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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1265, Mon May 15 22:36:59 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
4            generics lowerTriMatrix and upperTriMatrix along with methods for
5            the Csparse virtual class.  Also added a C function Csparse_band
6            that implements these methods by calling cholmod_band.
7    
8    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
11            erased when it was NULL.  This led to invalid subselections!
12    
13    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
16            in method for "t" so as not to lose the unit diagonal property.
17    
18    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
21            and methods.  This is now an option to the ranef method for the
22            mer class.
23    
24            * src/cs_utils.c: Ensure that the nz component is -1 for a
25            compressed column-oriented matrix.  Minor formatting cleanup.
26    
27            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
28            objects.
29    
30    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
33            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
34    
35    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
38            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
39    
40            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
41            for the dtCMatrix class.
42    
43    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
46            and methods for it.
47    
48    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
51            arguments, such that M %*% 1:6 now works
52            * Tests/matprod.R: test the above
53    
54    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
57            the ranef.lmer class.
58    
59            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
60            methods to extract the posterior variances from the bVar slot.
61    
62    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
65            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
66    
67            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
68            * tests/simple: (extended)
69    
70            * R/sparseMatrix.R (isTriangular): now using much improved
71            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
72    
73    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
76            (problem report from Franklin Parlamis).  This should be done
77            generally.
78    
79    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
82            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
83            update the plot methods.
84    
85    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/lmer.R (resid and ranef methods):  Added methods for the
88            "residuals" and "resid" generic but only for linear mixed model
89            fits.  Changed the ranef method to return a list of data frames so
90            that the plot methods now work.
91    
92    2006-03-16  Douglas Bates  <bates@bates2>
93    
94            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
95            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
96    
97            * DESCRIPTION (Date): New release
98    
99    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
102    
103            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
104            * man/KNex.Rd: and other help files
105            * tests/*.R: several ones needed adaption
106            * inst/doc/Comparisons.Rnw: dito
107    
108    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
111    
112            * tests/indexing.R: tests for new [<- methods for sparse matrices.
113    
114    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
117    
118            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
119    
120    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/dMatrix.R: enable things like  M [ M < 10 ]
123            * R/dgeMatrix.R: implement it
124    
125    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R: define "summary.mer" and "*.lmer"
128            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
129            * R/lmer.R (show): now works with summary()
130    
131    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
134            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
135                    support the above
136    
137    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
140            Use glmFit$prior.weights for weights in a glmm.
141            Allow an option usePQL = FALSE to skip the PQL steps for the
142            Laplace method (and, in time, the AGQ method).
143    
144            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
145            into a separate function internal_mer_Xfactor to be able to call
146            it from internal_bhat.
147    
148    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * tests/Class+Meth.R (tstMatrixClass): function for much better
151            testing; now again of all actual classes.
152    
153            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
154                    use macros and define make_d_matrix_* and make_i_matrix_*
155                    where _i_ is for the ldense routines:
156    
157            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
158            * src/ldense.c (lsyMatrix_as_lgeMatrix):
159    
160            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
161    
162    
163    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
166                    many different kinds of matrices.
167            * R/*.R: quite a few new methods were needed for R CMD check with
168                    new Matrix().  Very good for users playing around.
169    
170    
171    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * src/dgeMatrix.c (dMatrix_validate): new
174            * src/Mutils.c (dense_nonpacked_validate): new
175    
176            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
177    
178    
179    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
182    
183    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * DESCRIPTION (Version): 0.99-6 released to CRAN
186    
187            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
188            segfault in cases with multiple non-nested grouping factors.
189    
190    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
193                    (Depends): also on 'utils'
194    
195            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
196            * R/diagMatrix.R (Diagonal): constructor and methods for
197            diagonal matrices
198    
199            * R/ltTMatrix.R: new "minimal methods"
200    
201    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
204            all methods (and help files).
205    
206    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
209                    for case (dimn.  op  no_dimn.)
210    
211    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
212    
213            * DESCRIPTION (Version): 0.99-2  released to CRAN
214    
215    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
218            by Julian Faraway.
219    
220    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/Auxiliaries.R (try_as): new utility
223            * R/sparseMatrix.R: use try_as() in coercion to original class
224    
225    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
228    
229    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/Auxiliaries.R (dimNamesCheck): added
232    
233            * R/Matrix.R (as.array), (as.vector): new
234    
235    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
238                    default.
239            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
240                    "pMatrix" now contains "sparseMatrix"
241    
242    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * tests/Class+Meth.R: new tests; t(t(m)) == m
245    
246            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
247    
248            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
249            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
250    
251            * R/dspMatrix.R: typo in "t" method
252    
253    2005-09-18  Douglas Bates  <bates@wisc.edu>
254    
255            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
256            * R/Tsparse.R: instead of R/gTMatrix.R
257            * R/Csparse.R: new
258            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
259            * src/Tsparse.c: new; many trivial methods calling cholmod_()
260            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
261                            via cholmod
262    
263    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Auxiliaries.R (non0ind): new function using new C code
266            * src/dgCMatrix.c (compressed_non_0_ij): new utility
267    
268    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
269    
270            * src/chm_common.h: header file required by all C sources that
271            call CHOLMOD functions.  It defines a cholmod_common structure
272            called 'c' whose address is passed as the last argument to
273            (virtually) every CHOLMOD function.
274    
275            * src/Pattern.c: Simple example of the use of CHOLMOD.
276    
277            * src/init.c: initialize and finalize the cholmod_common structure.
278    
279            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
280            LDL and CCOLAMD from the U. of Florida sparse matrix library.
281    
282    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * inst/test-tools.R: new file collecting the utility functions used
285                    in ./tests/*.R
286    
287            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
288            * R/Matrix.R (cbind2): methods for NULL and missing
289    
290    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/AllClass.R: new "index" class for "[" and "[<-":
293                    First cut at "symmetricMatrix" and "triangularMatrix"
294            * R/gTMatrix.R (.ind.prep): new function;
295                    Logical and character indexing now work too.
296            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
297            * tests/indexing.R: new, including *.Rout.save
298            * tests/dgTMatrix.R: new
299    
300    2005-08-29  Douglas Bates  <bates@wisc.edu>
301    
302            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
303            indicator pos not being updated.  Also enforced upper triangular
304            for symmetric case.  Need to coerce edges component of elements of
305            edge list - grr! (Why don't they define their classes cleanly?)
306    
307    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Matrix.R:  added first "[<-" methods; not yet functional
310            * R/denseMatrix.R: dito
311            * man/Subassign-methods.Rd: new help file for these
312    
313    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * DESCRIPTION (Version): 0.98-6
316    
317            * R/denseMatrix.R: new file for "[" fallback methods for all dense
318            matrices.
319    
320    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
323                    as( <logical>, "matrix")
324    
325            * R/pMatrix.R: coercion to "lgTMatrix"
326    
327            * R/gTMatrix.R: new virtual class to define "[" methods for.
328            * man/gTMatrix-class.Rd:
329            * General slight re-organization of where "[" methods are defined.
330              more to come.
331    
332    2005-08-18  Douglas Bates  <bates@wisc.edu>
333    
334            * DESCRIPTION (Version): 0.98-5  released to CRAN
335    
336            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
337            * .....
338    
339    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
340    
341            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
342            or glmer objects.
343    
344    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
347    
348    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
349    
350            * R/HBMM.R: finish re-writing R-only code.
351    
352    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
353    
354            * man/externalFormats.Rd: move documentation for writeHB and
355            writeMM here.
356    
357            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
358            (suggested by Paul Roecker).
359    
360            * tests/validObj.R (assertError): Comment out test that is failing
361            after recent changes in r-devel.
362    
363    
364    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/AllClass.R: intermediate virtual class "denseMatrix"
367            * man/denseMatrix-class.Rd
368            * NAMESPACE: export it, and also export
369            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
370    
371    2005-08-10  Douglas Bates  <bates@wisc.edu>
372    
373            * DESCRIPTION (Version): 0.98-3 to CRAN
374    
375            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
376            matrix_solve code (which was really, really wrong).
377    
378    2005-08-07  Douglas Bates  <bates@wisc.edu>
379    
380            * DESCRIPTION (Version): 0.98-2
381    
382            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
383    
384            * R/lmer.R (abbrvNms): new
385            * R/lmer.R (mcmcsamp): allow transformed parameters
386            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
387            for the Harwell-Boeing and the MatrixMarket formats.
388    
389    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * man/dtrMatrix-class.Rd: add examples
392            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
393    
394            * TODO: note the dtpMatrix (docu) bug
395    
396            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
397            in order to ensure that new as.matrix() is used by old functions,
398            e.g., svd(), qr(), eigen(), dist(),..;
399                  apply(), also matplot() or pairs().
400    
401    
402    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
405              add comments about 'control' / lmerControl() arguments
406    
407    2005-07-27  Douglas Bates  <bates@wisc.edu>
408    
409            * man/sleepstudy.Rd: Added the sleep data set.
410            * DESCRIPTION (Version): 0.98-1  released to CRAN
411    
412    2005-07-12  Douglas Bates  <bates@wisc.edu>
413            * man/sleepstudy.Rd: Added the sleep data set.
414    
415            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
416            .Call calls that were producing spurious output.
417    
418    2005-07-05  Douglas Bates  <bates@wisc.edu>
419    
420            * R/lmer.R (lmer): stored updated variance component estimates in
421            mer object for the generalized model.  (Bug reported by Renaud
422            Lancelot).
423    
424    2005-07-03  Douglas Bates  <bates@wisc.edu>
425    
426            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
427            unidimensional case.
428    
429    2005-06-08  Douglas Bates  <bates@wisc.edu>
430    
431            * DESCRIPTION (Version): 0.96-1
432    
433            * moved  lmer-class' R and C code moved from lme4 to here
434    
435    2005-06-04  Douglas Bates  <bates@wisc.edu>
436    
437            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
438            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
439    
440    2005-06-02  Douglas Bates  <bates@wisc.edu>
441    
442            * src/Makefile.win: Forgot to update this when Makefile changed.
443    
444    2005-05-11  Douglas Bates  <bates@wisc.edu>
445    
446            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
447            bug reported by Kurt Hornik and Michael Hahsler.
448    
449    2005-05-10  Douglas Bates  <bates@wisc.edu>
450    
451            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
452            logical sparse matrices.  These will also be used in the symbolic
453            analysis for lmer objects.
454    
455            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
456            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
457    
458    2005-05-06  Douglas Bates  <bates@wisc.edu>
459    
460            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
461            colMeans, colSums, rowMeans and rowSums.
462    
463    2005-04-18  Douglas Bates  <bates@wisc.edu>
464    
465            * src/lgCMatrix.[ch]: code for _validate method and stub for
466            multiplication operation.
467    
468            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
469            to dgetrs.
470    
471            * src/init.c: Fix cut-and-paste error in definition of
472            dgeMatrix_matrix_solve
473    
474            * src/{many files}: Tighten code by using ALLOC_SLOT.
475    
476    2005-04-15  Douglas Bates  <bates@wisc.edu>
477    
478            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
479    
480            * DESCRIPTION: Eliminate import of stats.
481    
482    
483    2005-04-06  Douglas Bates  <bates@wisc.edu>
484    
485            * R/AllClass.R : add logical sparse matrix classes
486    
487    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/dgTMatrix.R: add "[" method for triplet matrices
490            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
491    
492    2005-03-31  Douglas Bates  <bates@wisc.edu>
493    
494            * DESCRIPTION (Version): release 0.95-5 to CRAN
495    
496            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
497            * R/sparseMatrix.R: %*%, crossprod()
498            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
499            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
500            * src/lmer.c (lmer_fitted): fix thinko
501    
502    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/AllClass.R: add two virtual sparse classes ``on top''
505    
506    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
509                    correspondingly fix examples and tests/ since new()
510                    doesn't work for virtual classes.
511    
512    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Matrix.R (as.matrix): method and one for unname()
515            * tests/dpoMatrix.R: tests should now be less platform dependent;
516              also run for R 2.1.0; using as.matrix()
517    
518    2005-03-15  Douglas Bates  <bates@wisc.edu>
519    
520            * R/pMatrix.R: "pMatrix" class added
521            * ....
522    
523    2005-03-14  Douglas Bates  <bates@wisc.edu>
524    
525            * R/dtpMatrix.R: Add unpack method and an example.
526    
527            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
528            of general symmetric matrices and associated S4 methods.
529    
530    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
531            +
532    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/dgeMatrix.R (setAs): and many other files: more coercion,
535              crossprod() and "%*%" methods added; tests, too.
536            * tests/matprod.R: new, for testing these
537    
538    2005-03-03  Douglas Bates  <bates@wisc.edu>
539    
540            * src/lmer.c (lmer_fitted): Added.
541    
542    2005-03-02  Douglas Bates  <bates@wisc.edu>
543    
544            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
545    
546    2005-02-28  Douglas Bates  <bates@wisc.edu>
547    
548            * src/*.c,po/,inst/po: Internationalization and localization of
549            the package.
550    
551            * src/ldl.[ch]: Removed these as their contents are referenced in the
552            R_ldl.c file.
553    
554            * src/flame.[ch]: Removed these source files.
555    
556            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
557    
558            * src/LU.[ch],src/init.c: absorb in factorizations
559    
560            * src/Mutils.h: prepare for internationalization
561    
562            * src/cblas.h: move the enum definitions to Mutils.h and remove
563            this file
564    
565    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
568    
569            * R/dtrMatrix.R: fix t() method
570    
571            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
572            * NAMESPACE: export them (and import generics from "methods")
573            * tests/group-methods.R : and test them.
574    
575            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
576            border case
577    
578    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * DESCRIPTION (Version): 0.95-2  released to CRAN
581    
582            * src/dgBCMatrix.c:
583            * src/lmer.c: many changes
584            * ...
585    
586    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Matrix.R: add more sophisticated show() method.
589    
590    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
591    
592            * */* : almost complete reorganization of classes.
593    
594    2005-01-26  Douglas Bates  <bates@wisc.edu>
595    
596            * R/AllGeneric.R: Added matrix exponential generic expm and a method
597            for the geMatrix class.
598    
599    2005-01-24  Douglas Bates  <bates@wisc.edu>
600    
601            * src/Makefile (clean): Remove *.a and *.so
602    
603            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
604    
605    2005-01-23  Douglas Bates  <bates@wisc.edu>
606    
607            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
608            had an effect in cases with more than 2 grouping factors.
609    
610    2005-01-03  Douglas Bates  <bates@wisc.edu>
611    
612            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
613    
614    2004-12-23  Douglas Bates  <bates@wisc.edu>
615    
616            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
617            and R_useDynamicSymbols (suggested by B.D.Ripley).
618    
619    2004-12-14  Douglas Bates  <bates@wisc.edu>
620    
621            * R/sscMatrix.R: Add determinant methods
622    
623            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
624            for tripletMatrix to matrix.
625    
626    2004-12-13  Douglas Bates  <bates@wisc.edu>
627    
628            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
629            no longer used.
630    
631            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
632            with dynamic allocation of scratch arrays.
633    
634            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
635            for multivariate random effects with multiple grouping factors.
636            Fixes part but not all of #15.
637    
638    2004-12-03  Douglas Bates  <bates@wisc.edu>
639    
640            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
641            scalar grouping factors corrected.
642    
643    2004-11-29  Douglas Bates  <bates@wisc.edu>
644    
645            * src/bCrosstab.c: remove diag_update which is no longer used
646    
647    2004-11-16  Douglas Bates  <bates@wisc.edu>
648    
649          * 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
650          .h file can be included.          .h file can be included.
651    
652  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
653    
654          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
655          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
656    
657          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
658    
659  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
660    
661          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
662    
663  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
664    
665          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
666    
667  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
668    
669          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
670    
671  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
672    
673          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
674    
675  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
676    
677          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
678          routines.          routines.
679    
680  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
681    
682          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
683    
684  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
685    
686          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
687    

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