SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1600, Fri Sep 29 13:37:25 2006 UTC
# Line 1  Line 1 
1    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
4    
5            * R/lsTMatrix.R: new files w/ missing methods
6            * R/nsTMatrix.R:  "  'for completeness'
7    
8            * tests/Class+Meth.R: a bit less 'not.ok.classes'
9    
10            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
11    
12    
13    2006-09-28  Douglas Bates  <bates@R-project.org>
14    
15            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
16            included.
17    
18            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
19            Export C-callable functions used in Zt_create in lme4.
20    
21    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * DESCRIPTION (Version): 0.9975-1
24    
25            * tests/simple.R: less checks fail; using NA, found that our
26                    kronecker() is not base-compatible with NA's.
27    
28            * R/dMatrix.R: "Compare" method now implemented for all cases
29    
30            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
31    
32            * man/dtpMatrix-class.Rd: mention length of 'x' slot
33    
34            * src/dtpMatrix.c (dtpMatrix_validate): fix check
35            * src/dspMatrix.c (dspMatrix_validate): ditto
36    
37            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
38              including coercion to [nl]tTMatrix.
39    
40            * R/diagMatrix.R (show): print a header line as for other classes.
41    
42    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/Makefile.win (SUBDIRS): fix typo
45    
46    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
49    
50    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
53            symmetric and y missing in R code using %*% (cholmod_aat doesn't
54            accept a symmetric matrix).
55            * tests/group-methods.R: Uncomment test of crossprod applied to
56            lsCMatrix objects.
57    
58    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/AllClass.R (symmetricMatrix): add validity method (available
61            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
62    
63            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
64    
65            * tests/indexing.Rout.save:
66            * tests/indexing.R: additions, mainly for 'lsparse'
67    
68            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
69            case.
70    
71            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
72    
73    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
76                    as 'N' (1-letter - Ok?)
77    
78            * tests/group-methods.R: add test for logical + NAs
79    
80            * R/dMatrix.R ("Compare"): fix to work with NA's
81    
82            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
83    
84            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
85                    which is implemented.
86    
87    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/chm_common.c: coerce logical <-> double instead of
90            typecasting;  needed for "l" matrix handling in cholmod.
91    
92            * tests/other-pkgs.R (graph): small extension in "graph" checks.
93    
94            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
95            (Tsp2grNEL): other fixes needed
96    
97    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
100                    Matrices, since "lMatrix", also "lsparseM" can have NA
101            * R/ndenseMatrix.R, etc: new source files
102            * man/nsparseMatrix-classes.Rd, etc: new help files
103            * tests/: adaptions
104            * src/chm_common.c (chm_dense_to_SEXP): and others:
105                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
106            * src/Csparse.c, etc: ditto
107    
108    2006-09-11  Douglas Bates  <bates@R-project.org>
109    
110            * src/Mutils.[ch],init.c inst/include/*.h: Move the
111            alloc_d**Matrix functions to the lme4 package.
112    
113    2006-09-09  Douglas Bates  <bates@R-project.org>
114    
115            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
116            fixed
117    
118    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/lMatrix.R: new
121    
122            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
123    
124            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
125            * man/tcrossprod.Rd: ditto
126    
127    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
130            for exported functions
131            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
132            Remove partitioning algorithms for sparse matrix reordering.  The
133            copyright on the Metis code was problematic and the methods were
134            rarely used.
135            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
136            operations are now done entirely in CHOLMOD code.
137    
138    2006-09-06  Douglas Bates  <bates@R-project.org>
139    
140            * src/Mutils.h: Remove functions that are no longer used.
141    
142    2006-09-04  Douglas Bates  <bates@R-project.org>
143    
144            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
145            * src/DEPS.mkf: update
146    
147    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * created branches/Matrix-for-R-2.3.x;  on trunk: do
150            * DESCRIPTION (Version): 0.9975-0
151            (Depends): R (>= 2.4.0)
152    
153    2006-09-01  Douglas Bates  <bates@R-project.org>
154    
155            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
156    
157    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
160            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
161    
162            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
163    
164    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
167            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
168            * R/dsparseMatrix.R: ditto
169            * R/Csparse.R: ditto
170    
171    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R (Compare): improve availability of "<", etc
174            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
175    
176    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
179            of a 0-index which was used as 1-index (..hmm)
180    
181            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
182    
183            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
184            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
185            (.is.diagonal): ditto
186    
187            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
188    
189            * R/Matrix.R (Matrix): also work for NA data
190    
191    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
194            in all cases.
195    
196    2006-08-27  Douglas Bates  <bates@R-project.org>
197    
198            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
199            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
200    
201    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
204            subclasses of "ddenseMatrix"
205            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
206            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
207            instead of half dozen specialized ones.
208    
209    2006-08-25  Douglas Bates  <bates@R-project.org>
210    
211            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
212            <tillard@cirad.fr> - ordering standard errors to match effects.
213    
214    2006-08-24  Douglas Bates  <bates@R-project.org>
215    
216            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
217            on R_ldl.
218            * R/lCholCMatrix.R,
219            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
220            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
221            * many files in ./R and ./src: Use more general version of
222            dup_mMatrix_as_dgeMatrix to simplify method definitions.
223            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
224            dtpMatrix, dspMatrix and dppMatrix conversions.
225    
226    
227    2006-08-23  Douglas Bates  <bates@R-project.org>
228    
229            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
230            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
231            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
232            dgeMatrix_crossprod (may need to do this in other places).
233            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
234            generic and method for dsCMatrix.  Use CHOLMOD for chol().
235    
236    2006-08-22  Douglas Bates  <bates@R-project.org>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
239            types of classed Matrices, matrices or numeric or logical vectors.
240            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
241            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
242            to Mutils.h (as an inline) and change name to Matrix_check_class;
243            fixes in as_cholmod_factor and chm_factor_to_SEXP.
244            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
245            dsCMatrix_matrix_solve.  Comment out vestigial functions.
246            * src/Csparse.c: use diag_P and uplo_P macros.
247    
248    2006-08-21  Douglas Bates  <bates@R-project.org>
249    
250            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
251            valgrind.
252            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
253            inverses.
254            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
255            -Wall warnings.
256            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
257            Use dup_mMatrix_as_dgeMatrix.
258    
259    2006-08-20  Douglas Bates  <bates@R-project.org>
260    
261            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
262            * tests/sparseQR.R: Added
263            * man/sparseQR-class.Rd: Document methods for qr.* generics
264            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
265    
266    2006-08-19  Douglas Bates  <bates@R-project.org>
267    
268            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
269            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
270            and qr.fitted.
271            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
272            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
273    
274    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
277            the base version has no "..." argument.
278    
279            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
280    
281            * R/Matrix.R: define and
282            * NAMESPACE: export as.numeric() and as.logical() methods.
283                    Let's hope these do not badly slow down something...
284            Finally export the zapsmall() method.
285    
286    2006-08-17  Douglas Bates  <bates@R-project.org>
287    
288            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
289            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
290            * src/dtCMatrix.c :Remove code that is no longer used
291            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
292    
293    2006-08-14  Douglas Bates  <bates@R-project.org>
294    
295            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
296            Csparse_to_logical and Csparse_symmetric_to_general.
297            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
298            coercion methods between CsparseMatrix and TsparseMatrix.
299    
300    2006-08-14  Douglas Bates  <bates@R-project.org>
301    
302            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
303            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
304            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
305            possible.
306    
307  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
308    
309          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

Legend:
Removed from v.1368  
changed lines
  Added in v.1600

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge