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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1257, Wed Apr 19 14:22:07 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
4            and methods.  This is now an option to the ranef method for the
5            mer class.
6    
7            * src/cs_utils.c: Ensure that the nz component is -1 for a
8            compressed column-oriented matrix.  Minor formatting cleanup.
9    
10            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
11            objects.
12    
13    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
16            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
17    
18    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
21            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
22    
23            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
24            for the dtCMatrix class.
25    
26    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
29            and methods for it.
30    
31    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
34            arguments, such that M %*% 1:6 now works
35            * Tests/matprod.R: test the above
36    
37    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
38    
39            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
40            the ranef.lmer class.
41    
42            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
43            methods to extract the posterior variances from the bVar slot.
44    
45    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
48            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
49    
50            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
51            * tests/simple: (extended)
52    
53            * R/sparseMatrix.R (isTriangular): now using much improved
54            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
55    
56    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
59            (problem report from Franklin Parlamis).  This should be done
60            generally.
61    
62    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
63    
64            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
65            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
66            update the plot methods.
67    
68    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
69    
70            * R/lmer.R (resid and ranef methods):  Added methods for the
71            "residuals" and "resid" generic but only for linear mixed model
72            fits.  Changed the ranef method to return a list of data frames so
73            that the plot methods now work.
74    
75    2006-03-16  Douglas Bates  <bates@bates2>
76    
77            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
78            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
79    
80            * DESCRIPTION (Date): New release
81    
82    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
85    
86            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
87            * man/KNex.Rd: and other help files
88            * tests/*.R: several ones needed adaption
89            * inst/doc/Comparisons.Rnw: dito
90    
91    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
94    
95            * tests/indexing.R: tests for new [<- methods for sparse matrices.
96    
97    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
100    
101            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
102    
103    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/dMatrix.R: enable things like  M [ M < 10 ]
106            * R/dgeMatrix.R: implement it
107    
108    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/AllClass.R: define "summary.mer" and "*.lmer"
111            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
112            * R/lmer.R (show): now works with summary()
113    
114    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
117            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
118                    support the above
119    
120    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
121    
122            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
123            Use glmFit$prior.weights for weights in a glmm.
124            Allow an option usePQL = FALSE to skip the PQL steps for the
125            Laplace method (and, in time, the AGQ method).
126    
127            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
128            into a separate function internal_mer_Xfactor to be able to call
129            it from internal_bhat.
130    
131    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * tests/Class+Meth.R (tstMatrixClass): function for much better
134            testing; now again of all actual classes.
135    
136            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
137                    use macros and define make_d_matrix_* and make_i_matrix_*
138                    where _i_ is for the ldense routines:
139    
140            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
141            * src/ldense.c (lsyMatrix_as_lgeMatrix):
142    
143            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
144    
145    
146    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
149                    many different kinds of matrices.
150            * R/*.R: quite a few new methods were needed for R CMD check with
151                    new Matrix().  Very good for users playing around.
152    
153    
154    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/dgeMatrix.c (dMatrix_validate): new
157            * src/Mutils.c (dense_nonpacked_validate): new
158    
159            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
160    
161    
162    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
165    
166    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
167    
168            * DESCRIPTION (Version): 0.99-6 released to CRAN
169    
170            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
171            segfault in cases with multiple non-nested grouping factors.
172    
173    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
176                    (Depends): also on 'utils'
177    
178            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
179            * R/diagMatrix.R (Diagonal): constructor and methods for
180            diagonal matrices
181    
182            * R/ltTMatrix.R: new "minimal methods"
183    
184    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
187            all methods (and help files).
188    
189    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
192                    for case (dimn.  op  no_dimn.)
193    
194    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * DESCRIPTION (Version): 0.99-2  released to CRAN
197    
198    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
201            by Julian Faraway.
202    
203    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (try_as): new utility
206            * R/sparseMatrix.R: use try_as() in coercion to original class
207    
208    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
211    
212    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Auxiliaries.R (dimNamesCheck): added
215    
216            * R/Matrix.R (as.array), (as.vector): new
217    
218    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
221                    default.
222            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
223                    "pMatrix" now contains "sparseMatrix"
224    
225    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * tests/Class+Meth.R: new tests; t(t(m)) == m
228    
229            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
230    
231            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
232            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
233    
234            * R/dspMatrix.R: typo in "t" method
235    
236    2005-09-18  Douglas Bates  <bates@wisc.edu>
237    
238            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
239            * R/Tsparse.R: instead of R/gTMatrix.R
240            * R/Csparse.R: new
241            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
242            * src/Tsparse.c: new; many trivial methods calling cholmod_()
243            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
244                            via cholmod
245    
246    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Auxiliaries.R (non0ind): new function using new C code
249            * src/dgCMatrix.c (compressed_non_0_ij): new utility
250    
251    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
252    
253            * src/chm_common.h: header file required by all C sources that
254            call CHOLMOD functions.  It defines a cholmod_common structure
255            called 'c' whose address is passed as the last argument to
256            (virtually) every CHOLMOD function.
257    
258            * src/Pattern.c: Simple example of the use of CHOLMOD.
259    
260            * src/init.c: initialize and finalize the cholmod_common structure.
261    
262            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
263            LDL and CCOLAMD from the U. of Florida sparse matrix library.
264    
265    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * inst/test-tools.R: new file collecting the utility functions used
268                    in ./tests/*.R
269    
270            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
271            * R/Matrix.R (cbind2): methods for NULL and missing
272    
273    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/AllClass.R: new "index" class for "[" and "[<-":
276                    First cut at "symmetricMatrix" and "triangularMatrix"
277            * R/gTMatrix.R (.ind.prep): new function;
278                    Logical and character indexing now work too.
279            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
280            * tests/indexing.R: new, including *.Rout.save
281            * tests/dgTMatrix.R: new
282    
283    2005-08-29  Douglas Bates  <bates@wisc.edu>
284    
285            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
286            indicator pos not being updated.  Also enforced upper triangular
287            for symmetric case.  Need to coerce edges component of elements of
288            edge list - grr! (Why don't they define their classes cleanly?)
289    
290    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Matrix.R:  added first "[<-" methods; not yet functional
293            * R/denseMatrix.R: dito
294            * man/Subassign-methods.Rd: new help file for these
295    
296    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * DESCRIPTION (Version): 0.98-6
299    
300            * R/denseMatrix.R: new file for "[" fallback methods for all dense
301            matrices.
302    
303    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
306                    as( <logical>, "matrix")
307    
308            * R/pMatrix.R: coercion to "lgTMatrix"
309    
310            * R/gTMatrix.R: new virtual class to define "[" methods for.
311            * man/gTMatrix-class.Rd:
312            * General slight re-organization of where "[" methods are defined.
313              more to come.
314    
315    2005-08-18  Douglas Bates  <bates@wisc.edu>
316    
317            * DESCRIPTION (Version): 0.98-5  released to CRAN
318    
319            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
320            * .....
321    
322    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
323    
324            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
325            or glmer objects.
326    
327    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
330    
331    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
332    
333            * R/HBMM.R: finish re-writing R-only code.
334    
335    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
336    
337            * man/externalFormats.Rd: move documentation for writeHB and
338            writeMM here.
339    
340            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
341            (suggested by Paul Roecker).
342    
343            * tests/validObj.R (assertError): Comment out test that is failing
344            after recent changes in r-devel.
345    
346    
347    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/AllClass.R: intermediate virtual class "denseMatrix"
350            * man/denseMatrix-class.Rd
351            * NAMESPACE: export it, and also export
352            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
353    
354    2005-08-10  Douglas Bates  <bates@wisc.edu>
355    
356            * DESCRIPTION (Version): 0.98-3 to CRAN
357    
358            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
359            matrix_solve code (which was really, really wrong).
360    
361    2005-08-07  Douglas Bates  <bates@wisc.edu>
362    
363            * DESCRIPTION (Version): 0.98-2
364    
365            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
366    
367            * R/lmer.R (abbrvNms): new
368            * R/lmer.R (mcmcsamp): allow transformed parameters
369            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
370            for the Harwell-Boeing and the MatrixMarket formats.
371    
372    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * man/dtrMatrix-class.Rd: add examples
375            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
376    
377            * TODO: note the dtpMatrix (docu) bug
378    
379            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
380            in order to ensure that new as.matrix() is used by old functions,
381            e.g., svd(), qr(), eigen(), dist(),..;
382                  apply(), also matplot() or pairs().
383    
384    
385    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
388              add comments about 'control' / lmerControl() arguments
389    
390    2005-07-27  Douglas Bates  <bates@wisc.edu>
391    
392            * man/sleepstudy.Rd: Added the sleep data set.
393            * DESCRIPTION (Version): 0.98-1  released to CRAN
394    
395    2005-07-12  Douglas Bates  <bates@wisc.edu>
396            * man/sleepstudy.Rd: Added the sleep data set.
397    
398            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
399            .Call calls that were producing spurious output.
400    
401    2005-07-05  Douglas Bates  <bates@wisc.edu>
402    
403            * R/lmer.R (lmer): stored updated variance component estimates in
404            mer object for the generalized model.  (Bug reported by Renaud
405            Lancelot).
406    
407    2005-07-03  Douglas Bates  <bates@wisc.edu>
408    
409            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
410            unidimensional case.
411    
412    2005-06-08  Douglas Bates  <bates@wisc.edu>
413    
414            * DESCRIPTION (Version): 0.96-1
415    
416            * moved  lmer-class' R and C code moved from lme4 to here
417    
418    2005-06-04  Douglas Bates  <bates@wisc.edu>
419    
420            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
421            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
422    
423    2005-06-02  Douglas Bates  <bates@wisc.edu>
424    
425            * src/Makefile.win: Forgot to update this when Makefile changed.
426    
427    2005-05-11  Douglas Bates  <bates@wisc.edu>
428    
429            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
430            bug reported by Kurt Hornik and Michael Hahsler.
431    
432    2005-05-10  Douglas Bates  <bates@wisc.edu>
433    
434            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
435            logical sparse matrices.  These will also be used in the symbolic
436            analysis for lmer objects.
437    
438            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
439            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
440    
441    2005-05-06  Douglas Bates  <bates@wisc.edu>
442    
443            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
444            colMeans, colSums, rowMeans and rowSums.
445    
446    2005-04-18  Douglas Bates  <bates@wisc.edu>
447    
448            * src/lgCMatrix.[ch]: code for _validate method and stub for
449            multiplication operation.
450    
451            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
452            to dgetrs.
453    
454            * src/init.c: Fix cut-and-paste error in definition of
455            dgeMatrix_matrix_solve
456    
457            * src/{many files}: Tighten code by using ALLOC_SLOT.
458    
459    2005-04-15  Douglas Bates  <bates@wisc.edu>
460    
461            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
462    
463            * DESCRIPTION: Eliminate import of stats.
464    
465    
466    2005-04-06  Douglas Bates  <bates@wisc.edu>
467    
468            * R/AllClass.R : add logical sparse matrix classes
469    
470    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/dgTMatrix.R: add "[" method for triplet matrices
473            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
474    
475    2005-03-31  Douglas Bates  <bates@wisc.edu>
476    
477            * DESCRIPTION (Version): release 0.95-5 to CRAN
478    
479            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
480            * R/sparseMatrix.R: %*%, crossprod()
481            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
482            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
483            * src/lmer.c (lmer_fitted): fix thinko
484    
485    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/AllClass.R: add two virtual sparse classes ``on top''
488    
489    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
492                    correspondingly fix examples and tests/ since new()
493                    doesn't work for virtual classes.
494    
495    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * R/Matrix.R (as.matrix): method and one for unname()
498            * tests/dpoMatrix.R: tests should now be less platform dependent;
499              also run for R 2.1.0; using as.matrix()
500    
501    2005-03-15  Douglas Bates  <bates@wisc.edu>
502    
503            * R/pMatrix.R: "pMatrix" class added
504            * ....
505    
506    2005-03-14  Douglas Bates  <bates@wisc.edu>
507    
508            * R/dtpMatrix.R: Add unpack method and an example.
509    
510            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
511            of general symmetric matrices and associated S4 methods.
512    
513    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
514            +
515    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/dgeMatrix.R (setAs): and many other files: more coercion,
518              crossprod() and "%*%" methods added; tests, too.
519            * tests/matprod.R: new, for testing these
520    
521    2005-03-03  Douglas Bates  <bates@wisc.edu>
522    
523            * src/lmer.c (lmer_fitted): Added.
524    
525    2005-03-02  Douglas Bates  <bates@wisc.edu>
526    
527            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
528    
529    2005-02-28  Douglas Bates  <bates@wisc.edu>
530    
531            * src/*.c,po/,inst/po: Internationalization and localization of
532            the package.
533    
534            * src/ldl.[ch]: Removed these as their contents are referenced in the
535            R_ldl.c file.
536    
537            * src/flame.[ch]: Removed these source files.
538    
539            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
540    
541            * src/LU.[ch],src/init.c: absorb in factorizations
542    
543            * src/Mutils.h: prepare for internationalization
544    
545            * src/cblas.h: move the enum definitions to Mutils.h and remove
546            this file
547    
548    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
551    
552            * R/dtrMatrix.R: fix t() method
553    
554            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
555            * NAMESPACE: export them (and import generics from "methods")
556            * tests/group-methods.R : and test them.
557    
558            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
559            border case
560    
561    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * DESCRIPTION (Version): 0.95-2  released to CRAN
564    
565            * src/dgBCMatrix.c:
566            * src/lmer.c: many changes
567            * ...
568    
569    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Matrix.R: add more sophisticated show() method.
572    
573    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
574    
575            * */* : almost complete reorganization of classes.
576    
577    2005-01-26  Douglas Bates  <bates@wisc.edu>
578    
579            * R/AllGeneric.R: Added matrix exponential generic expm and a method
580            for the geMatrix class.
581    
582    2005-01-24  Douglas Bates  <bates@wisc.edu>
583    
584            * src/Makefile (clean): Remove *.a and *.so
585    
586            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
587    
588    2005-01-23  Douglas Bates  <bates@wisc.edu>
589    
590            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
591            had an effect in cases with more than 2 grouping factors.
592    
593    2005-01-03  Douglas Bates  <bates@wisc.edu>
594    
595            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
596    
597    2004-12-23  Douglas Bates  <bates@wisc.edu>
598    
599            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
600            and R_useDynamicSymbols (suggested by B.D.Ripley).
601    
602    2004-12-14  Douglas Bates  <bates@wisc.edu>
603    
604          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
605    
606          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
607          for tripletMatrix to matrix.          for tripletMatrix to matrix.
608    
609  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
610    
611          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
612          no longer used.          no longer used.
# Line 17  Line 618 
618          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
619          Fixes part but not all of #15.          Fixes part but not all of #15.
620    
621  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
622    
623          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
624          scalar grouping factors corrected.          scalar grouping factors corrected.
625    
626  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
627    
628          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
629    
630  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
631    
632          * 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
633          .h file can be included.          .h file can be included.
634    
635  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
636    
637          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
638          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
639    
640          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
641    
642  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
643    
644          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
645    
646  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
647    
648          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
649    
650  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
651    
652          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
653    
654  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
655    
656          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
657    
658  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
659    
660          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
661          routines.          routines.
662    
663  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
664    
665          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
666    
667  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
668    
669          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
670    

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