.R, etc: new source files
45            * man/nsparseMatrix-classes.Rd, etc: new help files
46            * tests/: adaptions
47            * src/chm_common.c (chm_dense_to_SEXP): and others:
48                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
49            * src/Csparse.c, etc: dito
50    
51    2006-09-11  Douglas Bates  <bates@R-project.org>
52    
53            * src/Mutils.[ch],init.c inst/include/*.h: Move the
54            alloc_d**Matrix functions to the lme4 package.
55    
56    2006-09-09  Douglas Bates  <bates@R-project.org>
57    
58            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
59            fixed
60    
61    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/lMatrix.R: new
64    
65            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
66    
67            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
68            * man/tcrossprod.Rd: dito
69    
70    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
71    
72            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
73            for exported functions
74            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
75            Remove partitioning algorithms for sparse matrix reordering.  The
76            copyright on the Metis code was problematic and the methods were
77            rarely used.
78            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
79            operations are now done entirely in CHOLMOD code.
80    
81    2006-09-06  Douglas Bates  <bates@R-project.org>
82    
83            * src/Mutils.h: Remove functions that are no longer used.
84    
85    2006-09-04  Douglas Bates  <bates@R-project.org>
86    
87            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
88            * src/DEPS.mkf: update
89    
90    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * created branches/Matrix-for-R-2.3.x;  on trunk: do
93            * DESCRIPTION (Version): 0.9975-0
94            (Depends): R (>= 2.4.0)
95    
96    2006-09-01  Douglas Bates  <bates@R-project.org>
97    
98            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
99    
100    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
103            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
104    
105            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
106    
107    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
110            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
111            * R/dsparseMatrix.R: dito
112            * R/Csparse.R: dito
113    
114    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dMatrix.R (Compare): improve availability of "<", etc
117            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
118    
119    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
122            of a 0-index which was used as 1-index (..hmm)
123    
124            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
125    
126            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
127            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
128            (.is.diagonal): dito
129    
130            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
131    
132            * R/Matrix.R (Matrix): also work for NA data
133    
134    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
137            in all cases.
138    
139    2006-08-27  Douglas Bates  <bates@R-project.org>
140    
141            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
142            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
143    
144    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
147            subclasses of "ddenseMatrix"
148            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
149            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
150            instead of half dozen specialized ones.
151    
152    2006-08-25  Douglas Bates  <bates@R-project.org>
153    
154            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
155            <tillard@cirad.fr> - ordering standard errors to match effects.
156    
157    2006-08-24  Douglas Bates  <bates@R-project.org>
158    
159            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
160            on R_ldl.
161            * R/lCholCMatrix.R,
162            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
163            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
164            * many files in ./R and ./src: Use more general version of
165            dup_mMatrix_as_dgeMatrix to simplify method definitions.
166            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
167            dtpMatrix, dspMatrix and dppMatrix conversions.
168    
169    
170    2006-08-23  Douglas Bates  <bates@R-project.org>
171    
172            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
173            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
174            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
175            dgeMatrix_crossprod (may need to do this in other places).
176            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
177            generic and method for dsCMatrix.  Use CHOLMOD for chol().
178    
179    2006-08-22  Douglas Bates  <bates@R-project.org>
180    
181            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
182            types of classed Matrices, matrices or numeric or logical vectors.
183            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
184            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
185            to Mutils.h (as an inline) and change name to Matrix_check_class;
186            fixes in as_cholmod_factor and chm_factor_to_SEXP.
187            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
188            dsCMatrix_matrix_solve.  Comment out vestigial functions.
189            * src/Csparse.c: use diag_P and uplo_P macros.
190    
191    2006-08-21  Douglas Bates  <bates@R-project.org>
192    
193            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
194            valgrind.
195            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
196            inverses.
197            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
198            -Wall warnings.
199            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
200            Use dup_mMatrix_as_dgeMatrix.
201    
202    2006-08-20  Douglas Bates  <bates@R-project.org>
203    
204            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
205            * tests/sparseQR.R: Added
206            * man/sparseQR-class.Rd: Document methods for qr.* generics
207            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
208    
209    2006-08-19  Douglas Bates  <bates@R-project.org>
210    
211            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
212            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
213            and qr.fitted.
214            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
215            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
216    
217    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
220            the base version has no "..." argument.
221    
222            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
223    
224            * R/Matrix.R: define and
225            * NAMESPACE: export as.numeric() and as.logical() methods.
226                    Let's hope these do not badly slow down something...
227            Finally export the zapsmall() method.
228    
229    2006-08-17  Douglas Bates  <bates@R-project.org>
230    
231            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
232            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
233            * src/dtCMatrix.c :Remove code that is no longer used
234            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
235    
236    2006-08-14  Douglas Bates  <bates@R-project.org>
237    
238            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
239            Csparse_to_logical and Csparse_symmetric_to_general.
240            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
241            coercion methods between CsparseMatrix and TsparseMatrix.
242    
243    2006-08-14  Douglas Bates  <bates@R-project.org>
244    
245            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
246            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
247            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
248            possible.
249    
250  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
251    
252          * 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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