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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1595, Thu Sep 28 22:32:23 2006 UTC
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1    2006-09-28  Douglas Bates  <bates@R-project.org>
2    
3            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
4            included.
5    
6            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
7            Export C-callable functions used in Zt_create in lme4.
8    
9    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * DESCRIPTION (Version): 0.9975-1
12    
13            * tests/simple.R: less checks fail; using NA, found that our
14                    kronecker() is not base-compatible with NA's.
15    
16            * R/dMatrix.R: "Compare" method now implemented for all cases
17    
18            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
19    
20            * man/dtpMatrix-class.Rd: mention length of 'x' slot
21    
22            * src/dtpMatrix.c (dtpMatrix_validate): fix check
23            * src/dspMatrix.c (dspMatrix_validate): ditto
24    
25            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
26              including coercion to [nl]tTMatrix.
27    
28            * R/diagMatrix.R (show): print a header line as for other classes.
29    
30    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/Makefile.win (SUBDIRS): fix typo
33    
34    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
37    
38    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
41            symmetric and y missing in R code using %*% (cholmod_aat doesn't
42            accept a symmetric matrix).
43            * tests/group-methods.R: Uncomment test of crossprod applied to
44            lsCMatrix objects.
45    
46    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/AllClass.R (symmetricMatrix): add validity method (available
49            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
50    
51            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
52    
53            * tests/indexing.Rout.save:
54            * tests/indexing.R: additions, mainly for 'lsparse'
55    
56            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
57            case.
58    
59            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
60    
61    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
64                    as 'N' (1-letter - Ok?)
65    
66            * tests/group-methods.R: add test for logical + NAs
67    
68            * R/dMatrix.R ("Compare"): fix to work with NA's
69    
70            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
71    
72            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
73                    which is implemented.
74    
75    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/chm_common.c: coerce logical <-> double instead of
78            typecasting;  needed for "l" matrix handling in cholmod.
79    
80            * tests/other-pkgs.R (graph): small extension in "graph" checks.
81    
82            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
83            (Tsp2grNEL): other fixes needed
84    
85    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
88                    Matrices, since "lMatrix", also "lsparseM" can have NA
89            * R/ndenseMatrix.R, etc: new source files
90            * man/nsparseMatrix-classes.Rd, etc: new help files
91            * tests/: adaptions
92            * src/chm_common.c (chm_dense_to_SEXP): and others:
93                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
94            * src/Csparse.c, etc: ditto
95    
96    2006-09-11  Douglas Bates  <bates@R-project.org>
97    
98            * src/Mutils.[ch],init.c inst/include/*.h: Move the
99            alloc_d**Matrix functions to the lme4 package.
100    
101    2006-09-09  Douglas Bates  <bates@R-project.org>
102    
103            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
104            fixed
105    
106    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/lMatrix.R: new
109    
110            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
111    
112            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
113            * man/tcrossprod.Rd: ditto
114    
115    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
118            for exported functions
119            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
120            Remove partitioning algorithms for sparse matrix reordering.  The
121            copyright on the Metis code was problematic and the methods were
122            rarely used.
123            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
124            operations are now done entirely in CHOLMOD code.
125    
126    2006-09-06  Douglas Bates  <bates@R-project.org>
127    
128            * src/Mutils.h: Remove functions that are no longer used.
129    
130    2006-09-04  Douglas Bates  <bates@R-project.org>
131    
132            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
133            * src/DEPS.mkf: update
134    
135    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * created branches/Matrix-for-R-2.3.x;  on trunk: do
138            * DESCRIPTION (Version): 0.9975-0
139            (Depends): R (>= 2.4.0)
140    
141    2006-09-01  Douglas Bates  <bates@R-project.org>
142    
143            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
144    
145    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
148            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
149    
150            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
151    
152    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
155            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
156            * R/dsparseMatrix.R: ditto
157            * R/Csparse.R: ditto
158    
159    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/dMatrix.R (Compare): improve availability of "<", etc
162            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
163    
164    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
167            of a 0-index which was used as 1-index (..hmm)
168    
169            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
170    
171            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
172            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
173            (.is.diagonal): ditto
174    
175            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
176    
177            * R/Matrix.R (Matrix): also work for NA data
178    
179    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
182            in all cases.
183    
184    2006-08-27  Douglas Bates  <bates@R-project.org>
185    
186            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
187            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
188    
189    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
192            subclasses of "ddenseMatrix"
193            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
194            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
195            instead of half dozen specialized ones.
196    
197    2006-08-25  Douglas Bates  <bates@R-project.org>
198    
199            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
200            <tillard@cirad.fr> - ordering standard errors to match effects.
201    
202    2006-08-24  Douglas Bates  <bates@R-project.org>
203    
204            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
205            on R_ldl.
206            * R/lCholCMatrix.R,
207            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
208            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
209            * many files in ./R and ./src: Use more general version of
210            dup_mMatrix_as_dgeMatrix to simplify method definitions.
211            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
212            dtpMatrix, dspMatrix and dppMatrix conversions.
213    
214    
215    2006-08-23  Douglas Bates  <bates@R-project.org>
216    
217            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
218            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
219            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
220            dgeMatrix_crossprod (may need to do this in other places).
221            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
222            generic and method for dsCMatrix.  Use CHOLMOD for chol().
223    
224    2006-08-22  Douglas Bates  <bates@R-project.org>
225    
226            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
227            types of classed Matrices, matrices or numeric or logical vectors.
228            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
229            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
230            to Mutils.h (as an inline) and change name to Matrix_check_class;
231            fixes in as_cholmod_factor and chm_factor_to_SEXP.
232            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
233            dsCMatrix_matrix_solve.  Comment out vestigial functions.
234            * src/Csparse.c: use diag_P and uplo_P macros.
235    
236    2006-08-21  Douglas Bates  <bates@R-project.org>
237    
238            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
239            valgrind.
240            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
241            inverses.
242            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
243            -Wall warnings.
244            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
245            Use dup_mMatrix_as_dgeMatrix.
246    
247    2006-08-20  Douglas Bates  <bates@R-project.org>
248    
249            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
250            * tests/sparseQR.R: Added
251            * man/sparseQR-class.Rd: Document methods for qr.* generics
252            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
253    
254    2006-08-19  Douglas Bates  <bates@R-project.org>
255    
256            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
257            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
258            and qr.fitted.
259            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
260            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
261    
262    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
265            the base version has no "..." argument.
266    
267            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
268    
269            * R/Matrix.R: define and
270            * NAMESPACE: export as.numeric() and as.logical() methods.
271                    Let's hope these do not badly slow down something...
272            Finally export the zapsmall() method.
273    
274    2006-08-17  Douglas Bates  <bates@R-project.org>
275    
276            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
277            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
278            * src/dtCMatrix.c :Remove code that is no longer used
279            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
280    
281    2006-08-14  Douglas Bates  <bates@R-project.org>
282    
283            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
284            Csparse_to_logical and Csparse_symmetric_to_general.
285            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
286            coercion methods between CsparseMatrix and TsparseMatrix.
287    
288    2006-08-14  Douglas Bates  <bates@R-project.org>
289    
290            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
291            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
292            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
293            possible.
294    
295  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
296    
297          * 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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