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revision 1389, Fri Aug 18 13:53:33 2006 UTC revision 1646, Sun Oct 22 22:42:40 2006 UTC
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1    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
4    
5    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/AllClass.R (corMatrix): add 'validity' check;
8                    comment out unused "LDL" class definition
9            * NAMESPACE: mention, but do not export "LDL" class
10            * R/corMatrix.R: new (simple), needed for R-devel with
11            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
12              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
13    
14    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
15    
16            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
17            use Rprintf and R's error handling.
18    
19    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
22            * tests/matprod.R: add tests for the bug fixed.
23    
24    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
27            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
28    
29    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
30    
31            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
32    
33    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * DESCRIPTION (Version): 0.9975-3
36    
37            * R/diagMatrix.R (bdiag): new function constructing block diagonal
38            (sparse) matrices.
39            * man/bdiag.Rd: docu + examples
40    
41            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
42    
43            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
44            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
45    
46            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
47            that result is sparse or diagonal (and not dense).
48    
49            * man/Subassign-methods.Rd: fix examples
50    
51            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
52            should always return a sparse (and not sometimes a diagonal) matrix.
53    
54    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
57    
58    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * DESCRIPTION (Version): 0.9975-2
61    
62            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
63    
64    2006-10-02  Douglas Bates  <bates@R-project.org>
65    
66            * tests/dg_Matrix.R: Simplify test taking into account new code.
67    
68    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
71    
72            * R/lsTMatrix.R: new files w/ missing methods
73            * R/nsTMatrix.R:  "  'for completeness'
74    
75            * tests/Class+Meth.R: a bit less 'not.ok.classes'
76    
77            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
78    
79    
80    2006-09-28  Douglas Bates  <bates@R-project.org>
81    
82            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
83            included.
84    
85            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
86            Export C-callable functions used in Zt_create in lme4.
87    
88    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * DESCRIPTION (Version): 0.9975-1
91    
92            * tests/simple.R: less checks fail; using NA, found that our
93                    kronecker() is not base-compatible with NA's.
94    
95            * R/dMatrix.R: "Compare" method now implemented for all cases
96    
97            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
98    
99            * man/dtpMatrix-class.Rd: mention length of 'x' slot
100    
101            * src/dtpMatrix.c (dtpMatrix_validate): fix check
102            * src/dspMatrix.c (dspMatrix_validate): ditto
103    
104            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
105              including coercion to [nl]tTMatrix.
106    
107            * R/diagMatrix.R (show): print a header line as for other classes.
108    
109    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/Makefile.win (SUBDIRS): fix typo
112    
113    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
116    
117    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
120            symmetric and y missing in R code using %*% (cholmod_aat doesn't
121            accept a symmetric matrix).
122            * tests/group-methods.R: Uncomment test of crossprod applied to
123            lsCMatrix objects.
124    
125    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R (symmetricMatrix): add validity method (available
128            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
129    
130            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
131    
132            * tests/indexing.Rout.save:
133            * tests/indexing.R: additions, mainly for 'lsparse'
134    
135            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
136            case.
137    
138            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
139    
140    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
143                    as 'N' (1-letter - Ok?)
144    
145            * tests/group-methods.R: add test for logical + NAs
146    
147            * R/dMatrix.R ("Compare"): fix to work with NA's
148    
149            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
150    
151            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
152                    which is implemented.
153    
154    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/chm_common.c: coerce logical <-> double instead of
157            typecasting;  needed for "l" matrix handling in cholmod.
158    
159            * tests/other-pkgs.R (graph): small extension in "graph" checks.
160    
161            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
162            (Tsp2grNEL): other fixes needed
163    
164    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
167                    Matrices, since "lMatrix", also "lsparseM" can have NA
168            * R/ndenseMatrix.R, etc: new source files
169            * man/nsparseMatrix-classes.Rd, etc: new help files
170            * tests/: adaptions
171            * src/chm_common.c (chm_dense_to_SEXP): and others:
172                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
173            * src/Csparse.c, etc: ditto
174    
175    2006-09-11  Douglas Bates  <bates@R-project.org>
176    
177            * src/Mutils.[ch],init.c inst/include/*.h: Move the
178            alloc_d**Matrix functions to the lme4 package.
179    
180    2006-09-09  Douglas Bates  <bates@R-project.org>
181    
182            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
183            fixed
184    
185    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/lMatrix.R: new
188    
189            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
190    
191            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
192            * man/tcrossprod.Rd: ditto
193    
194    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
197            for exported functions
198            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
199            Remove partitioning algorithms for sparse matrix reordering.  The
200            copyright on the Metis code was problematic and the methods were
201            rarely used.
202            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
203            operations are now done entirely in CHOLMOD code.
204    
205    2006-09-06  Douglas Bates  <bates@R-project.org>
206    
207            * src/Mutils.h: Remove functions that are no longer used.
208    
209    2006-09-04  Douglas Bates  <bates@R-project.org>
210    
211            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
212            * src/DEPS.mkf: update
213    
214    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * created branches/Matrix-for-R-2.3.x;  on trunk: do
217            * DESCRIPTION (Version): 0.9975-0
218            (Depends): R (>= 2.4.0)
219    
220    2006-09-01  Douglas Bates  <bates@R-project.org>
221    
222            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
223    
224    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
227            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
228    
229            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
230    
231    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
234            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
235            * R/dsparseMatrix.R: ditto
236            * R/Csparse.R: ditto
237    
238    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dMatrix.R (Compare): improve availability of "<", etc
241            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
242    
243    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
246            of a 0-index which was used as 1-index (..hmm)
247    
248            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
249    
250            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
251            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
252            (.is.diagonal): ditto
253    
254            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
255    
256            * R/Matrix.R (Matrix): also work for NA data
257    
258    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
261            in all cases.
262    
263    2006-08-27  Douglas Bates  <bates@R-project.org>
264    
265            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
266            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
267    
268    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
271            subclasses of "ddenseMatrix"
272            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
273            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
274            instead of half dozen specialized ones.
275    
276    2006-08-25  Douglas Bates  <bates@R-project.org>
277    
278            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
279            <tillard@cirad.fr> - ordering standard errors to match effects.
280    
281    2006-08-24  Douglas Bates  <bates@R-project.org>
282    
283            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
284            on R_ldl.
285            * R/lCholCMatrix.R,
286            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
287            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
288            * many files in ./R and ./src: Use more general version of
289            dup_mMatrix_as_dgeMatrix to simplify method definitions.
290            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
291            dtpMatrix, dspMatrix and dppMatrix conversions.
292    
293    
294    2006-08-23  Douglas Bates  <bates@R-project.org>
295    
296            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
297            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
298            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
299            dgeMatrix_crossprod (may need to do this in other places).
300            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
301            generic and method for dsCMatrix.  Use CHOLMOD for chol().
302    
303    2006-08-22  Douglas Bates  <bates@R-project.org>
304    
305            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
306            types of classed Matrices, matrices or numeric or logical vectors.
307            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
308            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
309            to Mutils.h (as an inline) and change name to Matrix_check_class;
310            fixes in as_cholmod_factor and chm_factor_to_SEXP.
311            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
312            dsCMatrix_matrix_solve.  Comment out vestigial functions.
313            * src/Csparse.c: use diag_P and uplo_P macros.
314    
315    2006-08-21  Douglas Bates  <bates@R-project.org>
316    
317            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
318            valgrind.
319            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
320            inverses.
321            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
322            -Wall warnings.
323            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
324            Use dup_mMatrix_as_dgeMatrix.
325    
326    2006-08-20  Douglas Bates  <bates@R-project.org>
327    
328            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
329            * tests/sparseQR.R: Added
330            * man/sparseQR-class.Rd: Document methods for qr.* generics
331            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
332    
333    2006-08-19  Douglas Bates  <bates@R-project.org>
334    
335            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
336            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
337            and qr.fitted.
338            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
339            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
340    
341  2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343          * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since          * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since

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