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revision 726, Thu May 12 14:59:04 2005 UTC revision 1331, Sat Jul 22 17:59:53 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
4            via new smart
5            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
6            utility functions.
7    
8    
9    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/Csparse.R (tril, triu, band): do return *triangular* classed
12            matrices when appropriate; band() even symmetric ones.
13            (replCmat): extend to potentially all "CsparseMatrix"
14            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
15            allow subassignment for special sparse matrices.
16    
17            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
18    
19            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
20            argument; in glmer_*(): print only if(verbose).
21    
22            speed-optimize a few places by moving REAL(.) out of loops.
23    
24            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
25    
26    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
29                    since that wrongly triggers also for M[ logi , ]
30    
31            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
32            a symmetric matrix that results in a non-symmetric one.
33            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
34    
35            * R/dMatrix.R: make round(M) work as round(M, 0)
36    
37            * R/dgTMatrix.R (image): coordinate system and axis now use
38            1-based indices, not 0-based ones.
39    
40            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
41            * tests/indexing.R: test it.
42    
43            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
44            * man/isSymmetric-methods.Rd: and document it.
45    
46            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
47            * man/SparseM-conv.Rd: docu them
48    
49            * tests/other-pkgs.R: renamed from tests/graph.R and add example
50                    for 'SparseM' conversions
51    
52    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
53    
54            * R/Matrix.R (head): added head() and tail() methods.
55    
56    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): 0.995-12 released to CRAN
59    
60    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * tests/simple.R: add check for correct dsT -> dgT coercion;
63                    add check for correct printing of symmetric sparse matrices.
64    
65            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
66            for sparse symmetric matrices.
67    
68            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
69            diagonal twice.
70    
71    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
72    
73            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
74            being applied to the x slot (detected by Brian Ripley).
75    
76    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
79    
80            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
81    
82    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/lgCMatrix.c (lgCMatrix_diag): new function
85            * R/lgCMatrix.R (diag): for new method
86    
87            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
88                 ==> construction of illegal "*gTMatrix" via new() should
89                 now be much less easy:
90            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
91    
92            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
93                    directly.
94            * man/Matrix.Rd: documents it.
95    
96    2006-07-06  Douglas Bates  <bates@R-project.org>
97    
98            * src/pedigree.c (pedigree_inbreeding): Correction in
99            initialization.  This function is not currently being used and is
100            not fully tested.
101    
102            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
103            Introduced the glmer class.  Added code for mcmcmsamp on glmer
104            objects.  Modified validity check on pedigree objects to account
105            for nonparallel patterns of missingness of parents.
106    
107            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
108            class.
109    
110    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/pMatrix.R: coercion pMatrix -> Tsparse
113    
114    2006-06-12  Douglas Bates  <bates@R-project.org>
115    
116            * DESCRIPTION (Version): 0.995-11 released to CRAN
117    
118            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
119            the output from mcmcsamp.
120    
121    2006-06-10  Douglas Bates  <bates@R-project.org>
122    
123            * R/lmer.R (simulestimate): added C code for calculating the trace
124            of the hat matrix.
125    
126    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
129            classes.
130            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
131    
132    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dgTMatrix.R (colSums): etc. All four of
135            colSums(), rowSums(), colMeans(), rowMeans() now should work for
136            all "Matrices".
137    
138    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
139    
140            * R/lmer.R (panel.ci): Add a reference line at zero and a
141            background grid to the qqmath plot of ranef.lmer.
142    
143    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
146            grouping factors to be specified in the formula as (1|foo/bar).
147    
148    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/lmer.R (findbars and others): Change check of is.numeric to
151            !is.language to resolve the bug reported by Jacob Wegelin.
152    
153            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
154            code to evaluate inbreeding coefficients without calculating T,
155            based on code in Sargolzaei and Iwaisaki's paper.
156    
157    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
160            generic and mer methods for isNested and denomDF. This denomDF was
161            an attempt to emulate that in lme but I don't think that makes
162            sense.  Use the trace of the hat matrix instead.
163    
164    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
167            the C code depending on a slot structure that's no longer valid.
168            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
169    
170    
171    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
172    
173            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
174            of lowerTriMatrix generic and methods to tril (also upper to triu)
175            and added a general band extractor.
176    
177    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
178    
179            * R/pedigree.R (pedigree): Replace sire and dam values outside the
180            allowable range with NAs. Added a corresponding check in the
181            validity check for the pedigree class.
182    
183            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
184            crossprod methods now inherits from symmetricMatrix.
185    
186    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
187    
188            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
189            generics lowerTriMatrix and upperTriMatrix along with methods for
190            the Csparse virtual class.  Also added a C function Csparse_band
191            that implements these methods by calling cholmod_band.
192    
193    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
196            erased when it was NULL.  This led to invalid subselections!
197    
198    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
201            in method for "t" so as not to lose the unit diagonal property.
202    
203    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
206            and methods.  This is now an option to the ranef method for the
207            mer class.
208    
209            * src/cs_utils.c: Ensure that the nz component is -1 for a
210            compressed column-oriented matrix.  Minor formatting cleanup.
211    
212            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
213            objects.
214    
215    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
218            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
219    
220    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
223            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
224    
225            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
226            for the dtCMatrix class.
227    
228    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
229    
230            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
231            and methods for it.
232    
233    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
236            arguments, such that M %*% 1:6 now works
237            * Tests/matprod.R: test the above
238    
239    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
242            the ranef.lmer class.
243    
244            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
245            methods to extract the posterior variances from the bVar slot.
246    
247    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
250            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
251    
252            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
253            * tests/simple: (extended)
254    
255            * R/sparseMatrix.R (isTriangular): now using much improved
256            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
257    
258    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
261            (problem report from Franklin Parlamis).  This should be done
262            generally.
263    
264    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
267            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
268            update the plot methods.
269    
270    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/lmer.R (resid and ranef methods):  Added methods for the
273            "residuals" and "resid" generic but only for linear mixed model
274            fits.  Changed the ranef method to return a list of data frames so
275            that the plot methods now work.
276    
277    2006-03-16  Douglas Bates  <bates@bates2>
278    
279            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
280            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
281    
282            * DESCRIPTION (Date): New release
283    
284    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
287    
288            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
289            * man/KNex.Rd: and other help files
290            * tests/*.R: several ones needed adaption
291            * inst/doc/Comparisons.Rnw: dito
292    
293    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
296    
297            * tests/indexing.R: tests for new [<- methods for sparse matrices.
298    
299    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
302    
303            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
304    
305    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/dMatrix.R: enable things like  M [ M < 10 ]
308            * R/dgeMatrix.R: implement it
309    
310    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/AllClass.R: define "summary.mer" and "*.lmer"
313            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
314            * R/lmer.R (show): now works with summary()
315    
316    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
319            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
320                    support the above
321    
322    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
323    
324            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
325            Use glmFit$prior.weights for weights in a glmm.
326            Allow an option usePQL = FALSE to skip the PQL steps for the
327            Laplace method (and, in time, the AGQ method).
328    
329            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
330            into a separate function internal_mer_Xfactor to be able to call
331            it from internal_bhat.
332    
333    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * tests/Class+Meth.R (tstMatrixClass): function for much better
336            testing; now again of all actual classes.
337    
338            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
339                    use macros and define make_d_matrix_* and make_i_matrix_*
340                    where _i_ is for the ldense routines:
341    
342            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
343            * src/ldense.c (lsyMatrix_as_lgeMatrix):
344    
345            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
346    
347    
348    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
351                    many different kinds of matrices.
352            * R/*.R: quite a few new methods were needed for R CMD check with
353                    new Matrix().  Very good for users playing around.
354    
355    
356    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/dgeMatrix.c (dMatrix_validate): new
359            * src/Mutils.c (dense_nonpacked_validate): new
360    
361            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
362    
363    
364    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
367    
368    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
369    
370            * DESCRIPTION (Version): 0.99-6 released to CRAN
371    
372            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
373            segfault in cases with multiple non-nested grouping factors.
374    
375    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
378                    (Depends): also on 'utils'
379    
380            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
381            * R/diagMatrix.R (Diagonal): constructor and methods for
382            diagonal matrices
383    
384            * R/ltTMatrix.R: new "minimal methods"
385    
386    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
389            all methods (and help files).
390    
391    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
394                    for case (dimn.  op  no_dimn.)
395    
396    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
397    
398            * DESCRIPTION (Version): 0.99-2  released to CRAN
399    
400    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
401    
402            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
403            by Julian Faraway.
404    
405    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/Auxiliaries.R (try_as): new utility
408            * R/sparseMatrix.R: use try_as() in coercion to original class
409    
410    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
413    
414    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Auxiliaries.R (dimNamesCheck): added
417    
418            * R/Matrix.R (as.array), (as.vector): new
419    
420    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
423                    default.
424            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
425                    "pMatrix" now contains "sparseMatrix"
426    
427    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * tests/Class+Meth.R: new tests; t(t(m)) == m
430    
431            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
432    
433            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
434            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
435    
436            * R/dspMatrix.R: typo in "t" method
437    
438    2005-09-18  Douglas Bates  <bates@wisc.edu>
439    
440            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
441            * R/Tsparse.R: instead of R/gTMatrix.R
442            * R/Csparse.R: new
443            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
444            * src/Tsparse.c: new; many trivial methods calling cholmod_()
445            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
446                            via cholmod
447    
448    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/Auxiliaries.R (non0ind): new function using new C code
451            * src/dgCMatrix.c (compressed_non_0_ij): new utility
452    
453    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
454    
455            * src/chm_common.h: header file required by all C sources that
456            call CHOLMOD functions.  It defines a cholmod_common structure
457            called 'c' whose address is passed as the last argument to
458            (virtually) every CHOLMOD function.
459    
460            * src/Pattern.c: Simple example of the use of CHOLMOD.
461    
462            * src/init.c: initialize and finalize the cholmod_common structure.
463    
464            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
465            LDL and CCOLAMD from the U. of Florida sparse matrix library.
466    
467    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * inst/test-tools.R: new file collecting the utility functions used
470                    in ./tests/*.R
471    
472            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
473            * R/Matrix.R (cbind2): methods for NULL and missing
474    
475    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/AllClass.R: new "index" class for "[" and "[<-":
478                    First cut at "symmetricMatrix" and "triangularMatrix"
479            * R/gTMatrix.R (.ind.prep): new function;
480                    Logical and character indexing now work too.
481            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
482            * tests/indexing.R: new, including *.Rout.save
483            * tests/dgTMatrix.R: new
484    
485    2005-08-29  Douglas Bates  <bates@wisc.edu>
486    
487            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
488            indicator pos not being updated.  Also enforced upper triangular
489            for symmetric case.  Need to coerce edges component of elements of
490            edge list - grr! (Why don't they define their classes cleanly?)
491    
492    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/Matrix.R:  added first "[<-" methods; not yet functional
495            * R/denseMatrix.R: dito
496            * man/Subassign-methods.Rd: new help file for these
497    
498    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * DESCRIPTION (Version): 0.98-6
501    
502            * R/denseMatrix.R: new file for "[" fallback methods for all dense
503            matrices.
504    
505    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
508                    as( <logical>, "matrix")
509    
510            * R/pMatrix.R: coercion to "lgTMatrix"
511    
512            * R/gTMatrix.R: new virtual class to define "[" methods for.
513            * man/gTMatrix-class.Rd:
514            * General slight re-organization of where "[" methods are defined.
515              more to come.
516    
517    2005-08-18  Douglas Bates  <bates@wisc.edu>
518    
519            * DESCRIPTION (Version): 0.98-5  released to CRAN
520    
521            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
522            * .....
523    
524    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
525    
526            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
527            or glmer objects.
528    
529    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
532    
533    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
534    
535            * R/HBMM.R: finish re-writing R-only code.
536    
537    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
538    
539            * man/externalFormats.Rd: move documentation for writeHB and
540            writeMM here.
541    
542            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
543            (suggested by Paul Roecker).
544    
545            * tests/validObj.R (assertError): Comment out test that is failing
546            after recent changes in r-devel.
547    
548    
549    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/AllClass.R: intermediate virtual class "denseMatrix"
552            * man/denseMatrix-class.Rd
553            * NAMESPACE: export it, and also export
554            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
555    
556    2005-08-10  Douglas Bates  <bates@wisc.edu>
557    
558            * DESCRIPTION (Version): 0.98-3 to CRAN
559    
560            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
561            matrix_solve code (which was really, really wrong).
562    
563    2005-08-07  Douglas Bates  <bates@wisc.edu>
564    
565            * DESCRIPTION (Version): 0.98-2
566    
567            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
568    
569            * R/lmer.R (abbrvNms): new
570            * R/lmer.R (mcmcsamp): allow transformed parameters
571            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
572            for the Harwell-Boeing and the MatrixMarket formats.
573    
574    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * man/dtrMatrix-class.Rd: add examples
577            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
578    
579            * TODO: note the dtpMatrix (docu) bug
580    
581            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
582            in order to ensure that new as.matrix() is used by old functions,
583            e.g., svd(), qr(), eigen(), dist(),..;
584                  apply(), also matplot() or pairs().
585    
586    
587    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
590              add comments about 'control' / lmerControl() arguments
591    
592    2005-07-27  Douglas Bates  <bates@wisc.edu>
593    
594            * man/sleepstudy.Rd: Added the sleep data set.
595            * DESCRIPTION (Version): 0.98-1  released to CRAN
596    
597    2005-07-12  Douglas Bates  <bates@wisc.edu>
598            * man/sleepstudy.Rd: Added the sleep data set.
599    
600            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
601            .Call calls that were producing spurious output.
602    
603    2005-07-05  Douglas Bates  <bates@wisc.edu>
604    
605            * R/lmer.R (lmer): stored updated variance component estimates in
606            mer object for the generalized model.  (Bug reported by Renaud
607            Lancelot).
608    
609    2005-07-03  Douglas Bates  <bates@wisc.edu>
610    
611            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
612            unidimensional case.
613    
614    2005-06-08  Douglas Bates  <bates@wisc.edu>
615    
616            * DESCRIPTION (Version): 0.96-1
617    
618            * moved  lmer-class' R and C code moved from lme4 to here
619    
620    2005-06-04  Douglas Bates  <bates@wisc.edu>
621    
622            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
623            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
624    
625    2005-06-02  Douglas Bates  <bates@wisc.edu>
626    
627            * src/Makefile.win: Forgot to update this when Makefile changed.
628    
629    2005-05-11  Douglas Bates  <bates@wisc.edu>
630    
631          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
632          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
633    
634  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
635    
636          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
637          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 640 
640          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
641          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
642    
643  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
644    
645          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
646          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
647    
648  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
649    
650          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
651          multiplication operation.          multiplication operation.
# Line 30  Line 658 
658    
659          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
660    
661  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
662    
663          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
664    
665          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
666    
667    
668  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
669    
670          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
671    
# Line 46  Line 674 
674          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
675          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
676    
677  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
678    
679          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
680    
# Line 72  Line 700 
700          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
701            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
702    
703  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
704    
705          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
706          * ....          * ....
707    
708  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
709    
710          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
711    
# Line 92  Line 720 
720            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
721          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
722    
723  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
724    
725          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
726    
727  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
728    
729          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
730    
731  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
732    
733          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
734          the package.          the package.
# Line 148  Line 776 
776    
777          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
778    
779  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
780    
781          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
782          for the geMatrix class.          for the geMatrix class.
783    
784  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
785    
786          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
787    
788          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
789    
790  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
791    
792          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
793          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
794    
795  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
796    
797          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
798    
799  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
800    
801          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
802          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
803    
804  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
805    
806          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
807    
808          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
809          for tripletMatrix to matrix.          for tripletMatrix to matrix.
810    
811  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
812    
813          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
814          no longer used.          no longer used.
# Line 192  Line 820 
820          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
821          Fixes part but not all of #15.          Fixes part but not all of #15.
822    
823  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
824    
825          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
826          scalar grouping factors corrected.          scalar grouping factors corrected.
827    
828  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
829    
830          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
831    
832  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
833    
834          * 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
835          .h file can be included.          .h file can be included.
836    
837  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
838    
839          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
840          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
841    
842          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
843    
844  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
845    
846          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
847    
848  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
849    
850          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
851    
852  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
853    
854          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
855    
856  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
857    
858          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
859    
860  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
861    
862          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
863          routines.          routines.
864    
865  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
866    
867          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
868    
869  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
870    
871          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
872    

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