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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1335, Mon Jul 31 12:11:35 2006 UTC
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1    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE:    change  "correlation" to "corMatrix"
4            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
5            * R/dpoMatrix.R: dito
6            * R/lmer.R:      dito
7    
8    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
11            via new smart
12            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
13            utility functions.
14    
15    
16    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Csparse.R (tril, triu, band): do return *triangular* classed
19            matrices when appropriate; band() even symmetric ones.
20            (replCmat): extend to potentially all "CsparseMatrix"
21            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
22            allow subassignment for special sparse matrices.
23    
24            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
25    
26            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
27            argument; in glmer_*(): print only if(verbose).
28    
29            speed-optimize a few places by moving REAL(.) out of loops.
30    
31            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
32    
33    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
36                    since that wrongly triggers also for M[ logi , ]
37    
38            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
39            a symmetric matrix that results in a non-symmetric one.
40            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
41    
42            * R/dMatrix.R: make round(M) work as round(M, 0)
43    
44            * R/dgTMatrix.R (image): coordinate system and axis now use
45            1-based indices, not 0-based ones.
46    
47            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
48            * tests/indexing.R: test it.
49    
50            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
51            * man/isSymmetric-methods.Rd: and document it.
52    
53            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
54            * man/SparseM-conv.Rd: docu them
55    
56            * tests/other-pkgs.R: renamed from tests/graph.R and add example
57                    for 'SparseM' conversions
58    
59    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
60    
61            * R/Matrix.R (head): added head() and tail() methods.
62    
63    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * DESCRIPTION (Version): 0.995-12 released to CRAN
66    
67    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * tests/simple.R: add check for correct dsT -> dgT coercion;
70                    add check for correct printing of symmetric sparse matrices.
71    
72            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
73            for sparse symmetric matrices.
74    
75            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
76            diagonal twice.
77    
78    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
79    
80            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
81            being applied to the x slot (detected by Brian Ripley).
82    
83    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
86    
87            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
88    
89    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/lgCMatrix.c (lgCMatrix_diag): new function
92            * R/lgCMatrix.R (diag): for new method
93    
94            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
95                 ==> construction of illegal "*gTMatrix" via new() should
96                 now be much less easy:
97            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
98    
99            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
100                    directly.
101            * man/Matrix.Rd: documents it.
102    
103    2006-07-06  Douglas Bates  <bates@R-project.org>
104    
105            * src/pedigree.c (pedigree_inbreeding): Correction in
106            initialization.  This function is not currently being used and is
107            not fully tested.
108    
109            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
110            Introduced the glmer class.  Added code for mcmcmsamp on glmer
111            objects.  Modified validity check on pedigree objects to account
112            for nonparallel patterns of missingness of parents.
113    
114            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
115            class.
116    
117    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/pMatrix.R: coercion pMatrix -> Tsparse
120    
121    2006-06-12  Douglas Bates  <bates@R-project.org>
122    
123            * DESCRIPTION (Version): 0.995-11 released to CRAN
124    
125            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
126            the output from mcmcsamp.
127    
128    2006-06-10  Douglas Bates  <bates@R-project.org>
129    
130            * R/lmer.R (simulestimate): added C code for calculating the trace
131            of the hat matrix.
132    
133    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
136            classes.
137            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
138    
139    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/dgTMatrix.R (colSums): etc. All four of
142            colSums(), rowSums(), colMeans(), rowMeans() now should work for
143            all "Matrices".
144    
145    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
146    
147            * R/lmer.R (panel.ci): Add a reference line at zero and a
148            background grid to the qqmath plot of ranef.lmer.
149    
150    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
153            grouping factors to be specified in the formula as (1|foo/bar).
154    
155    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * R/lmer.R (findbars and others): Change check of is.numeric to
158            !is.language to resolve the bug reported by Jacob Wegelin.
159    
160            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
161            code to evaluate inbreeding coefficients without calculating T,
162            based on code in Sargolzaei and Iwaisaki's paper.
163    
164    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
167            generic and mer methods for isNested and denomDF. This denomDF was
168            an attempt to emulate that in lme but I don't think that makes
169            sense.  Use the trace of the hat matrix instead.
170    
171    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
174            the C code depending on a slot structure that's no longer valid.
175            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
176    
177    
178    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
179    
180            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
181            of lowerTriMatrix generic and methods to tril (also upper to triu)
182            and added a general band extractor.
183    
184    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * R/pedigree.R (pedigree): Replace sire and dam values outside the
187            allowable range with NAs. Added a corresponding check in the
188            validity check for the pedigree class.
189    
190            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
191            crossprod methods now inherits from symmetricMatrix.
192    
193    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
196            generics lowerTriMatrix and upperTriMatrix along with methods for
197            the Csparse virtual class.  Also added a C function Csparse_band
198            that implements these methods by calling cholmod_band.
199    
200    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
203            erased when it was NULL.  This led to invalid subselections!
204    
205    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
208            in method for "t" so as not to lose the unit diagonal property.
209    
210    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
211    
212            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
213            and methods.  This is now an option to the ranef method for the
214            mer class.
215    
216            * src/cs_utils.c: Ensure that the nz component is -1 for a
217            compressed column-oriented matrix.  Minor formatting cleanup.
218    
219            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
220            objects.
221    
222    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
225            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
226    
227    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
230            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
231    
232            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
233            for the dtCMatrix class.
234    
235    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
238            and methods for it.
239    
240    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
243            arguments, such that M %*% 1:6 now works
244            * Tests/matprod.R: test the above
245    
246    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
249            the ranef.lmer class.
250    
251            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
252            methods to extract the posterior variances from the bVar slot.
253    
254    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
257            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
258    
259            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
260            * tests/simple: (extended)
261    
262            * R/sparseMatrix.R (isTriangular): now using much improved
263            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
264    
265    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
268            (problem report from Franklin Parlamis).  This should be done
269            generally.
270    
271    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
274            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
275            update the plot methods.
276    
277    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
278    
279            * R/lmer.R (resid and ranef methods):  Added methods for the
280            "residuals" and "resid" generic but only for linear mixed model
281            fits.  Changed the ranef method to return a list of data frames so
282            that the plot methods now work.
283    
284    2006-03-16  Douglas Bates  <bates@bates2>
285    
286            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
287            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
288    
289            * DESCRIPTION (Date): New release
290    
291    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
294    
295            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
296            * man/KNex.Rd: and other help files
297            * tests/*.R: several ones needed adaption
298            * inst/doc/Comparisons.Rnw: dito
299    
300    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
303    
304            * tests/indexing.R: tests for new [<- methods for sparse matrices.
305    
306    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
309    
310            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
311    
312    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/dMatrix.R: enable things like  M [ M < 10 ]
315            * R/dgeMatrix.R: implement it
316    
317    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R: define "summary.mer" and "*.lmer"
320            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
321            * R/lmer.R (show): now works with summary()
322    
323    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
326            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
327                    support the above
328    
329    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
332            Use glmFit$prior.weights for weights in a glmm.
333            Allow an option usePQL = FALSE to skip the PQL steps for the
334            Laplace method (and, in time, the AGQ method).
335    
336            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
337            into a separate function internal_mer_Xfactor to be able to call
338            it from internal_bhat.
339    
340    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * tests/Class+Meth.R (tstMatrixClass): function for much better
343            testing; now again of all actual classes.
344    
345            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
346                    use macros and define make_d_matrix_* and make_i_matrix_*
347                    where _i_ is for the ldense routines:
348    
349            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
350            * src/ldense.c (lsyMatrix_as_lgeMatrix):
351    
352            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
353    
354    
355    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
358                    many different kinds of matrices.
359            * R/*.R: quite a few new methods were needed for R CMD check with
360                    new Matrix().  Very good for users playing around.
361    
362    
363    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * src/dgeMatrix.c (dMatrix_validate): new
366            * src/Mutils.c (dense_nonpacked_validate): new
367    
368            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
369    
370    
371    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
374    
375    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
376    
377            * DESCRIPTION (Version): 0.99-6 released to CRAN
378    
379            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
380            segfault in cases with multiple non-nested grouping factors.
381    
382    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
385                    (Depends): also on 'utils'
386    
387            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
388            * R/diagMatrix.R (Diagonal): constructor and methods for
389            diagonal matrices
390    
391            * R/ltTMatrix.R: new "minimal methods"
392    
393    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
396            all methods (and help files).
397    
398    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
401                    for case (dimn.  op  no_dimn.)
402    
403    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
404    
405            * DESCRIPTION (Version): 0.99-2  released to CRAN
406    
407    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
408    
409            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
410            by Julian Faraway.
411    
412    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/Auxiliaries.R (try_as): new utility
415            * R/sparseMatrix.R: use try_as() in coercion to original class
416    
417    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
420    
421    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/Auxiliaries.R (dimNamesCheck): added
424    
425            * R/Matrix.R (as.array), (as.vector): new
426    
427    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
430                    default.
431            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
432                    "pMatrix" now contains "sparseMatrix"
433    
434    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * tests/Class+Meth.R: new tests; t(t(m)) == m
437    
438            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
439    
440            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
441            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
442    
443            * R/dspMatrix.R: typo in "t" method
444    
445    2005-09-18  Douglas Bates  <bates@wisc.edu>
446    
447            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
448            * R/Tsparse.R: instead of R/gTMatrix.R
449            * R/Csparse.R: new
450            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
451            * src/Tsparse.c: new; many trivial methods calling cholmod_()
452            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
453                            via cholmod
454    
455    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Auxiliaries.R (non0ind): new function using new C code
458            * src/dgCMatrix.c (compressed_non_0_ij): new utility
459    
460    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
461    
462            * src/chm_common.h: header file required by all C sources that
463            call CHOLMOD functions.  It defines a cholmod_common structure
464            called 'c' whose address is passed as the last argument to
465            (virtually) every CHOLMOD function.
466    
467            * src/Pattern.c: Simple example of the use of CHOLMOD.
468    
469            * src/init.c: initialize and finalize the cholmod_common structure.
470    
471            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
472            LDL and CCOLAMD from the U. of Florida sparse matrix library.
473    
474    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * inst/test-tools.R: new file collecting the utility functions used
477                    in ./tests/*.R
478    
479            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
480            * R/Matrix.R (cbind2): methods for NULL and missing
481    
482    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/AllClass.R: new "index" class for "[" and "[<-":
485                    First cut at "symmetricMatrix" and "triangularMatrix"
486            * R/gTMatrix.R (.ind.prep): new function;
487                    Logical and character indexing now work too.
488            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
489            * tests/indexing.R: new, including *.Rout.save
490            * tests/dgTMatrix.R: new
491    
492    2005-08-29  Douglas Bates  <bates@wisc.edu>
493    
494            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
495            indicator pos not being updated.  Also enforced upper triangular
496            for symmetric case.  Need to coerce edges component of elements of
497            edge list - grr! (Why don't they define their classes cleanly?)
498    
499    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/Matrix.R:  added first "[<-" methods; not yet functional
502            * R/denseMatrix.R: dito
503            * man/Subassign-methods.Rd: new help file for these
504    
505    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Version): 0.98-6
508    
509            * R/denseMatrix.R: new file for "[" fallback methods for all dense
510            matrices.
511    
512    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
515                    as( <logical>, "matrix")
516    
517            * R/pMatrix.R: coercion to "lgTMatrix"
518    
519            * R/gTMatrix.R: new virtual class to define "[" methods for.
520            * man/gTMatrix-class.Rd:
521            * General slight re-organization of where "[" methods are defined.
522              more to come.
523    
524    2005-08-18  Douglas Bates  <bates@wisc.edu>
525    
526            * DESCRIPTION (Version): 0.98-5  released to CRAN
527    
528            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
529            * .....
530    
531    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
532    
533            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
534            or glmer objects.
535    
536    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
539    
540    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
541    
542            * R/HBMM.R: finish re-writing R-only code.
543    
544    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
545    
546            * man/externalFormats.Rd: move documentation for writeHB and
547            writeMM here.
548    
549            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
550            (suggested by Paul Roecker).
551    
552            * tests/validObj.R (assertError): Comment out test that is failing
553            after recent changes in r-devel.
554    
555    
556    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/AllClass.R: intermediate virtual class "denseMatrix"
559            * man/denseMatrix-class.Rd
560            * NAMESPACE: export it, and also export
561            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
562    
563    2005-08-10  Douglas Bates  <bates@wisc.edu>
564    
565            * DESCRIPTION (Version): 0.98-3 to CRAN
566    
567            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
568            matrix_solve code (which was really, really wrong).
569    
570    2005-08-07  Douglas Bates  <bates@wisc.edu>
571    
572            * DESCRIPTION (Version): 0.98-2
573    
574            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
575    
576            * R/lmer.R (abbrvNms): new
577            * R/lmer.R (mcmcsamp): allow transformed parameters
578            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
579            for the Harwell-Boeing and the MatrixMarket formats.
580    
581    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * man/dtrMatrix-class.Rd: add examples
584            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
585    
586            * TODO: note the dtpMatrix (docu) bug
587    
588            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
589            in order to ensure that new as.matrix() is used by old functions,
590            e.g., svd(), qr(), eigen(), dist(),..;
591                  apply(), also matplot() or pairs().
592    
593    
594    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
597              add comments about 'control' / lmerControl() arguments
598    
599    2005-07-27  Douglas Bates  <bates@wisc.edu>
600    
601            * man/sleepstudy.Rd: Added the sleep data set.
602            * DESCRIPTION (Version): 0.98-1  released to CRAN
603    
604    2005-07-12  Douglas Bates  <bates@wisc.edu>
605            * man/sleepstudy.Rd: Added the sleep data set.
606    
607            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
608            .Call calls that were producing spurious output.
609    
610    2005-07-05  Douglas Bates  <bates@wisc.edu>
611    
612            * R/lmer.R (lmer): stored updated variance component estimates in
613            mer object for the generalized model.  (Bug reported by Renaud
614            Lancelot).
615    
616    2005-07-03  Douglas Bates  <bates@wisc.edu>
617    
618            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
619            unidimensional case.
620    
621    2005-06-08  Douglas Bates  <bates@wisc.edu>
622    
623            * DESCRIPTION (Version): 0.96-1
624    
625            * moved  lmer-class' R and C code moved from lme4 to here
626    
627    2005-06-04  Douglas Bates  <bates@wisc.edu>
628    
629            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
630            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
631    
632    2005-06-02  Douglas Bates  <bates@wisc.edu>
633    
634            * src/Makefile.win: Forgot to update this when Makefile changed.
635    
636    2005-05-11  Douglas Bates  <bates@wisc.edu>
637    
638            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
639            bug reported by Kurt Hornik and Michael Hahsler.
640    
641    2005-05-10  Douglas Bates  <bates@wisc.edu>
642    
643            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
644            logical sparse matrices.  These will also be used in the symbolic
645            analysis for lmer objects.
646    
647            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
648            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
649    
650    2005-05-06  Douglas Bates  <bates@wisc.edu>
651    
652            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
653            colMeans, colSums, rowMeans and rowSums.
654    
655    2005-04-18  Douglas Bates  <bates@wisc.edu>
656    
657            * src/lgCMatrix.[ch]: code for _validate method and stub for
658            multiplication operation.
659    
660            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
661            to dgetrs.
662    
663            * src/init.c: Fix cut-and-paste error in definition of
664            dgeMatrix_matrix_solve
665    
666            * src/{many files}: Tighten code by using ALLOC_SLOT.
667    
668    2005-04-15  Douglas Bates  <bates@wisc.edu>
669    
670            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
671    
672            * DESCRIPTION: Eliminate import of stats.
673    
674    
675    2005-04-06  Douglas Bates  <bates@wisc.edu>
676    
677            * R/AllClass.R : add logical sparse matrix classes
678    
679  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
682          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
683    
684  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
685    
686          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
687    
# Line 29  Line 707 
707          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
708            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
709    
710  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
711    
712          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
713          * ....          * ....
714    
715  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
716    
717          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
718    
# Line 49  Line 727 
727            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
728          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
729    
730  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
731    
732          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
733    
734  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
735    
736          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
737    
738  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
739    
740          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
741          the package.          the package.
# Line 105  Line 783 
783    
784          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
785    
786  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
787    
788          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
789          for the geMatrix class.          for the geMatrix class.
790    
791  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
792    
793          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
794    
795          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
796    
797  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
798    
799          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
800          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
801    
802  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
803    
804          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
805    
806  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
807    
808          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
809          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
810    
811  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
812    
813          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
814    
815          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
816          for tripletMatrix to matrix.          for tripletMatrix to matrix.
817    
818  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
819    
820          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
821          no longer used.          no longer used.
# Line 149  Line 827 
827          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
828          Fixes part but not all of #15.          Fixes part but not all of #15.
829    
830  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
831    
832          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
833          scalar grouping factors corrected.          scalar grouping factors corrected.
834    
835  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
836    
837          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
838    
839  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
840    
841          * 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
842          .h file can be included.          .h file can be included.
843    
844  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
845    
846          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
847          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
848    
849          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
850    
851  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
852    
853          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
854    
855  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
856    
857          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
858    
859  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
860    
861          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
862    
863  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
864    
865          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
866    
867  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
868    
869          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
870          routines.          routines.
871    
872  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
873    
874          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
875    
876  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
877    
878          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
879    

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