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revision 726, Thu May 12 14:59:04 2005 UTC revision 1338, Mon Jul 31 23:06:01 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-07-31  Douglas Bates  <bates@R-project.org>
2    
3            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
4            function which calls the C function mer_hat_trace2.
5    
6            * man/ranef.Rd: Include description of "postVar" argument.
7    
8    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * NAMESPACE:    change  "correlation" to "corMatrix"
11            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
12            * R/dpoMatrix.R: dito
13            * R/lmer.R:      dito
14    
15    2006-07-28  Douglas Bates  <bates@R-project.org>
16    
17            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
18            RZXinv slot's contents into a separate internal function that can
19            be used in mer_hat_trace.
20    
21    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
24            via new smart
25            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
26            utility functions.
27    
28    
29    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Csparse.R (tril, triu, band): do return *triangular* classed
32            matrices when appropriate; band() even symmetric ones.
33            (replCmat): extend to potentially all "CsparseMatrix"
34            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
35            allow subassignment for special sparse matrices.
36    
37            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
38    
39            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
40            argument; in glmer_*(): print only if(verbose).
41    
42            speed-optimize a few places by moving REAL(.) out of loops.
43    
44            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
45    
46    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
49                    since that wrongly triggers also for M[ logi , ]
50    
51            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
52            a symmetric matrix that results in a non-symmetric one.
53            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
54    
55            * R/dMatrix.R: make round(M) work as round(M, 0)
56    
57            * R/dgTMatrix.R (image): coordinate system and axis now use
58            1-based indices, not 0-based ones.
59    
60            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
61            * tests/indexing.R: test it.
62    
63            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
64            * man/isSymmetric-methods.Rd: and document it.
65    
66            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
67            * man/SparseM-conv.Rd: docu them
68    
69            * tests/other-pkgs.R: renamed from tests/graph.R and add example
70                    for 'SparseM' conversions
71    
72    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
73    
74            * R/Matrix.R (head): added head() and tail() methods.
75    
76    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * DESCRIPTION (Version): 0.995-12 released to CRAN
79    
80    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * tests/simple.R: add check for correct dsT -> dgT coercion;
83                    add check for correct printing of symmetric sparse matrices.
84    
85            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
86            for sparse symmetric matrices.
87    
88            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
89            diagonal twice.
90    
91    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
92    
93            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
94            being applied to the x slot (detected by Brian Ripley).
95    
96    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
99    
100            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
101    
102    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * src/lgCMatrix.c (lgCMatrix_diag): new function
105            * R/lgCMatrix.R (diag): for new method
106    
107            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
108                 ==> construction of illegal "*gTMatrix" via new() should
109                 now be much less easy:
110            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
111    
112            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
113                    directly.
114            * man/Matrix.Rd: documents it.
115    
116    2006-07-06  Douglas Bates  <bates@R-project.org>
117    
118            * src/pedigree.c (pedigree_inbreeding): Correction in
119            initialization.  This function is not currently being used and is
120            not fully tested.
121    
122            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
123            Introduced the glmer class.  Added code for mcmcmsamp on glmer
124            objects.  Modified validity check on pedigree objects to account
125            for nonparallel patterns of missingness of parents.
126    
127            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
128            class.
129    
130    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/pMatrix.R: coercion pMatrix -> Tsparse
133    
134    2006-06-12  Douglas Bates  <bates@R-project.org>
135    
136            * DESCRIPTION (Version): 0.995-11 released to CRAN
137    
138            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
139            the output from mcmcsamp.
140    
141    2006-06-10  Douglas Bates  <bates@R-project.org>
142    
143            * R/lmer.R (simulestimate): added C code for calculating the trace
144            of the hat matrix.
145    
146    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
149            classes.
150            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
151    
152    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/dgTMatrix.R (colSums): etc. All four of
155            colSums(), rowSums(), colMeans(), rowMeans() now should work for
156            all "Matrices".
157    
158    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
159    
160            * R/lmer.R (panel.ci): Add a reference line at zero and a
161            background grid to the qqmath plot of ranef.lmer.
162    
163    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
166            grouping factors to be specified in the formula as (1|foo/bar).
167    
168    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/lmer.R (findbars and others): Change check of is.numeric to
171            !is.language to resolve the bug reported by Jacob Wegelin.
172    
173            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
174            code to evaluate inbreeding coefficients without calculating T,
175            based on code in Sargolzaei and Iwaisaki's paper.
176    
177    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
178    
179            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
180            generic and mer methods for isNested and denomDF. This denomDF was
181            an attempt to emulate that in lme but I don't think that makes
182            sense.  Use the trace of the hat matrix instead.
183    
184    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
187            the C code depending on a slot structure that's no longer valid.
188            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
189    
190    
191    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
192    
193            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
194            of lowerTriMatrix generic and methods to tril (also upper to triu)
195            and added a general band extractor.
196    
197    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
198    
199            * R/pedigree.R (pedigree): Replace sire and dam values outside the
200            allowable range with NAs. Added a corresponding check in the
201            validity check for the pedigree class.
202    
203            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
204            crossprod methods now inherits from symmetricMatrix.
205    
206    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
209            generics lowerTriMatrix and upperTriMatrix along with methods for
210            the Csparse virtual class.  Also added a C function Csparse_band
211            that implements these methods by calling cholmod_band.
212    
213    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
216            erased when it was NULL.  This led to invalid subselections!
217    
218    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
219    
220            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
221            in method for "t" so as not to lose the unit diagonal property.
222    
223    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
226            and methods.  This is now an option to the ranef method for the
227            mer class.
228    
229            * src/cs_utils.c: Ensure that the nz component is -1 for a
230            compressed column-oriented matrix.  Minor formatting cleanup.
231    
232            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
233            objects.
234    
235    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
238            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
239    
240    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
241    
242            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
243            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
244    
245            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
246            for the dtCMatrix class.
247    
248    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
251            and methods for it.
252    
253    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
256            arguments, such that M %*% 1:6 now works
257            * Tests/matprod.R: test the above
258    
259    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
262            the ranef.lmer class.
263    
264            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
265            methods to extract the posterior variances from the bVar slot.
266    
267    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
270            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
271    
272            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
273            * tests/simple: (extended)
274    
275            * R/sparseMatrix.R (isTriangular): now using much improved
276            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
277    
278    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
281            (problem report from Franklin Parlamis).  This should be done
282            generally.
283    
284    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
287            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
288            update the plot methods.
289    
290    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/lmer.R (resid and ranef methods):  Added methods for the
293            "residuals" and "resid" generic but only for linear mixed model
294            fits.  Changed the ranef method to return a list of data frames so
295            that the plot methods now work.
296    
297    2006-03-16  Douglas Bates  <bates@bates2>
298    
299            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
300            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
301    
302            * DESCRIPTION (Date): New release
303    
304    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
307    
308            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
309            * man/KNex.Rd: and other help files
310            * tests/*.R: several ones needed adaption
311            * inst/doc/Comparisons.Rnw: dito
312    
313    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
316    
317            * tests/indexing.R: tests for new [<- methods for sparse matrices.
318    
319    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
322    
323            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
324    
325    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dMatrix.R: enable things like  M [ M < 10 ]
328            * R/dgeMatrix.R: implement it
329    
330    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/AllClass.R: define "summary.mer" and "*.lmer"
333            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
334            * R/lmer.R (show): now works with summary()
335    
336    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
339            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
340                    support the above
341    
342    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
345            Use glmFit$prior.weights for weights in a glmm.
346            Allow an option usePQL = FALSE to skip the PQL steps for the
347            Laplace method (and, in time, the AGQ method).
348    
349            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
350            into a separate function internal_mer_Xfactor to be able to call
351            it from internal_bhat.
352    
353    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * tests/Class+Meth.R (tstMatrixClass): function for much better
356            testing; now again of all actual classes.
357    
358            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
359                    use macros and define make_d_matrix_* and make_i_matrix_*
360                    where _i_ is for the ldense routines:
361    
362            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
363            * src/ldense.c (lsyMatrix_as_lgeMatrix):
364    
365            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
366    
367    
368    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
371                    many different kinds of matrices.
372            * R/*.R: quite a few new methods were needed for R CMD check with
373                    new Matrix().  Very good for users playing around.
374    
375    
376    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * src/dgeMatrix.c (dMatrix_validate): new
379            * src/Mutils.c (dense_nonpacked_validate): new
380    
381            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
382    
383    
384    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
387    
388    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
389    
390            * DESCRIPTION (Version): 0.99-6 released to CRAN
391    
392            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
393            segfault in cases with multiple non-nested grouping factors.
394    
395    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
398                    (Depends): also on 'utils'
399    
400            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
401            * R/diagMatrix.R (Diagonal): constructor and methods for
402            diagonal matrices
403    
404            * R/ltTMatrix.R: new "minimal methods"
405    
406    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
409            all methods (and help files).
410    
411    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
414                    for case (dimn.  op  no_dimn.)
415    
416    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * DESCRIPTION (Version): 0.99-2  released to CRAN
419    
420    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
421    
422            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
423            by Julian Faraway.
424    
425    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Auxiliaries.R (try_as): new utility
428            * R/sparseMatrix.R: use try_as() in coercion to original class
429    
430    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
433    
434    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/Auxiliaries.R (dimNamesCheck): added
437    
438            * R/Matrix.R (as.array), (as.vector): new
439    
440    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
443                    default.
444            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
445                    "pMatrix" now contains "sparseMatrix"
446    
447    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/Class+Meth.R: new tests; t(t(m)) == m
450    
451            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
452    
453            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
454            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
455    
456            * R/dspMatrix.R: typo in "t" method
457    
458    2005-09-18  Douglas Bates  <bates@wisc.edu>
459    
460            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
461            * R/Tsparse.R: instead of R/gTMatrix.R
462            * R/Csparse.R: new
463            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
464            * src/Tsparse.c: new; many trivial methods calling cholmod_()
465            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
466                            via cholmod
467    
468    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/Auxiliaries.R (non0ind): new function using new C code
471            * src/dgCMatrix.c (compressed_non_0_ij): new utility
472    
473    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
474    
475            * src/chm_common.h: header file required by all C sources that
476            call CHOLMOD functions.  It defines a cholmod_common structure
477            called 'c' whose address is passed as the last argument to
478            (virtually) every CHOLMOD function.
479    
480            * src/Pattern.c: Simple example of the use of CHOLMOD.
481    
482            * src/init.c: initialize and finalize the cholmod_common structure.
483    
484            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
485            LDL and CCOLAMD from the U. of Florida sparse matrix library.
486    
487    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * inst/test-tools.R: new file collecting the utility functions used
490                    in ./tests/*.R
491    
492            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
493            * R/Matrix.R (cbind2): methods for NULL and missing
494    
495    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * R/AllClass.R: new "index" class for "[" and "[<-":
498                    First cut at "symmetricMatrix" and "triangularMatrix"
499            * R/gTMatrix.R (.ind.prep): new function;
500                    Logical and character indexing now work too.
501            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
502            * tests/indexing.R: new, including *.Rout.save
503            * tests/dgTMatrix.R: new
504    
505    2005-08-29  Douglas Bates  <bates@wisc.edu>
506    
507            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
508            indicator pos not being updated.  Also enforced upper triangular
509            for symmetric case.  Need to coerce edges component of elements of
510            edge list - grr! (Why don't they define their classes cleanly?)
511    
512    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Matrix.R:  added first "[<-" methods; not yet functional
515            * R/denseMatrix.R: dito
516            * man/Subassign-methods.Rd: new help file for these
517    
518    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * DESCRIPTION (Version): 0.98-6
521    
522            * R/denseMatrix.R: new file for "[" fallback methods for all dense
523            matrices.
524    
525    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
528                    as( <logical>, "matrix")
529    
530            * R/pMatrix.R: coercion to "lgTMatrix"
531    
532            * R/gTMatrix.R: new virtual class to define "[" methods for.
533            * man/gTMatrix-class.Rd:
534            * General slight re-organization of where "[" methods are defined.
535              more to come.
536    
537    2005-08-18  Douglas Bates  <bates@wisc.edu>
538    
539            * DESCRIPTION (Version): 0.98-5  released to CRAN
540    
541            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
542            * .....
543    
544    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
545    
546            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
547            or glmer objects.
548    
549    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
552    
553    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
554    
555            * R/HBMM.R: finish re-writing R-only code.
556    
557    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
558    
559            * man/externalFormats.Rd: move documentation for writeHB and
560            writeMM here.
561    
562            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
563            (suggested by Paul Roecker).
564    
565            * tests/validObj.R (assertError): Comment out test that is failing
566            after recent changes in r-devel.
567    
568    
569    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/AllClass.R: intermediate virtual class "denseMatrix"
572            * man/denseMatrix-class.Rd
573            * NAMESPACE: export it, and also export
574            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
575    
576    2005-08-10  Douglas Bates  <bates@wisc.edu>
577    
578            * DESCRIPTION (Version): 0.98-3 to CRAN
579    
580            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
581            matrix_solve code (which was really, really wrong).
582    
583    2005-08-07  Douglas Bates  <bates@wisc.edu>
584    
585            * DESCRIPTION (Version): 0.98-2
586    
587            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
588    
589            * R/lmer.R (abbrvNms): new
590            * R/lmer.R (mcmcsamp): allow transformed parameters
591            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
592            for the Harwell-Boeing and the MatrixMarket formats.
593    
594    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * man/dtrMatrix-class.Rd: add examples
597            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
598    
599            * TODO: note the dtpMatrix (docu) bug
600    
601            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
602            in order to ensure that new as.matrix() is used by old functions,
603            e.g., svd(), qr(), eigen(), dist(),..;
604                  apply(), also matplot() or pairs().
605    
606    
607    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
610              add comments about 'control' / lmerControl() arguments
611    
612    2005-07-27  Douglas Bates  <bates@wisc.edu>
613    
614            * man/sleepstudy.Rd: Added the sleep data set.
615            * DESCRIPTION (Version): 0.98-1  released to CRAN
616    
617    2005-07-12  Douglas Bates  <bates@wisc.edu>
618            * man/sleepstudy.Rd: Added the sleep data set.
619    
620            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
621            .Call calls that were producing spurious output.
622    
623    2005-07-05  Douglas Bates  <bates@wisc.edu>
624    
625            * R/lmer.R (lmer): stored updated variance component estimates in
626            mer object for the generalized model.  (Bug reported by Renaud
627            Lancelot).
628    
629    2005-07-03  Douglas Bates  <bates@wisc.edu>
630    
631            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
632            unidimensional case.
633    
634    2005-06-08  Douglas Bates  <bates@wisc.edu>
635    
636            * DESCRIPTION (Version): 0.96-1
637    
638            * moved  lmer-class' R and C code moved from lme4 to here
639    
640    2005-06-04  Douglas Bates  <bates@wisc.edu>
641    
642            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
643            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
644    
645    2005-06-02  Douglas Bates  <bates@wisc.edu>
646    
647            * src/Makefile.win: Forgot to update this when Makefile changed.
648    
649    2005-05-11  Douglas Bates  <bates@wisc.edu>
650    
651          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
652          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
653    
654  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
655    
656          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
657          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 660 
660          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
661          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
662    
663  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
664    
665          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
666          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
667    
668  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
669    
670          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
671          multiplication operation.          multiplication operation.
# Line 30  Line 678 
678    
679          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
680    
681  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
682    
683          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
684    
685          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
686    
687    
688  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
689    
690          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
691    
# Line 46  Line 694 
694          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
695          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
696    
697  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
698    
699          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
700    
# Line 72  Line 720 
720          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
721            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
722    
723  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
724    
725          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
726          * ....          * ....
727    
728  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
729    
730          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
731    
# Line 92  Line 740 
740            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
741          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
742    
743  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
744    
745          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
746    
747  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
748    
749          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
750    
751  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
752    
753          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
754          the package.          the package.
# Line 148  Line 796 
796    
797          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
798    
799  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
800    
801          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
802          for the geMatrix class.          for the geMatrix class.
803    
804  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
805    
806          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
807    
808          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
809    
810  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
811    
812          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
813          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
814    
815  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
816    
817          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
818    
819  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
820    
821          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
822          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
823    
824  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
825    
826          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
827    
828          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
829          for tripletMatrix to matrix.          for tripletMatrix to matrix.
830    
831  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
832    
833          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
834          no longer used.          no longer used.
# Line 192  Line 840 
840          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
841          Fixes part but not all of #15.          Fixes part but not all of #15.
842    
843  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
844    
845          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
846          scalar grouping factors corrected.          scalar grouping factors corrected.
847    
848  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
849    
850          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
851    
852  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
853    
854          * 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
855          .h file can be included.          .h file can be included.
856    
857  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
858    
859          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
860          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
861    
862          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
863    
864  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
865    
866          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
867    
868  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
869    
870          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
871    
872  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
873    
874          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
875    
876  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
877    
878          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
879    
880  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
881    
882          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
883          routines.          routines.
884    
885  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
886    
887          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
888    
889  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
890    
891          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
892    

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