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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1619, Fri Oct 6 21:29:15 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            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
10    
11            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
12            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
13    
14            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
15            that result is sparse or diagonal (and not dense).
16    
17            * man/Subassign-methods.Rd: fix examples
18    
19            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
20            should always return a sparse (and not sometimes a diagonal) matrix.
21    
22    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
25    
26    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * DESCRIPTION (Version): 0.9975-2
29    
30            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
31    
32    2006-10-02  Douglas Bates  <bates@R-project.org>
33    
34            * tests/dg_Matrix.R: Simplify test taking into account new code.
35    
36    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
39    
40            * R/lsTMatrix.R: new files w/ missing methods
41            * R/nsTMatrix.R:  "  'for completeness'
42    
43            * tests/Class+Meth.R: a bit less 'not.ok.classes'
44    
45            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
46    
47    
48    2006-09-28  Douglas Bates  <bates@R-project.org>
49    
50            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
51            included.
52    
53            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
54            Export C-callable functions used in Zt_create in lme4.
55    
56    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): 0.9975-1
59    
60            * tests/simple.R: less checks fail; using NA, found that our
61                    kronecker() is not base-compatible with NA's.
62    
63            * R/dMatrix.R: "Compare" method now implemented for all cases
64    
65            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
66    
67            * man/dtpMatrix-class.Rd: mention length of 'x' slot
68    
69            * src/dtpMatrix.c (dtpMatrix_validate): fix check
70            * src/dspMatrix.c (dspMatrix_validate): ditto
71    
72            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
73              including coercion to [nl]tTMatrix.
74    
75            * R/diagMatrix.R (show): print a header line as for other classes.
76    
77    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/Makefile.win (SUBDIRS): fix typo
80    
81    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
84    
85    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
88            symmetric and y missing in R code using %*% (cholmod_aat doesn't
89            accept a symmetric matrix).
90            * tests/group-methods.R: Uncomment test of crossprod applied to
91            lsCMatrix objects.
92    
93    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/AllClass.R (symmetricMatrix): add validity method (available
96            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
97    
98            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
99    
100            * tests/indexing.Rout.save:
101            * tests/indexing.R: additions, mainly for 'lsparse'
102    
103            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
104            case.
105    
106            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
107    
108    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
111                    as 'N' (1-letter - Ok?)
112    
113            * tests/group-methods.R: add test for logical + NAs
114    
115            * R/dMatrix.R ("Compare"): fix to work with NA's
116    
117            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
118    
119            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
120                    which is implemented.
121    
122    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/chm_common.c: coerce logical <-> double instead of
125            typecasting;  needed for "l" matrix handling in cholmod.
126    
127            * tests/other-pkgs.R (graph): small extension in "graph" checks.
128    
129            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
130            (Tsp2grNEL): other fixes needed
131    
132    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
135                    Matrices, since "lMatrix", also "lsparseM" can have NA
136            * R/ndenseMatrix.R, etc: new source files
137            * man/nsparseMatrix-classes.Rd, etc: new help files
138            * tests/: adaptions
139            * src/chm_common.c (chm_dense_to_SEXP): and others:
140                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
141            * src/Csparse.c, etc: ditto
142    
143    2006-09-11  Douglas Bates  <bates@R-project.org>
144    
145            * src/Mutils.[ch],init.c inst/include/*.h: Move the
146            alloc_d**Matrix functions to the lme4 package.
147    
148    2006-09-09  Douglas Bates  <bates@R-project.org>
149    
150            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
151            fixed
152    
153    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/lMatrix.R: new
156    
157            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
158    
159            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
160            * man/tcrossprod.Rd: ditto
161    
162    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
165            for exported functions
166            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
167            Remove partitioning algorithms for sparse matrix reordering.  The
168            copyright on the Metis code was problematic and the methods were
169            rarely used.
170            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
171            operations are now done entirely in CHOLMOD code.
172    
173    2006-09-06  Douglas Bates  <bates@R-project.org>
174    
175            * src/Mutils.h: Remove functions that are no longer used.
176    
177    2006-09-04  Douglas Bates  <bates@R-project.org>
178    
179            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
180            * src/DEPS.mkf: update
181    
182    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * created branches/Matrix-for-R-2.3.x;  on trunk: do
185            * DESCRIPTION (Version): 0.9975-0
186            (Depends): R (>= 2.4.0)
187    
188    2006-09-01  Douglas Bates  <bates@R-project.org>
189    
190            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
191    
192    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
195            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
196    
197            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
198    
199    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
202            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
203            * R/dsparseMatrix.R: ditto
204            * R/Csparse.R: ditto
205    
206    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dMatrix.R (Compare): improve availability of "<", etc
209            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
210    
211    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
214            of a 0-index which was used as 1-index (..hmm)
215    
216            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
217    
218            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
219            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
220            (.is.diagonal): ditto
221    
222            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
223    
224            * R/Matrix.R (Matrix): also work for NA data
225    
226    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
229            in all cases.
230    
231    2006-08-27  Douglas Bates  <bates@R-project.org>
232    
233            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
234            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
235    
236    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
239            subclasses of "ddenseMatrix"
240            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
241            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
242            instead of half dozen specialized ones.
243    
244    2006-08-25  Douglas Bates  <bates@R-project.org>
245    
246            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
247            <tillard@cirad.fr> - ordering standard errors to match effects.
248    
249    2006-08-24  Douglas Bates  <bates@R-project.org>
250    
251            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
252            on R_ldl.
253            * R/lCholCMatrix.R,
254            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
255            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
256            * many files in ./R and ./src: Use more general version of
257            dup_mMatrix_as_dgeMatrix to simplify method definitions.
258            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
259            dtpMatrix, dspMatrix and dppMatrix conversions.
260    
261    
262    2006-08-23  Douglas Bates  <bates@R-project.org>
263    
264            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
265            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
266            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
267            dgeMatrix_crossprod (may need to do this in other places).
268            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
269            generic and method for dsCMatrix.  Use CHOLMOD for chol().
270    
271    2006-08-22  Douglas Bates  <bates@R-project.org>
272    
273            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
274            types of classed Matrices, matrices or numeric or logical vectors.
275            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
276            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
277            to Mutils.h (as an inline) and change name to Matrix_check_class;
278            fixes in as_cholmod_factor and chm_factor_to_SEXP.
279            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
280            dsCMatrix_matrix_solve.  Comment out vestigial functions.
281            * src/Csparse.c: use diag_P and uplo_P macros.
282    
283    2006-08-21  Douglas Bates  <bates@R-project.org>
284    
285            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
286            valgrind.
287            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
288            inverses.
289            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
290            -Wall warnings.
291            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
292            Use dup_mMatrix_as_dgeMatrix.
293    
294    2006-08-20  Douglas Bates  <bates@R-project.org>
295    
296            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
297            * tests/sparseQR.R: Added
298            * man/sparseQR-class.Rd: Document methods for qr.* generics
299            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
300    
301    2006-08-19  Douglas Bates  <bates@R-project.org>
302    
303            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
304            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
305            and qr.fitted.
306            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
307            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
308    
309    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
312            the base version has no "..." argument.
313    
314            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
315    
316            * R/Matrix.R: define and
317            * NAMESPACE: export as.numeric() and as.logical() methods.
318                    Let's hope these do not badly slow down something...
319            Finally export the zapsmall() method.
320    
321    2006-08-17  Douglas Bates  <bates@R-project.org>
322    
323            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
324            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
325            * src/dtCMatrix.c :Remove code that is no longer used
326            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
327    
328    2006-08-14  Douglas Bates  <bates@R-project.org>
329    
330            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
331            Csparse_to_logical and Csparse_symmetric_to_general.
332            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
333            coercion methods between CsparseMatrix and TsparseMatrix.
334    
335    2006-08-14  Douglas Bates  <bates@R-project.org>
336    
337            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
338            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
339            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
340            possible.
341    
342    2006-08-12  Douglas Bates  <bates@R-project.org>
343    
344            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
345              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
346              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
347              generalize conversions between TsparseMatrix, CsparseMatrix,
348              denseMatrix and matrix.  Preserve triangularity property and
349              propagate Dimnames in the easy cases.
350    
351    2006-08-10  Douglas Bates  <bates@R-project.org>
352    
353            * src/lmer.c: adjust checks in glmer_init for S4SXP
354            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
355            before S4SXP but for the wrong reasons.
356    
357    2006-08-08  Douglas Bates  <bates@R-project.org>
358    
359            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
360            Later modified to return the upper triangle only.
361            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
362    
363    2006-08-07  Douglas Bates  <bates@R-project.org>
364    
365            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
366            R-level conversion to a sparse symmetric class.
367            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
368            Remove conversion to sparse symmetric classes (now done in C code).
369    
370    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
373            * man/band.Rd:  adapt the \dontshow{} unit test.
374    
375    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * DESCRIPTION (Version): 0.995-14  for CRAN
378    
379            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
380    
381            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
382            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
383    
384            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
385            * R/Tsparse.R (tril, triu, band): methods
386            * R/dgRMatrix.R (tril, ...):    ditto
387            * man/band.Rd:                  ditto
388    
389    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Matrix.R (head, tail): directly use utils:::head.matrix
392                    to be up-to-date automatically.
393    
394    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
397    
398            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
399            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
400            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
401            such that the S4 objects are always created by the current version
402            of R and 'Matrix' class definitions.
403    
404    2006-08-01  Douglas Bates  <bates@R-project.org>
405    
406            * R/lmer.R (LMEoptimize method), tests/lmer.R,
407            inst/external/test3comp.rda: Added warnings for convergence on
408            boundary and test cases.
409    
410            * src/lmer.c (mer_postVar): Modified to return the variances that
411            are marginal to the fixed effects, not conditional on them (which
412            is what the bVar slot contents represent).
413    
414    2006-07-31  Douglas Bates  <bates@R-project.org>
415    
416            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
417            function which calls the C function mer_hat_trace2.
418    
419            * man/ranef.Rd: Include description of "postVar" argument and
420            producing a caterpillar plot.
421    
422    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * NAMESPACE:    change  "correlation" to "corMatrix"
425            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
426            * R/dpoMatrix.R: ditto
427            * R/lmer.R:      ditto
428    
429    2006-07-28  Douglas Bates  <bates@R-project.org>
430    
431            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
432            RZXinv slot's contents into a separate internal function that can
433            be used in mer_hat_trace.
434    
435    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
438            via new smart
439            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
440            utility functions.
441    
442    
443    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/Csparse.R (tril, triu, band): do return *triangular* classed
446            matrices when appropriate; band() even symmetric ones.
447            (replCmat): extend to potentially all "CsparseMatrix"
448            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
449            allow subassignment for special sparse matrices.
450    
451            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
452    
453            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
454            argument; in glmer_*(): print only if(verbose).
455    
456            speed-optimize a few places by moving REAL(.) out of loops.
457    
458            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
459    
460    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
463                    since that wrongly triggers also for M[ logi , ]
464    
465            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
466            a symmetric matrix that results in a non-symmetric one.
467            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
468    
469            * R/dMatrix.R: make round(M) work as round(M, 0)
470    
471            * R/dgTMatrix.R (image): coordinate system and axis now use
472            1-based indices, not 0-based ones.
473    
474            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
475            * tests/indexing.R: test it.
476    
477            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
478            * man/isSymmetric-methods.Rd: and document it.
479    
480            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
481            * man/SparseM-conv.Rd: docu them
482    
483            * tests/other-pkgs.R: renamed from tests/graph.R and add example
484                    for 'SparseM' conversions
485    
486    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
487    
488            * R/Matrix.R (head): added head() and tail() methods.
489    
490    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * DESCRIPTION (Version): 0.995-12 released to CRAN
493    
494    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * tests/simple.R: add check for correct dsT -> dgT coercion;
497                    add check for correct printing of symmetric sparse matrices.
498    
499            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
500            for sparse symmetric matrices.
501    
502            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
503            diagonal twice.
504    
505    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
506    
507            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
508            being applied to the x slot (detected by Brian Ripley).
509    
510    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
513    
514            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
515    
516    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * src/lgCMatrix.c (lgCMatrix_diag): new function
519            * R/lgCMatrix.R (diag): for new method
520    
521            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
522                 ==> construction of illegal "*gTMatrix" via new() should
523                 now be much less easy:
524            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
525    
526            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
527                    directly.
528            * man/Matrix.Rd: documents it.
529    
530    2006-07-06  Douglas Bates  <bates@R-project.org>
531    
532            * src/pedigree.c (pedigree_inbreeding): Correction in
533            initialization.  This function is not currently being used and is
534            not fully tested.
535    
536            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
537            Introduced the glmer class.  Added code for mcmcmsamp on glmer
538            objects.  Modified validity check on pedigree objects to account
539            for nonparallel patterns of missingness of parents.
540    
541            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
542            class.
543    
544    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/pMatrix.R: coercion pMatrix -> Tsparse
547    
548    2006-06-12  Douglas Bates  <bates@R-project.org>
549    
550            * DESCRIPTION (Version): 0.995-11 released to CRAN
551    
552            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
553            the output from mcmcsamp.
554    
555    2006-06-10  Douglas Bates  <bates@R-project.org>
556    
557            * R/lmer.R (simulestimate): added C code for calculating the trace
558            of the hat matrix.
559    
560    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
563            classes.
564            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
565    
566    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/dgTMatrix.R (colSums): etc. All four of
569            colSums(), rowSums(), colMeans(), rowMeans() now should work for
570            all "Matrices".
571    
572  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
573    
574          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 599 
599    
600          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
601          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.
602          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
603    
604    
605  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 722 
722          * 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)
723          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
724          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
725          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
726    
727  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
# Line 355  Line 926 
926  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
927    
928          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
929          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
930          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
931    
932  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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