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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1330, Fri Jul 21 08:28:18 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
4            argument; in glmer_*(): print only if(verbose).
5    
6            speed-optimize a few places by moving REAL(.) out of loops.
7    
8            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
9    
10    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
13                    since that wrongly triggers also for M[ logi , ]
14    
15            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
16            a symmetric matrix that results in a non-symmetric one.
17            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
18    
19            * R/dMatrix.R: make round(M) work as round(M, 0)
20    
21            * R/dgTMatrix.R (image): coordinate system and axis now use
22            1-based indices, not 0-based ones.
23    
24            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
25            * tests/indexing.R: test it.
26    
27            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
28            * man/isSymmetric-methods.Rd: and document it.
29    
30            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
31            * man/SparseM-conv.Rd: docu them
32    
33            * tests/other-pkgs.R: renamed from tests/graph.R and add example
34                    for 'SparseM' conversions
35    
36    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
37    
38            * R/Matrix.R (head): added head() and tail() methods.
39    
40    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * DESCRIPTION (Version): 0.995-12 released to CRAN
43    
44    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * tests/simple.R: add check for correct dsT -> dgT coercion;
47                    add check for correct printing of symmetric sparse matrices.
48    
49            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
50            for sparse symmetric matrices.
51    
52            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
53            diagonal twice.
54    
55    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
56    
57            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
58            being applied to the x slot (detected by Brian Ripley).
59    
60    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
63    
64            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
65    
66    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * src/lgCMatrix.c (lgCMatrix_diag): new function
69            * R/lgCMatrix.R (diag): for new method
70    
71            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
72                 ==> construction of illegal "*gTMatrix" via new() should
73                 now be much less easy:
74            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
75    
76            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
77                    directly.
78            * man/Matrix.Rd: documents it.
79    
80    2006-07-06  Douglas Bates  <bates@R-project.org>
81    
82            * src/pedigree.c (pedigree_inbreeding): Correction in
83            initialization.  This function is not currently being used and is
84            not fully tested.
85    
86            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
87            Introduced the glmer class.  Added code for mcmcmsamp on glmer
88            objects.  Modified validity check on pedigree objects to account
89            for nonparallel patterns of missingness of parents.
90    
91            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
92            class.
93    
94    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/pMatrix.R: coercion pMatrix -> Tsparse
97    
98    2006-06-12  Douglas Bates  <bates@R-project.org>
99    
100            * DESCRIPTION (Version): 0.995-11 released to CRAN
101    
102            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
103            the output from mcmcsamp.
104    
105    2006-06-10  Douglas Bates  <bates@R-project.org>
106    
107            * R/lmer.R (simulestimate): added C code for calculating the trace
108            of the hat matrix.
109    
110    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
113            classes.
114            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
115    
116    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/dgTMatrix.R (colSums): etc. All four of
119            colSums(), rowSums(), colMeans(), rowMeans() now should work for
120            all "Matrices".
121    
122    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * R/lmer.R (panel.ci): Add a reference line at zero and a
125            background grid to the qqmath plot of ranef.lmer.
126    
127    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
130            grouping factors to be specified in the formula as (1|foo/bar).
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/lmer.R (findbars and others): Change check of is.numeric to
135            !is.language to resolve the bug reported by Jacob Wegelin.
136    
137            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
138            code to evaluate inbreeding coefficients without calculating T,
139            based on code in Sargolzaei and Iwaisaki's paper.
140    
141    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
144            generic and mer methods for isNested and denomDF. This denomDF was
145            an attempt to emulate that in lme but I don't think that makes
146            sense.  Use the trace of the hat matrix instead.
147    
148    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
151            the C code depending on a slot structure that's no longer valid.
152            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
153    
154    
155    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
156    
157            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
158            of lowerTriMatrix generic and methods to tril (also upper to triu)
159            and added a general band extractor.
160    
161    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * R/pedigree.R (pedigree): Replace sire and dam values outside the
164            allowable range with NAs. Added a corresponding check in the
165            validity check for the pedigree class.
166    
167            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
168            crossprod methods now inherits from symmetricMatrix.
169    
170    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
171    
172            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
173            generics lowerTriMatrix and upperTriMatrix along with methods for
174            the Csparse virtual class.  Also added a C function Csparse_band
175            that implements these methods by calling cholmod_band.
176    
177    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
180            erased when it was NULL.  This led to invalid subselections!
181    
182    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
183    
184            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
185            in method for "t" so as not to lose the unit diagonal property.
186    
187    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
190            and methods.  This is now an option to the ranef method for the
191            mer class.
192    
193            * src/cs_utils.c: Ensure that the nz component is -1 for a
194            compressed column-oriented matrix.  Minor formatting cleanup.
195    
196            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
197            objects.
198    
199    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
202            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
203    
204    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
207            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
208    
209            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
210            for the dtCMatrix class.
211    
212    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
215            and methods for it.
216    
217    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
220            arguments, such that M %*% 1:6 now works
221            * Tests/matprod.R: test the above
222    
223    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
226            the ranef.lmer class.
227    
228            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
229            methods to extract the posterior variances from the bVar slot.
230    
231    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
234            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
235    
236            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
237            * tests/simple: (extended)
238    
239            * R/sparseMatrix.R (isTriangular): now using much improved
240            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
241    
242    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
245            (problem report from Franklin Parlamis).  This should be done
246            generally.
247    
248    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
251            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
252            update the plot methods.
253    
254    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
255    
256            * R/lmer.R (resid and ranef methods):  Added methods for the
257            "residuals" and "resid" generic but only for linear mixed model
258            fits.  Changed the ranef method to return a list of data frames so
259            that the plot methods now work.
260    
261    2006-03-16  Douglas Bates  <bates@bates2>
262    
263            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
264            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
265    
266            * DESCRIPTION (Date): New release
267    
268    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
271    
272            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
273            * man/KNex.Rd: and other help files
274            * tests/*.R: several ones needed adaption
275            * inst/doc/Comparisons.Rnw: dito
276    
277    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
280    
281            * tests/indexing.R: tests for new [<- methods for sparse matrices.
282    
283    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
286    
287            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
288    
289    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dMatrix.R: enable things like  M [ M < 10 ]
292            * R/dgeMatrix.R: implement it
293    
294    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/AllClass.R: define "summary.mer" and "*.lmer"
297            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
298            * R/lmer.R (show): now works with summary()
299    
300    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
303            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
304                    support the above
305    
306    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
307    
308            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
309            Use glmFit$prior.weights for weights in a glmm.
310            Allow an option usePQL = FALSE to skip the PQL steps for the
311            Laplace method (and, in time, the AGQ method).
312    
313            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
314            into a separate function internal_mer_Xfactor to be able to call
315            it from internal_bhat.
316    
317    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * tests/Class+Meth.R (tstMatrixClass): function for much better
320            testing; now again of all actual classes.
321    
322            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
323                    use macros and define make_d_matrix_* and make_i_matrix_*
324                    where _i_ is for the ldense routines:
325    
326            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
327            * src/ldense.c (lsyMatrix_as_lgeMatrix):
328    
329            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
330    
331    
332    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
335                    many different kinds of matrices.
336            * R/*.R: quite a few new methods were needed for R CMD check with
337                    new Matrix().  Very good for users playing around.
338    
339    
340    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * src/dgeMatrix.c (dMatrix_validate): new
343            * src/Mutils.c (dense_nonpacked_validate): new
344    
345            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
346    
347    
348    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
351    
352    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
353    
354            * DESCRIPTION (Version): 0.99-6 released to CRAN
355    
356            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
357            segfault in cases with multiple non-nested grouping factors.
358    
359    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
362                    (Depends): also on 'utils'
363    
364            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
365            * R/diagMatrix.R (Diagonal): constructor and methods for
366            diagonal matrices
367    
368            * R/ltTMatrix.R: new "minimal methods"
369    
370    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
373            all methods (and help files).
374    
375    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
378                    for case (dimn.  op  no_dimn.)
379    
380    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
381    
382            * DESCRIPTION (Version): 0.99-2  released to CRAN
383    
384    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
387            by Julian Faraway.
388    
389    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Auxiliaries.R (try_as): new utility
392            * R/sparseMatrix.R: use try_as() in coercion to original class
393    
394    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
397    
398    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Auxiliaries.R (dimNamesCheck): added
401    
402            * R/Matrix.R (as.array), (as.vector): new
403    
404    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
407                    default.
408            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
409                    "pMatrix" now contains "sparseMatrix"
410    
411    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * tests/Class+Meth.R: new tests; t(t(m)) == m
414    
415            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
416    
417            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
418            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
419    
420            * R/dspMatrix.R: typo in "t" method
421    
422    2005-09-18  Douglas Bates  <bates@wisc.edu>
423    
424            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
425            * R/Tsparse.R: instead of R/gTMatrix.R
426            * R/Csparse.R: new
427            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
428            * src/Tsparse.c: new; many trivial methods calling cholmod_()
429            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
430                            via cholmod
431    
432    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/Auxiliaries.R (non0ind): new function using new C code
435            * src/dgCMatrix.c (compressed_non_0_ij): new utility
436    
437    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
438    
439            * src/chm_common.h: header file required by all C sources that
440            call CHOLMOD functions.  It defines a cholmod_common structure
441            called 'c' whose address is passed as the last argument to
442            (virtually) every CHOLMOD function.
443    
444            * src/Pattern.c: Simple example of the use of CHOLMOD.
445    
446            * src/init.c: initialize and finalize the cholmod_common structure.
447    
448            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
449            LDL and CCOLAMD from the U. of Florida sparse matrix library.
450    
451    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * inst/test-tools.R: new file collecting the utility functions used
454                    in ./tests/*.R
455    
456            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
457            * R/Matrix.R (cbind2): methods for NULL and missing
458    
459    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/AllClass.R: new "index" class for "[" and "[<-":
462                    First cut at "symmetricMatrix" and "triangularMatrix"
463            * R/gTMatrix.R (.ind.prep): new function;
464                    Logical and character indexing now work too.
465            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
466            * tests/indexing.R: new, including *.Rout.save
467            * tests/dgTMatrix.R: new
468    
469    2005-08-29  Douglas Bates  <bates@wisc.edu>
470    
471            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
472            indicator pos not being updated.  Also enforced upper triangular
473            for symmetric case.  Need to coerce edges component of elements of
474            edge list - grr! (Why don't they define their classes cleanly?)
475    
476    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Matrix.R:  added first "[<-" methods; not yet functional
479            * R/denseMatrix.R: dito
480            * man/Subassign-methods.Rd: new help file for these
481    
482    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * DESCRIPTION (Version): 0.98-6
485    
486            * R/denseMatrix.R: new file for "[" fallback methods for all dense
487            matrices.
488    
489    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
492                    as( <logical>, "matrix")
493    
494            * R/pMatrix.R: coercion to "lgTMatrix"
495    
496            * R/gTMatrix.R: new virtual class to define "[" methods for.
497            * man/gTMatrix-class.Rd:
498            * General slight re-organization of where "[" methods are defined.
499              more to come.
500    
501    2005-08-18  Douglas Bates  <bates@wisc.edu>
502    
503            * DESCRIPTION (Version): 0.98-5  released to CRAN
504    
505            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
506            * .....
507    
508    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
509    
510            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
511            or glmer objects.
512    
513    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
516    
517    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
518    
519            * R/HBMM.R: finish re-writing R-only code.
520    
521    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
522    
523            * man/externalFormats.Rd: move documentation for writeHB and
524            writeMM here.
525    
526            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
527            (suggested by Paul Roecker).
528    
529            * tests/validObj.R (assertError): Comment out test that is failing
530            after recent changes in r-devel.
531    
532    
533    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/AllClass.R: intermediate virtual class "denseMatrix"
536            * man/denseMatrix-class.Rd
537            * NAMESPACE: export it, and also export
538            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
539    
540    2005-08-10  Douglas Bates  <bates@wisc.edu>
541    
542            * DESCRIPTION (Version): 0.98-3 to CRAN
543    
544            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
545            matrix_solve code (which was really, really wrong).
546    
547    2005-08-07  Douglas Bates  <bates@wisc.edu>
548    
549            * DESCRIPTION (Version): 0.98-2
550    
551            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
552    
553            * R/lmer.R (abbrvNms): new
554            * R/lmer.R (mcmcsamp): allow transformed parameters
555            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
556            for the Harwell-Boeing and the MatrixMarket formats.
557    
558    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * man/dtrMatrix-class.Rd: add examples
561            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
562    
563            * TODO: note the dtpMatrix (docu) bug
564    
565            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
566            in order to ensure that new as.matrix() is used by old functions,
567            e.g., svd(), qr(), eigen(), dist(),..;
568                  apply(), also matplot() or pairs().
569    
570    
571    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
574              add comments about 'control' / lmerControl() arguments
575    
576    2005-07-27  Douglas Bates  <bates@wisc.edu>
577    
578            * man/sleepstudy.Rd: Added the sleep data set.
579            * DESCRIPTION (Version): 0.98-1  released to CRAN
580    
581    2005-07-12  Douglas Bates  <bates@wisc.edu>
582            * man/sleepstudy.Rd: Added the sleep data set.
583    
584            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
585            .Call calls that were producing spurious output.
586    
587    2005-07-05  Douglas Bates  <bates@wisc.edu>
588    
589            * R/lmer.R (lmer): stored updated variance component estimates in
590            mer object for the generalized model.  (Bug reported by Renaud
591            Lancelot).
592    
593    2005-07-03  Douglas Bates  <bates@wisc.edu>
594    
595            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
596            unidimensional case.
597    
598    2005-06-08  Douglas Bates  <bates@wisc.edu>
599    
600            * DESCRIPTION (Version): 0.96-1
601    
602            * moved  lmer-class' R and C code moved from lme4 to here
603    
604    2005-06-04  Douglas Bates  <bates@wisc.edu>
605    
606            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
607            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
608    
609    2005-06-02  Douglas Bates  <bates@wisc.edu>
610    
611            * src/Makefile.win: Forgot to update this when Makefile changed.
612    
613    2005-05-11  Douglas Bates  <bates@wisc.edu>
614    
615            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
616            bug reported by Kurt Hornik and Michael Hahsler.
617    
618    2005-05-10  Douglas Bates  <bates@wisc.edu>
619    
620            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
621            logical sparse matrices.  These will also be used in the symbolic
622            analysis for lmer objects.
623    
624            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
625            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
626    
627    2005-05-06  Douglas Bates  <bates@wisc.edu>
628    
629            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
630            colMeans, colSums, rowMeans and rowSums.
631    
632    2005-04-18  Douglas Bates  <bates@wisc.edu>
633    
634            * src/lgCMatrix.[ch]: code for _validate method and stub for
635            multiplication operation.
636    
637            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
638            to dgetrs.
639    
640            * src/init.c: Fix cut-and-paste error in definition of
641            dgeMatrix_matrix_solve
642    
643            * src/{many files}: Tighten code by using ALLOC_SLOT.
644    
645    2005-04-15  Douglas Bates  <bates@wisc.edu>
646    
647            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
648    
649            * DESCRIPTION: Eliminate import of stats.
650    
651    
652    2005-04-06  Douglas Bates  <bates@wisc.edu>
653    
654            * R/AllClass.R : add logical sparse matrix classes
655    
656    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/dgTMatrix.R: add "[" method for triplet matrices
659            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
660    
661    2005-03-31  Douglas Bates  <bates@wisc.edu>
662    
663            * DESCRIPTION (Version): release 0.95-5 to CRAN
664    
665            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
666            * R/sparseMatrix.R: %*%, crossprod()
667            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
668            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
669            * src/lmer.c (lmer_fitted): fix thinko
670    
671    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/AllClass.R: add two virtual sparse classes ``on top''
674    
675    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
678                    correspondingly fix examples and tests/ since new()
679                    doesn't work for virtual classes.
680    
681    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Matrix.R (as.matrix): method and one for unname()
684            * tests/dpoMatrix.R: tests should now be less platform dependent;
685              also run for R 2.1.0; using as.matrix()
686    
687    2005-03-15  Douglas Bates  <bates@wisc.edu>
688    
689            * R/pMatrix.R: "pMatrix" class added
690            * ....
691    
692    2005-03-14  Douglas Bates  <bates@wisc.edu>
693    
694            * R/dtpMatrix.R: Add unpack method and an example.
695    
696            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
697            of general symmetric matrices and associated S4 methods.
698    
699    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
700            +
701    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/dgeMatrix.R (setAs): and many other files: more coercion,
704              crossprod() and "%*%" methods added; tests, too.
705            * tests/matprod.R: new, for testing these
706    
707    2005-03-03  Douglas Bates  <bates@wisc.edu>
708    
709            * src/lmer.c (lmer_fitted): Added.
710    
711    2005-03-02  Douglas Bates  <bates@wisc.edu>
712    
713            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
714    
715    2005-02-28  Douglas Bates  <bates@wisc.edu>
716    
717            * src/*.c,po/,inst/po: Internationalization and localization of
718            the package.
719    
720            * src/ldl.[ch]: Removed these as their contents are referenced in the
721            R_ldl.c file.
722    
723            * src/flame.[ch]: Removed these source files.
724    
725            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
726    
727            * src/LU.[ch],src/init.c: absorb in factorizations
728    
729            * src/Mutils.h: prepare for internationalization
730    
731            * src/cblas.h: move the enum definitions to Mutils.h and remove
732            this file
733    
734    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
737    
738            * R/dtrMatrix.R: fix t() method
739    
740            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
741            * NAMESPACE: export them (and import generics from "methods")
742            * tests/group-methods.R : and test them.
743    
744            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
745            border case
746    
747    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
748    
749            * DESCRIPTION (Version): 0.95-2  released to CRAN
750    
751            * src/dgBCMatrix.c:
752            * src/lmer.c: many changes
753            * ...
754    
755    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/Matrix.R: add more sophisticated show() method.
758    
759    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * */* : almost complete reorganization of classes.
762    
763    2005-01-26  Douglas Bates  <bates@wisc.edu>
764    
765            * R/AllGeneric.R: Added matrix exponential generic expm and a method
766            for the geMatrix class.
767    
768    2005-01-24  Douglas Bates  <bates@wisc.edu>
769    
770            * src/Makefile (clean): Remove *.a and *.so
771    
772            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
773    
774    2005-01-23  Douglas Bates  <bates@wisc.edu>
775    
776            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
777            had an effect in cases with more than 2 grouping factors.
778    
779    2005-01-03  Douglas Bates  <bates@wisc.edu>
780    
781            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
782    
783    2004-12-23  Douglas Bates  <bates@wisc.edu>
784    
785            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
786            and R_useDynamicSymbols (suggested by B.D.Ripley).
787    
788    2004-12-14  Douglas Bates  <bates@wisc.edu>
789    
790          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
791    
792          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
793          for tripletMatrix to matrix.          for tripletMatrix to matrix.
794    
795  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
796    
797          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
798          no longer used.          no longer used.
# Line 17  Line 804 
804          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
805          Fixes part but not all of #15.          Fixes part but not all of #15.
806    
807  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
808    
809          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
810          scalar grouping factors corrected.          scalar grouping factors corrected.
811    
812  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
813    
814          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
815    
816  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
817    
818          * 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
819          .h file can be included.          .h file can be included.
820    
821  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
822    
823          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
824          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
825    
826          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
827    
828  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
829    
830          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
831    
832  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
833    
834          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
835    
836  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
837    
838          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
839    
840  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
841    
842          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
843    
844  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
845    
846          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
847          routines.          routines.
848    
849  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
850    
851          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
852    
853  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
854    
855          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
856    

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