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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1613, Wed Oct 4 22:41:49 2006 UTC
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1    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): 0.9975-2
4    
5            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
6    
7    2006-10-02  Douglas Bates  <bates@R-project.org>
8    
9            * tests/dg_Matrix.R: Simplify test taking into account new code.
10    
11    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
14    
15            * R/lsTMatrix.R: new files w/ missing methods
16            * R/nsTMatrix.R:  "  'for completeness'
17    
18            * tests/Class+Meth.R: a bit less 'not.ok.classes'
19    
20            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
21    
22    
23    2006-09-28  Douglas Bates  <bates@R-project.org>
24    
25            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
26            included.
27    
28            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
29            Export C-callable functions used in Zt_create in lme4.
30    
31    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.9975-1
34    
35            * tests/simple.R: less checks fail; using NA, found that our
36                    kronecker() is not base-compatible with NA's.
37    
38            * R/dMatrix.R: "Compare" method now implemented for all cases
39    
40            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
41    
42            * man/dtpMatrix-class.Rd: mention length of 'x' slot
43    
44            * src/dtpMatrix.c (dtpMatrix_validate): fix check
45            * src/dspMatrix.c (dspMatrix_validate): ditto
46    
47            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
48              including coercion to [nl]tTMatrix.
49    
50            * R/diagMatrix.R (show): print a header line as for other classes.
51    
52    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/Makefile.win (SUBDIRS): fix typo
55    
56    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
59    
60    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
63            symmetric and y missing in R code using %*% (cholmod_aat doesn't
64            accept a symmetric matrix).
65            * tests/group-methods.R: Uncomment test of crossprod applied to
66            lsCMatrix objects.
67    
68    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllClass.R (symmetricMatrix): add validity method (available
71            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
72    
73            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
74    
75            * tests/indexing.Rout.save:
76            * tests/indexing.R: additions, mainly for 'lsparse'
77    
78            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
79            case.
80    
81            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
82    
83    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
86                    as 'N' (1-letter - Ok?)
87    
88            * tests/group-methods.R: add test for logical + NAs
89    
90            * R/dMatrix.R ("Compare"): fix to work with NA's
91    
92            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
93    
94            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
95                    which is implemented.
96    
97    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * src/chm_common.c: coerce logical <-> double instead of
100            typecasting;  needed for "l" matrix handling in cholmod.
101    
102            * tests/other-pkgs.R (graph): small extension in "graph" checks.
103    
104            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
105            (Tsp2grNEL): other fixes needed
106    
107    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
110                    Matrices, since "lMatrix", also "lsparseM" can have NA
111            * R/ndenseMatrix.R, etc: new source files
112            * man/nsparseMatrix-classes.Rd, etc: new help files
113            * tests/: adaptions
114            * src/chm_common.c (chm_dense_to_SEXP): and others:
115                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
116            * src/Csparse.c, etc: ditto
117    
118    2006-09-11  Douglas Bates  <bates@R-project.org>
119    
120            * src/Mutils.[ch],init.c inst/include/*.h: Move the
121            alloc_d**Matrix functions to the lme4 package.
122    
123    2006-09-09  Douglas Bates  <bates@R-project.org>
124    
125            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
126            fixed
127    
128    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/lMatrix.R: new
131    
132            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
133    
134            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
135            * man/tcrossprod.Rd: ditto
136    
137    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
140            for exported functions
141            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
142            Remove partitioning algorithms for sparse matrix reordering.  The
143            copyright on the Metis code was problematic and the methods were
144            rarely used.
145            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
146            operations are now done entirely in CHOLMOD code.
147    
148    2006-09-06  Douglas Bates  <bates@R-project.org>
149    
150            * src/Mutils.h: Remove functions that are no longer used.
151    
152    2006-09-04  Douglas Bates  <bates@R-project.org>
153    
154            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
155            * src/DEPS.mkf: update
156    
157    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * created branches/Matrix-for-R-2.3.x;  on trunk: do
160            * DESCRIPTION (Version): 0.9975-0
161            (Depends): R (>= 2.4.0)
162    
163    2006-09-01  Douglas Bates  <bates@R-project.org>
164    
165            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
166    
167    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
170            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
171    
172            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
173    
174    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
177            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
178            * R/dsparseMatrix.R: ditto
179            * R/Csparse.R: ditto
180    
181    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/dMatrix.R (Compare): improve availability of "<", etc
184            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
185    
186    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
189            of a 0-index which was used as 1-index (..hmm)
190    
191            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
192    
193            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
194            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
195            (.is.diagonal): ditto
196    
197            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
198    
199            * R/Matrix.R (Matrix): also work for NA data
200    
201    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
204            in all cases.
205    
206    2006-08-27  Douglas Bates  <bates@R-project.org>
207    
208            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
209            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
210    
211    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
214            subclasses of "ddenseMatrix"
215            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
216            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
217            instead of half dozen specialized ones.
218    
219    2006-08-25  Douglas Bates  <bates@R-project.org>
220    
221            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
222            <tillard@cirad.fr> - ordering standard errors to match effects.
223    
224    2006-08-24  Douglas Bates  <bates@R-project.org>
225    
226            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
227            on R_ldl.
228            * R/lCholCMatrix.R,
229            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
230            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
231            * many files in ./R and ./src: Use more general version of
232            dup_mMatrix_as_dgeMatrix to simplify method definitions.
233            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
234            dtpMatrix, dspMatrix and dppMatrix conversions.
235    
236    
237    2006-08-23  Douglas Bates  <bates@R-project.org>
238    
239            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
240            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
241            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
242            dgeMatrix_crossprod (may need to do this in other places).
243            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
244            generic and method for dsCMatrix.  Use CHOLMOD for chol().
245    
246    2006-08-22  Douglas Bates  <bates@R-project.org>
247    
248            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
249            types of classed Matrices, matrices or numeric or logical vectors.
250            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
251            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
252            to Mutils.h (as an inline) and change name to Matrix_check_class;
253            fixes in as_cholmod_factor and chm_factor_to_SEXP.
254            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
255            dsCMatrix_matrix_solve.  Comment out vestigial functions.
256            * src/Csparse.c: use diag_P and uplo_P macros.
257    
258    2006-08-21  Douglas Bates  <bates@R-project.org>
259    
260            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
261            valgrind.
262            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
263            inverses.
264            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
265            -Wall warnings.
266            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
267            Use dup_mMatrix_as_dgeMatrix.
268    
269    2006-08-20  Douglas Bates  <bates@R-project.org>
270    
271            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
272            * tests/sparseQR.R: Added
273            * man/sparseQR-class.Rd: Document methods for qr.* generics
274            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
275    
276    2006-08-19  Douglas Bates  <bates@R-project.org>
277    
278            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
279            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
280            and qr.fitted.
281            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
282            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
283    
284    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
287            the base version has no "..." argument.
288    
289            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
290    
291            * R/Matrix.R: define and
292            * NAMESPACE: export as.numeric() and as.logical() methods.
293                    Let's hope these do not badly slow down something...
294            Finally export the zapsmall() method.
295    
296    2006-08-17  Douglas Bates  <bates@R-project.org>
297    
298            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
299            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
300            * src/dtCMatrix.c :Remove code that is no longer used
301            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
302    
303    2006-08-14  Douglas Bates  <bates@R-project.org>
304    
305            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
306            Csparse_to_logical and Csparse_symmetric_to_general.
307            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
308            coercion methods between CsparseMatrix and TsparseMatrix.
309    
310    2006-08-14  Douglas Bates  <bates@R-project.org>
311    
312            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
313            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
314            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
315            possible.
316    
317    2006-08-12  Douglas Bates  <bates@R-project.org>
318    
319            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
320              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
321              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
322              generalize conversions between TsparseMatrix, CsparseMatrix,
323              denseMatrix and matrix.  Preserve triangularity property and
324              propagate Dimnames in the easy cases.
325    
326    2006-08-10  Douglas Bates  <bates@R-project.org>
327    
328            * src/lmer.c: adjust checks in glmer_init for S4SXP
329            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
330            before S4SXP but for the wrong reasons.
331    
332    2006-08-08  Douglas Bates  <bates@R-project.org>
333    
334            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
335            Later modified to return the upper triangle only.
336            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
337    
338    2006-08-07  Douglas Bates  <bates@R-project.org>
339    
340            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
341            R-level conversion to a sparse symmetric class.
342            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
343            Remove conversion to sparse symmetric classes (now done in C code).
344    
345    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
348            * man/band.Rd:  adapt the \dontshow{} unit test.
349    
350    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * DESCRIPTION (Version): 0.995-14  for CRAN
353    
354            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
355    
356            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
357            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
358    
359            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
360            * R/Tsparse.R (tril, triu, band): methods
361            * R/dgRMatrix.R (tril, ...):    ditto
362            * man/band.Rd:                  ditto
363    
364    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Matrix.R (head, tail): directly use utils:::head.matrix
367                    to be up-to-date automatically.
368    
369    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
372    
373            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
374            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
375            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
376            such that the S4 objects are always created by the current version
377            of R and 'Matrix' class definitions.
378    
379    2006-08-01  Douglas Bates  <bates@R-project.org>
380    
381            * R/lmer.R (LMEoptimize method), tests/lmer.R,
382            inst/external/test3comp.rda: Added warnings for convergence on
383            boundary and test cases.
384    
385            * src/lmer.c (mer_postVar): Modified to return the variances that
386            are marginal to the fixed effects, not conditional on them (which
387            is what the bVar slot contents represent).
388    
389    2006-07-31  Douglas Bates  <bates@R-project.org>
390    
391            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
392            function which calls the C function mer_hat_trace2.
393    
394            * man/ranef.Rd: Include description of "postVar" argument and
395            producing a caterpillar plot.
396    
397    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * NAMESPACE:    change  "correlation" to "corMatrix"
400            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
401            * R/dpoMatrix.R: ditto
402            * R/lmer.R:      ditto
403    
404    2006-07-28  Douglas Bates  <bates@R-project.org>
405    
406            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
407            RZXinv slot's contents into a separate internal function that can
408            be used in mer_hat_trace.
409    
410    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
413            via new smart
414            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
415            utility functions.
416    
417    
418    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/Csparse.R (tril, triu, band): do return *triangular* classed
421            matrices when appropriate; band() even symmetric ones.
422            (replCmat): extend to potentially all "CsparseMatrix"
423            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
424            allow subassignment for special sparse matrices.
425    
426            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
427    
428            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
429            argument; in glmer_*(): print only if(verbose).
430    
431            speed-optimize a few places by moving REAL(.) out of loops.
432    
433            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
434    
435    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
438                    since that wrongly triggers also for M[ logi , ]
439    
440            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
441            a symmetric matrix that results in a non-symmetric one.
442            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
443    
444            * R/dMatrix.R: make round(M) work as round(M, 0)
445    
446            * R/dgTMatrix.R (image): coordinate system and axis now use
447            1-based indices, not 0-based ones.
448    
449            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
450            * tests/indexing.R: test it.
451    
452            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
453            * man/isSymmetric-methods.Rd: and document it.
454    
455            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
456            * man/SparseM-conv.Rd: docu them
457    
458            * tests/other-pkgs.R: renamed from tests/graph.R and add example
459                    for 'SparseM' conversions
460    
461    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
462    
463            * R/Matrix.R (head): added head() and tail() methods.
464    
465    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * DESCRIPTION (Version): 0.995-12 released to CRAN
468    
469    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/simple.R: add check for correct dsT -> dgT coercion;
472                    add check for correct printing of symmetric sparse matrices.
473    
474            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
475            for sparse symmetric matrices.
476    
477            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
478            diagonal twice.
479    
480    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
481    
482            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
483            being applied to the x slot (detected by Brian Ripley).
484    
485    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
488    
489            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
490    
491    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * src/lgCMatrix.c (lgCMatrix_diag): new function
494            * R/lgCMatrix.R (diag): for new method
495    
496            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
497                 ==> construction of illegal "*gTMatrix" via new() should
498                 now be much less easy:
499            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
500    
501            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
502                    directly.
503            * man/Matrix.Rd: documents it.
504    
505    2006-07-06  Douglas Bates  <bates@R-project.org>
506    
507            * src/pedigree.c (pedigree_inbreeding): Correction in
508            initialization.  This function is not currently being used and is
509            not fully tested.
510    
511            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
512            Introduced the glmer class.  Added code for mcmcmsamp on glmer
513            objects.  Modified validity check on pedigree objects to account
514            for nonparallel patterns of missingness of parents.
515    
516            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
517            class.
518    
519    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/pMatrix.R: coercion pMatrix -> Tsparse
522    
523    2006-06-12  Douglas Bates  <bates@R-project.org>
524    
525            * DESCRIPTION (Version): 0.995-11 released to CRAN
526    
527            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
528            the output from mcmcsamp.
529    
530    2006-06-10  Douglas Bates  <bates@R-project.org>
531    
532            * R/lmer.R (simulestimate): added C code for calculating the trace
533            of the hat matrix.
534    
535    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
538            classes.
539            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
540    
541    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/dgTMatrix.R (colSums): etc. All four of
544            colSums(), rowSums(), colMeans(), rowMeans() now should work for
545            all "Matrices".
546    
547  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
548    
549          * 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 574 
574    
575          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
576          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.
577          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
578    
579    
580  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 697 
697          * 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)
698          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
699          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
700          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
701    
702  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
# Line 355  Line 901 
901  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
904          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
905          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
906    
907  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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