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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1618, Fri Oct 6 15:44:01 2006 UTC
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1    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-3
4    
5            * R/diagMatrix.R (bdiag): new function constructing block diagonal
6            (sparse) matrices.
7            * man/bdiag.Rd: docu + examples
8    
9            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
10            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
11    
12            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
13            that result is sparse or diagonal (and not dense).
14    
15            * man/Subassign-methods.Rd: fix examples
16    
17            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
18            should always return a sparse (and not sometimes a diagonal) matrix.
19    
20    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
23    
24    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
25    
26            * DESCRIPTION (Version): 0.9975-2
27    
28            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
29    
30    2006-10-02  Douglas Bates  <bates@R-project.org>
31    
32            * tests/dg_Matrix.R: Simplify test taking into account new code.
33    
34    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
37    
38            * R/lsTMatrix.R: new files w/ missing methods
39            * R/nsTMatrix.R:  "  'for completeness'
40    
41            * tests/Class+Meth.R: a bit less 'not.ok.classes'
42    
43            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
44    
45    
46    2006-09-28  Douglas Bates  <bates@R-project.org>
47    
48            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
49            included.
50    
51            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
52            Export C-callable functions used in Zt_create in lme4.
53    
54    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Version): 0.9975-1
57    
58            * tests/simple.R: less checks fail; using NA, found that our
59                    kronecker() is not base-compatible with NA's.
60    
61            * R/dMatrix.R: "Compare" method now implemented for all cases
62    
63            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
64    
65            * man/dtpMatrix-class.Rd: mention length of 'x' slot
66    
67            * src/dtpMatrix.c (dtpMatrix_validate): fix check
68            * src/dspMatrix.c (dspMatrix_validate): ditto
69    
70            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
71              including coercion to [nl]tTMatrix.
72    
73            * R/diagMatrix.R (show): print a header line as for other classes.
74    
75    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/Makefile.win (SUBDIRS): fix typo
78    
79    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
82    
83    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
86            symmetric and y missing in R code using %*% (cholmod_aat doesn't
87            accept a symmetric matrix).
88            * tests/group-methods.R: Uncomment test of crossprod applied to
89            lsCMatrix objects.
90    
91    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/AllClass.R (symmetricMatrix): add validity method (available
94            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
95    
96            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
97    
98            * tests/indexing.Rout.save:
99            * tests/indexing.R: additions, mainly for 'lsparse'
100    
101            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
102            case.
103    
104            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
105    
106    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
109                    as 'N' (1-letter - Ok?)
110    
111            * tests/group-methods.R: add test for logical + NAs
112    
113            * R/dMatrix.R ("Compare"): fix to work with NA's
114    
115            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
116    
117            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
118                    which is implemented.
119    
120    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/chm_common.c: coerce logical <-> double instead of
123            typecasting;  needed for "l" matrix handling in cholmod.
124    
125            * tests/other-pkgs.R (graph): small extension in "graph" checks.
126    
127            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
128            (Tsp2grNEL): other fixes needed
129    
130    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
133                    Matrices, since "lMatrix", also "lsparseM" can have NA
134            * R/ndenseMatrix.R, etc: new source files
135            * man/nsparseMatrix-classes.Rd, etc: new help files
136            * tests/: adaptions
137            * src/chm_common.c (chm_dense_to_SEXP): and others:
138                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
139            * src/Csparse.c, etc: ditto
140    
141    2006-09-11  Douglas Bates  <bates@R-project.org>
142    
143            * src/Mutils.[ch],init.c inst/include/*.h: Move the
144            alloc_d**Matrix functions to the lme4 package.
145    
146    2006-09-09  Douglas Bates  <bates@R-project.org>
147    
148            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
149            fixed
150    
151    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/lMatrix.R: new
154    
155            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
156    
157            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
158            * man/tcrossprod.Rd: ditto
159    
160    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
161    
162            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
163            for exported functions
164            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
165            Remove partitioning algorithms for sparse matrix reordering.  The
166            copyright on the Metis code was problematic and the methods were
167            rarely used.
168            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
169            operations are now done entirely in CHOLMOD code.
170    
171    2006-09-06  Douglas Bates  <bates@R-project.org>
172    
173            * src/Mutils.h: Remove functions that are no longer used.
174    
175    2006-09-04  Douglas Bates  <bates@R-project.org>
176    
177            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
178            * src/DEPS.mkf: update
179    
180    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * created branches/Matrix-for-R-2.3.x;  on trunk: do
183            * DESCRIPTION (Version): 0.9975-0
184            (Depends): R (>= 2.4.0)
185    
186    2006-09-01  Douglas Bates  <bates@R-project.org>
187    
188            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
189    
190    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
193            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
194    
195            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
196    
197    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
200            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
201            * R/dsparseMatrix.R: ditto
202            * R/Csparse.R: ditto
203    
204    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dMatrix.R (Compare): improve availability of "<", etc
207            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
208    
209    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
212            of a 0-index which was used as 1-index (..hmm)
213    
214            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
215    
216            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
217            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
218            (.is.diagonal): ditto
219    
220            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
221    
222            * R/Matrix.R (Matrix): also work for NA data
223    
224    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
227            in all cases.
228    
229    2006-08-27  Douglas Bates  <bates@R-project.org>
230    
231            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
232            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
233    
234    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
237            subclasses of "ddenseMatrix"
238            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
239            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
240            instead of half dozen specialized ones.
241    
242    2006-08-25  Douglas Bates  <bates@R-project.org>
243    
244            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
245            <tillard@cirad.fr> - ordering standard errors to match effects.
246    
247    2006-08-24  Douglas Bates  <bates@R-project.org>
248    
249            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
250            on R_ldl.
251            * R/lCholCMatrix.R,
252            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
253            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
254            * many files in ./R and ./src: Use more general version of
255            dup_mMatrix_as_dgeMatrix to simplify method definitions.
256            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
257            dtpMatrix, dspMatrix and dppMatrix conversions.
258    
259    
260    2006-08-23  Douglas Bates  <bates@R-project.org>
261    
262            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
263            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
264            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
265            dgeMatrix_crossprod (may need to do this in other places).
266            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
267            generic and method for dsCMatrix.  Use CHOLMOD for chol().
268    
269    2006-08-22  Douglas Bates  <bates@R-project.org>
270    
271            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
272            types of classed Matrices, matrices or numeric or logical vectors.
273            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
274            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
275            to Mutils.h (as an inline) and change name to Matrix_check_class;
276            fixes in as_cholmod_factor and chm_factor_to_SEXP.
277            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
278            dsCMatrix_matrix_solve.  Comment out vestigial functions.
279            * src/Csparse.c: use diag_P and uplo_P macros.
280    
281    2006-08-21  Douglas Bates  <bates@R-project.org>
282    
283            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
284            valgrind.
285            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
286            inverses.
287            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
288            -Wall warnings.
289            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
290            Use dup_mMatrix_as_dgeMatrix.
291    
292    2006-08-20  Douglas Bates  <bates@R-project.org>
293    
294            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
295            * tests/sparseQR.R: Added
296            * man/sparseQR-class.Rd: Document methods for qr.* generics
297            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
298    
299    2006-08-19  Douglas Bates  <bates@R-project.org>
300    
301            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
302            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
303            and qr.fitted.
304            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
305            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
306    
307    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
310            the base version has no "..." argument.
311    
312            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
313    
314            * R/Matrix.R: define and
315            * NAMESPACE: export as.numeric() and as.logical() methods.
316                    Let's hope these do not badly slow down something...
317            Finally export the zapsmall() method.
318    
319    2006-08-17  Douglas Bates  <bates@R-project.org>
320    
321            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
322            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
323            * src/dtCMatrix.c :Remove code that is no longer used
324            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
325    
326    2006-08-14  Douglas Bates  <bates@R-project.org>
327    
328            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
329            Csparse_to_logical and Csparse_symmetric_to_general.
330            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
331            coercion methods between CsparseMatrix and TsparseMatrix.
332    
333    2006-08-14  Douglas Bates  <bates@R-project.org>
334    
335            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
336            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
337            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
338            possible.
339    
340    2006-08-12  Douglas Bates  <bates@R-project.org>
341    
342            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
343              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
344              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
345              generalize conversions between TsparseMatrix, CsparseMatrix,
346              denseMatrix and matrix.  Preserve triangularity property and
347              propagate Dimnames in the easy cases.
348    
349    2006-08-10  Douglas Bates  <bates@R-project.org>
350    
351            * src/lmer.c: adjust checks in glmer_init for S4SXP
352            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
353            before S4SXP but for the wrong reasons.
354    
355    2006-08-08  Douglas Bates  <bates@R-project.org>
356    
357            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
358            Later modified to return the upper triangle only.
359            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
360    
361    2006-08-07  Douglas Bates  <bates@R-project.org>
362    
363            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
364            R-level conversion to a sparse symmetric class.
365            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
366            Remove conversion to sparse symmetric classes (now done in C code).
367    
368    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
371            * man/band.Rd:  adapt the \dontshow{} unit test.
372    
373    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Version): 0.995-14  for CRAN
376    
377            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
378    
379            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
380            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
381    
382            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
383            * R/Tsparse.R (tril, triu, band): methods
384            * R/dgRMatrix.R (tril, ...):    ditto
385            * man/band.Rd:                  ditto
386    
387    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Matrix.R (head, tail): directly use utils:::head.matrix
390                    to be up-to-date automatically.
391    
392    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
395    
396            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
397            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
398            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
399            such that the S4 objects are always created by the current version
400            of R and 'Matrix' class definitions.
401    
402    2006-08-01  Douglas Bates  <bates@R-project.org>
403    
404            * R/lmer.R (LMEoptimize method), tests/lmer.R,
405            inst/external/test3comp.rda: Added warnings for convergence on
406            boundary and test cases.
407    
408            * src/lmer.c (mer_postVar): Modified to return the variances that
409            are marginal to the fixed effects, not conditional on them (which
410            is what the bVar slot contents represent).
411    
412    2006-07-31  Douglas Bates  <bates@R-project.org>
413    
414            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
415            function which calls the C function mer_hat_trace2.
416    
417            * man/ranef.Rd: Include description of "postVar" argument and
418            producing a caterpillar plot.
419    
420    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * NAMESPACE:    change  "correlation" to "corMatrix"
423            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
424            * R/dpoMatrix.R: ditto
425            * R/lmer.R:      ditto
426    
427    2006-07-28  Douglas Bates  <bates@R-project.org>
428    
429            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
430            RZXinv slot's contents into a separate internal function that can
431            be used in mer_hat_trace.
432    
433    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
436            via new smart
437            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
438            utility functions.
439    
440    
441    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Csparse.R (tril, triu, band): do return *triangular* classed
444            matrices when appropriate; band() even symmetric ones.
445            (replCmat): extend to potentially all "CsparseMatrix"
446            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
447            allow subassignment for special sparse matrices.
448    
449            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
450    
451            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
452            argument; in glmer_*(): print only if(verbose).
453    
454            speed-optimize a few places by moving REAL(.) out of loops.
455    
456            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
457    
458    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
461                    since that wrongly triggers also for M[ logi , ]
462    
463            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
464            a symmetric matrix that results in a non-symmetric one.
465            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
466    
467            * R/dMatrix.R: make round(M) work as round(M, 0)
468    
469            * R/dgTMatrix.R (image): coordinate system and axis now use
470            1-based indices, not 0-based ones.
471    
472            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
473            * tests/indexing.R: test it.
474    
475            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
476            * man/isSymmetric-methods.Rd: and document it.
477    
478            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
479            * man/SparseM-conv.Rd: docu them
480    
481            * tests/other-pkgs.R: renamed from tests/graph.R and add example
482                    for 'SparseM' conversions
483    
484    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
485    
486            * R/Matrix.R (head): added head() and tail() methods.
487    
488    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * DESCRIPTION (Version): 0.995-12 released to CRAN
491    
492    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * tests/simple.R: add check for correct dsT -> dgT coercion;
495                    add check for correct printing of symmetric sparse matrices.
496    
497            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
498            for sparse symmetric matrices.
499    
500            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
501            diagonal twice.
502    
503    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
504    
505            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
506            being applied to the x slot (detected by Brian Ripley).
507    
508    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
511    
512            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
513    
514    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * src/lgCMatrix.c (lgCMatrix_diag): new function
517            * R/lgCMatrix.R (diag): for new method
518    
519            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
520                 ==> construction of illegal "*gTMatrix" via new() should
521                 now be much less easy:
522            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
523    
524            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
525                    directly.
526            * man/Matrix.Rd: documents it.
527    
528  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
529    
530          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 536 
536          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
537          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
538    
539            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
540            class.
541    
542    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/pMatrix.R: coercion pMatrix -> Tsparse
545    
546  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
547    
548            * DESCRIPTION (Version): 0.995-11 released to CRAN
549    
550          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
551          the output from mcmcsamp.          the output from mcmcsamp.
552    
# Line 23  Line 559 
559    
560          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
561          classes.          classes.
562            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
563    
564  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
# Line 60  Line 597 
597    
598          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
599          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.
600          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
601    
602    
603  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 720 
720          * 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)
721          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
722          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
723          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
724    
725  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
# Line 387  Line 924 
924  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
927          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
928          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
929    
930  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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