SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 28, Sun Mar 28 17:06:05 2004 UTC revision 1288, Thu Jun 1 20:41:20 2006 UTC
# Line 1  Line 1 
1    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (panel.ci): Add a reference line at zero and a
4            background grid to the qqmath plot of ranef.lmer.
5    
6    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
9            grouping factors to be specified in the formula as (1|foo/bar).
10    
11    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R (findbars and others): Change check of is.numeric to
14            !is.language to resolve the bug reported by Jacob Wegelin.
15    
16            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
17            code to evaluate inbreeding coefficients without calculating T,
18            based on code in Sargolzaei and Iwaisaki's paper.
19    
20    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
23            generic and mer methods for isNested and denomDF. This denomDF was
24            an attempt to emulate that in lme but I don't think that makes
25            sense.  Use the trace of the hat matrix instead.
26    
27    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
30            the C code depending on a slot structure that's no longer valid.
31            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
32    
33    
34    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
35    
36            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
37            of lowerTriMatrix generic and methods to tril (also upper to triu)
38            and added a general band extractor.
39    
40    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/pedigree.R (pedigree): Replace sire and dam values outside the
43            allowable range with NAs. Added a corresponding check in the
44            validity check for the pedigree class.
45    
46            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
47            crossprod methods now inherits from symmetricMatrix.
48    
49    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
50    
51            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
52            generics lowerTriMatrix and upperTriMatrix along with methods for
53            the Csparse virtual class.  Also added a C function Csparse_band
54            that implements these methods by calling cholmod_band.
55    
56    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
59            erased when it was NULL.  This led to invalid subselections!
60    
61    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
64            in method for "t" so as not to lose the unit diagonal property.
65    
66    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
69            and methods.  This is now an option to the ranef method for the
70            mer class.
71    
72            * src/cs_utils.c: Ensure that the nz component is -1 for a
73            compressed column-oriented matrix.  Minor formatting cleanup.
74    
75            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
76            objects.
77    
78    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
81            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
82    
83    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
86            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
87    
88            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
89            for the dtCMatrix class.
90    
91    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
94            and methods for it.
95    
96    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
99            arguments, such that M %*% 1:6 now works
100            * Tests/matprod.R: test the above
101    
102    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
105            the ranef.lmer class.
106    
107            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
108            methods to extract the posterior variances from the bVar slot.
109    
110    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
113            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
114    
115            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
116            * tests/simple: (extended)
117    
118            * R/sparseMatrix.R (isTriangular): now using much improved
119            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
120    
121    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
124            (problem report from Franklin Parlamis).  This should be done
125            generally.
126    
127    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
130            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
131            update the plot methods.
132    
133    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/lmer.R (resid and ranef methods):  Added methods for the
136            "residuals" and "resid" generic but only for linear mixed model
137            fits.  Changed the ranef method to return a list of data frames so
138            that the plot methods now work.
139    
140    2006-03-16  Douglas Bates  <bates@bates2>
141    
142            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
143            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
144    
145            * DESCRIPTION (Date): New release
146    
147    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
150    
151            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
152            * man/KNex.Rd: and other help files
153            * tests/*.R: several ones needed adaption
154            * inst/doc/Comparisons.Rnw: dito
155    
156    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
159    
160            * tests/indexing.R: tests for new [<- methods for sparse matrices.
161    
162    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
165    
166            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
167    
168    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dMatrix.R: enable things like  M [ M < 10 ]
171            * R/dgeMatrix.R: implement it
172    
173    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/AllClass.R: define "summary.mer" and "*.lmer"
176            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
177            * R/lmer.R (show): now works with summary()
178    
179    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
182            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
183                    support the above
184    
185    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
186    
187            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
188            Use glmFit$prior.weights for weights in a glmm.
189            Allow an option usePQL = FALSE to skip the PQL steps for the
190            Laplace method (and, in time, the AGQ method).
191    
192            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
193            into a separate function internal_mer_Xfactor to be able to call
194            it from internal_bhat.
195    
196    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * tests/Class+Meth.R (tstMatrixClass): function for much better
199            testing; now again of all actual classes.
200    
201            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
202                    use macros and define make_d_matrix_* and make_i_matrix_*
203                    where _i_ is for the ldense routines:
204    
205            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
206            * src/ldense.c (lsyMatrix_as_lgeMatrix):
207    
208            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
209    
210    
211    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
214                    many different kinds of matrices.
215            * R/*.R: quite a few new methods were needed for R CMD check with
216                    new Matrix().  Very good for users playing around.
217    
218    
219    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * src/dgeMatrix.c (dMatrix_validate): new
222            * src/Mutils.c (dense_nonpacked_validate): new
223    
224            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
225    
226    
227    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
230    
231    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * DESCRIPTION (Version): 0.99-6 released to CRAN
234    
235            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
236            segfault in cases with multiple non-nested grouping factors.
237    
238    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
241                    (Depends): also on 'utils'
242    
243            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
244            * R/diagMatrix.R (Diagonal): constructor and methods for
245            diagonal matrices
246    
247            * R/ltTMatrix.R: new "minimal methods"
248    
249    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
252            all methods (and help files).
253    
254    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
257                    for case (dimn.  op  no_dimn.)
258    
259    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * DESCRIPTION (Version): 0.99-2  released to CRAN
262    
263    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
266            by Julian Faraway.
267    
268    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Auxiliaries.R (try_as): new utility
271            * R/sparseMatrix.R: use try_as() in coercion to original class
272    
273    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
276    
277    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (dimNamesCheck): added
280    
281            * R/Matrix.R (as.array), (as.vector): new
282    
283    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
286                    default.
287            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
288                    "pMatrix" now contains "sparseMatrix"
289    
290    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * tests/Class+Meth.R: new tests; t(t(m)) == m
293    
294            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
295    
296            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
297            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
298    
299            * R/dspMatrix.R: typo in "t" method
300    
301    2005-09-18  Douglas Bates  <bates@wisc.edu>
302    
303            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
304            * R/Tsparse.R: instead of R/gTMatrix.R
305            * R/Csparse.R: new
306            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
307            * src/Tsparse.c: new; many trivial methods calling cholmod_()
308            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
309                            via cholmod
310    
311    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Auxiliaries.R (non0ind): new function using new C code
314            * src/dgCMatrix.c (compressed_non_0_ij): new utility
315    
316    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
317    
318            * src/chm_common.h: header file required by all C sources that
319            call CHOLMOD functions.  It defines a cholmod_common structure
320            called 'c' whose address is passed as the last argument to
321            (virtually) every CHOLMOD function.
322    
323            * src/Pattern.c: Simple example of the use of CHOLMOD.
324    
325            * src/init.c: initialize and finalize the cholmod_common structure.
326    
327            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
328            LDL and CCOLAMD from the U. of Florida sparse matrix library.
329    
330    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * inst/test-tools.R: new file collecting the utility functions used
333                    in ./tests/*.R
334    
335            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
336            * R/Matrix.R (cbind2): methods for NULL and missing
337    
338    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/AllClass.R: new "index" class for "[" and "[<-":
341                    First cut at "symmetricMatrix" and "triangularMatrix"
342            * R/gTMatrix.R (.ind.prep): new function;
343                    Logical and character indexing now work too.
344            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
345            * tests/indexing.R: new, including *.Rout.save
346            * tests/dgTMatrix.R: new
347    
348    2005-08-29  Douglas Bates  <bates@wisc.edu>
349    
350            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
351            indicator pos not being updated.  Also enforced upper triangular
352            for symmetric case.  Need to coerce edges component of elements of
353            edge list - grr! (Why don't they define their classes cleanly?)
354    
355    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Matrix.R:  added first "[<-" methods; not yet functional
358            * R/denseMatrix.R: dito
359            * man/Subassign-methods.Rd: new help file for these
360    
361    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * DESCRIPTION (Version): 0.98-6
364    
365            * R/denseMatrix.R: new file for "[" fallback methods for all dense
366            matrices.
367    
368    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
371                    as( <logical>, "matrix")
372    
373            * R/pMatrix.R: coercion to "lgTMatrix"
374    
375            * R/gTMatrix.R: new virtual class to define "[" methods for.
376            * man/gTMatrix-class.Rd:
377            * General slight re-organization of where "[" methods are defined.
378              more to come.
379    
380    2005-08-18  Douglas Bates  <bates@wisc.edu>
381    
382            * DESCRIPTION (Version): 0.98-5  released to CRAN
383    
384            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
385            * .....
386    
387    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
388    
389            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
390            or glmer objects.
391    
392    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
395    
396    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
397    
398            * R/HBMM.R: finish re-writing R-only code.
399    
400    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
401    
402            * man/externalFormats.Rd: move documentation for writeHB and
403            writeMM here.
404    
405            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
406            (suggested by Paul Roecker).
407    
408            * tests/validObj.R (assertError): Comment out test that is failing
409            after recent changes in r-devel.
410    
411    
412    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/AllClass.R: intermediate virtual class "denseMatrix"
415            * man/denseMatrix-class.Rd
416            * NAMESPACE: export it, and also export
417            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
418    
419    2005-08-10  Douglas Bates  <bates@wisc.edu>
420    
421            * DESCRIPTION (Version): 0.98-3 to CRAN
422    
423            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
424            matrix_solve code (which was really, really wrong).
425    
426    2005-08-07  Douglas Bates  <bates@wisc.edu>
427    
428            * DESCRIPTION (Version): 0.98-2
429    
430            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
431    
432            * R/lmer.R (abbrvNms): new
433            * R/lmer.R (mcmcsamp): allow transformed parameters
434            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
435            for the Harwell-Boeing and the MatrixMarket formats.
436    
437    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * man/dtrMatrix-class.Rd: add examples
440            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
441    
442            * TODO: note the dtpMatrix (docu) bug
443    
444            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
445            in order to ensure that new as.matrix() is used by old functions,
446            e.g., svd(), qr(), eigen(), dist(),..;
447                  apply(), also matplot() or pairs().
448    
449    
450    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
453              add comments about 'control' / lmerControl() arguments
454    
455    2005-07-27  Douglas Bates  <bates@wisc.edu>
456    
457            * man/sleepstudy.Rd: Added the sleep data set.
458            * DESCRIPTION (Version): 0.98-1  released to CRAN
459    
460    2005-07-12  Douglas Bates  <bates@wisc.edu>
461            * man/sleepstudy.Rd: Added the sleep data set.
462    
463            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
464            .Call calls that were producing spurious output.
465    
466    2005-07-05  Douglas Bates  <bates@wisc.edu>
467    
468            * R/lmer.R (lmer): stored updated variance component estimates in
469            mer object for the generalized model.  (Bug reported by Renaud
470            Lancelot).
471    
472    2005-07-03  Douglas Bates  <bates@wisc.edu>
473    
474            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
475            unidimensional case.
476    
477    2005-06-08  Douglas Bates  <bates@wisc.edu>
478    
479            * DESCRIPTION (Version): 0.96-1
480    
481            * moved  lmer-class' R and C code moved from lme4 to here
482    
483    2005-06-04  Douglas Bates  <bates@wisc.edu>
484    
485            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
486            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
487    
488    2005-06-02  Douglas Bates  <bates@wisc.edu>
489    
490            * src/Makefile.win: Forgot to update this when Makefile changed.
491    
492    2005-05-11  Douglas Bates  <bates@wisc.edu>
493    
494            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
495            bug reported by Kurt Hornik and Michael Hahsler.
496    
497    2005-05-10  Douglas Bates  <bates@wisc.edu>
498    
499            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
500            logical sparse matrices.  These will also be used in the symbolic
501            analysis for lmer objects.
502    
503            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
504            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
505    
506    2005-05-06  Douglas Bates  <bates@wisc.edu>
507    
508            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
509            colMeans, colSums, rowMeans and rowSums.
510    
511    2005-04-18  Douglas Bates  <bates@wisc.edu>
512    
513            * src/lgCMatrix.[ch]: code for _validate method and stub for
514            multiplication operation.
515    
516            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
517            to dgetrs.
518    
519            * src/init.c: Fix cut-and-paste error in definition of
520            dgeMatrix_matrix_solve
521    
522            * src/{many files}: Tighten code by using ALLOC_SLOT.
523    
524    2005-04-15  Douglas Bates  <bates@wisc.edu>
525    
526            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
527    
528            * DESCRIPTION: Eliminate import of stats.
529    
530    
531    2005-04-06  Douglas Bates  <bates@wisc.edu>
532    
533            * R/AllClass.R : add logical sparse matrix classes
534    
535    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/dgTMatrix.R: add "[" method for triplet matrices
538            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
539    
540    2005-03-31  Douglas Bates  <bates@wisc.edu>
541    
542            * DESCRIPTION (Version): release 0.95-5 to CRAN
543    
544            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
545            * R/sparseMatrix.R: %*%, crossprod()
546            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
547            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
548            * src/lmer.c (lmer_fitted): fix thinko
549    
550    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/AllClass.R: add two virtual sparse classes ``on top''
553    
554    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
557                    correspondingly fix examples and tests/ since new()
558                    doesn't work for virtual classes.
559    
560    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/Matrix.R (as.matrix): method and one for unname()
563            * tests/dpoMatrix.R: tests should now be less platform dependent;
564              also run for R 2.1.0; using as.matrix()
565    
566    2005-03-15  Douglas Bates  <bates@wisc.edu>
567    
568            * R/pMatrix.R: "pMatrix" class added
569            * ....
570    
571    2005-03-14  Douglas Bates  <bates@wisc.edu>
572    
573            * R/dtpMatrix.R: Add unpack method and an example.
574    
575            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
576            of general symmetric matrices and associated S4 methods.
577    
578    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
579            +
580    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/dgeMatrix.R (setAs): and many other files: more coercion,
583              crossprod() and "%*%" methods added; tests, too.
584            * tests/matprod.R: new, for testing these
585    
586    2005-03-03  Douglas Bates  <bates@wisc.edu>
587    
588            * src/lmer.c (lmer_fitted): Added.
589    
590    2005-03-02  Douglas Bates  <bates@wisc.edu>
591    
592            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
593    
594    2005-02-28  Douglas Bates  <bates@wisc.edu>
595    
596            * src/*.c,po/,inst/po: Internationalization and localization of
597            the package.
598    
599            * src/ldl.[ch]: Removed these as their contents are referenced in the
600            R_ldl.c file.
601    
602            * src/flame.[ch]: Removed these source files.
603    
604            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
605    
606            * src/LU.[ch],src/init.c: absorb in factorizations
607    
608            * src/Mutils.h: prepare for internationalization
609    
610            * src/cblas.h: move the enum definitions to Mutils.h and remove
611            this file
612    
613    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
616    
617            * R/dtrMatrix.R: fix t() method
618    
619            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
620            * NAMESPACE: export them (and import generics from "methods")
621            * tests/group-methods.R : and test them.
622    
623            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
624            border case
625    
626    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
627    
628            * DESCRIPTION (Version): 0.95-2  released to CRAN
629    
630            * src/dgBCMatrix.c:
631            * src/lmer.c: many changes
632            * ...
633    
634    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Matrix.R: add more sophisticated show() method.
637    
638    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
639    
640            * */* : almost complete reorganization of classes.
641    
642    2005-01-26  Douglas Bates  <bates@wisc.edu>
643    
644            * R/AllGeneric.R: Added matrix exponential generic expm and a method
645            for the geMatrix class.
646    
647    2005-01-24  Douglas Bates  <bates@wisc.edu>
648    
649            * src/Makefile (clean): Remove *.a and *.so
650    
651            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
652    
653    2005-01-23  Douglas Bates  <bates@wisc.edu>
654    
655            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
656            had an effect in cases with more than 2 grouping factors.
657    
658    2005-01-03  Douglas Bates  <bates@wisc.edu>
659    
660            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
661    
662    2004-12-23  Douglas Bates  <bates@wisc.edu>
663    
664            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
665            and R_useDynamicSymbols (suggested by B.D.Ripley).
666    
667    2004-12-14  Douglas Bates  <bates@wisc.edu>
668    
669            * R/sscMatrix.R: Add determinant methods
670    
671            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
672            for tripletMatrix to matrix.
673    
674    2004-12-13  Douglas Bates  <bates@wisc.edu>
675    
676            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
677            no longer used.
678    
679            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
680            with dynamic allocation of scratch arrays.
681    
682            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
683            for multivariate random effects with multiple grouping factors.
684            Fixes part but not all of #15.
685    
686    2004-12-03  Douglas Bates  <bates@wisc.edu>
687    
688            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
689            scalar grouping factors corrected.
690    
691    2004-11-29  Douglas Bates  <bates@wisc.edu>
692    
693            * src/bCrosstab.c: remove diag_update which is no longer used
694    
695    2004-11-16  Douglas Bates  <bates@wisc.edu>
696    
697            * src/Metis_utils.c: Move metis.h include to C sources so that the
698            .h file can be included.
699    
700    2004-11-12  Douglas Bates  <bates@wisc.edu>
701    
702            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
703            Complete allocation of slots in NEW_OBJECT.
704    
705            * src/Mutils.h: Moved list of symbols to an include file
706    
707    2004-11-11  Douglas Bates  <bates@wisc.edu>
708    
709            * src/geMutils.c (Matrix_init): remove unused function
710    
711    2004-11-10  Douglas Bates  <bates@wisc.edu>
712    
713            * src/cscMatrix.c (csc_to_imagemat): removed unused function
714    
715    2004-11-05  Douglas Bates  <bates@wisc.edu>
716    
717            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
718    
719    2004-10-27  Douglas Bates  <bates@wisc.edu>
720    
721            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
722    
723    2004-10-04  Douglas Bates  <bates@wisc.edu>
724    
725            * src/init.c: Created R_init_Matrix and added registration of C
726            routines.
727    
728    2004-10-02  Douglas Bates  <bates@wisc.edu>
729    
730            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
731    
732    2004-06-15  Douglas Bates  <bates@wisc.edu>
733    
734            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
735    
736    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
739    
740    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
741    
742            * src/ssclme.c (ssclme_update_mm): fix logic error in
743            ssclme_update_mm
744    
745    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
746    
747            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
748            in the order of unconstrained and constrained parameters.
749            (ssclme_gradient): Added the gradients (not yet correct for
750            multidimensional, unconstrained case).
751    
752    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
753    
754            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
755    
756            * src/Makefile.win: Remove unneeded ranlib call
757    
758    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * DESCRIPTION (Version): New release
761    
762            * src/Makefile.win: Update Makefile.win to umfpack removal.
763    
764    2004-04-05  Douglas Bates  <bates@bates2_home>
765    
766            * src/triplet_to_col.c: Create triplet_to_col as a native
767            function, not the version from umfpack.  There were problems with
768            the configuration of UMFPACK for 64-bit processors and there was
769            only one umfpack routine being used so I moved it here.
770    
771    2004-04-04  Douglas Bates  <bates@bates2_home>
772    
773            * src/ssclme.c (ssclme_variances): New function.
774    
775  2004-03-28  Douglas Bates  <bates@bates2_home>  2004-03-28  Douglas Bates  <bates@bates2_home>
776    
777          * src/ssclme.c (ssclme_fitted): Added function.          * src/ssclme.c (ssclme_fitted): Added function.

Legend:
Removed from v.28  
changed lines
  Added in v.1288

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge