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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1599, Fri Sep 29 09:39:50 2006 UTC
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1    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/lsTMatrix.R: new files w/ missing methods
4            * R/nsTMatrix.R:  "  'for completeness'
5    
6            * tests/Class+Meth.R: a bit less 'not.ok.classes'
7    
8            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
9    
10    
11    2006-09-28  Douglas Bates  <bates@R-project.org>
12    
13            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
14            included.
15    
16            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
17            Export C-callable functions used in Zt_create in lme4.
18    
19    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * DESCRIPTION (Version): 0.9975-1
22    
23            * tests/simple.R: less checks fail; using NA, found that our
24                    kronecker() is not base-compatible with NA's.
25    
26            * R/dMatrix.R: "Compare" method now implemented for all cases
27    
28            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
29    
30            * man/dtpMatrix-class.Rd: mention length of 'x' slot
31    
32            * src/dtpMatrix.c (dtpMatrix_validate): fix check
33            * src/dspMatrix.c (dspMatrix_validate): ditto
34    
35            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
36              including coercion to [nl]tTMatrix.
37    
38            * R/diagMatrix.R (show): print a header line as for other classes.
39    
40    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * src/Makefile.win (SUBDIRS): fix typo
43    
44    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
47    
48    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
49    
50            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
51            symmetric and y missing in R code using %*% (cholmod_aat doesn't
52            accept a symmetric matrix).
53            * tests/group-methods.R: Uncomment test of crossprod applied to
54            lsCMatrix objects.
55    
56    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (symmetricMatrix): add validity method (available
59            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
60    
61            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
62    
63            * tests/indexing.Rout.save:
64            * tests/indexing.R: additions, mainly for 'lsparse'
65    
66            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
67            case.
68    
69            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
70    
71    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
74                    as 'N' (1-letter - Ok?)
75    
76            * tests/group-methods.R: add test for logical + NAs
77    
78            * R/dMatrix.R ("Compare"): fix to work with NA's
79    
80            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
81    
82            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
83                    which is implemented.
84    
85    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * src/chm_common.c: coerce logical <-> double instead of
88            typecasting;  needed for "l" matrix handling in cholmod.
89    
90            * tests/other-pkgs.R (graph): small extension in "graph" checks.
91    
92            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
93            (Tsp2grNEL): other fixes needed
94    
95    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
98                    Matrices, since "lMatrix", also "lsparseM" can have NA
99            * R/ndenseMatrix.R, etc: new source files
100            * man/nsparseMatrix-classes.Rd, etc: new help files
101            * tests/: adaptions
102            * src/chm_common.c (chm_dense_to_SEXP): and others:
103                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
104            * src/Csparse.c, etc: ditto
105    
106    2006-09-11  Douglas Bates  <bates@R-project.org>
107    
108            * src/Mutils.[ch],init.c inst/include/*.h: Move the
109            alloc_d**Matrix functions to the lme4 package.
110    
111    2006-09-09  Douglas Bates  <bates@R-project.org>
112    
113            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
114            fixed
115    
116    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/lMatrix.R: new
119    
120            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
121    
122            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
123            * man/tcrossprod.Rd: ditto
124    
125    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
126    
127            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
128            for exported functions
129            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
130            Remove partitioning algorithms for sparse matrix reordering.  The
131            copyright on the Metis code was problematic and the methods were
132            rarely used.
133            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
134            operations are now done entirely in CHOLMOD code.
135    
136    2006-09-06  Douglas Bates  <bates@R-project.org>
137    
138            * src/Mutils.h: Remove functions that are no longer used.
139    
140    2006-09-04  Douglas Bates  <bates@R-project.org>
141    
142            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
143            * src/DEPS.mkf: update
144    
145    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * created branches/Matrix-for-R-2.3.x;  on trunk: do
148            * DESCRIPTION (Version): 0.9975-0
149            (Depends): R (>= 2.4.0)
150    
151    2006-09-01  Douglas Bates  <bates@R-project.org>
152    
153            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
154    
155    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
158            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
159    
160            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
161    
162    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
165            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
166            * R/dsparseMatrix.R: ditto
167            * R/Csparse.R: ditto
168    
169    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/dMatrix.R (Compare): improve availability of "<", etc
172            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
173    
174    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
177            of a 0-index which was used as 1-index (..hmm)
178    
179            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
180    
181            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
182            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
183            (.is.diagonal): ditto
184    
185            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
186    
187            * R/Matrix.R (Matrix): also work for NA data
188    
189    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
192            in all cases.
193    
194    2006-08-27  Douglas Bates  <bates@R-project.org>
195    
196            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
197            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
198    
199    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
202            subclasses of "ddenseMatrix"
203            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
204            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
205            instead of half dozen specialized ones.
206    
207    2006-08-25  Douglas Bates  <bates@R-project.org>
208    
209            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
210            <tillard@cirad.fr> - ordering standard errors to match effects.
211    
212    2006-08-24  Douglas Bates  <bates@R-project.org>
213    
214            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
215            on R_ldl.
216            * R/lCholCMatrix.R,
217            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
218            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
219            * many files in ./R and ./src: Use more general version of
220            dup_mMatrix_as_dgeMatrix to simplify method definitions.
221            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
222            dtpMatrix, dspMatrix and dppMatrix conversions.
223    
224    
225    2006-08-23  Douglas Bates  <bates@R-project.org>
226    
227            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
228            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
229            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
230            dgeMatrix_crossprod (may need to do this in other places).
231            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
232            generic and method for dsCMatrix.  Use CHOLMOD for chol().
233    
234    2006-08-22  Douglas Bates  <bates@R-project.org>
235    
236            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
237            types of classed Matrices, matrices or numeric or logical vectors.
238            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
239            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
240            to Mutils.h (as an inline) and change name to Matrix_check_class;
241            fixes in as_cholmod_factor and chm_factor_to_SEXP.
242            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
243            dsCMatrix_matrix_solve.  Comment out vestigial functions.
244            * src/Csparse.c: use diag_P and uplo_P macros.
245    
246    2006-08-21  Douglas Bates  <bates@R-project.org>
247    
248            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
249            valgrind.
250            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
251            inverses.
252            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
253            -Wall warnings.
254            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
255            Use dup_mMatrix_as_dgeMatrix.
256    
257    2006-08-20  Douglas Bates  <bates@R-project.org>
258    
259            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
260            * tests/sparseQR.R: Added
261            * man/sparseQR-class.Rd: Document methods for qr.* generics
262            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
263    
264    2006-08-19  Douglas Bates  <bates@R-project.org>
265    
266            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
267            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
268            and qr.fitted.
269            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
270            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
271    
272    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
275            the base version has no "..." argument.
276    
277            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
278    
279            * R/Matrix.R: define and
280            * NAMESPACE: export as.numeric() and as.logical() methods.
281                    Let's hope these do not badly slow down something...
282            Finally export the zapsmall() method.
283    
284    2006-08-17  Douglas Bates  <bates@R-project.org>
285    
286            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
287            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
288            * src/dtCMatrix.c :Remove code that is no longer used
289            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
290    
291    2006-08-14  Douglas Bates  <bates@R-project.org>
292    
293            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
294            Csparse_to_logical and Csparse_symmetric_to_general.
295            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
296            coercion methods between CsparseMatrix and TsparseMatrix.
297    
298    2006-08-14  Douglas Bates  <bates@R-project.org>
299    
300            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
301            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
302            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
303            possible.
304    
305    2006-08-12  Douglas Bates  <bates@R-project.org>
306    
307            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
308              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
309              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
310              generalize conversions between TsparseMatrix, CsparseMatrix,
311              denseMatrix and matrix.  Preserve triangularity property and
312              propagate Dimnames in the easy cases.
313    
314    2006-08-10  Douglas Bates  <bates@R-project.org>
315    
316            * src/lmer.c: adjust checks in glmer_init for S4SXP
317            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
318            before S4SXP but for the wrong reasons.
319    
320    2006-08-08  Douglas Bates  <bates@R-project.org>
321    
322            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
323            Later modified to return the upper triangle only.
324            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
325    
326    2006-08-07  Douglas Bates  <bates@R-project.org>
327    
328            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
329            R-level conversion to a sparse symmetric class.
330            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
331            Remove conversion to sparse symmetric classes (now done in C code).
332    
333    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
336            * man/band.Rd:  adapt the \dontshow{} unit test.
337    
338    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * DESCRIPTION (Version): 0.995-14  for CRAN
341    
342            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
343    
344            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
345            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
346    
347            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
348            * R/Tsparse.R (tril, triu, band): methods
349            * R/dgRMatrix.R (tril, ...):    ditto
350            * man/band.Rd:                  ditto
351    
352    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/Matrix.R (head, tail): directly use utils:::head.matrix
355                    to be up-to-date automatically.
356    
357    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
360    
361            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
362            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
363            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
364            such that the S4 objects are always created by the current version
365            of R and 'Matrix' class definitions.
366    
367    2006-08-01  Douglas Bates  <bates@R-project.org>
368    
369            * R/lmer.R (LMEoptimize method), tests/lmer.R,
370            inst/external/test3comp.rda: Added warnings for convergence on
371            boundary and test cases.
372    
373            * src/lmer.c (mer_postVar): Modified to return the variances that
374            are marginal to the fixed effects, not conditional on them (which
375            is what the bVar slot contents represent).
376    
377    2006-07-31  Douglas Bates  <bates@R-project.org>
378    
379            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
380            function which calls the C function mer_hat_trace2.
381    
382            * man/ranef.Rd: Include description of "postVar" argument and
383            producing a caterpillar plot.
384    
385    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * NAMESPACE:    change  "correlation" to "corMatrix"
388            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
389            * R/dpoMatrix.R: ditto
390            * R/lmer.R:      ditto
391    
392    2006-07-28  Douglas Bates  <bates@R-project.org>
393    
394            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
395            RZXinv slot's contents into a separate internal function that can
396            be used in mer_hat_trace.
397    
398    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
401            via new smart
402            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
403            utility functions.
404    
405    
406    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Csparse.R (tril, triu, band): do return *triangular* classed
409            matrices when appropriate; band() even symmetric ones.
410            (replCmat): extend to potentially all "CsparseMatrix"
411            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
412            allow subassignment for special sparse matrices.
413    
414            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
415    
416            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
417            argument; in glmer_*(): print only if(verbose).
418    
419            speed-optimize a few places by moving REAL(.) out of loops.
420    
421            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
422    
423    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
426                    since that wrongly triggers also for M[ logi , ]
427    
428            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
429            a symmetric matrix that results in a non-symmetric one.
430            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
431    
432            * R/dMatrix.R: make round(M) work as round(M, 0)
433    
434            * R/dgTMatrix.R (image): coordinate system and axis now use
435            1-based indices, not 0-based ones.
436    
437            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
438            * tests/indexing.R: test it.
439    
440            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
441            * man/isSymmetric-methods.Rd: and document it.
442    
443            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
444            * man/SparseM-conv.Rd: docu them
445    
446            * tests/other-pkgs.R: renamed from tests/graph.R and add example
447                    for 'SparseM' conversions
448    
449    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
450    
451            * R/Matrix.R (head): added head() and tail() methods.
452    
453    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * DESCRIPTION (Version): 0.995-12 released to CRAN
456    
457    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * tests/simple.R: add check for correct dsT -> dgT coercion;
460                    add check for correct printing of symmetric sparse matrices.
461    
462            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
463            for sparse symmetric matrices.
464    
465            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
466            diagonal twice.
467    
468    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
469    
470            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
471            being applied to the x slot (detected by Brian Ripley).
472    
473    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
476    
477            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
478    
479    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * src/lgCMatrix.c (lgCMatrix_diag): new function
482            * R/lgCMatrix.R (diag): for new method
483    
484            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
485                 ==> construction of illegal "*gTMatrix" via new() should
486                 now be much less easy:
487            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
488    
489            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
490                    directly.
491            * man/Matrix.Rd: documents it.
492    
493    2006-07-06  Douglas Bates  <bates@R-project.org>
494    
495            * src/pedigree.c (pedigree_inbreeding): Correction in
496            initialization.  This function is not currently being used and is
497            not fully tested.
498    
499            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
500            Introduced the glmer class.  Added code for mcmcmsamp on glmer
501            objects.  Modified validity check on pedigree objects to account
502            for nonparallel patterns of missingness of parents.
503    
504            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
505            class.
506    
507    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/pMatrix.R: coercion pMatrix -> Tsparse
510    
511    2006-06-12  Douglas Bates  <bates@R-project.org>
512    
513            * DESCRIPTION (Version): 0.995-11 released to CRAN
514    
515            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
516            the output from mcmcsamp.
517    
518    2006-06-10  Douglas Bates  <bates@R-project.org>
519    
520            * R/lmer.R (simulestimate): added C code for calculating the trace
521            of the hat matrix.
522    
523    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
526            classes.
527            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
528    
529    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/dgTMatrix.R (colSums): etc. All four of
532            colSums(), rowSums(), colMeans(), rowMeans() now should work for
533            all "Matrices".
534    
535    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
536    
537            * R/lmer.R (panel.ci): Add a reference line at zero and a
538            background grid to the qqmath plot of ranef.lmer.
539    
540    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
541    
542            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
543            grouping factors to be specified in the formula as (1|foo/bar).
544    
545    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
546    
547            * R/lmer.R (findbars and others): Change check of is.numeric to
548            !is.language to resolve the bug reported by Jacob Wegelin.
549    
550            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
551            code to evaluate inbreeding coefficients without calculating T,
552            based on code in Sargolzaei and Iwaisaki's paper.
553    
554    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
555    
556            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
557            generic and mer methods for isNested and denomDF. This denomDF was
558            an attempt to emulate that in lme but I don't think that makes
559            sense.  Use the trace of the hat matrix instead.
560    
561  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
564          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.
565          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
566    
567    
568  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 685 
685          * 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)
686          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
687          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
688          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
689    
690  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
# Line 329  Line 889 
889  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
892          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
893          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
894    
895  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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