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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1657, Wed Nov 1 16:29:53 2006 UTC
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1    2006-11-01  Douglas Bates  <bates@r-project.org>
2    
3            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
4            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
5            <CsparseMatrix>) added
6    
7    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * tests/matprod.R: add a variation of Harri's example
10    
11            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
12            recursive infinitely.
13    
14            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
15    
16            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
17    
18    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
21            matrix if possible; test m+m == 2*m; now test dgRMatrix.
22            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
23            satisfy the above test.
24    
25    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
28    
29            * R/dgCMatrix.R: solve(a, b="missing") based on
30            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
31            RHS = NULL.
32    
33            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
34            add more (needed) [t]crossprod() methods.
35    
36            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
37    
38            * R/Auxiliaries.R (as_CspClass): cleanup
39            (drop0): internal utility for "Csparse_drop(*, 0)"
40            (.bail.out.2): encourage active feedback
41    
42    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dMatrix.R(Compare): new(), then slots [no validity check]
45    
46            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
47            non-valid or 'sorted' case).
48    
49            * R/dsparseMatrix.R: add "chol" method.
50            * R/ddenseMatrix.R: ditto
51    
52            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
53            * NAMESPACE (Ops)
54            * R/diagMatrix.R (diag2T): simple utility used "higher level"
55            coercion; deprecating direct lower level coercions.
56    
57            * R/*.R (seq): use seq_len() and seq_along() where possible.
58    
59    
60    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Version): 0.9975-5 ready for release
63    
64    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
67    
68    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllClass.R (corMatrix): add 'validity' check;
71                    comment out unused "LDL" class definition
72            * NAMESPACE: mention, but do not export "LDL" class
73            * R/corMatrix.R: new (simple), needed for R-devel with
74            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
75              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
76    
77    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
80            use Rprintf and R's error handling.
81    
82    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
85            * tests/matprod.R: add tests for the bug fixed.
86    
87    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
88    
89            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
90            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
91    
92    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
95    
96    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * DESCRIPTION (Version): 0.9975-3
99    
100            * R/diagMatrix.R (bdiag): new function constructing block diagonal
101            (sparse) matrices.
102            * man/bdiag.Rd: docu + examples
103    
104            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
105    
106            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
107            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
108    
109            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
110            that result is sparse or diagonal (and not dense).
111    
112            * man/Subassign-methods.Rd: fix examples
113    
114            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
115            should always return a sparse (and not sometimes a diagonal) matrix.
116    
117    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
120    
121    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * DESCRIPTION (Version): 0.9975-2
124    
125            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
126    
127    2006-10-02  Douglas Bates  <bates@R-project.org>
128    
129            * tests/dg_Matrix.R: Simplify test taking into account new code.
130    
131    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
134    
135            * R/lsTMatrix.R: new files w/ missing methods
136            * R/nsTMatrix.R:  "  'for completeness'
137    
138            * tests/Class+Meth.R: a bit less 'not.ok.classes'
139    
140            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
141    
142    
143    2006-09-28  Douglas Bates  <bates@R-project.org>
144    
145            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
146            included.
147    
148            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
149            Export C-callable functions used in Zt_create in lme4.
150    
151    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.9975-1
154    
155            * tests/simple.R: less checks fail; using NA, found that our
156                    kronecker() is not base-compatible with NA's.
157    
158            * R/dMatrix.R: "Compare" method now implemented for all cases
159    
160            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
161    
162            * man/dtpMatrix-class.Rd: mention length of 'x' slot
163    
164            * src/dtpMatrix.c (dtpMatrix_validate): fix check
165            * src/dspMatrix.c (dspMatrix_validate): ditto
166    
167            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
168              including coercion to [nl]tTMatrix.
169    
170            * R/diagMatrix.R (show): print a header line as for other classes.
171    
172    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * src/Makefile.win (SUBDIRS): fix typo
175    
176    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
179    
180    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
181    
182            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
183            symmetric and y missing in R code using %*% (cholmod_aat doesn't
184            accept a symmetric matrix).
185            * tests/group-methods.R: Uncomment test of crossprod applied to
186            lsCMatrix objects.
187    
188    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllClass.R (symmetricMatrix): add validity method (available
191            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
192    
193            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
194    
195            * tests/indexing.Rout.save:
196            * tests/indexing.R: additions, mainly for 'lsparse'
197    
198            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
199            case.
200    
201            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
202    
203    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
206                    as 'N' (1-letter - Ok?)
207    
208            * tests/group-methods.R: add test for logical + NAs
209    
210            * R/dMatrix.R ("Compare"): fix to work with NA's
211    
212            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
213    
214            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
215                    which is implemented.
216    
217    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/chm_common.c: coerce logical <-> double instead of
220            typecasting;  needed for "l" matrix handling in cholmod.
221    
222            * tests/other-pkgs.R (graph): small extension in "graph" checks.
223    
224            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
225            (Tsp2grNEL): other fixes needed
226    
227    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
230                    Matrices, since "lMatrix", also "lsparseM" can have NA
231            * R/ndenseMatrix.R, etc: new source files
232            * man/nsparseMatrix-classes.Rd, etc: new help files
233            * tests/: adaptions
234            * src/chm_common.c (chm_dense_to_SEXP): and others:
235                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
236            * src/Csparse.c, etc: ditto
237    
238    2006-09-11  Douglas Bates  <bates@R-project.org>
239    
240            * src/Mutils.[ch],init.c inst/include/*.h: Move the
241            alloc_d**Matrix functions to the lme4 package.
242    
243    2006-09-09  Douglas Bates  <bates@R-project.org>
244    
245            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
246            fixed
247    
248    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/lMatrix.R: new
251    
252            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
253    
254            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
255            * man/tcrossprod.Rd: ditto
256    
257    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
260            for exported functions
261            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
262            Remove partitioning algorithms for sparse matrix reordering.  The
263            copyright on the Metis code was problematic and the methods were
264            rarely used.
265            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
266            operations are now done entirely in CHOLMOD code.
267    
268    2006-09-06  Douglas Bates  <bates@R-project.org>
269    
270            * src/Mutils.h: Remove functions that are no longer used.
271    
272    2006-09-04  Douglas Bates  <bates@R-project.org>
273    
274            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
275            * src/DEPS.mkf: update
276    
277    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * created branches/Matrix-for-R-2.3.x;  on trunk: do
280            * DESCRIPTION (Version): 0.9975-0
281            (Depends): R (>= 2.4.0)
282    
283    2006-09-01  Douglas Bates  <bates@R-project.org>
284    
285            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
286    
287    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
290            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
291    
292            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
293    
294    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
297            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
298            * R/dsparseMatrix.R: ditto
299            * R/Csparse.R: ditto
300    
301    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/dMatrix.R (Compare): improve availability of "<", etc
304            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
305    
306    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
309            of a 0-index which was used as 1-index (..hmm)
310    
311            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
312    
313            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
314            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
315            (.is.diagonal): ditto
316    
317            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
318    
319            * R/Matrix.R (Matrix): also work for NA data
320    
321  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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