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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1295, Fri Jun 9 21:47:22 2006 UTC
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1    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
4            classes.
5    
6    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dgTMatrix.R (colSums): etc. All four of
9            colSums(), rowSums(), colMeans(), rowMeans() now should work for
10            all "Matrices".
11    
12    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (panel.ci): Add a reference line at zero and a
15            background grid to the qqmath plot of ranef.lmer.
16    
17    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
20            grouping factors to be specified in the formula as (1|foo/bar).
21    
22    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/lmer.R (findbars and others): Change check of is.numeric to
25            !is.language to resolve the bug reported by Jacob Wegelin.
26    
27            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
28            code to evaluate inbreeding coefficients without calculating T,
29            based on code in Sargolzaei and Iwaisaki's paper.
30    
31    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
34            generic and mer methods for isNested and denomDF. This denomDF was
35            an attempt to emulate that in lme but I don't think that makes
36            sense.  Use the trace of the hat matrix instead.
37    
38    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
41            the C code depending on a slot structure that's no longer valid.
42            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
43    
44    
45    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
46    
47            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
48            of lowerTriMatrix generic and methods to tril (also upper to triu)
49            and added a general band extractor.
50    
51    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * R/pedigree.R (pedigree): Replace sire and dam values outside the
54            allowable range with NAs. Added a corresponding check in the
55            validity check for the pedigree class.
56    
57            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
58            crossprod methods now inherits from symmetricMatrix.
59    
60    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
63            generics lowerTriMatrix and upperTriMatrix along with methods for
64            the Csparse virtual class.  Also added a C function Csparse_band
65            that implements these methods by calling cholmod_band.
66    
67    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
70            erased when it was NULL.  This led to invalid subselections!
71    
72    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
75            in method for "t" so as not to lose the unit diagonal property.
76    
77    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
80            and methods.  This is now an option to the ranef method for the
81            mer class.
82    
83            * src/cs_utils.c: Ensure that the nz component is -1 for a
84            compressed column-oriented matrix.  Minor formatting cleanup.
85    
86            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
87            objects.
88    
89    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
92            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
93    
94    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
97            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
98    
99            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
100            for the dtCMatrix class.
101    
102    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
105            and methods for it.
106    
107    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
110            arguments, such that M %*% 1:6 now works
111            * Tests/matprod.R: test the above
112    
113    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
116            the ranef.lmer class.
117    
118            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
119            methods to extract the posterior variances from the bVar slot.
120    
121    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
124            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
125    
126            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
127            * tests/simple: (extended)
128    
129            * R/sparseMatrix.R (isTriangular): now using much improved
130            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
131    
132    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
135            (problem report from Franklin Parlamis).  This should be done
136            generally.
137    
138    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
139    
140            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
141            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
142            update the plot methods.
143    
144    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * R/lmer.R (resid and ranef methods):  Added methods for the
147            "residuals" and "resid" generic but only for linear mixed model
148            fits.  Changed the ranef method to return a list of data frames so
149            that the plot methods now work.
150    
151    2006-03-16  Douglas Bates  <bates@bates2>
152    
153            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
154            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
155    
156            * DESCRIPTION (Date): New release
157    
158    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
161    
162            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
163            * man/KNex.Rd: and other help files
164            * tests/*.R: several ones needed adaption
165            * inst/doc/Comparisons.Rnw: dito
166    
167    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
170    
171            * tests/indexing.R: tests for new [<- methods for sparse matrices.
172    
173    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
176    
177            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
178    
179    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dMatrix.R: enable things like  M [ M < 10 ]
182            * R/dgeMatrix.R: implement it
183    
184    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/AllClass.R: define "summary.mer" and "*.lmer"
187            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
188            * R/lmer.R (show): now works with summary()
189    
190    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
193            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
194                    support the above
195    
196    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
197    
198            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
199            Use glmFit$prior.weights for weights in a glmm.
200            Allow an option usePQL = FALSE to skip the PQL steps for the
201            Laplace method (and, in time, the AGQ method).
202    
203            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
204            into a separate function internal_mer_Xfactor to be able to call
205            it from internal_bhat.
206    
207    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * tests/Class+Meth.R (tstMatrixClass): function for much better
210            testing; now again of all actual classes.
211    
212            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
213                    use macros and define make_d_matrix_* and make_i_matrix_*
214                    where _i_ is for the ldense routines:
215    
216            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
217            * src/ldense.c (lsyMatrix_as_lgeMatrix):
218    
219            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
220    
221    
222    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
225                    many different kinds of matrices.
226            * R/*.R: quite a few new methods were needed for R CMD check with
227                    new Matrix().  Very good for users playing around.
228    
229    
230    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dgeMatrix.c (dMatrix_validate): new
233            * src/Mutils.c (dense_nonpacked_validate): new
234    
235            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
236    
237    
238    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
239    
240            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
241    
242    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * DESCRIPTION (Version): 0.99-6 released to CRAN
245    
246            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
247            segfault in cases with multiple non-nested grouping factors.
248    
249    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
252                    (Depends): also on 'utils'
253    
254            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
255            * R/diagMatrix.R (Diagonal): constructor and methods for
256            diagonal matrices
257    
258            * R/ltTMatrix.R: new "minimal methods"
259    
260    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
263            all methods (and help files).
264    
265    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
268                    for case (dimn.  op  no_dimn.)
269    
270    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * DESCRIPTION (Version): 0.99-2  released to CRAN
273    
274    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
277            by Julian Faraway.
278    
279    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (try_as): new utility
282            * R/sparseMatrix.R: use try_as() in coercion to original class
283    
284    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
287    
288    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/Auxiliaries.R (dimNamesCheck): added
291    
292            * R/Matrix.R (as.array), (as.vector): new
293    
294    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
297                    default.
298            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
299                    "pMatrix" now contains "sparseMatrix"
300    
301    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * tests/Class+Meth.R: new tests; t(t(m)) == m
304    
305            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
306    
307            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
308            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
309    
310            * R/dspMatrix.R: typo in "t" method
311    
312    2005-09-18  Douglas Bates  <bates@wisc.edu>
313    
314            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
315            * R/Tsparse.R: instead of R/gTMatrix.R
316            * R/Csparse.R: new
317            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
318            * src/Tsparse.c: new; many trivial methods calling cholmod_()
319            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
320                            via cholmod
321    
322    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (non0ind): new function using new C code
325            * src/dgCMatrix.c (compressed_non_0_ij): new utility
326    
327    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
328    
329            * src/chm_common.h: header file required by all C sources that
330            call CHOLMOD functions.  It defines a cholmod_common structure
331            called 'c' whose address is passed as the last argument to
332            (virtually) every CHOLMOD function.
333    
334            * src/Pattern.c: Simple example of the use of CHOLMOD.
335    
336            * src/init.c: initialize and finalize the cholmod_common structure.
337    
338            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
339            LDL and CCOLAMD from the U. of Florida sparse matrix library.
340    
341    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * inst/test-tools.R: new file collecting the utility functions used
344                    in ./tests/*.R
345    
346            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
347            * R/Matrix.R (cbind2): methods for NULL and missing
348    
349    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/AllClass.R: new "index" class for "[" and "[<-":
352                    First cut at "symmetricMatrix" and "triangularMatrix"
353            * R/gTMatrix.R (.ind.prep): new function;
354                    Logical and character indexing now work too.
355            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
356            * tests/indexing.R: new, including *.Rout.save
357            * tests/dgTMatrix.R: new
358    
359    2005-08-29  Douglas Bates  <bates@wisc.edu>
360    
361            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
362            indicator pos not being updated.  Also enforced upper triangular
363            for symmetric case.  Need to coerce edges component of elements of
364            edge list - grr! (Why don't they define their classes cleanly?)
365    
366    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Matrix.R:  added first "[<-" methods; not yet functional
369            * R/denseMatrix.R: dito
370            * man/Subassign-methods.Rd: new help file for these
371    
372    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * DESCRIPTION (Version): 0.98-6
375    
376            * R/denseMatrix.R: new file for "[" fallback methods for all dense
377            matrices.
378    
379    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
382                    as( <logical>, "matrix")
383    
384            * R/pMatrix.R: coercion to "lgTMatrix"
385    
386            * R/gTMatrix.R: new virtual class to define "[" methods for.
387            * man/gTMatrix-class.Rd:
388            * General slight re-organization of where "[" methods are defined.
389              more to come.
390    
391    2005-08-18  Douglas Bates  <bates@wisc.edu>
392    
393            * DESCRIPTION (Version): 0.98-5  released to CRAN
394    
395            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
396            * .....
397    
398    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
399    
400            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
401            or glmer objects.
402    
403    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
406    
407    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
408    
409            * R/HBMM.R: finish re-writing R-only code.
410    
411    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
412    
413            * man/externalFormats.Rd: move documentation for writeHB and
414            writeMM here.
415    
416            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
417            (suggested by Paul Roecker).
418    
419            * tests/validObj.R (assertError): Comment out test that is failing
420            after recent changes in r-devel.
421    
422    
423    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/AllClass.R: intermediate virtual class "denseMatrix"
426            * man/denseMatrix-class.Rd
427            * NAMESPACE: export it, and also export
428            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
429    
430    2005-08-10  Douglas Bates  <bates@wisc.edu>
431    
432            * DESCRIPTION (Version): 0.98-3 to CRAN
433    
434            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
435            matrix_solve code (which was really, really wrong).
436    
437    2005-08-07  Douglas Bates  <bates@wisc.edu>
438    
439            * DESCRIPTION (Version): 0.98-2
440    
441            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
442    
443            * R/lmer.R (abbrvNms): new
444            * R/lmer.R (mcmcsamp): allow transformed parameters
445            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
446            for the Harwell-Boeing and the MatrixMarket formats.
447    
448    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * man/dtrMatrix-class.Rd: add examples
451            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
452    
453            * TODO: note the dtpMatrix (docu) bug
454    
455            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
456            in order to ensure that new as.matrix() is used by old functions,
457            e.g., svd(), qr(), eigen(), dist(),..;
458                  apply(), also matplot() or pairs().
459    
460    
461    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
464              add comments about 'control' / lmerControl() arguments
465    
466    2005-07-27  Douglas Bates  <bates@wisc.edu>
467    
468            * man/sleepstudy.Rd: Added the sleep data set.
469            * DESCRIPTION (Version): 0.98-1  released to CRAN
470    
471    2005-07-12  Douglas Bates  <bates@wisc.edu>
472            * man/sleepstudy.Rd: Added the sleep data set.
473    
474            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
475            .Call calls that were producing spurious output.
476    
477    2005-07-05  Douglas Bates  <bates@wisc.edu>
478    
479            * R/lmer.R (lmer): stored updated variance component estimates in
480            mer object for the generalized model.  (Bug reported by Renaud
481            Lancelot).
482    
483    2005-07-03  Douglas Bates  <bates@wisc.edu>
484    
485            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
486            unidimensional case.
487    
488    2005-06-08  Douglas Bates  <bates@wisc.edu>
489    
490            * DESCRIPTION (Version): 0.96-1
491    
492            * moved  lmer-class' R and C code moved from lme4 to here
493    
494    2005-06-04  Douglas Bates  <bates@wisc.edu>
495    
496            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
497            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
498    
499    2005-06-02  Douglas Bates  <bates@wisc.edu>
500    
501            * src/Makefile.win: Forgot to update this when Makefile changed.
502    
503    2005-05-11  Douglas Bates  <bates@wisc.edu>
504    
505            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
506            bug reported by Kurt Hornik and Michael Hahsler.
507    
508    2005-05-10  Douglas Bates  <bates@wisc.edu>
509    
510            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
511            logical sparse matrices.  These will also be used in the symbolic
512            analysis for lmer objects.
513    
514            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
515            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
516    
517    2005-05-06  Douglas Bates  <bates@wisc.edu>
518    
519            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
520            colMeans, colSums, rowMeans and rowSums.
521    
522    2005-04-18  Douglas Bates  <bates@wisc.edu>
523    
524            * src/lgCMatrix.[ch]: code for _validate method and stub for
525            multiplication operation.
526    
527            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
528            to dgetrs.
529    
530            * src/init.c: Fix cut-and-paste error in definition of
531            dgeMatrix_matrix_solve
532    
533            * src/{many files}: Tighten code by using ALLOC_SLOT.
534    
535    2005-04-15  Douglas Bates  <bates@wisc.edu>
536    
537            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
538    
539            * DESCRIPTION: Eliminate import of stats.
540    
541    
542    2005-04-06  Douglas Bates  <bates@wisc.edu>
543    
544            * R/AllClass.R : add logical sparse matrix classes
545    
546  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
549          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
550    
551  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
552    
553          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
554    
# Line 29  Line 574 
574          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
575            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
576    
577  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
578    
579          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
580          * ....          * ....
581    
582  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
583    
584          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
585    
# Line 49  Line 594 
594            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
595          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
596    
597  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
598    
599          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
600    
601  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
602    
603          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
604    
605  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
606    
607          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
608          the package.          the package.
# Line 105  Line 650 
650    
651          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
652    
653  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
654    
655          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
656          for the geMatrix class.          for the geMatrix class.
657    
658  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
659    
660          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
661    
662          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
663    
664  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
665    
666          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
667          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
668    
669  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
670    
671          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
672    
673  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
674    
675          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
676          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
677    
678  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
679    
680          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
681    
682          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
683          for tripletMatrix to matrix.          for tripletMatrix to matrix.
684    
685  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
686    
687          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
688          no longer used.          no longer used.
# Line 149  Line 694 
694          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
695          Fixes part but not all of #15.          Fixes part but not all of #15.
696    
697  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
698    
699          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
700          scalar grouping factors corrected.          scalar grouping factors corrected.
701    
702  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
703    
704          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
705    
706  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
707    
708          * 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
709          .h file can be included.          .h file can be included.
710    
711  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
712    
713          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
714          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
715    
716          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
717    
718  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
719    
720          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
721    
722  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
723    
724          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
725    
726  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
727    
728          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
729    
730  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
731    
732          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
733    
734  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
735    
736          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
737          routines.          routines.
738    
739  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
740    
741          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
742    
743  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
744    
745          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
746    

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