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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1349, Mon Aug 7 09:05:42 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-14  for CRAN
4    
5            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
6    
7            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
8            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
9    
10            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
11            * R/Tsparse.R (tril, triu, band): methods
12            * R/dgRMatrix.R (tril, ...):    dito
13            * man/band.Rd:                  dito
14    
15    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (head, tail): directly use utils:::head.matrix
18                    to be up-to-date automatically.
19    
20    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
23    
24            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
25            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
26            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
27            such that the S4 objects are always created by the current version
28            of R and 'Matrix' class definitions.
29    
30    2006-08-01  Douglas Bates  <bates@R-project.org>
31    
32            * R/lmer.R (LMEoptimize method), tests/lmer.R,
33            inst/external/test3comp.rda: Added warnings for convergence on
34            boundary and test cases.
35    
36            * src/lmer.c (mer_postVar): Modified to return the variances that
37            are marginal to the fixed effects, not conditional on them (which
38            is what the bVar slot contents represent).
39    
40    2006-07-31  Douglas Bates  <bates@R-project.org>
41    
42            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
43            function which calls the C function mer_hat_trace2.
44    
45            * man/ranef.Rd: Include description of "postVar" argument and
46            producing a caterpillar plot.
47    
48    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * NAMESPACE:    change  "correlation" to "corMatrix"
51            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
52            * R/dpoMatrix.R: dito
53            * R/lmer.R:      dito
54    
55    2006-07-28  Douglas Bates  <bates@R-project.org>
56    
57            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
58            RZXinv slot's contents into a separate internal function that can
59            be used in mer_hat_trace.
60    
61    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
64            via new smart
65            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
66            utility functions.
67    
68    
69    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R (tril, triu, band): do return *triangular* classed
72            matrices when appropriate; band() even symmetric ones.
73            (replCmat): extend to potentially all "CsparseMatrix"
74            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
75            allow subassignment for special sparse matrices.
76    
77            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
78    
79            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
80            argument; in glmer_*(): print only if(verbose).
81    
82            speed-optimize a few places by moving REAL(.) out of loops.
83    
84            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
85    
86    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
89                    since that wrongly triggers also for M[ logi , ]
90    
91            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
92            a symmetric matrix that results in a non-symmetric one.
93            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
94    
95            * R/dMatrix.R: make round(M) work as round(M, 0)
96    
97            * R/dgTMatrix.R (image): coordinate system and axis now use
98            1-based indices, not 0-based ones.
99    
100            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
101            * tests/indexing.R: test it.
102    
103            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
104            * man/isSymmetric-methods.Rd: and document it.
105    
106            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
107            * man/SparseM-conv.Rd: docu them
108    
109            * tests/other-pkgs.R: renamed from tests/graph.R and add example
110                    for 'SparseM' conversions
111    
112    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
113    
114            * R/Matrix.R (head): added head() and tail() methods.
115    
116    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * DESCRIPTION (Version): 0.995-12 released to CRAN
119    
120    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/simple.R: add check for correct dsT -> dgT coercion;
123                    add check for correct printing of symmetric sparse matrices.
124    
125            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
126            for sparse symmetric matrices.
127    
128            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
129            diagonal twice.
130    
131    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
132    
133            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
134            being applied to the x slot (detected by Brian Ripley).
135    
136    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
139    
140            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
141    
142    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/lgCMatrix.c (lgCMatrix_diag): new function
145            * R/lgCMatrix.R (diag): for new method
146    
147            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
148                 ==> construction of illegal "*gTMatrix" via new() should
149                 now be much less easy:
150            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
151    
152            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
153                    directly.
154            * man/Matrix.Rd: documents it.
155    
156    2006-07-06  Douglas Bates  <bates@R-project.org>
157    
158            * src/pedigree.c (pedigree_inbreeding): Correction in
159            initialization.  This function is not currently being used and is
160            not fully tested.
161    
162            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
163            Introduced the glmer class.  Added code for mcmcmsamp on glmer
164            objects.  Modified validity check on pedigree objects to account
165            for nonparallel patterns of missingness of parents.
166    
167            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
168            class.
169    
170    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/pMatrix.R: coercion pMatrix -> Tsparse
173    
174    2006-06-12  Douglas Bates  <bates@R-project.org>
175    
176            * DESCRIPTION (Version): 0.995-11 released to CRAN
177    
178            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
179            the output from mcmcsamp.
180    
181    2006-06-10  Douglas Bates  <bates@R-project.org>
182    
183            * R/lmer.R (simulestimate): added C code for calculating the trace
184            of the hat matrix.
185    
186    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
189            classes.
190            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
191    
192    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dgTMatrix.R (colSums): etc. All four of
195            colSums(), rowSums(), colMeans(), rowMeans() now should work for
196            all "Matrices".
197    
198    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/lmer.R (panel.ci): Add a reference line at zero and a
201            background grid to the qqmath plot of ranef.lmer.
202    
203    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
206            grouping factors to be specified in the formula as (1|foo/bar).
207    
208    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (findbars and others): Change check of is.numeric to
211            !is.language to resolve the bug reported by Jacob Wegelin.
212    
213            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
214            code to evaluate inbreeding coefficients without calculating T,
215            based on code in Sargolzaei and Iwaisaki's paper.
216    
217    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
220            generic and mer methods for isNested and denomDF. This denomDF was
221            an attempt to emulate that in lme but I don't think that makes
222            sense.  Use the trace of the hat matrix instead.
223    
224    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
227            the C code depending on a slot structure that's no longer valid.
228            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
229    
230    
231    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
232    
233            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
234            of lowerTriMatrix generic and methods to tril (also upper to triu)
235            and added a general band extractor.
236    
237    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/pedigree.R (pedigree): Replace sire and dam values outside the
240            allowable range with NAs. Added a corresponding check in the
241            validity check for the pedigree class.
242    
243            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
244            crossprod methods now inherits from symmetricMatrix.
245    
246    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
249            generics lowerTriMatrix and upperTriMatrix along with methods for
250            the Csparse virtual class.  Also added a C function Csparse_band
251            that implements these methods by calling cholmod_band.
252    
253    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
256            erased when it was NULL.  This led to invalid subselections!
257    
258    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
261            in method for "t" so as not to lose the unit diagonal property.
262    
263    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
266            and methods.  This is now an option to the ranef method for the
267            mer class.
268    
269            * src/cs_utils.c: Ensure that the nz component is -1 for a
270            compressed column-oriented matrix.  Minor formatting cleanup.
271    
272            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
273            objects.
274    
275    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
278            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
279    
280    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
283            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
284    
285            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
286            for the dtCMatrix class.
287    
288    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
289    
290            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
291            and methods for it.
292    
293    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
296            arguments, such that M %*% 1:6 now works
297            * Tests/matprod.R: test the above
298    
299    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
300    
301            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
302            the ranef.lmer class.
303    
304            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
305            methods to extract the posterior variances from the bVar slot.
306    
307    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
310            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
311    
312            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
313            * tests/simple: (extended)
314    
315            * R/sparseMatrix.R (isTriangular): now using much improved
316            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
317    
318    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
321            (problem report from Franklin Parlamis).  This should be done
322            generally.
323    
324    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
325    
326            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
327            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
328            update the plot methods.
329    
330    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * R/lmer.R (resid and ranef methods):  Added methods for the
333            "residuals" and "resid" generic but only for linear mixed model
334            fits.  Changed the ranef method to return a list of data frames so
335            that the plot methods now work.
336    
337    2006-03-16  Douglas Bates  <bates@bates2>
338    
339            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
340            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
341    
342            * DESCRIPTION (Date): New release
343    
344    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
347    
348            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
349            * man/KNex.Rd: and other help files
350            * tests/*.R: several ones needed adaption
351            * inst/doc/Comparisons.Rnw: dito
352    
353    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
356    
357            * tests/indexing.R: tests for new [<- methods for sparse matrices.
358    
359    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
362    
363            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
364    
365    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/dMatrix.R: enable things like  M [ M < 10 ]
368            * R/dgeMatrix.R: implement it
369    
370    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllClass.R: define "summary.mer" and "*.lmer"
373            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
374            * R/lmer.R (show): now works with summary()
375    
376    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
379            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
380                    support the above
381    
382    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
383    
384            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
385            Use glmFit$prior.weights for weights in a glmm.
386            Allow an option usePQL = FALSE to skip the PQL steps for the
387            Laplace method (and, in time, the AGQ method).
388    
389            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
390            into a separate function internal_mer_Xfactor to be able to call
391            it from internal_bhat.
392    
393    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * tests/Class+Meth.R (tstMatrixClass): function for much better
396            testing; now again of all actual classes.
397    
398            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
399                    use macros and define make_d_matrix_* and make_i_matrix_*
400                    where _i_ is for the ldense routines:
401    
402            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
403            * src/ldense.c (lsyMatrix_as_lgeMatrix):
404    
405            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
406    
407    
408    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
411                    many different kinds of matrices.
412            * R/*.R: quite a few new methods were needed for R CMD check with
413                    new Matrix().  Very good for users playing around.
414    
415    
416    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * src/dgeMatrix.c (dMatrix_validate): new
419            * src/Mutils.c (dense_nonpacked_validate): new
420    
421            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
422    
423    
424    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
425    
426            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
427    
428    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * DESCRIPTION (Version): 0.99-6 released to CRAN
431    
432            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
433            segfault in cases with multiple non-nested grouping factors.
434    
435    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
438                    (Depends): also on 'utils'
439    
440            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
441            * R/diagMatrix.R (Diagonal): constructor and methods for
442            diagonal matrices
443    
444            * R/ltTMatrix.R: new "minimal methods"
445    
446    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
449            all methods (and help files).
450    
451    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
454                    for case (dimn.  op  no_dimn.)
455    
456    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
457    
458            * DESCRIPTION (Version): 0.99-2  released to CRAN
459    
460    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
461    
462            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
463            by Julian Faraway.
464    
465    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Auxiliaries.R (try_as): new utility
468            * R/sparseMatrix.R: use try_as() in coercion to original class
469    
470    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
473    
474    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Auxiliaries.R (dimNamesCheck): added
477    
478            * R/Matrix.R (as.array), (as.vector): new
479    
480    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
483                    default.
484            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
485                    "pMatrix" now contains "sparseMatrix"
486    
487    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * tests/Class+Meth.R: new tests; t(t(m)) == m
490    
491            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
492    
493            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
494            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
495    
496            * R/dspMatrix.R: typo in "t" method
497    
498    2005-09-18  Douglas Bates  <bates@wisc.edu>
499    
500            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
501            * R/Tsparse.R: instead of R/gTMatrix.R
502            * R/Csparse.R: new
503            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
504            * src/Tsparse.c: new; many trivial methods calling cholmod_()
505            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
506                            via cholmod
507    
508    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/Auxiliaries.R (non0ind): new function using new C code
511            * src/dgCMatrix.c (compressed_non_0_ij): new utility
512    
513    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
514    
515            * src/chm_common.h: header file required by all C sources that
516            call CHOLMOD functions.  It defines a cholmod_common structure
517            called 'c' whose address is passed as the last argument to
518            (virtually) every CHOLMOD function.
519    
520            * src/Pattern.c: Simple example of the use of CHOLMOD.
521    
522            * src/init.c: initialize and finalize the cholmod_common structure.
523    
524            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
525            LDL and CCOLAMD from the U. of Florida sparse matrix library.
526    
527    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * inst/test-tools.R: new file collecting the utility functions used
530                    in ./tests/*.R
531    
532            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
533            * R/Matrix.R (cbind2): methods for NULL and missing
534    
535    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/AllClass.R: new "index" class for "[" and "[<-":
538                    First cut at "symmetricMatrix" and "triangularMatrix"
539            * R/gTMatrix.R (.ind.prep): new function;
540                    Logical and character indexing now work too.
541            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
542            * tests/indexing.R: new, including *.Rout.save
543            * tests/dgTMatrix.R: new
544    
545    2005-08-29  Douglas Bates  <bates@wisc.edu>
546    
547            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
548            indicator pos not being updated.  Also enforced upper triangular
549            for symmetric case.  Need to coerce edges component of elements of
550            edge list - grr! (Why don't they define their classes cleanly?)
551    
552    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/Matrix.R:  added first "[<-" methods; not yet functional
555            * R/denseMatrix.R: dito
556            * man/Subassign-methods.Rd: new help file for these
557    
558    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * DESCRIPTION (Version): 0.98-6
561    
562            * R/denseMatrix.R: new file for "[" fallback methods for all dense
563            matrices.
564    
565    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
568                    as( <logical>, "matrix")
569    
570            * R/pMatrix.R: coercion to "lgTMatrix"
571    
572            * R/gTMatrix.R: new virtual class to define "[" methods for.
573            * man/gTMatrix-class.Rd:
574            * General slight re-organization of where "[" methods are defined.
575              more to come.
576    
577    2005-08-18  Douglas Bates  <bates@wisc.edu>
578    
579            * DESCRIPTION (Version): 0.98-5  released to CRAN
580    
581            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
582            * .....
583    
584    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
585    
586            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
587            or glmer objects.
588    
589    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
592    
593    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
594    
595            * R/HBMM.R: finish re-writing R-only code.
596    
597    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
598    
599            * man/externalFormats.Rd: move documentation for writeHB and
600            writeMM here.
601    
602            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
603            (suggested by Paul Roecker).
604    
605            * tests/validObj.R (assertError): Comment out test that is failing
606            after recent changes in r-devel.
607    
608    
609    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/AllClass.R: intermediate virtual class "denseMatrix"
612            * man/denseMatrix-class.Rd
613            * NAMESPACE: export it, and also export
614            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
615    
616    2005-08-10  Douglas Bates  <bates@wisc.edu>
617    
618            * DESCRIPTION (Version): 0.98-3 to CRAN
619    
620            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
621            matrix_solve code (which was really, really wrong).
622    
623    2005-08-07  Douglas Bates  <bates@wisc.edu>
624    
625            * DESCRIPTION (Version): 0.98-2
626    
627            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
628    
629            * R/lmer.R (abbrvNms): new
630            * R/lmer.R (mcmcsamp): allow transformed parameters
631            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
632            for the Harwell-Boeing and the MatrixMarket formats.
633    
634    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * man/dtrMatrix-class.Rd: add examples
637            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
638    
639            * TODO: note the dtpMatrix (docu) bug
640    
641            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
642            in order to ensure that new as.matrix() is used by old functions,
643            e.g., svd(), qr(), eigen(), dist(),..;
644                  apply(), also matplot() or pairs().
645    
646    
647    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
650              add comments about 'control' / lmerControl() arguments
651    
652    2005-07-27  Douglas Bates  <bates@wisc.edu>
653    
654            * man/sleepstudy.Rd: Added the sleep data set.
655            * DESCRIPTION (Version): 0.98-1  released to CRAN
656    
657    2005-07-12  Douglas Bates  <bates@wisc.edu>
658            * man/sleepstudy.Rd: Added the sleep data set.
659    
660            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
661            .Call calls that were producing spurious output.
662    
663    2005-07-05  Douglas Bates  <bates@wisc.edu>
664    
665            * R/lmer.R (lmer): stored updated variance component estimates in
666            mer object for the generalized model.  (Bug reported by Renaud
667            Lancelot).
668    
669    2005-07-03  Douglas Bates  <bates@wisc.edu>
670    
671            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
672            unidimensional case.
673    
674    2005-06-08  Douglas Bates  <bates@wisc.edu>
675    
676            * DESCRIPTION (Version): 0.96-1
677    
678            * moved  lmer-class' R and C code moved from lme4 to here
679    
680    2005-06-04  Douglas Bates  <bates@wisc.edu>
681    
682            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
683            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
684    
685    2005-06-02  Douglas Bates  <bates@wisc.edu>
686    
687            * src/Makefile.win: Forgot to update this when Makefile changed.
688    
689    2005-05-11  Douglas Bates  <bates@wisc.edu>
690    
691            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
692            bug reported by Kurt Hornik and Michael Hahsler.
693    
694    2005-05-10  Douglas Bates  <bates@wisc.edu>
695    
696            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
697            logical sparse matrices.  These will also be used in the symbolic
698            analysis for lmer objects.
699    
700            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
701            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
702    
703    2005-05-06  Douglas Bates  <bates@wisc.edu>
704    
705            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
706            colMeans, colSums, rowMeans and rowSums.
707    
708    2005-04-18  Douglas Bates  <bates@wisc.edu>
709    
710            * src/lgCMatrix.[ch]: code for _validate method and stub for
711            multiplication operation.
712    
713            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
714            to dgetrs.
715    
716            * src/init.c: Fix cut-and-paste error in definition of
717            dgeMatrix_matrix_solve
718    
719            * src/{many files}: Tighten code by using ALLOC_SLOT.
720    
721    2005-04-15  Douglas Bates  <bates@wisc.edu>
722    
723            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
724    
725            * DESCRIPTION: Eliminate import of stats.
726    
727    
728    2005-04-06  Douglas Bates  <bates@wisc.edu>
729    
730            * R/AllClass.R : add logical sparse matrix classes
731    
732    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/dgTMatrix.R: add "[" method for triplet matrices
735            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
736    
737    2005-03-31  Douglas Bates  <bates@wisc.edu>
738    
739            * DESCRIPTION (Version): release 0.95-5 to CRAN
740    
741            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
742            * R/sparseMatrix.R: %*%, crossprod()
743            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
744            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
745            * src/lmer.c (lmer_fitted): fix thinko
746    
747    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/AllClass.R: add two virtual sparse classes ``on top''
750    
751    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
754                    correspondingly fix examples and tests/ since new()
755                    doesn't work for virtual classes.
756    
757    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/Matrix.R (as.matrix): method and one for unname()
760            * tests/dpoMatrix.R: tests should now be less platform dependent;
761              also run for R 2.1.0; using as.matrix()
762    
763    2005-03-15  Douglas Bates  <bates@wisc.edu>
764    
765            * R/pMatrix.R: "pMatrix" class added
766            * ....
767    
768    2005-03-14  Douglas Bates  <bates@wisc.edu>
769    
770            * R/dtpMatrix.R: Add unpack method and an example.
771    
772            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
773            of general symmetric matrices and associated S4 methods.
774    
775    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
776            +
777    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/dgeMatrix.R (setAs): and many other files: more coercion,
780              crossprod() and "%*%" methods added; tests, too.
781            * tests/matprod.R: new, for testing these
782    
783    2005-03-03  Douglas Bates  <bates@wisc.edu>
784    
785            * src/lmer.c (lmer_fitted): Added.
786    
787    2005-03-02  Douglas Bates  <bates@wisc.edu>
788    
789            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
790    
791    2005-02-28  Douglas Bates  <bates@wisc.edu>
792    
793            * src/*.c,po/,inst/po: Internationalization and localization of
794            the package.
795    
796            * src/ldl.[ch]: Removed these as their contents are referenced in the
797            R_ldl.c file.
798    
799            * src/flame.[ch]: Removed these source files.
800    
801            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
802    
803            * src/LU.[ch],src/init.c: absorb in factorizations
804    
805            * src/Mutils.h: prepare for internationalization
806    
807            * src/cblas.h: move the enum definitions to Mutils.h and remove
808            this file
809    
810    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
813    
814            * R/dtrMatrix.R: fix t() method
815    
816            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
817            * NAMESPACE: export them (and import generics from "methods")
818            * tests/group-methods.R : and test them.
819    
820            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
821            border case
822    
823    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
824    
825            * DESCRIPTION (Version): 0.95-2  released to CRAN
826    
827            * src/dgBCMatrix.c:
828            * src/lmer.c: many changes
829            * ...
830    
831    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/Matrix.R: add more sophisticated show() method.
834    
835    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
836    
837            * */* : almost complete reorganization of classes.
838    
839    2005-01-26  Douglas Bates  <bates@wisc.edu>
840    
841            * R/AllGeneric.R: Added matrix exponential generic expm and a method
842            for the geMatrix class.
843    
844    2005-01-24  Douglas Bates  <bates@wisc.edu>
845    
846            * src/Makefile (clean): Remove *.a and *.so
847    
848            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
849    
850    2005-01-23  Douglas Bates  <bates@wisc.edu>
851    
852            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
853            had an effect in cases with more than 2 grouping factors.
854    
855    2005-01-03  Douglas Bates  <bates@wisc.edu>
856    
857            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
858    
859    2004-12-23  Douglas Bates  <bates@wisc.edu>
860    
861            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
862            and R_useDynamicSymbols (suggested by B.D.Ripley).
863    
864    2004-12-14  Douglas Bates  <bates@wisc.edu>
865    
866            * R/sscMatrix.R: Add determinant methods
867    
868            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
869            for tripletMatrix to matrix.
870    
871    2004-12-13  Douglas Bates  <bates@wisc.edu>
872    
873            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
874            no longer used.
875    
876          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
877          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 880 
880          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
881          Fixes part but not all of #15.          Fixes part but not all of #15.
882    
883  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
884    
885          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
886          scalar grouping factors corrected.          scalar grouping factors corrected.
887    
888  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
889    
890          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
891    
892  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
893    
894          * 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
895          .h file can be included.          .h file can be included.
896    
897  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
898    
899          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
900          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
901    
902          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
903    
904  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
905    
906          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
907    
908  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
909    
910          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
911    
912  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
913    
914          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
915    
916  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
917    
918          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
919    
920  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
921    
922          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
923          routines.          routines.
924    
925  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
926    
927          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
928    
929  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
930    
931          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
932    

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