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 1405, Mon Aug 21 14:43:00 2006 UTC revision 1661, Thu Nov 2 13:10:50 2006 UTC
# Line 1  Line 1 
1    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Tsparse.c: use xTsparse_validate() , and hence remove
4    
5            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
6    
7    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
10    
11            * tests/simple.R: validObject() checking the above.
12    
13            * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,
14            replacing both dgCMatrix_validate and lgCM*.
15    
16            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
17            fix dimnames setting in other places.
18            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
19    
20    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
23    
24            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
25            symmetry test, via
26            * R/Auxiliaries.R (.as.dgC.0.factors):
27    
28    2006-11-01  Douglas Bates  <bates@r-project.org>
29    
30            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
31            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
32            <CsparseMatrix>) added
33    
34    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * tests/matprod.R: add a variation of Harri's example
37    
38            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
39            recursive infinitely.
40    
41            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
42    
43            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
44    
45    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
48            matrix if possible; test m+m == 2*m; now test dgRMatrix.
49            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
50            satisfy the above test.
51    
52    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
55    
56            * R/dgCMatrix.R: solve(a, b="missing") based on
57            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
58            RHS = NULL.
59    
60            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
61            add more (needed) [t]crossprod() methods.
62    
63            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
64    
65            * R/Auxiliaries.R (as_CspClass): cleanup
66            (drop0): internal utility for "Csparse_drop(*, 0)"
67            (.bail.out.2): encourage active feedback
68    
69    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/dMatrix.R(Compare): new(), then slots [no validity check]
72    
73            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
74            non-valid or 'sorted' case).
75    
76            * R/dsparseMatrix.R: add "chol" method.
77            * R/ddenseMatrix.R: ditto
78    
79            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
80            * NAMESPACE (Ops)
81            * R/diagMatrix.R (diag2T): simple utility used "higher level"
82            coercion; deprecating direct lower level coercions.
83    
84            * R/*.R (seq): use seq_len() and seq_along() where possible.
85    
86    
87    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.9975-5 ready for release
90    
91    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
94    
95    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/AllClass.R (corMatrix): add 'validity' check;
98                    comment out unused "LDL" class definition
99            * NAMESPACE: mention, but do not export "LDL" class
100            * R/corMatrix.R: new (simple), needed for R-devel with
101            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
102              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
103    
104    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
107            use Rprintf and R's error handling.
108    
109    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
112            * tests/matprod.R: add tests for the bug fixed.
113    
114    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
117            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
118    
119    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
122    
123    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * DESCRIPTION (Version): 0.9975-3
126    
127            * R/diagMatrix.R (bdiag): new function constructing block diagonal
128            (sparse) matrices.
129            * man/bdiag.Rd: docu + examples
130    
131            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
132    
133            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
134            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
135    
136            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
137            that result is sparse or diagonal (and not dense).
138    
139            * man/Subassign-methods.Rd: fix examples
140    
141            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
142            should always return a sparse (and not sometimes a diagonal) matrix.
143    
144    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
147    
148    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * DESCRIPTION (Version): 0.9975-2
151    
152            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
153    
154    2006-10-02  Douglas Bates  <bates@R-project.org>
155    
156            * tests/dg_Matrix.R: Simplify test taking into account new code.
157    
158    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
161    
162            * R/lsTMatrix.R: new files w/ missing methods
163            * R/nsTMatrix.R:  "  'for completeness'
164    
165            * tests/Class+Meth.R: a bit less 'not.ok.classes'
166    
167            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
168    
169    
170    2006-09-28  Douglas Bates  <bates@R-project.org>
171    
172            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
173            included.
174    
175            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
176            Export C-callable functions used in Zt_create in lme4.
177    
178    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.9975-1
181    
182            * tests/simple.R: less checks fail; using NA, found that our
183                    kronecker() is not base-compatible with NA's.
184    
185            * R/dMatrix.R: "Compare" method now implemented for all cases
186    
187            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
188    
189            * man/dtpMatrix-class.Rd: mention length of 'x' slot
190    
191            * src/dtpMatrix.c (dtpMatrix_validate): fix check
192            * src/dspMatrix.c (dspMatrix_validate): ditto
193    
194            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
195              including coercion to [nl]tTMatrix.
196    
197            * R/diagMatrix.R (show): print a header line as for other classes.
198    
199    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/Makefile.win (SUBDIRS): fix typo
202    
203    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
206    
207    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
210            symmetric and y missing in R code using %*% (cholmod_aat doesn't
211            accept a symmetric matrix).
212            * tests/group-methods.R: Uncomment test of crossprod applied to
213            lsCMatrix objects.
214    
215    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/AllClass.R (symmetricMatrix): add validity method (available
218            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
219    
220            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
221    
222            * tests/indexing.Rout.save:
223            * tests/indexing.R: additions, mainly for 'lsparse'
224    
225            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
226            case.
227    
228            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
229    
230    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
233                    as 'N' (1-letter - Ok?)
234    
235            * tests/group-methods.R: add test for logical + NAs
236    
237            * R/dMatrix.R ("Compare"): fix to work with NA's
238    
239            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
240    
241            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
242                    which is implemented.
243    
244    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/chm_common.c: coerce logical <-> double instead of
247            typecasting;  needed for "l" matrix handling in cholmod.
248    
249            * tests/other-pkgs.R (graph): small extension in "graph" checks.
250    
251            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
252            (Tsp2grNEL): other fixes needed
253    
254    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
257                    Matrices, since "lMatrix", also "lsparseM" can have NA
258            * R/ndenseMatrix.R, etc: new source files
259            * man/nsparseMatrix-classes.Rd, etc: new help files
260            * tests/: adaptions
261            * src/chm_common.c (chm_dense_to_SEXP): and others:
262                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
263            * src/Csparse.c, etc: ditto
264    
265    2006-09-11  Douglas Bates  <bates@R-project.org>
266    
267            * src/Mutils.[ch],init.c inst/include/*.h: Move the
268            alloc_d**Matrix functions to the lme4 package.
269    
270    2006-09-09  Douglas Bates  <bates@R-project.org>
271    
272            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
273            fixed
274    
275    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/lMatrix.R: new
278    
279            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
280    
281            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
282            * man/tcrossprod.Rd: ditto
283    
284    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
287            for exported functions
288            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
289            Remove partitioning algorithms for sparse matrix reordering.  The
290            copyright on the Metis code was problematic and the methods were
291            rarely used.
292            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
293            operations are now done entirely in CHOLMOD code.
294    
295    2006-09-06  Douglas Bates  <bates@R-project.org>
296    
297            * src/Mutils.h: Remove functions that are no longer used.
298    
299    2006-09-04  Douglas Bates  <bates@R-project.org>
300    
301            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
302            * src/DEPS.mkf: update
303    
304    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * created branches/Matrix-for-R-2.3.x;  on trunk: do
307            * DESCRIPTION (Version): 0.9975-0
308            (Depends): R (>= 2.4.0)
309    
310    2006-09-01  Douglas Bates  <bates@R-project.org>
311    
312            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
313    
314    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
317            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
318    
319            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
320    
321    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
324            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
325            * R/dsparseMatrix.R: ditto
326            * R/Csparse.R: ditto
327    
328    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/dMatrix.R (Compare): improve availability of "<", etc
331            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
332    
333    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
336            of a 0-index which was used as 1-index (..hmm)
337    
338            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
339    
340            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
341            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
342            (.is.diagonal): ditto
343    
344            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
345    
346            * R/Matrix.R (Matrix): also work for NA data
347    
348    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
351            in all cases.
352    
353    2006-08-27  Douglas Bates  <bates@R-project.org>
354    
355            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
356            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
357    
358    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
361            subclasses of "ddenseMatrix"
362            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
363            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
364            instead of half dozen specialized ones.
365    
366    2006-08-25  Douglas Bates  <bates@R-project.org>
367    
368            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
369            <tillard@cirad.fr> - ordering standard errors to match effects.
370    
371    2006-08-24  Douglas Bates  <bates@R-project.org>
372    
373            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
374            on R_ldl.
375            * R/lCholCMatrix.R,
376            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
377            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
378            * many files in ./R and ./src: Use more general version of
379            dup_mMatrix_as_dgeMatrix to simplify method definitions.
380            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
381            dtpMatrix, dspMatrix and dppMatrix conversions.
382    
383    
384    2006-08-23  Douglas Bates  <bates@R-project.org>
385    
386            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
387            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
388            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
389            dgeMatrix_crossprod (may need to do this in other places).
390            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
391            generic and method for dsCMatrix.  Use CHOLMOD for chol().
392    
393    2006-08-22  Douglas Bates  <bates@R-project.org>
394    
395            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
396            types of classed Matrices, matrices or numeric or logical vectors.
397            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
398            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
399            to Mutils.h (as an inline) and change name to Matrix_check_class;
400            fixes in as_cholmod_factor and chm_factor_to_SEXP.
401            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
402            dsCMatrix_matrix_solve.  Comment out vestigial functions.
403            * src/Csparse.c: use diag_P and uplo_P macros.
404    
405  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
406    
407          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
408          valgrind.          valgrind.
409            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
410            inverses.
411            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
412            -Wall warnings.
413            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
414            Use dup_mMatrix_as_dgeMatrix.
415    
416  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
417    

Legend:
Removed from v.1405  
changed lines
  Added in v.1661

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