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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1599, Fri Sep 29 09:39:50 2006 UTC
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1    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/lsTMatrix.R: new files w/ missing methods
4            * R/nsTMatrix.R:  "  'for completeness'
5    
6            * tests/Class+Meth.R: a bit less 'not.ok.classes'
7    
8            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
9    
10    
11    2006-09-28  Douglas Bates  <bates@R-project.org>
12    
13            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
14            included.
15    
16            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
17            Export C-callable functions used in Zt_create in lme4.
18    
19    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * DESCRIPTION (Version): 0.9975-1
22    
23            * tests/simple.R: less checks fail; using NA, found that our
24                    kronecker() is not base-compatible with NA's.
25    
26            * R/dMatrix.R: "Compare" method now implemented for all cases
27    
28            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
29    
30            * man/dtpMatrix-class.Rd: mention length of 'x' slot
31    
32            * src/dtpMatrix.c (dtpMatrix_validate): fix check
33            * src/dspMatrix.c (dspMatrix_validate): ditto
34    
35            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
36              including coercion to [nl]tTMatrix.
37    
38            * R/diagMatrix.R (show): print a header line as for other classes.
39    
40    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * src/Makefile.win (SUBDIRS): fix typo
43    
44    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
47    
48    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
49    
50            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
51            symmetric and y missing in R code using %*% (cholmod_aat doesn't
52            accept a symmetric matrix).
53            * tests/group-methods.R: Uncomment test of crossprod applied to
54            lsCMatrix objects.
55    
56    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (symmetricMatrix): add validity method (available
59            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
60    
61            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
62    
63            * tests/indexing.Rout.save:
64            * tests/indexing.R: additions, mainly for 'lsparse'
65    
66            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
67            case.
68    
69            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
70    
71    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
74                    as 'N' (1-letter - Ok?)
75    
76            * tests/group-methods.R: add test for logical + NAs
77    
78            * R/dMatrix.R ("Compare"): fix to work with NA's
79    
80            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
81    
82            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
83                    which is implemented.
84    
85    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * src/chm_common.c: coerce logical <-> double instead of
88            typecasting;  needed for "l" matrix handling in cholmod.
89    
90            * tests/other-pkgs.R (graph): small extension in "graph" checks.
91    
92            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
93            (Tsp2grNEL): other fixes needed
94    
95    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
98                    Matrices, since "lMatrix", also "lsparseM" can have NA
99            * R/ndenseMatrix.R, etc: new source files
100            * man/nsparseMatrix-classes.Rd, etc: new help files
101            * tests/: adaptions
102            * src/chm_common.c (chm_dense_to_SEXP): and others:
103                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
104            * src/Csparse.c, etc: ditto
105    
106    2006-09-11  Douglas Bates  <bates@R-project.org>
107    
108            * src/Mutils.[ch],init.c inst/include/*.h: Move the
109            alloc_d**Matrix functions to the lme4 package.
110    
111    2006-09-09  Douglas Bates  <bates@R-project.org>
112    
113            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
114            fixed
115    
116    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/lMatrix.R: new
119    
120            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
121    
122            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
123            * man/tcrossprod.Rd: ditto
124    
125    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
126    
127            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
128            for exported functions
129            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
130            Remove partitioning algorithms for sparse matrix reordering.  The
131            copyright on the Metis code was problematic and the methods were
132            rarely used.
133            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
134            operations are now done entirely in CHOLMOD code.
135    
136    2006-09-06  Douglas Bates  <bates@R-project.org>
137    
138            * src/Mutils.h: Remove functions that are no longer used.
139    
140    2006-09-04  Douglas Bates  <bates@R-project.org>
141    
142            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
143            * src/DEPS.mkf: update
144    
145    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * created branches/Matrix-for-R-2.3.x;  on trunk: do
148            * DESCRIPTION (Version): 0.9975-0
149            (Depends): R (>= 2.4.0)
150    
151    2006-09-01  Douglas Bates  <bates@R-project.org>
152    
153            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
154    
155    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
158            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
159    
160            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
161    
162    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
165            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
166            * R/dsparseMatrix.R: ditto
167            * R/Csparse.R: ditto
168    
169    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/dMatrix.R (Compare): improve availability of "<", etc
172            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
173    
174    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
177            of a 0-index which was used as 1-index (..hmm)
178    
179            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
180    
181            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
182            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
183            (.is.diagonal): ditto
184    
185            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
186    
187            * R/Matrix.R (Matrix): also work for NA data
188    
189    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
192            in all cases.
193    
194    2006-08-27  Douglas Bates  <bates@R-project.org>
195    
196            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
197            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
198    
199    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
202            subclasses of "ddenseMatrix"
203            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
204            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
205            instead of half dozen specialized ones.
206    
207    2006-08-25  Douglas Bates  <bates@R-project.org>
208    
209            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
210            <tillard@cirad.fr> - ordering standard errors to match effects.
211    
212    2006-08-24  Douglas Bates  <bates@R-project.org>
213    
214            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
215            on R_ldl.
216            * R/lCholCMatrix.R,
217            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
218            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
219            * many files in ./R and ./src: Use more general version of
220            dup_mMatrix_as_dgeMatrix to simplify method definitions.
221            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
222            dtpMatrix, dspMatrix and dppMatrix conversions.
223    
224    
225    2006-08-23  Douglas Bates  <bates@R-project.org>
226    
227            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
228            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
229            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
230            dgeMatrix_crossprod (may need to do this in other places).
231            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
232            generic and method for dsCMatrix.  Use CHOLMOD for chol().
233    
234    2006-08-22  Douglas Bates  <bates@R-project.org>
235    
236            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
237            types of classed Matrices, matrices or numeric or logical vectors.
238            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
239            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
240            to Mutils.h (as an inline) and change name to Matrix_check_class;
241            fixes in as_cholmod_factor and chm_factor_to_SEXP.
242            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
243            dsCMatrix_matrix_solve.  Comment out vestigial functions.
244            * src/Csparse.c: use diag_P and uplo_P macros.
245    
246    2006-08-21  Douglas Bates  <bates@R-project.org>
247    
248            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
249            valgrind.
250            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
251            inverses.
252            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
253            -Wall warnings.
254            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
255            Use dup_mMatrix_as_dgeMatrix.
256    
257    2006-08-20  Douglas Bates  <bates@R-project.org>
258    
259            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
260            * tests/sparseQR.R: Added
261            * man/sparseQR-class.Rd: Document methods for qr.* generics
262            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
263    
264    2006-08-19  Douglas Bates  <bates@R-project.org>
265    
266            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
267            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
268            and qr.fitted.
269            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
270            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
271    
272    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
275            the base version has no "..." argument.
276    
277            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
278    
279            * R/Matrix.R: define and
280            * NAMESPACE: export as.numeric() and as.logical() methods.
281                    Let's hope these do not badly slow down something...
282            Finally export the zapsmall() method.
283    
284    2006-08-17  Douglas Bates  <bates@R-project.org>
285    
286            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
287            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
288            * src/dtCMatrix.c :Remove code that is no longer used
289            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
290    
291    2006-08-14  Douglas Bates  <bates@R-project.org>
292    
293            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
294            Csparse_to_logical and Csparse_symmetric_to_general.
295            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
296            coercion methods between CsparseMatrix and TsparseMatrix.
297    
298    2006-08-14  Douglas Bates  <bates@R-project.org>
299    
300            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
301            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
302            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
303            possible.
304    
305  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
306    
307          * 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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