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revision 1373, Mon Aug 14 21:15:38 2006 UTC revision 1642, Fri Oct 20 21:08:28 2006 UTC
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1    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R (corMatrix): add 'validity' check;
4                    comment out unused "LDL" class definition
5            * NAMESPACE: mention, but do not export "LDL" class
6            * R/corMatrix.R: new (simple), needed for R-devel with
7            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
8              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
9    
10    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
13            use Rprintf and R's error handling.
14    
15    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
18            * tests/matprod.R: add tests for the bug fixed.
19    
20    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
23            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
24    
25    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
26    
27            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
28    
29    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * DESCRIPTION (Version): 0.9975-3
32    
33            * R/diagMatrix.R (bdiag): new function constructing block diagonal
34            (sparse) matrices.
35            * man/bdiag.Rd: docu + examples
36    
37            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
38    
39            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
40            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
41    
42            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
43            that result is sparse or diagonal (and not dense).
44    
45            * man/Subassign-methods.Rd: fix examples
46    
47            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
48            should always return a sparse (and not sometimes a diagonal) matrix.
49    
50    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
53    
54    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * DESCRIPTION (Version): 0.9975-2
57    
58            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
59    
60    2006-10-02  Douglas Bates  <bates@R-project.org>
61    
62            * tests/dg_Matrix.R: Simplify test taking into account new code.
63    
64    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
67    
68            * R/lsTMatrix.R: new files w/ missing methods
69            * R/nsTMatrix.R:  "  'for completeness'
70    
71            * tests/Class+Meth.R: a bit less 'not.ok.classes'
72    
73            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
74    
75    
76    2006-09-28  Douglas Bates  <bates@R-project.org>
77    
78            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
79            included.
80    
81            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
82            Export C-callable functions used in Zt_create in lme4.
83    
84    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * DESCRIPTION (Version): 0.9975-1
87    
88            * tests/simple.R: less checks fail; using NA, found that our
89                    kronecker() is not base-compatible with NA's.
90    
91            * R/dMatrix.R: "Compare" method now implemented for all cases
92    
93            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
94    
95            * man/dtpMatrix-class.Rd: mention length of 'x' slot
96    
97            * src/dtpMatrix.c (dtpMatrix_validate): fix check
98            * src/dspMatrix.c (dspMatrix_validate): ditto
99    
100            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
101              including coercion to [nl]tTMatrix.
102    
103            * R/diagMatrix.R (show): print a header line as for other classes.
104    
105    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Makefile.win (SUBDIRS): fix typo
108    
109    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
112    
113    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
116            symmetric and y missing in R code using %*% (cholmod_aat doesn't
117            accept a symmetric matrix).
118            * tests/group-methods.R: Uncomment test of crossprod applied to
119            lsCMatrix objects.
120    
121    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/AllClass.R (symmetricMatrix): add validity method (available
124            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
125    
126            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
127    
128            * tests/indexing.Rout.save:
129            * tests/indexing.R: additions, mainly for 'lsparse'
130    
131            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
132            case.
133    
134            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
135    
136    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
139                    as 'N' (1-letter - Ok?)
140    
141            * tests/group-methods.R: add test for logical + NAs
142    
143            * R/dMatrix.R ("Compare"): fix to work with NA's
144    
145            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
146    
147            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
148                    which is implemented.
149    
150    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/chm_common.c: coerce logical <-> double instead of
153            typecasting;  needed for "l" matrix handling in cholmod.
154    
155            * tests/other-pkgs.R (graph): small extension in "graph" checks.
156    
157            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
158            (Tsp2grNEL): other fixes needed
159    
160    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
163                    Matrices, since "lMatrix", also "lsparseM" can have NA
164            * R/ndenseMatrix.R, etc: new source files
165            * man/nsparseMatrix-classes.Rd, etc: new help files
166            * tests/: adaptions
167            * src/chm_common.c (chm_dense_to_SEXP): and others:
168                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
169            * src/Csparse.c, etc: ditto
170    
171    2006-09-11  Douglas Bates  <bates@R-project.org>
172    
173            * src/Mutils.[ch],init.c inst/include/*.h: Move the
174            alloc_d**Matrix functions to the lme4 package.
175    
176    2006-09-09  Douglas Bates  <bates@R-project.org>
177    
178            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
179            fixed
180    
181    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/lMatrix.R: new
184    
185            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
186    
187            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
188            * man/tcrossprod.Rd: ditto
189    
190    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
191    
192            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
193            for exported functions
194            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
195            Remove partitioning algorithms for sparse matrix reordering.  The
196            copyright on the Metis code was problematic and the methods were
197            rarely used.
198            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
199            operations are now done entirely in CHOLMOD code.
200    
201    2006-09-06  Douglas Bates  <bates@R-project.org>
202    
203            * src/Mutils.h: Remove functions that are no longer used.
204    
205    2006-09-04  Douglas Bates  <bates@R-project.org>
206    
207            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
208            * src/DEPS.mkf: update
209    
210    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * created branches/Matrix-for-R-2.3.x;  on trunk: do
213            * DESCRIPTION (Version): 0.9975-0
214            (Depends): R (>= 2.4.0)
215    
216    2006-09-01  Douglas Bates  <bates@R-project.org>
217    
218            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
219    
220    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
223            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
224    
225            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
226    
227    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
230            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
231            * R/dsparseMatrix.R: ditto
232            * R/Csparse.R: ditto
233    
234    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dMatrix.R (Compare): improve availability of "<", etc
237            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
238    
239    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
242            of a 0-index which was used as 1-index (..hmm)
243    
244            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
245    
246            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
247            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
248            (.is.diagonal): ditto
249    
250            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
251    
252            * R/Matrix.R (Matrix): also work for NA data
253    
254    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
257            in all cases.
258    
259    2006-08-27  Douglas Bates  <bates@R-project.org>
260    
261            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
262            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
263    
264    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
267            subclasses of "ddenseMatrix"
268            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
269            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
270            instead of half dozen specialized ones.
271    
272    2006-08-25  Douglas Bates  <bates@R-project.org>
273    
274            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
275            <tillard@cirad.fr> - ordering standard errors to match effects.
276    
277    2006-08-24  Douglas Bates  <bates@R-project.org>
278    
279            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
280            on R_ldl.
281            * R/lCholCMatrix.R,
282            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
283            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
284            * many files in ./R and ./src: Use more general version of
285            dup_mMatrix_as_dgeMatrix to simplify method definitions.
286            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
287            dtpMatrix, dspMatrix and dppMatrix conversions.
288    
289    
290    2006-08-23  Douglas Bates  <bates@R-project.org>
291    
292            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
293            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
294            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
295            dgeMatrix_crossprod (may need to do this in other places).
296            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
297            generic and method for dsCMatrix.  Use CHOLMOD for chol().
298    
299    2006-08-22  Douglas Bates  <bates@R-project.org>
300    
301            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
302            types of classed Matrices, matrices or numeric or logical vectors.
303            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
304            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
305            to Mutils.h (as an inline) and change name to Matrix_check_class;
306            fixes in as_cholmod_factor and chm_factor_to_SEXP.
307            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
308            dsCMatrix_matrix_solve.  Comment out vestigial functions.
309            * src/Csparse.c: use diag_P and uplo_P macros.
310    
311    2006-08-21  Douglas Bates  <bates@R-project.org>
312    
313            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
314            valgrind.
315            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
316            inverses.
317            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
318            -Wall warnings.
319            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
320            Use dup_mMatrix_as_dgeMatrix.
321    
322    2006-08-20  Douglas Bates  <bates@R-project.org>
323    
324            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
325            * tests/sparseQR.R: Added
326            * man/sparseQR-class.Rd: Document methods for qr.* generics
327            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
328    
329    2006-08-19  Douglas Bates  <bates@R-project.org>
330    
331            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
332            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
333            and qr.fitted.
334            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
335            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
336    
337    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
340            the base version has no "..." argument.
341    
342            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
343    
344            * R/Matrix.R: define and
345            * NAMESPACE: export as.numeric() and as.logical() methods.
346                    Let's hope these do not badly slow down something...
347            Finally export the zapsmall() method.
348    
349    2006-08-17  Douglas Bates  <bates@R-project.org>
350    
351            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
352            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
353            * src/dtCMatrix.c :Remove code that is no longer used
354            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
355    
356  2006-08-14  Douglas Bates  <bates@R-project.org>  2006-08-14  Douglas Bates  <bates@R-project.org>
357    
358          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities

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