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 1298, Sat Jun 10 19:56:18 2006 UTC revision 1681, Wed Nov 29 15:55:03 2006 UTC
# Line 1  Line 1 
1    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
4            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
5            is exactly singular.
6    
7    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Date): updated -> release 0.9975-6
10    
11    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
14            now returns symmetric.
15    
16            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
17    
18            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
19            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
20    
21            * R/Auxiliaries.R (.type.kind): added
22    
23    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
26            running src/CSparse_install.sh
27    
28            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
29    
30    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
33            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
34    
35            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
36    
37            * tests/Class+Meth.R (tstMatrixClass): now assure
38            the (important in method programming) property :
39    
40                    ###>>  Every "Matrix" is either
41                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
42    
43                    (where "*" stands for "Matrix")
44    
45            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
46    
47            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
48            * tests/validObj.R: checks for "comparison"
49    
50            * R/sparseMatrix.R ([): improved indexing for sparse;
51                    trying to keep <symmetric>[ n, n] symmmetric
52    
53            * tests/indexing.R: indexing for logical sparse now ok
54    
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/Tsparse.c: use xTsparse_validate() , and hence remove
59    
60            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
61    
62    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
65    
66            * tests/simple.R: validObject() checking the above.
67    
68            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
69            replacing both dgCMatrix_validate and lgCM*.
70    
71            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
72            fix dimnames setting in other places.
73            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
74    
75    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
78    
79            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
80            symmetry test, via
81            * R/Auxiliaries.R (.as.dgC.0.factors):
82    
83    2006-11-01  Douglas Bates  <bates@r-project.org>
84    
85            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
86            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
87            <CsparseMatrix>) added
88    
89    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * tests/matprod.R: add a variation of Harri's example
92    
93            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
94            recursive infinitely.
95    
96            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
97    
98            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
99    
100    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
103            matrix if possible; test m+m == 2*m; now test dgRMatrix.
104            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
105            satisfy the above test.
106    
107    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
110    
111            * R/dgCMatrix.R: solve(a, b="missing") based on
112            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
113            RHS = NULL.
114    
115            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
116            add more (needed) [t]crossprod() methods.
117    
118            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
119    
120            * R/Auxiliaries.R (as_CspClass): cleanup
121            (drop0): internal utility for "Csparse_drop(*, 0)"
122            (.bail.out.2): encourage active feedback
123    
124    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dMatrix.R(Compare): new(), then slots [no validity check]
127    
128            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
129            non-valid or 'sorted' case).
130    
131            * R/dsparseMatrix.R: add "chol" method.
132            * R/ddenseMatrix.R: ditto
133    
134            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
135            * NAMESPACE (Ops)
136            * R/diagMatrix.R (diag2T): simple utility used "higher level"
137            coercion; deprecating direct lower level coercions.
138    
139            * R/*.R (seq): use seq_len() and seq_along() where possible.
140    
141    
142    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.9975-5 ready for release
145    
146    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
149    
150    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/AllClass.R (corMatrix): add 'validity' check;
153                    comment out unused "LDL" class definition
154            * NAMESPACE: mention, but do not export "LDL" class
155            * R/corMatrix.R: new (simple), needed for R-devel with
156            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
157              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
158    
159    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
162            use Rprintf and R's error handling.
163    
164    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
167            * tests/matprod.R: add tests for the bug fixed.
168    
169    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
172            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
173    
174    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
177    
178    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.9975-3
181    
182            * R/diagMatrix.R (bdiag): new function constructing block diagonal
183            (sparse) matrices.
184            * man/bdiag.Rd: docu + examples
185    
186            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
187    
188            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
189            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
190    
191            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
192            that result is sparse or diagonal (and not dense).
193    
194            * man/Subassign-methods.Rd: fix examples
195    
196            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
197            should always return a sparse (and not sometimes a diagonal) matrix.
198    
199    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
202    
203    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * DESCRIPTION (Version): 0.9975-2
206    
207            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
208    
209    2006-10-02  Douglas Bates  <bates@R-project.org>
210    
211            * tests/dg_Matrix.R: Simplify test taking into account new code.
212    
213    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
216    
217            * R/lsTMatrix.R: new files w/ missing methods
218            * R/nsTMatrix.R:  "  'for completeness'
219    
220            * tests/Class+Meth.R: a bit less 'not.ok.classes'
221    
222            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
223    
224    
225    2006-09-28  Douglas Bates  <bates@R-project.org>
226    
227            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
228            included.
229    
230            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
231            Export C-callable functions used in Zt_create in lme4.
232    
233    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.9975-1
236    
237            * tests/simple.R: less checks fail; using NA, found that our
238                    kronecker() is not base-compatible with NA's.
239    
240            * R/dMatrix.R: "Compare" method now implemented for all cases
241    
242            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
243    
244            * man/dtpMatrix-class.Rd: mention length of 'x' slot
245    
246            * src/dtpMatrix.c (dtpMatrix_validate): fix check
247            * src/dspMatrix.c (dspMatrix_validate): ditto
248    
249            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
250              including coercion to [nl]tTMatrix.
251    
252            * R/diagMatrix.R (show): print a header line as for other classes.
253    
254    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * src/Makefile.win (SUBDIRS): fix typo
257    
258    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
261    
262    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
265            symmetric and y missing in R code using %*% (cholmod_aat doesn't
266            accept a symmetric matrix).
267            * tests/group-methods.R: Uncomment test of crossprod applied to
268            lsCMatrix objects.
269    
270    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/AllClass.R (symmetricMatrix): add validity method (available
273            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
274    
275            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
276    
277            * tests/indexing.Rout.save:
278            * tests/indexing.R: additions, mainly for 'lsparse'
279    
280            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
281            case.
282    
283            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
284    
285    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
288                    as 'N' (1-letter - Ok?)
289    
290            * tests/group-methods.R: add test for logical + NAs
291    
292            * R/dMatrix.R ("Compare"): fix to work with NA's
293    
294            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
295    
296            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
297                    which is implemented.
298    
299    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/chm_common.c: coerce logical <-> double instead of
302            typecasting;  needed for "l" matrix handling in cholmod.
303    
304            * tests/other-pkgs.R (graph): small extension in "graph" checks.
305    
306            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
307            (Tsp2grNEL): other fixes needed
308    
309    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
312                    Matrices, since "lMatrix", also "lsparseM" can have NA
313            * R/ndenseMatrix.R, etc: new source files
314            * man/nsparseMatrix-classes.Rd, etc: new help files
315            * tests/: adaptions
316            * src/chm_common.c (chm_dense_to_SEXP): and others:
317                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
318            * src/Csparse.c, etc: ditto
319    
320    2006-09-11  Douglas Bates  <bates@R-project.org>
321    
322            * src/Mutils.[ch],init.c inst/include/*.h: Move the
323            alloc_d**Matrix functions to the lme4 package.
324    
325    2006-09-09  Douglas Bates  <bates@R-project.org>
326    
327            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
328            fixed
329    
330    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/lMatrix.R: new
333    
334            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
335    
336            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
337            * man/tcrossprod.Rd: ditto
338    
339    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
342            for exported functions
343            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
344            Remove partitioning algorithms for sparse matrix reordering.  The
345            copyright on the Metis code was problematic and the methods were
346            rarely used.
347            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
348            operations are now done entirely in CHOLMOD code.
349    
350    2006-09-06  Douglas Bates  <bates@R-project.org>
351    
352            * src/Mutils.h: Remove functions that are no longer used.
353    
354    2006-09-04  Douglas Bates  <bates@R-project.org>
355    
356            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
357            * src/DEPS.mkf: update
358    
359    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * created branches/Matrix-for-R-2.3.x;  on trunk: do
362            * DESCRIPTION (Version): 0.9975-0
363            (Depends): R (>= 2.4.0)
364    
365    2006-09-01  Douglas Bates  <bates@R-project.org>
366    
367            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
368    
369    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
372            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
373    
374            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
375    
376    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
379            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
380            * R/dsparseMatrix.R: ditto
381            * R/Csparse.R: ditto
382    
383    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/dMatrix.R (Compare): improve availability of "<", etc
386            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
387    
388    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
391            of a 0-index which was used as 1-index (..hmm)
392    
393            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
394    
395            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
396            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
397            (.is.diagonal): ditto
398    
399            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
400    
401            * R/Matrix.R (Matrix): also work for NA data
402    
403    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
406            in all cases.
407    
408    2006-08-27  Douglas Bates  <bates@R-project.org>
409    
410            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
411            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
412    
413    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
416            subclasses of "ddenseMatrix"
417            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
418            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
419            instead of half dozen specialized ones.
420    
421    2006-08-25  Douglas Bates  <bates@R-project.org>
422    
423            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
424            <tillard@cirad.fr> - ordering standard errors to match effects.
425    
426    2006-08-24  Douglas Bates  <bates@R-project.org>
427    
428            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
429            on R_ldl.
430            * R/lCholCMatrix.R,
431            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
432            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
433            * many files in ./R and ./src: Use more general version of
434            dup_mMatrix_as_dgeMatrix to simplify method definitions.
435            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
436            dtpMatrix, dspMatrix and dppMatrix conversions.
437    
438    
439    2006-08-23  Douglas Bates  <bates@R-project.org>
440    
441            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
442            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
443            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
444            dgeMatrix_crossprod (may need to do this in other places).
445            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
446            generic and method for dsCMatrix.  Use CHOLMOD for chol().
447    
448    2006-08-22  Douglas Bates  <bates@R-project.org>
449    
450            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
451            types of classed Matrices, matrices or numeric or logical vectors.
452            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
453            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
454            to Mutils.h (as an inline) and change name to Matrix_check_class;
455            fixes in as_cholmod_factor and chm_factor_to_SEXP.
456            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
457            dsCMatrix_matrix_solve.  Comment out vestigial functions.
458            * src/Csparse.c: use diag_P and uplo_P macros.
459    
460    2006-08-21  Douglas Bates  <bates@R-project.org>
461    
462            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
463            valgrind.
464            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
465            inverses.
466            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
467            -Wall warnings.
468            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
469            Use dup_mMatrix_as_dgeMatrix.
470    
471    2006-08-20  Douglas Bates  <bates@R-project.org>
472    
473            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
474            * tests/sparseQR.R: Added
475            * man/sparseQR-class.Rd: Document methods for qr.* generics
476            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
477    
478    2006-08-19  Douglas Bates  <bates@R-project.org>
479    
480            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
481            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
482            and qr.fitted.
483            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
484            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
485    
486    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
489            the base version has no "..." argument.
490    
491            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
492    
493            * R/Matrix.R: define and
494            * NAMESPACE: export as.numeric() and as.logical() methods.
495                    Let's hope these do not badly slow down something...
496            Finally export the zapsmall() method.
497    
498    2006-08-17  Douglas Bates  <bates@R-project.org>
499    
500            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
501            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
502            * src/dtCMatrix.c :Remove code that is no longer used
503            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
504    
505    2006-08-14  Douglas Bates  <bates@R-project.org>
506    
507            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
508            Csparse_to_logical and Csparse_symmetric_to_general.
509            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
510            coercion methods between CsparseMatrix and TsparseMatrix.
511    
512    2006-08-14  Douglas Bates  <bates@R-project.org>
513    
514            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
515            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
516            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
517            possible.
518    
519    2006-08-12  Douglas Bates  <bates@R-project.org>
520    
521            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
522              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
523              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
524              generalize conversions between TsparseMatrix, CsparseMatrix,
525              denseMatrix and matrix.  Preserve triangularity property and
526              propagate Dimnames in the easy cases.
527    
528    2006-08-10  Douglas Bates  <bates@R-project.org>
529    
530            * src/lmer.c: adjust checks in glmer_init for S4SXP
531            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
532            before S4SXP but for the wrong reasons.
533    
534    2006-08-08  Douglas Bates  <bates@R-project.org>
535    
536            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
537            Later modified to return the upper triangle only.
538            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
539    
540    2006-08-07  Douglas Bates  <bates@R-project.org>
541    
542            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
543            R-level conversion to a sparse symmetric class.
544            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
545            Remove conversion to sparse symmetric classes (now done in C code).
546    
547    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
550            * man/band.Rd:  adapt the \dontshow{} unit test.
551    
552    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * DESCRIPTION (Version): 0.995-14  for CRAN
555    
556            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
557    
558            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
559            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
560    
561            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
562            * R/Tsparse.R (tril, triu, band): methods
563            * R/dgRMatrix.R (tril, ...):    ditto
564            * man/band.Rd:                  ditto
565    
566    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/Matrix.R (head, tail): directly use utils:::head.matrix
569                    to be up-to-date automatically.
570    
571    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
574    
575            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
576            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
577            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
578            such that the S4 objects are always created by the current version
579            of R and 'Matrix' class definitions.
580    
581    2006-08-01  Douglas Bates  <bates@R-project.org>
582    
583            * R/lmer.R (LMEoptimize method), tests/lmer.R,
584            inst/external/test3comp.rda: Added warnings for convergence on
585            boundary and test cases.
586    
587            * src/lmer.c (mer_postVar): Modified to return the variances that
588            are marginal to the fixed effects, not conditional on them (which
589            is what the bVar slot contents represent).
590    
591    2006-07-31  Douglas Bates  <bates@R-project.org>
592    
593            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
594            function which calls the C function mer_hat_trace2.
595    
596            * man/ranef.Rd: Include description of "postVar" argument and
597            producing a caterpillar plot.
598    
599    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * NAMESPACE:    change  "correlation" to "corMatrix"
602            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
603            * R/dpoMatrix.R: ditto
604            * R/lmer.R:      ditto
605    
606    2006-07-28  Douglas Bates  <bates@R-project.org>
607    
608            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
609            RZXinv slot's contents into a separate internal function that can
610            be used in mer_hat_trace.
611    
612    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
615            via new smart
616            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
617            utility functions.
618    
619    
620    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Csparse.R (tril, triu, band): do return *triangular* classed
623            matrices when appropriate; band() even symmetric ones.
624            (replCmat): extend to potentially all "CsparseMatrix"
625            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
626            allow subassignment for special sparse matrices.
627    
628            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
629    
630            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
631            argument; in glmer_*(): print only if(verbose).
632    
633            speed-optimize a few places by moving REAL(.) out of loops.
634    
635            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
636    
637    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
640                    since that wrongly triggers also for M[ logi , ]
641    
642            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
643            a symmetric matrix that results in a non-symmetric one.
644            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
645    
646            * R/dMatrix.R: make round(M) work as round(M, 0)
647    
648            * R/dgTMatrix.R (image): coordinate system and axis now use
649            1-based indices, not 0-based ones.
650    
651            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
652            * tests/indexing.R: test it.
653    
654            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
655            * man/isSymmetric-methods.Rd: and document it.
656    
657            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
658            * man/SparseM-conv.Rd: docu them
659    
660            * tests/other-pkgs.R: renamed from tests/graph.R and add example
661                    for 'SparseM' conversions
662    
663    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
664    
665            * R/Matrix.R (head): added head() and tail() methods.
666    
667    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * DESCRIPTION (Version): 0.995-12 released to CRAN
670    
671    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * tests/simple.R: add check for correct dsT -> dgT coercion;
674                    add check for correct printing of symmetric sparse matrices.
675    
676            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
677            for sparse symmetric matrices.
678    
679            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
680            diagonal twice.
681    
682    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
683    
684            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
685            being applied to the x slot (detected by Brian Ripley).
686    
687    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
690    
691            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
692    
693    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * src/lgCMatrix.c (lgCMatrix_diag): new function
696            * R/lgCMatrix.R (diag): for new method
697    
698            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
699                 ==> construction of illegal "*gTMatrix" via new() should
700                 now be much less easy:
701            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
702    
703            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
704                    directly.
705            * man/Matrix.Rd: documents it.
706    
707    2006-07-06  Douglas Bates  <bates@R-project.org>
708    
709            * src/pedigree.c (pedigree_inbreeding): Correction in
710            initialization.  This function is not currently being used and is
711            not fully tested.
712    
713            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
714            Introduced the glmer class.  Added code for mcmcmsamp on glmer
715            objects.  Modified validity check on pedigree objects to account
716            for nonparallel patterns of missingness of parents.
717    
718            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
719            class.
720    
721    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/pMatrix.R: coercion pMatrix -> Tsparse
724    
725    2006-06-12  Douglas Bates  <bates@R-project.org>
726    
727            * DESCRIPTION (Version): 0.995-11 released to CRAN
728    
729            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
730            the output from mcmcsamp.
731    
732  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
733    
734          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
735            of the hat matrix.
736    
737  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
740          classes.          classes.
741            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
742    
743  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
# Line 43  Line 776 
776    
777          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
778          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
779          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
780    
781    
782  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 899 
899          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
900          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
901          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
902          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
903    
904  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
# Line 370  Line 1103 
1103  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1106          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1107          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1108    
1109  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1298  
changed lines
  Added in v.1681

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