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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1599, Fri Sep 29 09:39:50 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  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>
562    
563            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
564            the C code depending on a slot structure that's no longer valid.
565            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
566    
567    
568    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
569    
570            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
571            of lowerTriMatrix generic and methods to tril (also upper to triu)
572            and added a general band extractor.
573    
574    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
575    
576            * R/pedigree.R (pedigree): Replace sire and dam values outside the
577            allowable range with NAs. Added a corresponding check in the
578            validity check for the pedigree class.
579    
580            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
581            crossprod methods now inherits from symmetricMatrix.
582    
583    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
584    
585            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
586            generics lowerTriMatrix and upperTriMatrix along with methods for
587            the Csparse virtual class.  Also added a C function Csparse_band
588            that implements these methods by calling cholmod_band.
589    
590    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
593            erased when it was NULL.  This led to invalid subselections!
594    
595    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
596    
597            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
598            in method for "t" so as not to lose the unit diagonal property.
599    
600    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
603            and methods.  This is now an option to the ranef method for the
604            mer class.
605    
606            * src/cs_utils.c: Ensure that the nz component is -1 for a
607            compressed column-oriented matrix.  Minor formatting cleanup.
608    
609            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
610            objects.
611    
612    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
615            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
616    
617    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
618    
619            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
620            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
621    
622            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
623            for the dtCMatrix class.
624    
625    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
628            and methods for it.
629    
630    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
633            arguments, such that M %*% 1:6 now works
634            * Tests/matprod.R: test the above
635    
636    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
637    
638            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
639            the ranef.lmer class.
640    
641            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
642            methods to extract the posterior variances from the bVar slot.
643    
644    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
647            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
648    
649            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
650            * tests/simple: (extended)
651    
652            * R/sparseMatrix.R (isTriangular): now using much improved
653            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
654    
655    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
656    
657            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
658            (problem report from Franklin Parlamis).  This should be done
659            generally.
660    
661    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
664            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
665            update the plot methods.
666    
667    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/lmer.R (resid and ranef methods):  Added methods for the
670            "residuals" and "resid" generic but only for linear mixed model
671            fits.  Changed the ranef method to return a list of data frames so
672            that the plot methods now work.
673    
674    2006-03-16  Douglas Bates  <bates@bates2>
675    
676            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
677            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
678    
679            * DESCRIPTION (Date): New release
680    
681    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
684    
685            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
686            * man/KNex.Rd: and other help files
687            * tests/*.R: several ones needed adaption
688            * inst/doc/Comparisons.Rnw: ditto
689    
690    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
693    
694            * tests/indexing.R: tests for new [<- methods for sparse matrices.
695    
696    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
699    
700            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
701    
702    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/dMatrix.R: enable things like  M [ M < 10 ]
705            * R/dgeMatrix.R: implement it
706    
707    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/AllClass.R: define "summary.mer" and "*.lmer"
710            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
711            * R/lmer.R (show): now works with summary()
712    
713    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
716            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
717                    support the above
718    
719    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
720    
721            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
722            Use glmFit$prior.weights for weights in a glmm.
723            Allow an option usePQL = FALSE to skip the PQL steps for the
724            Laplace method (and, in time, the AGQ method).
725    
726            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
727            into a separate function internal_mer_Xfactor to be able to call
728            it from internal_bhat.
729    
730    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * tests/Class+Meth.R (tstMatrixClass): function for much better
733            testing; now again of all actual classes.
734    
735            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
736                    use macros and define make_d_matrix_* and make_i_matrix_*
737                    where _i_ is for the ldense routines:
738    
739            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
740            * src/ldense.c (lsyMatrix_as_lgeMatrix):
741    
742            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
743    
744    
745    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
748                    many different kinds of matrices.
749            * R/*.R: quite a few new methods were needed for R CMD check with
750                    new Matrix().  Very good for users playing around.
751    
752    
753    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * src/dgeMatrix.c (dMatrix_validate): new
756            * src/Mutils.c (dense_nonpacked_validate): new
757    
758            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
759    
760    
761    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
762    
763            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
764    
765    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
766    
767            * DESCRIPTION (Version): 0.99-6 released to CRAN
768    
769            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
770            segfault in cases with multiple non-nested grouping factors.
771    
772    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
775                    (Depends): also on 'utils'
776    
777            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
778            * R/diagMatrix.R (Diagonal): constructor and methods for
779            diagonal matrices
780    
781            * R/ltTMatrix.R: new "minimal methods"
782    
783    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
786            all methods (and help files).
787    
788    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
791                    for case (dimn.  op  no_dimn.)
792    
793    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * DESCRIPTION (Version): 0.99-2  released to CRAN
796    
797    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
798    
799            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
800            by Julian Faraway.
801    
802    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/Auxiliaries.R (try_as): new utility
805            * R/sparseMatrix.R: use try_as() in coercion to original class
806    
807    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
810    
811    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/Auxiliaries.R (dimNamesCheck): added
814    
815            * R/Matrix.R (as.array), (as.vector): new
816    
817    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
820                    default.
821            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
822                    "pMatrix" now contains "sparseMatrix"
823    
824    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * tests/Class+Meth.R: new tests; t(t(m)) == m
827    
828            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
829    
830            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
831            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
832    
833            * R/dspMatrix.R: typo in "t" method
834    
835    2005-09-18  Douglas Bates  <bates@wisc.edu>
836    
837            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
838            * R/Tsparse.R: instead of R/gTMatrix.R
839            * R/Csparse.R: new
840            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
841            * src/Tsparse.c: new; many trivial methods calling cholmod_()
842            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
843                            via cholmod
844    
845    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/Auxiliaries.R (non0ind): new function using new C code
848            * src/dgCMatrix.c (compressed_non_0_ij): new utility
849    
850    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
851    
852            * src/chm_common.h: header file required by all C sources that
853            call CHOLMOD functions.  It defines a cholmod_common structure
854            called 'c' whose address is passed as the last argument to
855            (virtually) every CHOLMOD function.
856    
857            * src/Pattern.c: Simple example of the use of CHOLMOD.
858    
859            * src/init.c: initialize and finalize the cholmod_common structure.
860    
861            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
862            LDL and CCOLAMD from the U. of Florida sparse matrix library.
863    
864    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * inst/test-tools.R: new file collecting the utility functions used
867                    in ./tests/*.R
868    
869            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
870            * R/Matrix.R (cbind2): methods for NULL and missing
871    
872    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/AllClass.R: new "index" class for "[" and "[<-":
875                    First cut at "symmetricMatrix" and "triangularMatrix"
876            * R/gTMatrix.R (.ind.prep): new function;
877                    Logical and character indexing now work too.
878            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
879            * tests/indexing.R: new, including *.Rout.save
880            * tests/dgTMatrix.R: new
881    
882    2005-08-29  Douglas Bates  <bates@wisc.edu>
883    
884            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
885            indicator pos not being updated.  Also enforced upper triangular
886            for symmetric case.  Need to coerce edges component of elements of
887            edge list - grr! (Why don't they define their classes cleanly?)
888    
889    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/Matrix.R:  added first "[<-" methods; not yet functional
892            * R/denseMatrix.R: ditto
893            * man/Subassign-methods.Rd: new help file for these
894    
895    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * DESCRIPTION (Version): 0.98-6
898    
899            * R/denseMatrix.R: new file for "[" fallback methods for all dense
900            matrices.
901    
902    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
903    
904            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
905                    as( <logical>, "matrix")
906    
907            * R/pMatrix.R: coercion to "lgTMatrix"
908    
909            * R/gTMatrix.R: new virtual class to define "[" methods for.
910            * man/gTMatrix-class.Rd:
911            * General slight re-organization of where "[" methods are defined.
912              more to come.
913    
914    2005-08-18  Douglas Bates  <bates@wisc.edu>
915    
916            * DESCRIPTION (Version): 0.98-5  released to CRAN
917    
918            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
919            * .....
920    
921    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
922    
923            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
924            or glmer objects.
925    
926    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
927    
928            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
929    
930    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
931    
932            * R/HBMM.R: finish re-writing R-only code.
933    
934    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
935    
936            * man/externalFormats.Rd: move documentation for writeHB and
937            writeMM here.
938    
939            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
940            (suggested by Paul Roecker).
941    
942            * tests/validObj.R (assertError): Comment out test that is failing
943            after recent changes in r-devel.
944    
945    
946    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/AllClass.R: intermediate virtual class "denseMatrix"
949            * man/denseMatrix-class.Rd
950            * NAMESPACE: export it, and also export
951            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
952    
953    2005-08-10  Douglas Bates  <bates@wisc.edu>
954    
955            * DESCRIPTION (Version): 0.98-3 to CRAN
956    
957            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
958            matrix_solve code (which was really, really wrong).
959    
960    2005-08-07  Douglas Bates  <bates@wisc.edu>
961    
962            * DESCRIPTION (Version): 0.98-2
963    
964            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
965    
966            * R/lmer.R (abbrvNms): new
967            * R/lmer.R (mcmcsamp): allow transformed parameters
968            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
969            for the Harwell-Boeing and the MatrixMarket formats.
970    
971    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * man/dtrMatrix-class.Rd: add examples
974            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
975    
976            * TODO: note the dtpMatrix (docu) bug
977    
978            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
979            in order to ensure that new as.matrix() is used by old functions,
980            e.g., svd(), qr(), eigen(), dist(),..;
981                  apply(), also matplot() or pairs().
982    
983    
984    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
987              add comments about 'control' / lmerControl() arguments
988    
989    2005-07-27  Douglas Bates  <bates@wisc.edu>
990    
991            * man/sleepstudy.Rd: Added the sleep data set.
992            * DESCRIPTION (Version): 0.98-1  released to CRAN
993    
994    2005-07-12  Douglas Bates  <bates@wisc.edu>
995            * man/sleepstudy.Rd: Added the sleep data set.
996    
997            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
998            .Call calls that were producing spurious output.
999    
1000    2005-07-05  Douglas Bates  <bates@wisc.edu>
1001    
1002            * R/lmer.R (lmer): stored updated variance component estimates in
1003            mer object for the generalized model.  (Bug reported by Renaud
1004            Lancelot).
1005    
1006    2005-07-03  Douglas Bates  <bates@wisc.edu>
1007    
1008            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1009            unidimensional case.
1010    
1011    2005-06-08  Douglas Bates  <bates@wisc.edu>
1012    
1013            * DESCRIPTION (Version): 0.96-1
1014    
1015            * moved  lmer-class' R and C code moved from lme4 to here
1016    
1017    2005-06-04  Douglas Bates  <bates@wisc.edu>
1018    
1019            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1020            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1021    
1022    2005-06-02  Douglas Bates  <bates@wisc.edu>
1023    
1024            * src/Makefile.win: Forgot to update this when Makefile changed.
1025    
1026    2005-05-11  Douglas Bates  <bates@wisc.edu>
1027    
1028            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1029            bug reported by Kurt Hornik and Michael Hahsler.
1030    
1031    2005-05-10  Douglas Bates  <bates@wisc.edu>
1032    
1033            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1034            logical sparse matrices.  These will also be used in the symbolic
1035            analysis for lmer objects.
1036    
1037            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1038            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1039    
1040    2005-05-06  Douglas Bates  <bates@wisc.edu>
1041    
1042            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1043            colMeans, colSums, rowMeans and rowSums.
1044    
1045    2005-04-18  Douglas Bates  <bates@wisc.edu>
1046    
1047            * src/lgCMatrix.[ch]: code for _validate method and stub for
1048            multiplication operation.
1049    
1050            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1051            to dgetrs.
1052    
1053            * src/init.c: Fix cut-and-paste error in definition of
1054            dgeMatrix_matrix_solve
1055    
1056            * src/{many files}: Tighten code by using ALLOC_SLOT.
1057    
1058    2005-04-15  Douglas Bates  <bates@wisc.edu>
1059    
1060            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1061    
1062            * DESCRIPTION: Eliminate import of stats.
1063    
1064    
1065    2005-04-06  Douglas Bates  <bates@wisc.edu>
1066    
1067            * R/AllClass.R : add logical sparse matrix classes
1068    
1069    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/dgTMatrix.R: add "[" method for triplet matrices
1072            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1073    
1074    2005-03-31  Douglas Bates  <bates@wisc.edu>
1075    
1076            * DESCRIPTION (Version): release 0.95-5 to CRAN
1077    
1078            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1079            * R/sparseMatrix.R: %*%, crossprod()
1080            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1081            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1082            * src/lmer.c (lmer_fitted): fix thinko
1083    
1084    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/AllClass.R: add two virtual sparse classes ``on top''
1087    
1088    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1091                    correspondingly fix examples and tests/ since new()
1092                    doesn't work for virtual classes.
1093    
1094    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/Matrix.R (as.matrix): method and one for unname()
1097            * tests/dpoMatrix.R: tests should now be less platform dependent;
1098              also run for R 2.1.0; using as.matrix()
1099    
1100    2005-03-15  Douglas Bates  <bates@wisc.edu>
1101    
1102            * R/pMatrix.R: "pMatrix" class added
1103            * ....
1104    
1105    2005-03-14  Douglas Bates  <bates@wisc.edu>
1106    
1107            * R/dtpMatrix.R: Add unpack method and an example.
1108    
1109            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1110            of general symmetric matrices and associated S4 methods.
1111    
1112    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1113            +
1114    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1117              crossprod() and "%*%" methods added; tests, too.
1118            * tests/matprod.R: new, for testing these
1119    
1120    2005-03-03  Douglas Bates  <bates@wisc.edu>
1121    
1122            * src/lmer.c (lmer_fitted): Added.
1123    
1124    2005-03-02  Douglas Bates  <bates@wisc.edu>
1125    
1126            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1127    
1128    2005-02-28  Douglas Bates  <bates@wisc.edu>
1129    
1130            * src/*.c,po/,inst/po: Internationalization and localization of
1131            the package.
1132    
1133            * src/ldl.[ch]: Removed these as their contents are referenced in the
1134            R_ldl.c file.
1135    
1136            * src/flame.[ch]: Removed these source files.
1137    
1138            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1139    
1140            * src/LU.[ch],src/init.c: absorb in factorizations
1141    
1142            * src/Mutils.h: prepare for internationalization
1143    
1144            * src/cblas.h: move the enum definitions to Mutils.h and remove
1145            this file
1146    
1147    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1150    
1151            * R/dtrMatrix.R: fix t() method
1152    
1153            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1154            * NAMESPACE: export them (and import generics from "methods")
1155            * tests/group-methods.R : and test them.
1156    
1157            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1158            border case
1159    
1160    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1161    
1162            * DESCRIPTION (Version): 0.95-2  released to CRAN
1163    
1164            * src/dgBCMatrix.c:
1165            * src/lmer.c: many changes
1166            * ...
1167    
1168    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/Matrix.R: add more sophisticated show() method.
1171    
1172    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1173    
1174            * */* : almost complete reorganization of classes.
1175    
1176    2005-01-26  Douglas Bates  <bates@wisc.edu>
1177    
1178            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1179            for the geMatrix class.
1180    
1181    2005-01-24  Douglas Bates  <bates@wisc.edu>
1182    
1183            * src/Makefile (clean): Remove *.a and *.so
1184    
1185            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1186    
1187    2005-01-23  Douglas Bates  <bates@wisc.edu>
1188    
1189            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1190            had an effect in cases with more than 2 grouping factors.
1191    
1192    2005-01-03  Douglas Bates  <bates@wisc.edu>
1193    
1194            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1195    
1196    2004-12-23  Douglas Bates  <bates@wisc.edu>
1197    
1198            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1199            and R_useDynamicSymbols (suggested by B.D.Ripley).
1200    
1201    2004-12-14  Douglas Bates  <bates@wisc.edu>
1202    
1203            * R/sscMatrix.R: Add determinant methods
1204    
1205            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1206            for tripletMatrix to matrix.
1207    
1208    2004-12-13  Douglas Bates  <bates@wisc.edu>
1209    
1210            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1211            no longer used.
1212    
1213            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1214            with dynamic allocation of scratch arrays.
1215    
1216            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1217            for multivariate random effects with multiple grouping factors.
1218            Fixes part but not all of #15.
1219    
1220    2004-12-03  Douglas Bates  <bates@wisc.edu>
1221    
1222            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1223            scalar grouping factors corrected.
1224    
1225    2004-11-29  Douglas Bates  <bates@wisc.edu>
1226    
1227            * src/bCrosstab.c: remove diag_update which is no longer used
1228    
1229    2004-11-16  Douglas Bates  <bates@wisc.edu>
1230    
1231          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1232          .h file can be included.          .h file can be included.
1233    
1234  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1235    
1236          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1237          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1238    
1239          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1240    
1241  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1242    
1243          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1244    
1245  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1246    
1247          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1248    
1249  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1250    
1251          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1252    
1253  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1254    
1255          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1256    
1257  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1258    
1259          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1260          routines.          routines.
1261    
1262  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1263    
1264          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1265    
1266  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1267    
1268          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1269    

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