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revision 726, Thu May 12 14:59:04 2005 UTC revision 1346, Thu Aug 3 17:17:55 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
4    
5            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
6            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
7            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
8            such that the S4 objects are always created by the current version
9            of R and 'Matrix' class definitions.
10    
11    2006-08-01  Douglas Bates  <bates@R-project.org>
12    
13            * R/lmer.R (LMEoptimize method), tests/lmer.R,
14            inst/external/test3comp.rda: Added warnings for convergence on
15            boundary and test cases.
16    
17            * src/lmer.c (mer_postVar): Modified to return the variances that
18            are marginal to the fixed effects, not conditional on them (which
19            is what the bVar slot contents represent).
20    
21    2006-07-31  Douglas Bates  <bates@R-project.org>
22    
23            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
24            function which calls the C function mer_hat_trace2.
25    
26            * man/ranef.Rd: Include description of "postVar" argument and
27            producing a caterpillar plot.
28    
29    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * NAMESPACE:    change  "correlation" to "corMatrix"
32            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
33            * R/dpoMatrix.R: dito
34            * R/lmer.R:      dito
35    
36    2006-07-28  Douglas Bates  <bates@R-project.org>
37    
38            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
39            RZXinv slot's contents into a separate internal function that can
40            be used in mer_hat_trace.
41    
42    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
45            via new smart
46            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
47            utility functions.
48    
49    
50    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Csparse.R (tril, triu, band): do return *triangular* classed
53            matrices when appropriate; band() even symmetric ones.
54            (replCmat): extend to potentially all "CsparseMatrix"
55            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
56            allow subassignment for special sparse matrices.
57    
58            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
59    
60            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
61            argument; in glmer_*(): print only if(verbose).
62    
63            speed-optimize a few places by moving REAL(.) out of loops.
64    
65            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
66    
67    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
70                    since that wrongly triggers also for M[ logi , ]
71    
72            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
73            a symmetric matrix that results in a non-symmetric one.
74            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
75    
76            * R/dMatrix.R: make round(M) work as round(M, 0)
77    
78            * R/dgTMatrix.R (image): coordinate system and axis now use
79            1-based indices, not 0-based ones.
80    
81            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
82            * tests/indexing.R: test it.
83    
84            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
85            * man/isSymmetric-methods.Rd: and document it.
86    
87            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
88            * man/SparseM-conv.Rd: docu them
89    
90            * tests/other-pkgs.R: renamed from tests/graph.R and add example
91                    for 'SparseM' conversions
92    
93    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
94    
95            * R/Matrix.R (head): added head() and tail() methods.
96    
97    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * DESCRIPTION (Version): 0.995-12 released to CRAN
100    
101    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * tests/simple.R: add check for correct dsT -> dgT coercion;
104                    add check for correct printing of symmetric sparse matrices.
105    
106            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
107            for sparse symmetric matrices.
108    
109            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
110            diagonal twice.
111    
112    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
113    
114            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
115            being applied to the x slot (detected by Brian Ripley).
116    
117    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
120    
121            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
122    
123    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * src/lgCMatrix.c (lgCMatrix_diag): new function
126            * R/lgCMatrix.R (diag): for new method
127    
128            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
129                 ==> construction of illegal "*gTMatrix" via new() should
130                 now be much less easy:
131            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
132    
133            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
134                    directly.
135            * man/Matrix.Rd: documents it.
136    
137    2006-07-06  Douglas Bates  <bates@R-project.org>
138    
139            * src/pedigree.c (pedigree_inbreeding): Correction in
140            initialization.  This function is not currently being used and is
141            not fully tested.
142    
143            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
144            Introduced the glmer class.  Added code for mcmcmsamp on glmer
145            objects.  Modified validity check on pedigree objects to account
146            for nonparallel patterns of missingness of parents.
147    
148            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
149            class.
150    
151    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/pMatrix.R: coercion pMatrix -> Tsparse
154    
155    2006-06-12  Douglas Bates  <bates@R-project.org>
156    
157            * DESCRIPTION (Version): 0.995-11 released to CRAN
158    
159            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
160            the output from mcmcsamp.
161    
162    2006-06-10  Douglas Bates  <bates@R-project.org>
163    
164            * R/lmer.R (simulestimate): added C code for calculating the trace
165            of the hat matrix.
166    
167    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
170            classes.
171            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
172    
173    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (colSums): etc. All four of
176            colSums(), rowSums(), colMeans(), rowMeans() now should work for
177            all "Matrices".
178    
179    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * R/lmer.R (panel.ci): Add a reference line at zero and a
182            background grid to the qqmath plot of ranef.lmer.
183    
184    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
187            grouping factors to be specified in the formula as (1|foo/bar).
188    
189    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
190    
191            * R/lmer.R (findbars and others): Change check of is.numeric to
192            !is.language to resolve the bug reported by Jacob Wegelin.
193    
194            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
195            code to evaluate inbreeding coefficients without calculating T,
196            based on code in Sargolzaei and Iwaisaki's paper.
197    
198    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
201            generic and mer methods for isNested and denomDF. This denomDF was
202            an attempt to emulate that in lme but I don't think that makes
203            sense.  Use the trace of the hat matrix instead.
204    
205    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
208            the C code depending on a slot structure that's no longer valid.
209            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
210    
211    
212    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
213    
214            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
215            of lowerTriMatrix generic and methods to tril (also upper to triu)
216            and added a general band extractor.
217    
218    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
219    
220            * R/pedigree.R (pedigree): Replace sire and dam values outside the
221            allowable range with NAs. Added a corresponding check in the
222            validity check for the pedigree class.
223    
224            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
225            crossprod methods now inherits from symmetricMatrix.
226    
227    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
230            generics lowerTriMatrix and upperTriMatrix along with methods for
231            the Csparse virtual class.  Also added a C function Csparse_band
232            that implements these methods by calling cholmod_band.
233    
234    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
237            erased when it was NULL.  This led to invalid subselections!
238    
239    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
242            in method for "t" so as not to lose the unit diagonal property.
243    
244    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
245    
246            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
247            and methods.  This is now an option to the ranef method for the
248            mer class.
249    
250            * src/cs_utils.c: Ensure that the nz component is -1 for a
251            compressed column-oriented matrix.  Minor formatting cleanup.
252    
253            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
254            objects.
255    
256    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
259            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
260    
261    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
264            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
265    
266            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
267            for the dtCMatrix class.
268    
269    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
270    
271            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
272            and methods for it.
273    
274    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
277            arguments, such that M %*% 1:6 now works
278            * Tests/matprod.R: test the above
279    
280    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
283            the ranef.lmer class.
284    
285            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
286            methods to extract the posterior variances from the bVar slot.
287    
288    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
291            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
292    
293            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
294            * tests/simple: (extended)
295    
296            * R/sparseMatrix.R (isTriangular): now using much improved
297            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
298    
299    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
300    
301            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
302            (problem report from Franklin Parlamis).  This should be done
303            generally.
304    
305    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
308            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
309            update the plot methods.
310    
311    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * R/lmer.R (resid and ranef methods):  Added methods for the
314            "residuals" and "resid" generic but only for linear mixed model
315            fits.  Changed the ranef method to return a list of data frames so
316            that the plot methods now work.
317    
318    2006-03-16  Douglas Bates  <bates@bates2>
319    
320            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
321            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
322    
323            * DESCRIPTION (Date): New release
324    
325    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
328    
329            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
330            * man/KNex.Rd: and other help files
331            * tests/*.R: several ones needed adaption
332            * inst/doc/Comparisons.Rnw: dito
333    
334    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
337    
338            * tests/indexing.R: tests for new [<- methods for sparse matrices.
339    
340    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
343    
344            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
345    
346    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/dMatrix.R: enable things like  M [ M < 10 ]
349            * R/dgeMatrix.R: implement it
350    
351    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/AllClass.R: define "summary.mer" and "*.lmer"
354            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
355            * R/lmer.R (show): now works with summary()
356    
357    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
360            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
361                    support the above
362    
363    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
366            Use glmFit$prior.weights for weights in a glmm.
367            Allow an option usePQL = FALSE to skip the PQL steps for the
368            Laplace method (and, in time, the AGQ method).
369    
370            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
371            into a separate function internal_mer_Xfactor to be able to call
372            it from internal_bhat.
373    
374    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * tests/Class+Meth.R (tstMatrixClass): function for much better
377            testing; now again of all actual classes.
378    
379            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
380                    use macros and define make_d_matrix_* and make_i_matrix_*
381                    where _i_ is for the ldense routines:
382    
383            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
384            * src/ldense.c (lsyMatrix_as_lgeMatrix):
385    
386            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
387    
388    
389    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
392                    many different kinds of matrices.
393            * R/*.R: quite a few new methods were needed for R CMD check with
394                    new Matrix().  Very good for users playing around.
395    
396    
397    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * src/dgeMatrix.c (dMatrix_validate): new
400            * src/Mutils.c (dense_nonpacked_validate): new
401    
402            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
403    
404    
405    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
406    
407            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
408    
409    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
410    
411            * DESCRIPTION (Version): 0.99-6 released to CRAN
412    
413            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
414            segfault in cases with multiple non-nested grouping factors.
415    
416    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
419                    (Depends): also on 'utils'
420    
421            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
422            * R/diagMatrix.R (Diagonal): constructor and methods for
423            diagonal matrices
424    
425            * R/ltTMatrix.R: new "minimal methods"
426    
427    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
430            all methods (and help files).
431    
432    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
435                    for case (dimn.  op  no_dimn.)
436    
437    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * DESCRIPTION (Version): 0.99-2  released to CRAN
440    
441    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
442    
443            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
444            by Julian Faraway.
445    
446    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/Auxiliaries.R (try_as): new utility
449            * R/sparseMatrix.R: use try_as() in coercion to original class
450    
451    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
454    
455    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Auxiliaries.R (dimNamesCheck): added
458    
459            * R/Matrix.R (as.array), (as.vector): new
460    
461    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
464                    default.
465            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
466                    "pMatrix" now contains "sparseMatrix"
467    
468    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * tests/Class+Meth.R: new tests; t(t(m)) == m
471    
472            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
473    
474            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
475            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
476    
477            * R/dspMatrix.R: typo in "t" method
478    
479    2005-09-18  Douglas Bates  <bates@wisc.edu>
480    
481            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
482            * R/Tsparse.R: instead of R/gTMatrix.R
483            * R/Csparse.R: new
484            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
485            * src/Tsparse.c: new; many trivial methods calling cholmod_()
486            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
487                            via cholmod
488    
489    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Auxiliaries.R (non0ind): new function using new C code
492            * src/dgCMatrix.c (compressed_non_0_ij): new utility
493    
494    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
495    
496            * src/chm_common.h: header file required by all C sources that
497            call CHOLMOD functions.  It defines a cholmod_common structure
498            called 'c' whose address is passed as the last argument to
499            (virtually) every CHOLMOD function.
500    
501            * src/Pattern.c: Simple example of the use of CHOLMOD.
502    
503            * src/init.c: initialize and finalize the cholmod_common structure.
504    
505            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
506            LDL and CCOLAMD from the U. of Florida sparse matrix library.
507    
508    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * inst/test-tools.R: new file collecting the utility functions used
511                    in ./tests/*.R
512    
513            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
514            * R/Matrix.R (cbind2): methods for NULL and missing
515    
516    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/AllClass.R: new "index" class for "[" and "[<-":
519                    First cut at "symmetricMatrix" and "triangularMatrix"
520            * R/gTMatrix.R (.ind.prep): new function;
521                    Logical and character indexing now work too.
522            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
523            * tests/indexing.R: new, including *.Rout.save
524            * tests/dgTMatrix.R: new
525    
526    2005-08-29  Douglas Bates  <bates@wisc.edu>
527    
528            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
529            indicator pos not being updated.  Also enforced upper triangular
530            for symmetric case.  Need to coerce edges component of elements of
531            edge list - grr! (Why don't they define their classes cleanly?)
532    
533    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/Matrix.R:  added first "[<-" methods; not yet functional
536            * R/denseMatrix.R: dito
537            * man/Subassign-methods.Rd: new help file for these
538    
539    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Version): 0.98-6
542    
543            * R/denseMatrix.R: new file for "[" fallback methods for all dense
544            matrices.
545    
546    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
549                    as( <logical>, "matrix")
550    
551            * R/pMatrix.R: coercion to "lgTMatrix"
552    
553            * R/gTMatrix.R: new virtual class to define "[" methods for.
554            * man/gTMatrix-class.Rd:
555            * General slight re-organization of where "[" methods are defined.
556              more to come.
557    
558    2005-08-18  Douglas Bates  <bates@wisc.edu>
559    
560            * DESCRIPTION (Version): 0.98-5  released to CRAN
561    
562            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
563            * .....
564    
565    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
566    
567            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
568            or glmer objects.
569    
570    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
573    
574    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
575    
576            * R/HBMM.R: finish re-writing R-only code.
577    
578    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
579    
580            * man/externalFormats.Rd: move documentation for writeHB and
581            writeMM here.
582    
583            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
584            (suggested by Paul Roecker).
585    
586            * tests/validObj.R (assertError): Comment out test that is failing
587            after recent changes in r-devel.
588    
589    
590    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/AllClass.R: intermediate virtual class "denseMatrix"
593            * man/denseMatrix-class.Rd
594            * NAMESPACE: export it, and also export
595            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
596    
597    2005-08-10  Douglas Bates  <bates@wisc.edu>
598    
599            * DESCRIPTION (Version): 0.98-3 to CRAN
600    
601            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
602            matrix_solve code (which was really, really wrong).
603    
604    2005-08-07  Douglas Bates  <bates@wisc.edu>
605    
606            * DESCRIPTION (Version): 0.98-2
607    
608            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
609    
610            * R/lmer.R (abbrvNms): new
611            * R/lmer.R (mcmcsamp): allow transformed parameters
612            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
613            for the Harwell-Boeing and the MatrixMarket formats.
614    
615    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * man/dtrMatrix-class.Rd: add examples
618            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
619    
620            * TODO: note the dtpMatrix (docu) bug
621    
622            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
623            in order to ensure that new as.matrix() is used by old functions,
624            e.g., svd(), qr(), eigen(), dist(),..;
625                  apply(), also matplot() or pairs().
626    
627    
628    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
631              add comments about 'control' / lmerControl() arguments
632    
633    2005-07-27  Douglas Bates  <bates@wisc.edu>
634    
635            * man/sleepstudy.Rd: Added the sleep data set.
636            * DESCRIPTION (Version): 0.98-1  released to CRAN
637    
638    2005-07-12  Douglas Bates  <bates@wisc.edu>
639            * man/sleepstudy.Rd: Added the sleep data set.
640    
641            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
642            .Call calls that were producing spurious output.
643    
644    2005-07-05  Douglas Bates  <bates@wisc.edu>
645    
646            * R/lmer.R (lmer): stored updated variance component estimates in
647            mer object for the generalized model.  (Bug reported by Renaud
648            Lancelot).
649    
650    2005-07-03  Douglas Bates  <bates@wisc.edu>
651    
652            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
653            unidimensional case.
654    
655    2005-06-08  Douglas Bates  <bates@wisc.edu>
656    
657            * DESCRIPTION (Version): 0.96-1
658    
659            * moved  lmer-class' R and C code moved from lme4 to here
660    
661    2005-06-04  Douglas Bates  <bates@wisc.edu>
662    
663            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
664            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
665    
666    2005-06-02  Douglas Bates  <bates@wisc.edu>
667    
668            * src/Makefile.win: Forgot to update this when Makefile changed.
669    
670    2005-05-11  Douglas Bates  <bates@wisc.edu>
671    
672          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
673          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
674    
675  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
676    
677          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
678          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 681 
681          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
682          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
683    
684  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
685    
686          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
687          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
688    
689  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
690    
691          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
692          multiplication operation.          multiplication operation.
# Line 30  Line 699 
699    
700          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
701    
702  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
703    
704          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
705    
706          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
707    
708    
709  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
710    
711          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
712    
# Line 46  Line 715 
715          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
716          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
717    
718  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
719    
720          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
721    
# Line 72  Line 741 
741          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
742            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
743    
744  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
745    
746          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
747          * ....          * ....
748    
749  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
750    
751          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
752    
# Line 92  Line 761 
761            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
762          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
763    
764  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
765    
766          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
767    
768  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
769    
770          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
771    
772  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
773    
774          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
775          the package.          the package.
# Line 148  Line 817 
817    
818          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
819    
820  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
821    
822          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
823          for the geMatrix class.          for the geMatrix class.
824    
825  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
826    
827          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
828    
829          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
830    
831  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
832    
833          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
834          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
835    
836  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
837    
838          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
839    
840  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
841    
842          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
843          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
844    
845  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
846    
847          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
848    
849          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
850          for tripletMatrix to matrix.          for tripletMatrix to matrix.
851    
852  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
853    
854          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
855          no longer used.          no longer used.
# Line 192  Line 861 
861          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
862          Fixes part but not all of #15.          Fixes part but not all of #15.
863    
864  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
865    
866          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
867          scalar grouping factors corrected.          scalar grouping factors corrected.
868    
869  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
870    
871          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
872    
873  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
874    
875          * 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
876          .h file can be included.          .h file can be included.
877    
878  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
879    
880          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
881          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
882    
883          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
884    
885  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
886    
887          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
888    
889  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
890    
891          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
892    
893  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
894    
895          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
896    
897  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
898    
899          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
900    
901  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
902    
903          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
904          routines.          routines.
905    
906  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
907    
908          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
909    
910  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
911    
912          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
913    

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