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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1615, Thu Oct 5 16:30:46 2006 UTC
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1    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
4    
5    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * DESCRIPTION (Version): 0.9975-2
8    
9            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
10    
11    2006-10-02  Douglas Bates  <bates@R-project.org>
12    
13            * tests/dg_Matrix.R: Simplify test taking into account new code.
14    
15    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
18    
19            * R/lsTMatrix.R: new files w/ missing methods
20            * R/nsTMatrix.R:  "  'for completeness'
21    
22            * tests/Class+Meth.R: a bit less 'not.ok.classes'
23    
24            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
25    
26    
27    2006-09-28  Douglas Bates  <bates@R-project.org>
28    
29            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
30            included.
31    
32            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
33            Export C-callable functions used in Zt_create in lme4.
34    
35    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * DESCRIPTION (Version): 0.9975-1
38    
39            * tests/simple.R: less checks fail; using NA, found that our
40                    kronecker() is not base-compatible with NA's.
41    
42            * R/dMatrix.R: "Compare" method now implemented for all cases
43    
44            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
45    
46            * man/dtpMatrix-class.Rd: mention length of 'x' slot
47    
48            * src/dtpMatrix.c (dtpMatrix_validate): fix check
49            * src/dspMatrix.c (dspMatrix_validate): ditto
50    
51            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
52              including coercion to [nl]tTMatrix.
53    
54            * R/diagMatrix.R (show): print a header line as for other classes.
55    
56    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/Makefile.win (SUBDIRS): fix typo
59    
60    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
63    
64    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
67            symmetric and y missing in R code using %*% (cholmod_aat doesn't
68            accept a symmetric matrix).
69            * tests/group-methods.R: Uncomment test of crossprod applied to
70            lsCMatrix objects.
71    
72    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/AllClass.R (symmetricMatrix): add validity method (available
75            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
76    
77            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
78    
79            * tests/indexing.Rout.save:
80            * tests/indexing.R: additions, mainly for 'lsparse'
81    
82            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
83            case.
84    
85            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
86    
87    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
90                    as 'N' (1-letter - Ok?)
91    
92            * tests/group-methods.R: add test for logical + NAs
93    
94            * R/dMatrix.R ("Compare"): fix to work with NA's
95    
96            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
97    
98            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
99                    which is implemented.
100    
101    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * src/chm_common.c: coerce logical <-> double instead of
104            typecasting;  needed for "l" matrix handling in cholmod.
105    
106            * tests/other-pkgs.R (graph): small extension in "graph" checks.
107    
108            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
109            (Tsp2grNEL): other fixes needed
110    
111    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
114                    Matrices, since "lMatrix", also "lsparseM" can have NA
115            * R/ndenseMatrix.R, etc: new source files
116            * man/nsparseMatrix-classes.Rd, etc: new help files
117            * tests/: adaptions
118            * src/chm_common.c (chm_dense_to_SEXP): and others:
119                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
120            * src/Csparse.c, etc: ditto
121    
122    2006-09-11  Douglas Bates  <bates@R-project.org>
123    
124            * src/Mutils.[ch],init.c inst/include/*.h: Move the
125            alloc_d**Matrix functions to the lme4 package.
126    
127    2006-09-09  Douglas Bates  <bates@R-project.org>
128    
129            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
130            fixed
131    
132    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/lMatrix.R: new
135    
136            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
137    
138            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
139            * man/tcrossprod.Rd: ditto
140    
141    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
144            for exported functions
145            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
146            Remove partitioning algorithms for sparse matrix reordering.  The
147            copyright on the Metis code was problematic and the methods were
148            rarely used.
149            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
150            operations are now done entirely in CHOLMOD code.
151    
152    2006-09-06  Douglas Bates  <bates@R-project.org>
153    
154            * src/Mutils.h: Remove functions that are no longer used.
155    
156    2006-09-04  Douglas Bates  <bates@R-project.org>
157    
158            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
159            * src/DEPS.mkf: update
160    
161    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * created branches/Matrix-for-R-2.3.x;  on trunk: do
164            * DESCRIPTION (Version): 0.9975-0
165            (Depends): R (>= 2.4.0)
166    
167    2006-09-01  Douglas Bates  <bates@R-project.org>
168    
169            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
170    
171    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
174            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
175    
176            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
177    
178    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
181            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
182            * R/dsparseMatrix.R: ditto
183            * R/Csparse.R: ditto
184    
185    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dMatrix.R (Compare): improve availability of "<", etc
188            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
189    
190    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
193            of a 0-index which was used as 1-index (..hmm)
194    
195            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
196    
197            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
198            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
199            (.is.diagonal): ditto
200    
201            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
202    
203            * R/Matrix.R (Matrix): also work for NA data
204    
205    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
208            in all cases.
209    
210    2006-08-27  Douglas Bates  <bates@R-project.org>
211    
212            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
213            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
214    
215    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
218            subclasses of "ddenseMatrix"
219            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
220            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
221            instead of half dozen specialized ones.
222    
223    2006-08-25  Douglas Bates  <bates@R-project.org>
224    
225            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
226            <tillard@cirad.fr> - ordering standard errors to match effects.
227    
228    2006-08-24  Douglas Bates  <bates@R-project.org>
229    
230            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
231            on R_ldl.
232            * R/lCholCMatrix.R,
233            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
234            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
235            * many files in ./R and ./src: Use more general version of
236            dup_mMatrix_as_dgeMatrix to simplify method definitions.
237            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
238            dtpMatrix, dspMatrix and dppMatrix conversions.
239    
240    
241    2006-08-23  Douglas Bates  <bates@R-project.org>
242    
243            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
244            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
245            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
246            dgeMatrix_crossprod (may need to do this in other places).
247            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
248            generic and method for dsCMatrix.  Use CHOLMOD for chol().
249    
250    2006-08-22  Douglas Bates  <bates@R-project.org>
251    
252            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
253            types of classed Matrices, matrices or numeric or logical vectors.
254            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
255            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
256            to Mutils.h (as an inline) and change name to Matrix_check_class;
257            fixes in as_cholmod_factor and chm_factor_to_SEXP.
258            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
259            dsCMatrix_matrix_solve.  Comment out vestigial functions.
260            * src/Csparse.c: use diag_P and uplo_P macros.
261    
262    2006-08-21  Douglas Bates  <bates@R-project.org>
263    
264            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
265            valgrind.
266            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
267            inverses.
268            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
269            -Wall warnings.
270            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
271            Use dup_mMatrix_as_dgeMatrix.
272    
273    2006-08-20  Douglas Bates  <bates@R-project.org>
274    
275            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
276            * tests/sparseQR.R: Added
277            * man/sparseQR-class.Rd: Document methods for qr.* generics
278            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
279    
280    2006-08-19  Douglas Bates  <bates@R-project.org>
281    
282            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
283            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
284            and qr.fitted.
285            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
286            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
287    
288    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
291            the base version has no "..." argument.
292    
293            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
294    
295            * R/Matrix.R: define and
296            * NAMESPACE: export as.numeric() and as.logical() methods.
297                    Let's hope these do not badly slow down something...
298            Finally export the zapsmall() method.
299    
300    2006-08-17  Douglas Bates  <bates@R-project.org>
301    
302            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
303            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
304            * src/dtCMatrix.c :Remove code that is no longer used
305            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
306    
307    2006-08-14  Douglas Bates  <bates@R-project.org>
308    
309            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
310            Csparse_to_logical and Csparse_symmetric_to_general.
311            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
312            coercion methods between CsparseMatrix and TsparseMatrix.
313    
314    2006-08-14  Douglas Bates  <bates@R-project.org>
315    
316            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
317            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
318            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
319            possible.
320    
321    2006-08-12  Douglas Bates  <bates@R-project.org>
322    
323            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
324              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
325              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
326              generalize conversions between TsparseMatrix, CsparseMatrix,
327              denseMatrix and matrix.  Preserve triangularity property and
328              propagate Dimnames in the easy cases.
329    
330    2006-08-10  Douglas Bates  <bates@R-project.org>
331    
332            * src/lmer.c: adjust checks in glmer_init for S4SXP
333            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
334            before S4SXP but for the wrong reasons.
335    
336    2006-08-08  Douglas Bates  <bates@R-project.org>
337    
338            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
339            Later modified to return the upper triangle only.
340            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
341    
342    2006-08-07  Douglas Bates  <bates@R-project.org>
343    
344            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
345            R-level conversion to a sparse symmetric class.
346            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
347            Remove conversion to sparse symmetric classes (now done in C code).
348    
349    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
352            * man/band.Rd:  adapt the \dontshow{} unit test.
353    
354    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.995-14  for CRAN
357    
358            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
359    
360            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
361            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
362    
363            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
364            * R/Tsparse.R (tril, triu, band): methods
365            * R/dgRMatrix.R (tril, ...):    ditto
366            * man/band.Rd:                  ditto
367    
368    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Matrix.R (head, tail): directly use utils:::head.matrix
371                    to be up-to-date automatically.
372    
373    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
376    
377            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
378            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
379            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
380            such that the S4 objects are always created by the current version
381            of R and 'Matrix' class definitions.
382    
383    2006-08-01  Douglas Bates  <bates@R-project.org>
384    
385            * R/lmer.R (LMEoptimize method), tests/lmer.R,
386            inst/external/test3comp.rda: Added warnings for convergence on
387            boundary and test cases.
388    
389            * src/lmer.c (mer_postVar): Modified to return the variances that
390            are marginal to the fixed effects, not conditional on them (which
391            is what the bVar slot contents represent).
392    
393    2006-07-31  Douglas Bates  <bates@R-project.org>
394    
395            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
396            function which calls the C function mer_hat_trace2.
397    
398            * man/ranef.Rd: Include description of "postVar" argument and
399            producing a caterpillar plot.
400    
401    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * NAMESPACE:    change  "correlation" to "corMatrix"
404            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
405            * R/dpoMatrix.R: ditto
406            * R/lmer.R:      ditto
407    
408    2006-07-28  Douglas Bates  <bates@R-project.org>
409    
410            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
411            RZXinv slot's contents into a separate internal function that can
412            be used in mer_hat_trace.
413    
414    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
417            via new smart
418            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
419            utility functions.
420    
421    
422    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/Csparse.R (tril, triu, band): do return *triangular* classed
425            matrices when appropriate; band() even symmetric ones.
426            (replCmat): extend to potentially all "CsparseMatrix"
427            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
428            allow subassignment for special sparse matrices.
429    
430            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
431    
432            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
433            argument; in glmer_*(): print only if(verbose).
434    
435            speed-optimize a few places by moving REAL(.) out of loops.
436    
437            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
438    
439    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
442                    since that wrongly triggers also for M[ logi , ]
443    
444            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
445            a symmetric matrix that results in a non-symmetric one.
446            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
447    
448            * R/dMatrix.R: make round(M) work as round(M, 0)
449    
450            * R/dgTMatrix.R (image): coordinate system and axis now use
451            1-based indices, not 0-based ones.
452    
453            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
454            * tests/indexing.R: test it.
455    
456            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
457            * man/isSymmetric-methods.Rd: and document it.
458    
459            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
460            * man/SparseM-conv.Rd: docu them
461    
462            * tests/other-pkgs.R: renamed from tests/graph.R and add example
463                    for 'SparseM' conversions
464    
465    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
466    
467            * R/Matrix.R (head): added head() and tail() methods.
468    
469    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Version): 0.995-12 released to CRAN
472    
473    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * tests/simple.R: add check for correct dsT -> dgT coercion;
476                    add check for correct printing of symmetric sparse matrices.
477    
478            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
479            for sparse symmetric matrices.
480    
481            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
482            diagonal twice.
483    
484    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
485    
486            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
487            being applied to the x slot (detected by Brian Ripley).
488    
489    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
492    
493            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
494    
495    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/lgCMatrix.c (lgCMatrix_diag): new function
498            * R/lgCMatrix.R (diag): for new method
499    
500            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
501                 ==> construction of illegal "*gTMatrix" via new() should
502                 now be much less easy:
503            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
504    
505            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
506                    directly.
507            * man/Matrix.Rd: documents it.
508    
509  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
510    
511          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 517 
517          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
518          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
519    
520            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
521            class.
522    
523    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/pMatrix.R: coercion pMatrix -> Tsparse
526    
527  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
528    
529            * DESCRIPTION (Version): 0.995-11 released to CRAN
530    
531          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
532          the output from mcmcsamp.          the output from mcmcsamp.
533    
# Line 23  Line 540 
540    
541          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
542          classes.          classes.
543            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
544    
545  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
# Line 60  Line 578 
578    
579          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
580          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.
581          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
582    
583    
584  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 701 
701          * 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)
702          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
703          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
704          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
705    
706  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
# Line 387  Line 905 
905  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
908          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
909          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
910    
911  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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