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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1619, Fri Oct 6 21:29:15 2006 UTC
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1    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-3
4    
5            * R/diagMatrix.R (bdiag): new function constructing block diagonal
6            (sparse) matrices.
7            * man/bdiag.Rd: docu + examples
8    
9            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
10    
11            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
12            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
13    
14            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
15            that result is sparse or diagonal (and not dense).
16    
17            * man/Subassign-methods.Rd: fix examples
18    
19            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
20            should always return a sparse (and not sometimes a diagonal) matrix.
21    
22    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
25    
26    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * DESCRIPTION (Version): 0.9975-2
29    
30            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
31    
32    2006-10-02  Douglas Bates  <bates@R-project.org>
33    
34            * tests/dg_Matrix.R: Simplify test taking into account new code.
35    
36    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
39    
40            * R/lsTMatrix.R: new files w/ missing methods
41            * R/nsTMatrix.R:  "  'for completeness'
42    
43            * tests/Class+Meth.R: a bit less 'not.ok.classes'
44    
45            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
46    
47    
48    2006-09-28  Douglas Bates  <bates@R-project.org>
49    
50            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
51            included.
52    
53            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
54            Export C-callable functions used in Zt_create in lme4.
55    
56    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): 0.9975-1
59    
60            * tests/simple.R: less checks fail; using NA, found that our
61                    kronecker() is not base-compatible with NA's.
62    
63            * R/dMatrix.R: "Compare" method now implemented for all cases
64    
65            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
66    
67            * man/dtpMatrix-class.Rd: mention length of 'x' slot
68    
69            * src/dtpMatrix.c (dtpMatrix_validate): fix check
70            * src/dspMatrix.c (dspMatrix_validate): ditto
71    
72            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
73              including coercion to [nl]tTMatrix.
74    
75            * R/diagMatrix.R (show): print a header line as for other classes.
76    
77    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/Makefile.win (SUBDIRS): fix typo
80    
81    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
84    
85    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
88            symmetric and y missing in R code using %*% (cholmod_aat doesn't
89            accept a symmetric matrix).
90            * tests/group-methods.R: Uncomment test of crossprod applied to
91            lsCMatrix objects.
92    
93    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/AllClass.R (symmetricMatrix): add validity method (available
96            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
97    
98            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
99    
100            * tests/indexing.Rout.save:
101            * tests/indexing.R: additions, mainly for 'lsparse'
102    
103            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
104            case.
105    
106            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
107    
108    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
111                    as 'N' (1-letter - Ok?)
112    
113            * tests/group-methods.R: add test for logical + NAs
114    
115            * R/dMatrix.R ("Compare"): fix to work with NA's
116    
117            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
118    
119            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
120                    which is implemented.
121    
122    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/chm_common.c: coerce logical <-> double instead of
125            typecasting;  needed for "l" matrix handling in cholmod.
126    
127            * tests/other-pkgs.R (graph): small extension in "graph" checks.
128    
129            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
130            (Tsp2grNEL): other fixes needed
131    
132    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
135                    Matrices, since "lMatrix", also "lsparseM" can have NA
136            * R/ndenseMatrix.R, etc: new source files
137            * man/nsparseMatrix-classes.Rd, etc: new help files
138            * tests/: adaptions
139            * src/chm_common.c (chm_dense_to_SEXP): and others:
140                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
141            * src/Csparse.c, etc: ditto
142    
143    2006-09-11  Douglas Bates  <bates@R-project.org>
144    
145            * src/Mutils.[ch],init.c inst/include/*.h: Move the
146            alloc_d**Matrix functions to the lme4 package.
147    
148    2006-09-09  Douglas Bates  <bates@R-project.org>
149    
150            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
151            fixed
152    
153    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/lMatrix.R: new
156    
157            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
158    
159            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
160            * man/tcrossprod.Rd: ditto
161    
162    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
165            for exported functions
166            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
167            Remove partitioning algorithms for sparse matrix reordering.  The
168            copyright on the Metis code was problematic and the methods were
169            rarely used.
170            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
171            operations are now done entirely in CHOLMOD code.
172    
173    2006-09-06  Douglas Bates  <bates@R-project.org>
174    
175            * src/Mutils.h: Remove functions that are no longer used.
176    
177    2006-09-04  Douglas Bates  <bates@R-project.org>
178    
179            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
180            * src/DEPS.mkf: update
181    
182    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * created branches/Matrix-for-R-2.3.x;  on trunk: do
185            * DESCRIPTION (Version): 0.9975-0
186            (Depends): R (>= 2.4.0)
187    
188    2006-09-01  Douglas Bates  <bates@R-project.org>
189    
190            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
191    
192    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
195            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
196    
197            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
198    
199    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
202            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
203            * R/dsparseMatrix.R: ditto
204            * R/Csparse.R: ditto
205    
206    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dMatrix.R (Compare): improve availability of "<", etc
209            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
210    
211    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
214            of a 0-index which was used as 1-index (..hmm)
215    
216            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
217    
218            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
219            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
220            (.is.diagonal): ditto
221    
222            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
223    
224            * R/Matrix.R (Matrix): also work for NA data
225    
226    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
229            in all cases.
230    
231    2006-08-27  Douglas Bates  <bates@R-project.org>
232    
233            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
234            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
235    
236    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
239            subclasses of "ddenseMatrix"
240            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
241            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
242            instead of half dozen specialized ones.
243    
244    2006-08-25  Douglas Bates  <bates@R-project.org>
245    
246            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
247            <tillard@cirad.fr> - ordering standard errors to match effects.
248    
249    2006-08-24  Douglas Bates  <bates@R-project.org>
250    
251            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
252            on R_ldl.
253            * R/lCholCMatrix.R,
254            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
255            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
256            * many files in ./R and ./src: Use more general version of
257            dup_mMatrix_as_dgeMatrix to simplify method definitions.
258            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
259            dtpMatrix, dspMatrix and dppMatrix conversions.
260    
261    
262    2006-08-23  Douglas Bates  <bates@R-project.org>
263    
264            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
265            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
266            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
267            dgeMatrix_crossprod (may need to do this in other places).
268            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
269            generic and method for dsCMatrix.  Use CHOLMOD for chol().
270    
271    2006-08-22  Douglas Bates  <bates@R-project.org>
272    
273            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
274            types of classed Matrices, matrices or numeric or logical vectors.
275            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
276            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
277            to Mutils.h (as an inline) and change name to Matrix_check_class;
278            fixes in as_cholmod_factor and chm_factor_to_SEXP.
279            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
280            dsCMatrix_matrix_solve.  Comment out vestigial functions.
281            * src/Csparse.c: use diag_P and uplo_P macros.
282    
283    2006-08-21  Douglas Bates  <bates@R-project.org>
284    
285            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
286            valgrind.
287            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
288            inverses.
289            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
290            -Wall warnings.
291            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
292            Use dup_mMatrix_as_dgeMatrix.
293    
294    2006-08-20  Douglas Bates  <bates@R-project.org>
295    
296            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
297            * tests/sparseQR.R: Added
298            * man/sparseQR-class.Rd: Document methods for qr.* generics
299            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
300    
301    2006-08-19  Douglas Bates  <bates@R-project.org>
302    
303            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
304            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
305            and qr.fitted.
306            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
307            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
308    
309    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
312            the base version has no "..." argument.
313    
314            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
315    
316            * R/Matrix.R: define and
317            * NAMESPACE: export as.numeric() and as.logical() methods.
318                    Let's hope these do not badly slow down something...
319            Finally export the zapsmall() method.
320    
321    2006-08-17  Douglas Bates  <bates@R-project.org>
322    
323            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
324            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
325            * src/dtCMatrix.c :Remove code that is no longer used
326            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
327    
328    2006-08-14  Douglas Bates  <bates@R-project.org>
329    
330            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
331            Csparse_to_logical and Csparse_symmetric_to_general.
332            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
333            coercion methods between CsparseMatrix and TsparseMatrix.
334    
335    2006-08-14  Douglas Bates  <bates@R-project.org>
336    
337            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
338            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
339            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
340            possible.
341    
342  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
343    
344          * 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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