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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1315, Mon Jul 10 16:08:05 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
4    
5            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
6    
7    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/lgCMatrix.c (lgCMatrix_diag): new function
10            * R/lgCMatrix.R (diag): for new method
11    
12            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
13                 ==> construction of illegal "*gTMatrix" via new() should
14                 now be much less easy:
15            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
16    
17            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
18                    directly.
19            * man/Matrix.Rd: documents it.
20    
21    2006-07-06  Douglas Bates  <bates@R-project.org>
22    
23            * src/pedigree.c (pedigree_inbreeding): Correction in
24            initialization.  This function is not currently being used and is
25            not fully tested.
26    
27            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
28            Introduced the glmer class.  Added code for mcmcmsamp on glmer
29            objects.  Modified validity check on pedigree objects to account
30            for nonparallel patterns of missingness of parents.
31    
32            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
33            class.
34    
35    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/pMatrix.R: coercion pMatrix -> Tsparse
38    
39    2006-06-12  Douglas Bates  <bates@R-project.org>
40    
41            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
42            the output from mcmcsamp.
43    
44    2006-06-10  Douglas Bates  <bates@R-project.org>
45    
46            * R/lmer.R (simulestimate): added C code for calculating the trace
47            of the hat matrix.
48    
49    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
52            classes.
53            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
54    
55    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgTMatrix.R (colSums): etc. All four of
58            colSums(), rowSums(), colMeans(), rowMeans() now should work for
59            all "Matrices".
60    
61    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/lmer.R (panel.ci): Add a reference line at zero and a
64            background grid to the qqmath plot of ranef.lmer.
65    
66    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
69            grouping factors to be specified in the formula as (1|foo/bar).
70    
71    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * R/lmer.R (findbars and others): Change check of is.numeric to
74            !is.language to resolve the bug reported by Jacob Wegelin.
75    
76            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
77            code to evaluate inbreeding coefficients without calculating T,
78            based on code in Sargolzaei and Iwaisaki's paper.
79    
80    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
81    
82            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
83            generic and mer methods for isNested and denomDF. This denomDF was
84            an attempt to emulate that in lme but I don't think that makes
85            sense.  Use the trace of the hat matrix instead.
86    
87    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
90            the C code depending on a slot structure that's no longer valid.
91            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
92    
93    
94    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
95    
96            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
97            of lowerTriMatrix generic and methods to tril (also upper to triu)
98            and added a general band extractor.
99    
100    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
101    
102            * R/pedigree.R (pedigree): Replace sire and dam values outside the
103            allowable range with NAs. Added a corresponding check in the
104            validity check for the pedigree class.
105    
106            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
107            crossprod methods now inherits from symmetricMatrix.
108    
109    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
110    
111            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
112            generics lowerTriMatrix and upperTriMatrix along with methods for
113            the Csparse virtual class.  Also added a C function Csparse_band
114            that implements these methods by calling cholmod_band.
115    
116    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
119            erased when it was NULL.  This led to invalid subselections!
120    
121    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
124            in method for "t" so as not to lose the unit diagonal property.
125    
126    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
129            and methods.  This is now an option to the ranef method for the
130            mer class.
131    
132            * src/cs_utils.c: Ensure that the nz component is -1 for a
133            compressed column-oriented matrix.  Minor formatting cleanup.
134    
135            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
136            objects.
137    
138    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
141            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
142    
143    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
146            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
147    
148            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
149            for the dtCMatrix class.
150    
151    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
152    
153            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
154            and methods for it.
155    
156    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
159            arguments, such that M %*% 1:6 now works
160            * Tests/matprod.R: test the above
161    
162    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
165            the ranef.lmer class.
166    
167            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
168            methods to extract the posterior variances from the bVar slot.
169    
170    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
173            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
174    
175            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
176            * tests/simple: (extended)
177    
178            * R/sparseMatrix.R (isTriangular): now using much improved
179            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
180    
181    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
182    
183            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
184            (problem report from Franklin Parlamis).  This should be done
185            generally.
186    
187    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
190            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
191            update the plot methods.
192    
193    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * R/lmer.R (resid and ranef methods):  Added methods for the
196            "residuals" and "resid" generic but only for linear mixed model
197            fits.  Changed the ranef method to return a list of data frames so
198            that the plot methods now work.
199    
200    2006-03-16  Douglas Bates  <bates@bates2>
201    
202            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
203            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
204    
205            * DESCRIPTION (Date): New release
206    
207    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
210    
211            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
212            * man/KNex.Rd: and other help files
213            * tests/*.R: several ones needed adaption
214            * inst/doc/Comparisons.Rnw: dito
215    
216    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
219    
220            * tests/indexing.R: tests for new [<- methods for sparse matrices.
221    
222    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
225    
226            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
227    
228    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dMatrix.R: enable things like  M [ M < 10 ]
231            * R/dgeMatrix.R: implement it
232    
233    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/AllClass.R: define "summary.mer" and "*.lmer"
236            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
237            * R/lmer.R (show): now works with summary()
238    
239    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
242            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
243                    support the above
244    
245    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
248            Use glmFit$prior.weights for weights in a glmm.
249            Allow an option usePQL = FALSE to skip the PQL steps for the
250            Laplace method (and, in time, the AGQ method).
251    
252            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
253            into a separate function internal_mer_Xfactor to be able to call
254            it from internal_bhat.
255    
256    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * tests/Class+Meth.R (tstMatrixClass): function for much better
259            testing; now again of all actual classes.
260    
261            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
262                    use macros and define make_d_matrix_* and make_i_matrix_*
263                    where _i_ is for the ldense routines:
264    
265            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
266            * src/ldense.c (lsyMatrix_as_lgeMatrix):
267    
268            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
269    
270    
271    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
274                    many different kinds of matrices.
275            * R/*.R: quite a few new methods were needed for R CMD check with
276                    new Matrix().  Very good for users playing around.
277    
278    
279    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/dgeMatrix.c (dMatrix_validate): new
282            * src/Mutils.c (dense_nonpacked_validate): new
283    
284            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
285    
286    
287    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
290    
291    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * DESCRIPTION (Version): 0.99-6 released to CRAN
294    
295            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
296            segfault in cases with multiple non-nested grouping factors.
297    
298    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
301                    (Depends): also on 'utils'
302    
303            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
304            * R/diagMatrix.R (Diagonal): constructor and methods for
305            diagonal matrices
306    
307            * R/ltTMatrix.R: new "minimal methods"
308    
309    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
312            all methods (and help files).
313    
314    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
317                    for case (dimn.  op  no_dimn.)
318    
319    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
320    
321            * DESCRIPTION (Version): 0.99-2  released to CRAN
322    
323    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
326            by Julian Faraway.
327    
328    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Auxiliaries.R (try_as): new utility
331            * R/sparseMatrix.R: use try_as() in coercion to original class
332    
333    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
336    
337    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Auxiliaries.R (dimNamesCheck): added
340    
341            * R/Matrix.R (as.array), (as.vector): new
342    
343    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
346                    default.
347            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
348                    "pMatrix" now contains "sparseMatrix"
349    
350    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * tests/Class+Meth.R: new tests; t(t(m)) == m
353    
354            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
355    
356            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
357            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
358    
359            * R/dspMatrix.R: typo in "t" method
360    
361    2005-09-18  Douglas Bates  <bates@wisc.edu>
362    
363            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
364            * R/Tsparse.R: instead of R/gTMatrix.R
365            * R/Csparse.R: new
366            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
367            * src/Tsparse.c: new; many trivial methods calling cholmod_()
368            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
369                            via cholmod
370    
371    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/Auxiliaries.R (non0ind): new function using new C code
374            * src/dgCMatrix.c (compressed_non_0_ij): new utility
375    
376    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
377    
378            * src/chm_common.h: header file required by all C sources that
379            call CHOLMOD functions.  It defines a cholmod_common structure
380            called 'c' whose address is passed as the last argument to
381            (virtually) every CHOLMOD function.
382    
383            * src/Pattern.c: Simple example of the use of CHOLMOD.
384    
385            * src/init.c: initialize and finalize the cholmod_common structure.
386    
387            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
388            LDL and CCOLAMD from the U. of Florida sparse matrix library.
389    
390    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * inst/test-tools.R: new file collecting the utility functions used
393                    in ./tests/*.R
394    
395            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
396            * R/Matrix.R (cbind2): methods for NULL and missing
397    
398    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllClass.R: new "index" class for "[" and "[<-":
401                    First cut at "symmetricMatrix" and "triangularMatrix"
402            * R/gTMatrix.R (.ind.prep): new function;
403                    Logical and character indexing now work too.
404            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
405            * tests/indexing.R: new, including *.Rout.save
406            * tests/dgTMatrix.R: new
407    
408    2005-08-29  Douglas Bates  <bates@wisc.edu>
409    
410            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
411            indicator pos not being updated.  Also enforced upper triangular
412            for symmetric case.  Need to coerce edges component of elements of
413            edge list - grr! (Why don't they define their classes cleanly?)
414    
415    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/Matrix.R:  added first "[<-" methods; not yet functional
418            * R/denseMatrix.R: dito
419            * man/Subassign-methods.Rd: new help file for these
420    
421    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * DESCRIPTION (Version): 0.98-6
424    
425            * R/denseMatrix.R: new file for "[" fallback methods for all dense
426            matrices.
427    
428    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
431                    as( <logical>, "matrix")
432    
433            * R/pMatrix.R: coercion to "lgTMatrix"
434    
435            * R/gTMatrix.R: new virtual class to define "[" methods for.
436            * man/gTMatrix-class.Rd:
437            * General slight re-organization of where "[" methods are defined.
438              more to come.
439    
440    2005-08-18  Douglas Bates  <bates@wisc.edu>
441    
442            * DESCRIPTION (Version): 0.98-5  released to CRAN
443    
444            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
445            * .....
446    
447    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
448    
449            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
450            or glmer objects.
451    
452    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
455    
456    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
457    
458            * R/HBMM.R: finish re-writing R-only code.
459    
460    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
461    
462            * man/externalFormats.Rd: move documentation for writeHB and
463            writeMM here.
464    
465            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
466            (suggested by Paul Roecker).
467    
468            * tests/validObj.R (assertError): Comment out test that is failing
469            after recent changes in r-devel.
470    
471    
472    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/AllClass.R: intermediate virtual class "denseMatrix"
475            * man/denseMatrix-class.Rd
476            * NAMESPACE: export it, and also export
477            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
478    
479    2005-08-10  Douglas Bates  <bates@wisc.edu>
480    
481            * DESCRIPTION (Version): 0.98-3 to CRAN
482    
483            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
484            matrix_solve code (which was really, really wrong).
485    
486    2005-08-07  Douglas Bates  <bates@wisc.edu>
487    
488            * DESCRIPTION (Version): 0.98-2
489    
490            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
491    
492            * R/lmer.R (abbrvNms): new
493            * R/lmer.R (mcmcsamp): allow transformed parameters
494            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
495            for the Harwell-Boeing and the MatrixMarket formats.
496    
497    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * man/dtrMatrix-class.Rd: add examples
500            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
501    
502            * TODO: note the dtpMatrix (docu) bug
503    
504            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
505            in order to ensure that new as.matrix() is used by old functions,
506            e.g., svd(), qr(), eigen(), dist(),..;
507                  apply(), also matplot() or pairs().
508    
509    
510    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
513              add comments about 'control' / lmerControl() arguments
514    
515    2005-07-27  Douglas Bates  <bates@wisc.edu>
516    
517            * man/sleepstudy.Rd: Added the sleep data set.
518            * DESCRIPTION (Version): 0.98-1  released to CRAN
519    
520    2005-07-12  Douglas Bates  <bates@wisc.edu>
521            * man/sleepstudy.Rd: Added the sleep data set.
522    
523            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
524            .Call calls that were producing spurious output.
525    
526    2005-07-05  Douglas Bates  <bates@wisc.edu>
527    
528            * R/lmer.R (lmer): stored updated variance component estimates in
529            mer object for the generalized model.  (Bug reported by Renaud
530            Lancelot).
531    
532    2005-07-03  Douglas Bates  <bates@wisc.edu>
533    
534            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
535            unidimensional case.
536    
537    2005-06-08  Douglas Bates  <bates@wisc.edu>
538    
539            * DESCRIPTION (Version): 0.96-1
540    
541            * moved  lmer-class' R and C code moved from lme4 to here
542    
543    2005-06-04  Douglas Bates  <bates@wisc.edu>
544    
545            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
546            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
547    
548    2005-06-02  Douglas Bates  <bates@wisc.edu>
549    
550            * src/Makefile.win: Forgot to update this when Makefile changed.
551    
552    2005-05-11  Douglas Bates  <bates@wisc.edu>
553    
554            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
555            bug reported by Kurt Hornik and Michael Hahsler.
556    
557    2005-05-10  Douglas Bates  <bates@wisc.edu>
558    
559            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
560            logical sparse matrices.  These will also be used in the symbolic
561            analysis for lmer objects.
562    
563            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
564            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
565    
566    2005-05-06  Douglas Bates  <bates@wisc.edu>
567    
568            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
569            colMeans, colSums, rowMeans and rowSums.
570    
571    2005-04-18  Douglas Bates  <bates@wisc.edu>
572    
573            * src/lgCMatrix.[ch]: code for _validate method and stub for
574            multiplication operation.
575    
576            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
577            to dgetrs.
578    
579            * src/init.c: Fix cut-and-paste error in definition of
580            dgeMatrix_matrix_solve
581    
582            * src/{many files}: Tighten code by using ALLOC_SLOT.
583    
584    2005-04-15  Douglas Bates  <bates@wisc.edu>
585    
586            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
587    
588            * DESCRIPTION: Eliminate import of stats.
589    
590    
591    2005-04-06  Douglas Bates  <bates@wisc.edu>
592    
593            * R/AllClass.R : add logical sparse matrix classes
594    
595    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/dgTMatrix.R: add "[" method for triplet matrices
598            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
599    
600    2005-03-31  Douglas Bates  <bates@wisc.edu>
601    
602            * DESCRIPTION (Version): release 0.95-5 to CRAN
603    
604            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
605            * R/sparseMatrix.R: %*%, crossprod()
606            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
607            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
608            * src/lmer.c (lmer_fitted): fix thinko
609    
610    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/AllClass.R: add two virtual sparse classes ``on top''
613    
614    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
617                    correspondingly fix examples and tests/ since new()
618                    doesn't work for virtual classes.
619    
620    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Matrix.R (as.matrix): method and one for unname()
623            * tests/dpoMatrix.R: tests should now be less platform dependent;
624              also run for R 2.1.0; using as.matrix()
625    
626    2005-03-15  Douglas Bates  <bates@wisc.edu>
627    
628            * R/pMatrix.R: "pMatrix" class added
629            * ....
630    
631    2005-03-14  Douglas Bates  <bates@wisc.edu>
632    
633            * R/dtpMatrix.R: Add unpack method and an example.
634    
635            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
636            of general symmetric matrices and associated S4 methods.
637    
638    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
639            +
640    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/dgeMatrix.R (setAs): and many other files: more coercion,
643              crossprod() and "%*%" methods added; tests, too.
644            * tests/matprod.R: new, for testing these
645    
646    2005-03-03  Douglas Bates  <bates@wisc.edu>
647    
648            * src/lmer.c (lmer_fitted): Added.
649    
650    2005-03-02  Douglas Bates  <bates@wisc.edu>
651    
652            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
653    
654    2005-02-28  Douglas Bates  <bates@wisc.edu>
655    
656            * src/*.c,po/,inst/po: Internationalization and localization of
657            the package.
658    
659            * src/ldl.[ch]: Removed these as their contents are referenced in the
660            R_ldl.c file.
661    
662            * src/flame.[ch]: Removed these source files.
663    
664            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
665    
666            * src/LU.[ch],src/init.c: absorb in factorizations
667    
668            * src/Mutils.h: prepare for internationalization
669    
670            * src/cblas.h: move the enum definitions to Mutils.h and remove
671            this file
672    
673    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
674    
675            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
676    
677            * R/dtrMatrix.R: fix t() method
678    
679            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
680            * NAMESPACE: export them (and import generics from "methods")
681            * tests/group-methods.R : and test them.
682    
683            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
684            border case
685    
686    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
687    
688            * DESCRIPTION (Version): 0.95-2  released to CRAN
689    
690            * src/dgBCMatrix.c:
691            * src/lmer.c: many changes
692            * ...
693    
694    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Matrix.R: add more sophisticated show() method.
697    
698    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
699    
700            * */* : almost complete reorganization of classes.
701    
702    2005-01-26  Douglas Bates  <bates@wisc.edu>
703    
704            * R/AllGeneric.R: Added matrix exponential generic expm and a method
705            for the geMatrix class.
706    
707    2005-01-24  Douglas Bates  <bates@wisc.edu>
708    
709            * src/Makefile (clean): Remove *.a and *.so
710    
711            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
712    
713    2005-01-23  Douglas Bates  <bates@wisc.edu>
714    
715            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
716            had an effect in cases with more than 2 grouping factors.
717    
718    2005-01-03  Douglas Bates  <bates@wisc.edu>
719    
720            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
721    
722    2004-12-23  Douglas Bates  <bates@wisc.edu>
723    
724            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
725            and R_useDynamicSymbols (suggested by B.D.Ripley).
726    
727    2004-12-14  Douglas Bates  <bates@wisc.edu>
728    
729            * R/sscMatrix.R: Add determinant methods
730    
731            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
732            for tripletMatrix to matrix.
733    
734    2004-12-13  Douglas Bates  <bates@wisc.edu>
735    
736            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
737            no longer used.
738    
739          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
740          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 743 
743          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
744          Fixes part but not all of #15.          Fixes part but not all of #15.
745    
746  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
747    
748          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
749          scalar grouping factors corrected.          scalar grouping factors corrected.
750    
751  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
752    
753          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
754    
755  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
756    
757          * 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
758          .h file can be included.          .h file can be included.
759    
760  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
761    
762          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
763          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
764    
765          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
766    
767  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
768    
769          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
770    
771  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
772    
773          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
774    
775  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
776    
777          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
778    
779  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
780    
781          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
782    
783  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
784    
785          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
786          routines.          routines.
787    
788  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
789    
790          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
791    
792  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
793    
794          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
795    

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