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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1647, Mon Oct 23 12:36:27 2006 UTC
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1    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-5 ready for release
4    
5    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
8    
9    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (corMatrix): add 'validity' check;
12                    comment out unused "LDL" class definition
13            * NAMESPACE: mention, but do not export "LDL" class
14            * R/corMatrix.R: new (simple), needed for R-devel with
15            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
16              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
17    
18    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
21            use Rprintf and R's error handling.
22    
23    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
26            * tests/matprod.R: add tests for the bug fixed.
27    
28    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
31            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
32    
33    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
36    
37    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.9975-3
40    
41            * R/diagMatrix.R (bdiag): new function constructing block diagonal
42            (sparse) matrices.
43            * man/bdiag.Rd: docu + examples
44    
45            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
46    
47            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
48            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
49    
50            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
51            that result is sparse or diagonal (and not dense).
52    
53            * man/Subassign-methods.Rd: fix examples
54    
55            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
56            should always return a sparse (and not sometimes a diagonal) matrix.
57    
58    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
61    
62    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
63    
64            * DESCRIPTION (Version): 0.9975-2
65    
66            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
67    
68    2006-10-02  Douglas Bates  <bates@R-project.org>
69    
70            * tests/dg_Matrix.R: Simplify test taking into account new code.
71    
72    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
75    
76            * R/lsTMatrix.R: new files w/ missing methods
77            * R/nsTMatrix.R:  "  'for completeness'
78    
79            * tests/Class+Meth.R: a bit less 'not.ok.classes'
80    
81            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
82    
83    
84    2006-09-28  Douglas Bates  <bates@R-project.org>
85    
86            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
87            included.
88    
89            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
90            Export C-callable functions used in Zt_create in lme4.
91    
92    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.9975-1
95    
96            * tests/simple.R: less checks fail; using NA, found that our
97                    kronecker() is not base-compatible with NA's.
98    
99            * R/dMatrix.R: "Compare" method now implemented for all cases
100    
101            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
102    
103            * man/dtpMatrix-class.Rd: mention length of 'x' slot
104    
105            * src/dtpMatrix.c (dtpMatrix_validate): fix check
106            * src/dspMatrix.c (dspMatrix_validate): ditto
107    
108            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
109              including coercion to [nl]tTMatrix.
110    
111            * R/diagMatrix.R (show): print a header line as for other classes.
112    
113    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/Makefile.win (SUBDIRS): fix typo
116    
117    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
120    
121    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
124            symmetric and y missing in R code using %*% (cholmod_aat doesn't
125            accept a symmetric matrix).
126            * tests/group-methods.R: Uncomment test of crossprod applied to
127            lsCMatrix objects.
128    
129    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/AllClass.R (symmetricMatrix): add validity method (available
132            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
133    
134            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
135    
136            * tests/indexing.Rout.save:
137            * tests/indexing.R: additions, mainly for 'lsparse'
138    
139            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
140            case.
141    
142            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
143    
144    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
147                    as 'N' (1-letter - Ok?)
148    
149            * tests/group-methods.R: add test for logical + NAs
150    
151            * R/dMatrix.R ("Compare"): fix to work with NA's
152    
153            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
154    
155            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
156                    which is implemented.
157    
158    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/chm_common.c: coerce logical <-> double instead of
161            typecasting;  needed for "l" matrix handling in cholmod.
162    
163            * tests/other-pkgs.R (graph): small extension in "graph" checks.
164    
165            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
166            (Tsp2grNEL): other fixes needed
167    
168    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
171                    Matrices, since "lMatrix", also "lsparseM" can have NA
172            * R/ndenseMatrix.R, etc: new source files
173            * man/nsparseMatrix-classes.Rd, etc: new help files
174            * tests/: adaptions
175            * src/chm_common.c (chm_dense_to_SEXP): and others:
176                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
177            * src/Csparse.c, etc: ditto
178    
179    2006-09-11  Douglas Bates  <bates@R-project.org>
180    
181            * src/Mutils.[ch],init.c inst/include/*.h: Move the
182            alloc_d**Matrix functions to the lme4 package.
183    
184    2006-09-09  Douglas Bates  <bates@R-project.org>
185    
186            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
187            fixed
188    
189    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/lMatrix.R: new
192    
193            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
194    
195            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
196            * man/tcrossprod.Rd: ditto
197    
198    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
201            for exported functions
202            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
203            Remove partitioning algorithms for sparse matrix reordering.  The
204            copyright on the Metis code was problematic and the methods were
205            rarely used.
206            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
207            operations are now done entirely in CHOLMOD code.
208    
209    2006-09-06  Douglas Bates  <bates@R-project.org>
210    
211            * src/Mutils.h: Remove functions that are no longer used.
212    
213    2006-09-04  Douglas Bates  <bates@R-project.org>
214    
215            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
216            * src/DEPS.mkf: update
217    
218    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * created branches/Matrix-for-R-2.3.x;  on trunk: do
221            * DESCRIPTION (Version): 0.9975-0
222            (Depends): R (>= 2.4.0)
223    
224    2006-09-01  Douglas Bates  <bates@R-project.org>
225    
226            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
227    
228    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
231            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
232    
233            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
234    
235    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
238            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
239            * R/dsparseMatrix.R: ditto
240            * R/Csparse.R: ditto
241    
242    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/dMatrix.R (Compare): improve availability of "<", etc
245            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
246    
247    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
250            of a 0-index which was used as 1-index (..hmm)
251    
252            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
253    
254            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
255            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
256            (.is.diagonal): ditto
257    
258            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
259    
260            * R/Matrix.R (Matrix): also work for NA data
261    
262    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
265            in all cases.
266    
267    2006-08-27  Douglas Bates  <bates@R-project.org>
268    
269            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
270            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
271    
272    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
275            subclasses of "ddenseMatrix"
276            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
277            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
278            instead of half dozen specialized ones.
279    
280    2006-08-25  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
283            <tillard@cirad.fr> - ordering standard errors to match effects.
284    
285    2006-08-24  Douglas Bates  <bates@R-project.org>
286    
287            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
288            on R_ldl.
289            * R/lCholCMatrix.R,
290            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
291            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
292            * many files in ./R and ./src: Use more general version of
293            dup_mMatrix_as_dgeMatrix to simplify method definitions.
294            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
295            dtpMatrix, dspMatrix and dppMatrix conversions.
296    
297    
298    2006-08-23  Douglas Bates  <bates@R-project.org>
299    
300            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
301            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
302            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
303            dgeMatrix_crossprod (may need to do this in other places).
304            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
305            generic and method for dsCMatrix.  Use CHOLMOD for chol().
306    
307    2006-08-22  Douglas Bates  <bates@R-project.org>
308    
309            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
310            types of classed Matrices, matrices or numeric or logical vectors.
311            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
312            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
313            to Mutils.h (as an inline) and change name to Matrix_check_class;
314            fixes in as_cholmod_factor and chm_factor_to_SEXP.
315            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
316            dsCMatrix_matrix_solve.  Comment out vestigial functions.
317            * src/Csparse.c: use diag_P and uplo_P macros.
318    
319    2006-08-21  Douglas Bates  <bates@R-project.org>
320    
321            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
322            valgrind.
323            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
324            inverses.
325            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
326            -Wall warnings.
327            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
328            Use dup_mMatrix_as_dgeMatrix.
329    
330    2006-08-20  Douglas Bates  <bates@R-project.org>
331    
332            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
333            * tests/sparseQR.R: Added
334            * man/sparseQR-class.Rd: Document methods for qr.* generics
335            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
336    
337    2006-08-19  Douglas Bates  <bates@R-project.org>
338    
339            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
340            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
341            and qr.fitted.
342            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
343            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
344    
345    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
348            the base version has no "..." argument.
349    
350            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
351    
352            * R/Matrix.R: define and
353            * NAMESPACE: export as.numeric() and as.logical() methods.
354                    Let's hope these do not badly slow down something...
355            Finally export the zapsmall() method.
356    
357    2006-08-17  Douglas Bates  <bates@R-project.org>
358    
359            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
360            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
361            * src/dtCMatrix.c :Remove code that is no longer used
362            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
363    
364    2006-08-14  Douglas Bates  <bates@R-project.org>
365    
366            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
367            Csparse_to_logical and Csparse_symmetric_to_general.
368            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
369            coercion methods between CsparseMatrix and TsparseMatrix.
370    
371    2006-08-14  Douglas Bates  <bates@R-project.org>
372    
373            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
374            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
375            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
376            possible.
377    
378  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
379    
380          * 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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