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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1259, Tue Apr 25 18:42:22 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
4            in method for "t" so as not to lose the unit diagonal property.
5    
6    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
9            and methods.  This is now an option to the ranef method for the
10            mer class.
11    
12            * src/cs_utils.c: Ensure that the nz component is -1 for a
13            compressed column-oriented matrix.  Minor formatting cleanup.
14    
15            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
16            objects.
17    
18    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
21            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
22    
23    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
24    
25            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
26            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
27    
28            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
29            for the dtCMatrix class.
30    
31    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
34            and methods for it.
35    
36    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
39            arguments, such that M %*% 1:6 now works
40            * Tests/matprod.R: test the above
41    
42    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
45            the ranef.lmer class.
46    
47            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
48            methods to extract the posterior variances from the bVar slot.
49    
50    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
53            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
54    
55            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
56            * tests/simple: (extended)
57    
58            * R/sparseMatrix.R (isTriangular): now using much improved
59            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
60    
61    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
64            (problem report from Franklin Parlamis).  This should be done
65            generally.
66    
67    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
68    
69            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
70            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
71            update the plot methods.
72    
73    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * R/lmer.R (resid and ranef methods):  Added methods for the
76            "residuals" and "resid" generic but only for linear mixed model
77            fits.  Changed the ranef method to return a list of data frames so
78            that the plot methods now work.
79    
80    2006-03-16  Douglas Bates  <bates@bates2>
81    
82            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
83            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
84    
85            * DESCRIPTION (Date): New release
86    
87    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
90    
91            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
92            * man/KNex.Rd: and other help files
93            * tests/*.R: several ones needed adaption
94            * inst/doc/Comparisons.Rnw: dito
95    
96    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
99    
100            * tests/indexing.R: tests for new [<- methods for sparse matrices.
101    
102    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
105    
106            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
107    
108    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dMatrix.R: enable things like  M [ M < 10 ]
111            * R/dgeMatrix.R: implement it
112    
113    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/AllClass.R: define "summary.mer" and "*.lmer"
116            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
117            * R/lmer.R (show): now works with summary()
118    
119    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
122            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
123                    support the above
124    
125    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
126    
127            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
128            Use glmFit$prior.weights for weights in a glmm.
129            Allow an option usePQL = FALSE to skip the PQL steps for the
130            Laplace method (and, in time, the AGQ method).
131    
132            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
133            into a separate function internal_mer_Xfactor to be able to call
134            it from internal_bhat.
135    
136    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/Class+Meth.R (tstMatrixClass): function for much better
139            testing; now again of all actual classes.
140    
141            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
142                    use macros and define make_d_matrix_* and make_i_matrix_*
143                    where _i_ is for the ldense routines:
144    
145            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
146            * src/ldense.c (lsyMatrix_as_lgeMatrix):
147    
148            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
149    
150    
151    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
154                    many different kinds of matrices.
155            * R/*.R: quite a few new methods were needed for R CMD check with
156                    new Matrix().  Very good for users playing around.
157    
158    
159    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/dgeMatrix.c (dMatrix_validate): new
162            * src/Mutils.c (dense_nonpacked_validate): new
163    
164            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
165    
166    
167    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
168    
169            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
170    
171    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * DESCRIPTION (Version): 0.99-6 released to CRAN
174    
175            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
176            segfault in cases with multiple non-nested grouping factors.
177    
178    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
181                    (Depends): also on 'utils'
182    
183            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
184            * R/diagMatrix.R (Diagonal): constructor and methods for
185            diagonal matrices
186    
187            * R/ltTMatrix.R: new "minimal methods"
188    
189    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
192            all methods (and help files).
193    
194    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
197                    for case (dimn.  op  no_dimn.)
198    
199    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * DESCRIPTION (Version): 0.99-2  released to CRAN
202    
203    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
206            by Julian Faraway.
207    
208    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Auxiliaries.R (try_as): new utility
211            * R/sparseMatrix.R: use try_as() in coercion to original class
212    
213    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
216    
217    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (dimNamesCheck): added
220    
221            * R/Matrix.R (as.array), (as.vector): new
222    
223    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
226                    default.
227            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
228                    "pMatrix" now contains "sparseMatrix"
229    
230    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * tests/Class+Meth.R: new tests; t(t(m)) == m
233    
234            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
235    
236            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
237            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
238    
239            * R/dspMatrix.R: typo in "t" method
240    
241    2005-09-18  Douglas Bates  <bates@wisc.edu>
242    
243            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
244            * R/Tsparse.R: instead of R/gTMatrix.R
245            * R/Csparse.R: new
246            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
247            * src/Tsparse.c: new; many trivial methods calling cholmod_()
248            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
249                            via cholmod
250    
251    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (non0ind): new function using new C code
254            * src/dgCMatrix.c (compressed_non_0_ij): new utility
255    
256    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
257    
258            * src/chm_common.h: header file required by all C sources that
259            call CHOLMOD functions.  It defines a cholmod_common structure
260            called 'c' whose address is passed as the last argument to
261            (virtually) every CHOLMOD function.
262    
263            * src/Pattern.c: Simple example of the use of CHOLMOD.
264    
265            * src/init.c: initialize and finalize the cholmod_common structure.
266    
267            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
268            LDL and CCOLAMD from the U. of Florida sparse matrix library.
269    
270    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * inst/test-tools.R: new file collecting the utility functions used
273                    in ./tests/*.R
274    
275            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
276            * R/Matrix.R (cbind2): methods for NULL and missing
277    
278    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/AllClass.R: new "index" class for "[" and "[<-":
281                    First cut at "symmetricMatrix" and "triangularMatrix"
282            * R/gTMatrix.R (.ind.prep): new function;
283                    Logical and character indexing now work too.
284            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
285            * tests/indexing.R: new, including *.Rout.save
286            * tests/dgTMatrix.R: new
287    
288    2005-08-29  Douglas Bates  <bates@wisc.edu>
289    
290            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
291            indicator pos not being updated.  Also enforced upper triangular
292            for symmetric case.  Need to coerce edges component of elements of
293            edge list - grr! (Why don't they define their classes cleanly?)
294    
295    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Matrix.R:  added first "[<-" methods; not yet functional
298            * R/denseMatrix.R: dito
299            * man/Subassign-methods.Rd: new help file for these
300    
301    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * DESCRIPTION (Version): 0.98-6
304    
305            * R/denseMatrix.R: new file for "[" fallback methods for all dense
306            matrices.
307    
308    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
311                    as( <logical>, "matrix")
312    
313            * R/pMatrix.R: coercion to "lgTMatrix"
314    
315            * R/gTMatrix.R: new virtual class to define "[" methods for.
316            * man/gTMatrix-class.Rd:
317            * General slight re-organization of where "[" methods are defined.
318              more to come.
319    
320    2005-08-18  Douglas Bates  <bates@wisc.edu>
321    
322            * DESCRIPTION (Version): 0.98-5  released to CRAN
323    
324            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
325            * .....
326    
327    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
328    
329            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
330            or glmer objects.
331    
332    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
335    
336    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
337    
338            * R/HBMM.R: finish re-writing R-only code.
339    
340    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
341    
342            * man/externalFormats.Rd: move documentation for writeHB and
343            writeMM here.
344    
345            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
346            (suggested by Paul Roecker).
347    
348            * tests/validObj.R (assertError): Comment out test that is failing
349            after recent changes in r-devel.
350    
351    
352    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/AllClass.R: intermediate virtual class "denseMatrix"
355            * man/denseMatrix-class.Rd
356            * NAMESPACE: export it, and also export
357            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
358    
359    2005-08-10  Douglas Bates  <bates@wisc.edu>
360    
361            * DESCRIPTION (Version): 0.98-3 to CRAN
362    
363            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
364            matrix_solve code (which was really, really wrong).
365    
366    2005-08-07  Douglas Bates  <bates@wisc.edu>
367    
368            * DESCRIPTION (Version): 0.98-2
369    
370            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
371    
372            * R/lmer.R (abbrvNms): new
373            * R/lmer.R (mcmcsamp): allow transformed parameters
374            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
375            for the Harwell-Boeing and the MatrixMarket formats.
376    
377    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * man/dtrMatrix-class.Rd: add examples
380            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
381    
382            * TODO: note the dtpMatrix (docu) bug
383    
384            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
385            in order to ensure that new as.matrix() is used by old functions,
386            e.g., svd(), qr(), eigen(), dist(),..;
387                  apply(), also matplot() or pairs().
388    
389    
390    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
393              add comments about 'control' / lmerControl() arguments
394    
395    2005-07-27  Douglas Bates  <bates@wisc.edu>
396    
397            * man/sleepstudy.Rd: Added the sleep data set.
398            * DESCRIPTION (Version): 0.98-1  released to CRAN
399    
400    2005-07-12  Douglas Bates  <bates@wisc.edu>
401            * man/sleepstudy.Rd: Added the sleep data set.
402    
403            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
404            .Call calls that were producing spurious output.
405    
406    2005-07-05  Douglas Bates  <bates@wisc.edu>
407    
408            * R/lmer.R (lmer): stored updated variance component estimates in
409            mer object for the generalized model.  (Bug reported by Renaud
410            Lancelot).
411    
412    2005-07-03  Douglas Bates  <bates@wisc.edu>
413    
414            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
415            unidimensional case.
416    
417    2005-06-08  Douglas Bates  <bates@wisc.edu>
418    
419            * DESCRIPTION (Version): 0.96-1
420    
421            * moved  lmer-class' R and C code moved from lme4 to here
422    
423    2005-06-04  Douglas Bates  <bates@wisc.edu>
424    
425            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
426            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
427    
428    2005-06-02  Douglas Bates  <bates@wisc.edu>
429    
430            * src/Makefile.win: Forgot to update this when Makefile changed.
431    
432    2005-05-11  Douglas Bates  <bates@wisc.edu>
433    
434            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
435            bug reported by Kurt Hornik and Michael Hahsler.
436    
437    2005-05-10  Douglas Bates  <bates@wisc.edu>
438    
439            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
440            logical sparse matrices.  These will also be used in the symbolic
441            analysis for lmer objects.
442    
443            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
444            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
445    
446    2005-05-06  Douglas Bates  <bates@wisc.edu>
447    
448            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
449            colMeans, colSums, rowMeans and rowSums.
450    
451    2005-04-18  Douglas Bates  <bates@wisc.edu>
452    
453            * src/lgCMatrix.[ch]: code for _validate method and stub for
454            multiplication operation.
455    
456            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
457            to dgetrs.
458    
459            * src/init.c: Fix cut-and-paste error in definition of
460            dgeMatrix_matrix_solve
461    
462            * src/{many files}: Tighten code by using ALLOC_SLOT.
463    
464    2005-04-15  Douglas Bates  <bates@wisc.edu>
465    
466            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
467    
468            * DESCRIPTION: Eliminate import of stats.
469    
470    
471    2005-04-06  Douglas Bates  <bates@wisc.edu>
472    
473            * R/AllClass.R : add logical sparse matrix classes
474    
475    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/dgTMatrix.R: add "[" method for triplet matrices
478            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
479    
480    2005-03-31  Douglas Bates  <bates@wisc.edu>
481    
482            * DESCRIPTION (Version): release 0.95-5 to CRAN
483    
484            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
485            * R/sparseMatrix.R: %*%, crossprod()
486            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
487            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
488            * src/lmer.c (lmer_fitted): fix thinko
489    
490    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/AllClass.R: add two virtual sparse classes ``on top''
493    
494    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
497                    correspondingly fix examples and tests/ since new()
498                    doesn't work for virtual classes.
499    
500    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Matrix.R (as.matrix): method and one for unname()
503            * tests/dpoMatrix.R: tests should now be less platform dependent;
504              also run for R 2.1.0; using as.matrix()
505    
506    2005-03-15  Douglas Bates  <bates@wisc.edu>
507    
508            * R/pMatrix.R: "pMatrix" class added
509            * ....
510    
511    2005-03-14  Douglas Bates  <bates@wisc.edu>
512    
513            * R/dtpMatrix.R: Add unpack method and an example.
514    
515            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
516            of general symmetric matrices and associated S4 methods.
517    
518    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
519            +
520    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/dgeMatrix.R (setAs): and many other files: more coercion,
523              crossprod() and "%*%" methods added; tests, too.
524            * tests/matprod.R: new, for testing these
525    
526    2005-03-03  Douglas Bates  <bates@wisc.edu>
527    
528            * src/lmer.c (lmer_fitted): Added.
529    
530    2005-03-02  Douglas Bates  <bates@wisc.edu>
531    
532            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
533    
534    2005-02-28  Douglas Bates  <bates@wisc.edu>
535    
536            * src/*.c,po/,inst/po: Internationalization and localization of
537            the package.
538    
539            * src/ldl.[ch]: Removed these as their contents are referenced in the
540            R_ldl.c file.
541    
542            * src/flame.[ch]: Removed these source files.
543    
544            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
545    
546            * src/LU.[ch],src/init.c: absorb in factorizations
547    
548            * src/Mutils.h: prepare for internationalization
549    
550            * src/cblas.h: move the enum definitions to Mutils.h and remove
551            this file
552    
553    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
556    
557            * R/dtrMatrix.R: fix t() method
558    
559            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
560            * NAMESPACE: export them (and import generics from "methods")
561            * tests/group-methods.R : and test them.
562    
563            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
564            border case
565    
566    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
567    
568            * DESCRIPTION (Version): 0.95-2  released to CRAN
569    
570            * src/dgBCMatrix.c:
571            * src/lmer.c: many changes
572            * ...
573    
574    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R: add more sophisticated show() method.
577    
578    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * */* : almost complete reorganization of classes.
581    
582    2005-01-26  Douglas Bates  <bates@wisc.edu>
583    
584            * R/AllGeneric.R: Added matrix exponential generic expm and a method
585            for the geMatrix class.
586    
587    2005-01-24  Douglas Bates  <bates@wisc.edu>
588    
589            * src/Makefile (clean): Remove *.a and *.so
590    
591            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
592    
593    2005-01-23  Douglas Bates  <bates@wisc.edu>
594    
595            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
596            had an effect in cases with more than 2 grouping factors.
597    
598    2005-01-03  Douglas Bates  <bates@wisc.edu>
599    
600            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
601    
602    2004-12-23  Douglas Bates  <bates@wisc.edu>
603    
604            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
605            and R_useDynamicSymbols (suggested by B.D.Ripley).
606    
607    2004-12-14  Douglas Bates  <bates@wisc.edu>
608    
609            * R/sscMatrix.R: Add determinant methods
610    
611            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
612            for tripletMatrix to matrix.
613    
614    2004-12-13  Douglas Bates  <bates@wisc.edu>
615    
616            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
617            no longer used.
618    
619          * 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
620          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 623 
623          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
624          Fixes part but not all of #15.          Fixes part but not all of #15.
625    
626  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
627    
628          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
629          scalar grouping factors corrected.          scalar grouping factors corrected.
630    
631  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
632    
633          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
634    
635  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
636    
637          * 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
638          .h file can be included.          .h file can be included.
639    
640  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
641    
642          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
643          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
644    
645          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
646    
647  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
648    
649          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
650    
651  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
652    
653          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
654    
655  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
656    
657          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
658    
659  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
660    
661          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
662    
663  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
664    
665          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
666          routines.          routines.
667    
668  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
669    
670          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
671    
672  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
673    
674          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
675    

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