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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1565, Fri Sep 15 14:02:48 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/other-pkgs.R (graph): small extenion in "graph" checks.
4    
5            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
6            (Tsp2grNEL): other fixes needed
7    
8    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
11                    Matrices, since "lMatrix", also "lsparseM" can have NA
12            * R/ndenseMatrix.R, etc: new source files
13            * man/nsparseMatrix-classes.Rd, etc: new help files
14            * tests/: adaptions
15            * src/chm_common.c (chm_dense_to_SEXP): and others:
16                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
17            * src/Csparse.c, etc: dito
18    
19    2006-09-11  Douglas Bates  <bates@R-project.org>
20    
21            * src/Mutils.[ch],init.c inst/include/*.h: Move the
22            alloc_d**Matrix functions to the lme4 package.
23    
24    2006-09-09  Douglas Bates  <bates@R-project.org>
25    
26            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
27            fixed
28    
29    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lMatrix.R: new
32    
33            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
34    
35            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
36            * man/tcrossprod.Rd: dito
37    
38    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
41            for exported functions
42            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
43            Remove partitioning algorithms for sparse matrix reordering.  The
44            copyright on the Metis code was problematic and the methods were
45            rarely used.
46            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
47            operations are now done entirely in CHOLMOD code.
48    
49    2006-09-06  Douglas Bates  <bates@R-project.org>
50    
51            * src/Mutils.h: Remove functions that are no longer used.
52    
53    2006-09-04  Douglas Bates  <bates@R-project.org>
54    
55            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
56            * src/DEPS.mkf: update
57    
58    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * created branches/Matrix-for-R-2.3.x;  on trunk: do
61            * DESCRIPTION (Version): 0.9975-0
62            (Depends): R (>= 2.4.0)
63    
64    2006-09-01  Douglas Bates  <bates@R-project.org>
65    
66            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
67    
68    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
71            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
72    
73            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
78            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
79            * R/dsparseMatrix.R: dito
80            * R/Csparse.R: dito
81    
82    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Compare): improve availability of "<", etc
85            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
86    
87    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
90            of a 0-index which was used as 1-index (..hmm)
91    
92            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
93    
94            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
95            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
96            (.is.diagonal): dito
97    
98            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
99    
100            * R/Matrix.R (Matrix): also work for NA data
101    
102    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
105            in all cases.
106    
107    2006-08-27  Douglas Bates  <bates@R-project.org>
108    
109            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
110            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
111    
112    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
115            subclasses of "ddenseMatrix"
116            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
117            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
118            instead of half dozen specialized ones.
119    
120    2006-08-25  Douglas Bates  <bates@R-project.org>
121    
122            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
123            <tillard@cirad.fr> - ordering standard errors to match effects.
124    
125    2006-08-24  Douglas Bates  <bates@R-project.org>
126    
127            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
128            on R_ldl.
129            * R/lCholCMatrix.R,
130            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
131            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
132            * many files in ./R and ./src: Use more general version of
133            dup_mMatrix_as_dgeMatrix to simplify method definitions.
134            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
135            dtpMatrix, dspMatrix and dppMatrix conversions.
136    
137    
138    2006-08-23  Douglas Bates  <bates@R-project.org>
139    
140            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
141            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
142            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
143            dgeMatrix_crossprod (may need to do this in other places).
144            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
145            generic and method for dsCMatrix.  Use CHOLMOD for chol().
146    
147    2006-08-22  Douglas Bates  <bates@R-project.org>
148    
149            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
150            types of classed Matrices, matrices or numeric or logical vectors.
151            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
152            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
153            to Mutils.h (as an inline) and change name to Matrix_check_class;
154            fixes in as_cholmod_factor and chm_factor_to_SEXP.
155            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
156            dsCMatrix_matrix_solve.  Comment out vestigial functions.
157            * src/Csparse.c: use diag_P and uplo_P macros.
158    
159    2006-08-21  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
162            valgrind.
163            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
164            inverses.
165            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
166            -Wall warnings.
167            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
168            Use dup_mMatrix_as_dgeMatrix.
169    
170    2006-08-20  Douglas Bates  <bates@R-project.org>
171    
172            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
173            * tests/sparseQR.R: Added
174            * man/sparseQR-class.Rd: Document methods for qr.* generics
175            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
176    
177    2006-08-19  Douglas Bates  <bates@R-project.org>
178    
179            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
180            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
181            and qr.fitted.
182            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
183            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
184    
185    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
188            the base version has no "..." argument.
189    
190            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
191    
192            * R/Matrix.R: define and
193            * NAMESPACE: export as.numeric() and as.logical() methods.
194                    Let's hope these do not badly slow down something...
195            Finally export the zapsmall() method.
196    
197    2006-08-17  Douglas Bates  <bates@R-project.org>
198    
199            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
200            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
201            * src/dtCMatrix.c :Remove code that is no longer used
202            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
207            Csparse_to_logical and Csparse_symmetric_to_general.
208            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
209            coercion methods between CsparseMatrix and TsparseMatrix.
210    
211    2006-08-14  Douglas Bates  <bates@R-project.org>
212    
213            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
214            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
215            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
216            possible.
217    
218    2006-08-12  Douglas Bates  <bates@R-project.org>
219    
220            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
221              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
222              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
223              generalize conversions between TsparseMatrix, CsparseMatrix,
224              denseMatrix and matrix.  Preserve triangularity property and
225              propagate Dimnames in the easy cases.
226    
227    2006-08-10  Douglas Bates  <bates@R-project.org>
228    
229            * src/lmer.c: adjust checks in glmer_init for S4SXP
230            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
231            before S4SXP but for the wrong reasons.
232    
233    2006-08-08  Douglas Bates  <bates@R-project.org>
234    
235            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
236            Later modified to return the upper triangle only.
237            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
238    
239    2006-08-07  Douglas Bates  <bates@R-project.org>
240    
241            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
242            R-level conversion to a sparse symmetric class.
243            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
244            Remove conversion to sparse symmetric classes (now done in C code).
245    
246    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
249            * man/band.Rd:  adapt the \dontshow{} unit test.
250    
251    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * DESCRIPTION (Version): 0.995-14  for CRAN
254    
255            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
256    
257            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
258            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
259    
260            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
261            * R/Tsparse.R (tril, triu, band): methods
262            * R/dgRMatrix.R (tril, ...):    ditto
263            * man/band.Rd:                  ditto
264    
265    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Matrix.R (head, tail): directly use utils:::head.matrix
268                    to be up-to-date automatically.
269    
270    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
273    
274            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
275            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
276            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
277            such that the S4 objects are always created by the current version
278            of R and 'Matrix' class definitions.
279    
280    2006-08-01  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (LMEoptimize method), tests/lmer.R,
283            inst/external/test3comp.rda: Added warnings for convergence on
284            boundary and test cases.
285    
286            * src/lmer.c (mer_postVar): Modified to return the variances that
287            are marginal to the fixed effects, not conditional on them (which
288            is what the bVar slot contents represent).
289    
290    2006-07-31  Douglas Bates  <bates@R-project.org>
291    
292            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
293            function which calls the C function mer_hat_trace2.
294    
295            * man/ranef.Rd: Include description of "postVar" argument and
296            producing a caterpillar plot.
297    
298    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * NAMESPACE:    change  "correlation" to "corMatrix"
301            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
302            * R/dpoMatrix.R: ditto
303            * R/lmer.R:      ditto
304    
305    2006-07-28  Douglas Bates  <bates@R-project.org>
306    
307            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
308            RZXinv slot's contents into a separate internal function that can
309            be used in mer_hat_trace.
310    
311    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
314            via new smart
315            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
316            utility functions.
317    
318    
319    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Csparse.R (tril, triu, band): do return *triangular* classed
322            matrices when appropriate; band() even symmetric ones.
323            (replCmat): extend to potentially all "CsparseMatrix"
324            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
325            allow subassignment for special sparse matrices.
326    
327            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
328    
329            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
330            argument; in glmer_*(): print only if(verbose).
331    
332            speed-optimize a few places by moving REAL(.) out of loops.
333    
334            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
335    
336    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
339                    since that wrongly triggers also for M[ logi , ]
340    
341            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
342            a symmetric matrix that results in a non-symmetric one.
343            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
344    
345            * R/dMatrix.R: make round(M) work as round(M, 0)
346    
347            * R/dgTMatrix.R (image): coordinate system and axis now use
348            1-based indices, not 0-based ones.
349    
350            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
351            * tests/indexing.R: test it.
352    
353            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
354            * man/isSymmetric-methods.Rd: and document it.
355    
356            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
357            * man/SparseM-conv.Rd: docu them
358    
359            * tests/other-pkgs.R: renamed from tests/graph.R and add example
360                    for 'SparseM' conversions
361    
362    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
363    
364            * R/Matrix.R (head): added head() and tail() methods.
365    
366    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version): 0.995-12 released to CRAN
369    
370    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * tests/simple.R: add check for correct dsT -> dgT coercion;
373                    add check for correct printing of symmetric sparse matrices.
374    
375            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
376            for sparse symmetric matrices.
377    
378            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
379            diagonal twice.
380    
381    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
382    
383            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
384            being applied to the x slot (detected by Brian Ripley).
385    
386    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
389    
390            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
391    
392    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/lgCMatrix.c (lgCMatrix_diag): new function
395            * R/lgCMatrix.R (diag): for new method
396    
397            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
398                 ==> construction of illegal "*gTMatrix" via new() should
399                 now be much less easy:
400            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
401    
402            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
403                    directly.
404            * man/Matrix.Rd: documents it.
405    
406    2006-07-06  Douglas Bates  <bates@R-project.org>
407    
408            * src/pedigree.c (pedigree_inbreeding): Correction in
409            initialization.  This function is not currently being used and is
410            not fully tested.
411    
412            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
413            Introduced the glmer class.  Added code for mcmcmsamp on glmer
414            objects.  Modified validity check on pedigree objects to account
415            for nonparallel patterns of missingness of parents.
416    
417            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
418            class.
419    
420    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/pMatrix.R: coercion pMatrix -> Tsparse
423    
424    2006-06-12  Douglas Bates  <bates@R-project.org>
425    
426            * DESCRIPTION (Version): 0.995-11 released to CRAN
427    
428            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
429            the output from mcmcsamp.
430    
431    2006-06-10  Douglas Bates  <bates@R-project.org>
432    
433            * R/lmer.R (simulestimate): added C code for calculating the trace
434            of the hat matrix.
435    
436    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
439            classes.
440            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
441    
442    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dgTMatrix.R (colSums): etc. All four of
445            colSums(), rowSums(), colMeans(), rowMeans() now should work for
446            all "Matrices".
447    
448    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/lmer.R (panel.ci): Add a reference line at zero and a
451            background grid to the qqmath plot of ranef.lmer.
452    
453    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
456            grouping factors to be specified in the formula as (1|foo/bar).
457    
458    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
459    
460            * R/lmer.R (findbars and others): Change check of is.numeric to
461            !is.language to resolve the bug reported by Jacob Wegelin.
462    
463            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
464            code to evaluate inbreeding coefficients without calculating T,
465            based on code in Sargolzaei and Iwaisaki's paper.
466    
467    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
470            generic and mer methods for isNested and denomDF. This denomDF was
471            an attempt to emulate that in lme but I don't think that makes
472            sense.  Use the trace of the hat matrix instead.
473    
474    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
477            the C code depending on a slot structure that's no longer valid.
478            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
479    
480    
481    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
482    
483            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
484            of lowerTriMatrix generic and methods to tril (also upper to triu)
485            and added a general band extractor.
486    
487    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
488    
489            * R/pedigree.R (pedigree): Replace sire and dam values outside the
490            allowable range with NAs. Added a corresponding check in the
491            validity check for the pedigree class.
492    
493            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
494            crossprod methods now inherits from symmetricMatrix.
495    
496    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
497    
498            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
499            generics lowerTriMatrix and upperTriMatrix along with methods for
500            the Csparse virtual class.  Also added a C function Csparse_band
501            that implements these methods by calling cholmod_band.
502    
503    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
506            erased when it was NULL.  This led to invalid subselections!
507    
508    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
509    
510            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
511            in method for "t" so as not to lose the unit diagonal property.
512    
513    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
516            and methods.  This is now an option to the ranef method for the
517            mer class.
518    
519            * src/cs_utils.c: Ensure that the nz component is -1 for a
520            compressed column-oriented matrix.  Minor formatting cleanup.
521    
522            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
523            objects.
524    
525    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
528            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
529    
530    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
533            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
534    
535            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
536            for the dtCMatrix class.
537    
538    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
539    
540            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
541            and methods for it.
542    
543    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
546            arguments, such that M %*% 1:6 now works
547            * Tests/matprod.R: test the above
548    
549    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
552            the ranef.lmer class.
553    
554            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
555            methods to extract the posterior variances from the bVar slot.
556    
557    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
560            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
561    
562            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
563            * tests/simple: (extended)
564    
565            * R/sparseMatrix.R (isTriangular): now using much improved
566            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
567    
568    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
569    
570            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
571            (problem report from Franklin Parlamis).  This should be done
572            generally.
573    
574    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
575    
576            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
577            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
578            update the plot methods.
579    
580    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/lmer.R (resid and ranef methods):  Added methods for the
583            "residuals" and "resid" generic but only for linear mixed model
584            fits.  Changed the ranef method to return a list of data frames so
585            that the plot methods now work.
586    
587    2006-03-16  Douglas Bates  <bates@bates2>
588    
589            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
590            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
591    
592            * DESCRIPTION (Date): New release
593    
594    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
597    
598            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
599            * man/KNex.Rd: and other help files
600            * tests/*.R: several ones needed adaption
601            * inst/doc/Comparisons.Rnw: ditto
602    
603    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
606    
607            * tests/indexing.R: tests for new [<- methods for sparse matrices.
608    
609    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
612    
613            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
614    
615    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/dMatrix.R: enable things like  M [ M < 10 ]
618            * R/dgeMatrix.R: implement it
619    
620    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/AllClass.R: define "summary.mer" and "*.lmer"
623            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
624            * R/lmer.R (show): now works with summary()
625    
626    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
629            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
630                    support the above
631    
632    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
633    
634            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
635            Use glmFit$prior.weights for weights in a glmm.
636            Allow an option usePQL = FALSE to skip the PQL steps for the
637            Laplace method (and, in time, the AGQ method).
638    
639            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
640            into a separate function internal_mer_Xfactor to be able to call
641            it from internal_bhat.
642    
643    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * tests/Class+Meth.R (tstMatrixClass): function for much better
646            testing; now again of all actual classes.
647    
648            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
649                    use macros and define make_d_matrix_* and make_i_matrix_*
650                    where _i_ is for the ldense routines:
651    
652            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
653            * src/ldense.c (lsyMatrix_as_lgeMatrix):
654    
655            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
656    
657    
658    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
661                    many different kinds of matrices.
662            * R/*.R: quite a few new methods were needed for R CMD check with
663                    new Matrix().  Very good for users playing around.
664    
665    
666    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/dgeMatrix.c (dMatrix_validate): new
669            * src/Mutils.c (dense_nonpacked_validate): new
670    
671            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
672    
673    
674    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
675    
676            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
677    
678    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
679    
680            * DESCRIPTION (Version): 0.99-6 released to CRAN
681    
682            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
683            segfault in cases with multiple non-nested grouping factors.
684    
685    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
688                    (Depends): also on 'utils'
689    
690            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
691            * R/diagMatrix.R (Diagonal): constructor and methods for
692            diagonal matrices
693    
694            * R/ltTMatrix.R: new "minimal methods"
695    
696    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
699            all methods (and help files).
700    
701    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
704                    for case (dimn.  op  no_dimn.)
705    
706    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * DESCRIPTION (Version): 0.99-2  released to CRAN
709    
710    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
713            by Julian Faraway.
714    
715    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Auxiliaries.R (try_as): new utility
718            * R/sparseMatrix.R: use try_as() in coercion to original class
719    
720    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
723    
724    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * R/Auxiliaries.R (dimNamesCheck): added
727    
728            * R/Matrix.R (as.array), (as.vector): new
729    
730    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
733                    default.
734            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
735                    "pMatrix" now contains "sparseMatrix"
736    
737    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * tests/Class+Meth.R: new tests; t(t(m)) == m
740    
741            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
742    
743            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
744            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
745    
746            * R/dspMatrix.R: typo in "t" method
747    
748    2005-09-18  Douglas Bates  <bates@wisc.edu>
749    
750            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
751            * R/Tsparse.R: instead of R/gTMatrix.R
752            * R/Csparse.R: new
753            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
754            * src/Tsparse.c: new; many trivial methods calling cholmod_()
755            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
756                            via cholmod
757    
758    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Auxiliaries.R (non0ind): new function using new C code
761            * src/dgCMatrix.c (compressed_non_0_ij): new utility
762    
763    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
764    
765            * src/chm_common.h: header file required by all C sources that
766            call CHOLMOD functions.  It defines a cholmod_common structure
767            called 'c' whose address is passed as the last argument to
768            (virtually) every CHOLMOD function.
769    
770            * src/Pattern.c: Simple example of the use of CHOLMOD.
771    
772            * src/init.c: initialize and finalize the cholmod_common structure.
773    
774            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
775            LDL and CCOLAMD from the U. of Florida sparse matrix library.
776    
777    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * inst/test-tools.R: new file collecting the utility functions used
780                    in ./tests/*.R
781    
782            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
783            * R/Matrix.R (cbind2): methods for NULL and missing
784    
785    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/AllClass.R: new "index" class for "[" and "[<-":
788                    First cut at "symmetricMatrix" and "triangularMatrix"
789            * R/gTMatrix.R (.ind.prep): new function;
790                    Logical and character indexing now work too.
791            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
792            * tests/indexing.R: new, including *.Rout.save
793            * tests/dgTMatrix.R: new
794    
795    2005-08-29  Douglas Bates  <bates@wisc.edu>
796    
797            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
798            indicator pos not being updated.  Also enforced upper triangular
799            for symmetric case.  Need to coerce edges component of elements of
800            edge list - grr! (Why don't they define their classes cleanly?)
801    
802    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/Matrix.R:  added first "[<-" methods; not yet functional
805            * R/denseMatrix.R: ditto
806            * man/Subassign-methods.Rd: new help file for these
807    
808    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * DESCRIPTION (Version): 0.98-6
811    
812            * R/denseMatrix.R: new file for "[" fallback methods for all dense
813            matrices.
814    
815    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
818                    as( <logical>, "matrix")
819    
820            * R/pMatrix.R: coercion to "lgTMatrix"
821    
822            * R/gTMatrix.R: new virtual class to define "[" methods for.
823            * man/gTMatrix-class.Rd:
824            * General slight re-organization of where "[" methods are defined.
825              more to come.
826    
827    2005-08-18  Douglas Bates  <bates@wisc.edu>
828    
829            * DESCRIPTION (Version): 0.98-5  released to CRAN
830    
831            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
832            * .....
833    
834    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
835    
836            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
837            or glmer objects.
838    
839    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
842    
843    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
844    
845            * R/HBMM.R: finish re-writing R-only code.
846    
847    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
848    
849            * man/externalFormats.Rd: move documentation for writeHB and
850            writeMM here.
851    
852            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
853            (suggested by Paul Roecker).
854    
855            * tests/validObj.R (assertError): Comment out test that is failing
856            after recent changes in r-devel.
857    
858    
859    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/AllClass.R: intermediate virtual class "denseMatrix"
862            * man/denseMatrix-class.Rd
863            * NAMESPACE: export it, and also export
864            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
865    
866    2005-08-10  Douglas Bates  <bates@wisc.edu>
867    
868            * DESCRIPTION (Version): 0.98-3 to CRAN
869    
870            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
871            matrix_solve code (which was really, really wrong).
872    
873    2005-08-07  Douglas Bates  <bates@wisc.edu>
874    
875            * DESCRIPTION (Version): 0.98-2
876    
877            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
878    
879            * R/lmer.R (abbrvNms): new
880            * R/lmer.R (mcmcsamp): allow transformed parameters
881            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
882            for the Harwell-Boeing and the MatrixMarket formats.
883    
884    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * man/dtrMatrix-class.Rd: add examples
887            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
888    
889            * TODO: note the dtpMatrix (docu) bug
890    
891            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
892            in order to ensure that new as.matrix() is used by old functions,
893            e.g., svd(), qr(), eigen(), dist(),..;
894                  apply(), also matplot() or pairs().
895    
896    
897    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
900              add comments about 'control' / lmerControl() arguments
901    
902    2005-07-27  Douglas Bates  <bates@wisc.edu>
903    
904            * man/sleepstudy.Rd: Added the sleep data set.
905            * DESCRIPTION (Version): 0.98-1  released to CRAN
906    
907    2005-07-12  Douglas Bates  <bates@wisc.edu>
908            * man/sleepstudy.Rd: Added the sleep data set.
909    
910            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
911            .Call calls that were producing spurious output.
912    
913    2005-07-05  Douglas Bates  <bates@wisc.edu>
914    
915            * R/lmer.R (lmer): stored updated variance component estimates in
916            mer object for the generalized model.  (Bug reported by Renaud
917            Lancelot).
918    
919    2005-07-03  Douglas Bates  <bates@wisc.edu>
920    
921            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
922            unidimensional case.
923    
924    2005-06-08  Douglas Bates  <bates@wisc.edu>
925    
926            * DESCRIPTION (Version): 0.96-1
927    
928            * moved  lmer-class' R and C code moved from lme4 to here
929    
930    2005-06-04  Douglas Bates  <bates@wisc.edu>
931    
932            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
933            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
934    
935    2005-06-02  Douglas Bates  <bates@wisc.edu>
936    
937            * src/Makefile.win: Forgot to update this when Makefile changed.
938    
939    2005-05-11  Douglas Bates  <bates@wisc.edu>
940    
941            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
942            bug reported by Kurt Hornik and Michael Hahsler.
943    
944    2005-05-10  Douglas Bates  <bates@wisc.edu>
945    
946            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
947            logical sparse matrices.  These will also be used in the symbolic
948            analysis for lmer objects.
949    
950            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
951            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
952    
953    2005-05-06  Douglas Bates  <bates@wisc.edu>
954    
955            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
956            colMeans, colSums, rowMeans and rowSums.
957    
958    2005-04-18  Douglas Bates  <bates@wisc.edu>
959    
960            * src/lgCMatrix.[ch]: code for _validate method and stub for
961            multiplication operation.
962    
963            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
964            to dgetrs.
965    
966            * src/init.c: Fix cut-and-paste error in definition of
967            dgeMatrix_matrix_solve
968    
969            * src/{many files}: Tighten code by using ALLOC_SLOT.
970    
971    2005-04-15  Douglas Bates  <bates@wisc.edu>
972    
973            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
974    
975            * DESCRIPTION: Eliminate import of stats.
976    
977    
978    2005-04-06  Douglas Bates  <bates@wisc.edu>
979    
980            * R/AllClass.R : add logical sparse matrix classes
981    
982    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * R/dgTMatrix.R: add "[" method for triplet matrices
985            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
986    
987    2005-03-31  Douglas Bates  <bates@wisc.edu>
988    
989            * DESCRIPTION (Version): release 0.95-5 to CRAN
990    
991            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
992            * R/sparseMatrix.R: %*%, crossprod()
993            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
994            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
995            * src/lmer.c (lmer_fitted): fix thinko
996    
997    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/AllClass.R: add two virtual sparse classes ``on top''
1000    
1001    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1002    
1003            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1004                    correspondingly fix examples and tests/ since new()
1005                    doesn't work for virtual classes.
1006    
1007    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * R/Matrix.R (as.matrix): method and one for unname()
1010            * tests/dpoMatrix.R: tests should now be less platform dependent;
1011              also run for R 2.1.0; using as.matrix()
1012    
1013    2005-03-15  Douglas Bates  <bates@wisc.edu>
1014    
1015            * R/pMatrix.R: "pMatrix" class added
1016            * ....
1017    
1018    2005-03-14  Douglas Bates  <bates@wisc.edu>
1019    
1020            * R/dtpMatrix.R: Add unpack method and an example.
1021    
1022            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1023            of general symmetric matrices and associated S4 methods.
1024    
1025    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1026            +
1027    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1030              crossprod() and "%*%" methods added; tests, too.
1031            * tests/matprod.R: new, for testing these
1032    
1033    2005-03-03  Douglas Bates  <bates@wisc.edu>
1034    
1035            * src/lmer.c (lmer_fitted): Added.
1036    
1037    2005-03-02  Douglas Bates  <bates@wisc.edu>
1038    
1039            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1040    
1041    2005-02-28  Douglas Bates  <bates@wisc.edu>
1042    
1043            * src/*.c,po/,inst/po: Internationalization and localization of
1044            the package.
1045    
1046            * src/ldl.[ch]: Removed these as their contents are referenced in the
1047            R_ldl.c file.
1048    
1049            * src/flame.[ch]: Removed these source files.
1050    
1051            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1052    
1053            * src/LU.[ch],src/init.c: absorb in factorizations
1054    
1055            * src/Mutils.h: prepare for internationalization
1056    
1057            * src/cblas.h: move the enum definitions to Mutils.h and remove
1058            this file
1059    
1060    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1063    
1064            * R/dtrMatrix.R: fix t() method
1065    
1066            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1067            * NAMESPACE: export them (and import generics from "methods")
1068            * tests/group-methods.R : and test them.
1069    
1070            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1071            border case
1072    
1073    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1074    
1075            * DESCRIPTION (Version): 0.95-2  released to CRAN
1076    
1077            * src/dgBCMatrix.c:
1078            * src/lmer.c: many changes
1079            * ...
1080    
1081    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * R/Matrix.R: add more sophisticated show() method.
1084    
1085    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1086    
1087            * */* : almost complete reorganization of classes.
1088    
1089    2005-01-26  Douglas Bates  <bates@wisc.edu>
1090    
1091            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1092            for the geMatrix class.
1093    
1094    2005-01-24  Douglas Bates  <bates@wisc.edu>
1095    
1096            * src/Makefile (clean): Remove *.a and *.so
1097    
1098            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1099    
1100    2005-01-23  Douglas Bates  <bates@wisc.edu>
1101    
1102            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1103            had an effect in cases with more than 2 grouping factors.
1104    
1105    2005-01-03  Douglas Bates  <bates@wisc.edu>
1106    
1107            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1108    
1109    2004-12-23  Douglas Bates  <bates@wisc.edu>
1110    
1111            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1112            and R_useDynamicSymbols (suggested by B.D.Ripley).
1113    
1114    2004-12-14  Douglas Bates  <bates@wisc.edu>
1115    
1116            * R/sscMatrix.R: Add determinant methods
1117    
1118            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1119            for tripletMatrix to matrix.
1120    
1121    2004-12-13  Douglas Bates  <bates@wisc.edu>
1122    
1123            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1124            no longer used.
1125    
1126          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1127          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1130 
1130          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1131          Fixes part but not all of #15.          Fixes part but not all of #15.
1132    
1133  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1134    
1135          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1136          scalar grouping factors corrected.          scalar grouping factors corrected.
1137    
1138  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1139    
1140          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1141    
1142  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1143    
1144          * 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
1145          .h file can be included.          .h file can be included.
1146    
1147  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1148    
1149          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1150          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1151    
1152          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1153    
1154  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1155    
1156          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1157    
1158  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1159    
1160          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1161    
1162  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1163    
1164          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1165    
1166  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1167    
1168          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1169    
1170  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1171    
1172          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1173          routines.          routines.
1174    
1175  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1176    
1177          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1178    
1179  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1180    
1181          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1182    

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