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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1351, Mon Aug 7 16:51:14 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
4            * man/band.Rd:  adapt the \dontshow{} unit test.
5    
6    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version): 0.995-14  for CRAN
9    
10            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
11    
12            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
13            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
14    
15            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
16            * R/Tsparse.R (tril, triu, band): methods
17            * R/dgRMatrix.R (tril, ...):    dito
18            * man/band.Rd:                  dito
19    
20    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (head, tail): directly use utils:::head.matrix
23                    to be up-to-date automatically.
24    
25    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
28    
29            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
30            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
31            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
32            such that the S4 objects are always created by the current version
33            of R and 'Matrix' class definitions.
34    
35    2006-08-01  Douglas Bates  <bates@R-project.org>
36    
37            * R/lmer.R (LMEoptimize method), tests/lmer.R,
38            inst/external/test3comp.rda: Added warnings for convergence on
39            boundary and test cases.
40    
41            * src/lmer.c (mer_postVar): Modified to return the variances that
42            are marginal to the fixed effects, not conditional on them (which
43            is what the bVar slot contents represent).
44    
45    2006-07-31  Douglas Bates  <bates@R-project.org>
46    
47            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
48            function which calls the C function mer_hat_trace2.
49    
50            * man/ranef.Rd: Include description of "postVar" argument and
51            producing a caterpillar plot.
52    
53    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * NAMESPACE:    change  "correlation" to "corMatrix"
56            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
57            * R/dpoMatrix.R: dito
58            * R/lmer.R:      dito
59    
60    2006-07-28  Douglas Bates  <bates@R-project.org>
61    
62            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
63            RZXinv slot's contents into a separate internal function that can
64            be used in mer_hat_trace.
65    
66    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
69            via new smart
70            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
71            utility functions.
72    
73    
74    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Csparse.R (tril, triu, band): do return *triangular* classed
77            matrices when appropriate; band() even symmetric ones.
78            (replCmat): extend to potentially all "CsparseMatrix"
79            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
80            allow subassignment for special sparse matrices.
81    
82            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
83    
84            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
85            argument; in glmer_*(): print only if(verbose).
86    
87            speed-optimize a few places by moving REAL(.) out of loops.
88    
89            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
90    
91    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
94                    since that wrongly triggers also for M[ logi , ]
95    
96            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
97            a symmetric matrix that results in a non-symmetric one.
98            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
99    
100            * R/dMatrix.R: make round(M) work as round(M, 0)
101    
102            * R/dgTMatrix.R (image): coordinate system and axis now use
103            1-based indices, not 0-based ones.
104    
105            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
106            * tests/indexing.R: test it.
107    
108            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
109            * man/isSymmetric-methods.Rd: and document it.
110    
111            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
112            * man/SparseM-conv.Rd: docu them
113    
114            * tests/other-pkgs.R: renamed from tests/graph.R and add example
115                    for 'SparseM' conversions
116    
117    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
118    
119            * R/Matrix.R (head): added head() and tail() methods.
120    
121    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * DESCRIPTION (Version): 0.995-12 released to CRAN
124    
125    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * tests/simple.R: add check for correct dsT -> dgT coercion;
128                    add check for correct printing of symmetric sparse matrices.
129    
130            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
131            for sparse symmetric matrices.
132    
133            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
134            diagonal twice.
135    
136    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
137    
138            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
139            being applied to the x slot (detected by Brian Ripley).
140    
141    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
144    
145            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
146    
147    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/lgCMatrix.c (lgCMatrix_diag): new function
150            * R/lgCMatrix.R (diag): for new method
151    
152            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
153                 ==> construction of illegal "*gTMatrix" via new() should
154                 now be much less easy:
155            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
156    
157            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
158                    directly.
159            * man/Matrix.Rd: documents it.
160    
161    2006-07-06  Douglas Bates  <bates@R-project.org>
162    
163            * src/pedigree.c (pedigree_inbreeding): Correction in
164            initialization.  This function is not currently being used and is
165            not fully tested.
166    
167            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
168            Introduced the glmer class.  Added code for mcmcmsamp on glmer
169            objects.  Modified validity check on pedigree objects to account
170            for nonparallel patterns of missingness of parents.
171    
172            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
173            class.
174    
175    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/pMatrix.R: coercion pMatrix -> Tsparse
178    
179    2006-06-12  Douglas Bates  <bates@R-project.org>
180    
181            * DESCRIPTION (Version): 0.995-11 released to CRAN
182    
183            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
184            the output from mcmcsamp.
185    
186    2006-06-10  Douglas Bates  <bates@R-project.org>
187    
188            * R/lmer.R (simulestimate): added C code for calculating the trace
189            of the hat matrix.
190    
191    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
194            classes.
195            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
196    
197    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/dgTMatrix.R (colSums): etc. All four of
200            colSums(), rowSums(), colMeans(), rowMeans() now should work for
201            all "Matrices".
202    
203    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (panel.ci): Add a reference line at zero and a
206            background grid to the qqmath plot of ranef.lmer.
207    
208    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
211            grouping factors to be specified in the formula as (1|foo/bar).
212    
213    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * R/lmer.R (findbars and others): Change check of is.numeric to
216            !is.language to resolve the bug reported by Jacob Wegelin.
217    
218            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
219            code to evaluate inbreeding coefficients without calculating T,
220            based on code in Sargolzaei and Iwaisaki's paper.
221    
222    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
225            generic and mer methods for isNested and denomDF. This denomDF was
226            an attempt to emulate that in lme but I don't think that makes
227            sense.  Use the trace of the hat matrix instead.
228    
229    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
232            the C code depending on a slot structure that's no longer valid.
233            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
234    
235    
236    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
237    
238            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
239            of lowerTriMatrix generic and methods to tril (also upper to triu)
240            and added a general band extractor.
241    
242    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * R/pedigree.R (pedigree): Replace sire and dam values outside the
245            allowable range with NAs. Added a corresponding check in the
246            validity check for the pedigree class.
247    
248            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
249            crossprod methods now inherits from symmetricMatrix.
250    
251    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
254            generics lowerTriMatrix and upperTriMatrix along with methods for
255            the Csparse virtual class.  Also added a C function Csparse_band
256            that implements these methods by calling cholmod_band.
257    
258    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
261            erased when it was NULL.  This led to invalid subselections!
262    
263    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
266            in method for "t" so as not to lose the unit diagonal property.
267    
268    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
269    
270            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
271            and methods.  This is now an option to the ranef method for the
272            mer class.
273    
274            * src/cs_utils.c: Ensure that the nz component is -1 for a
275            compressed column-oriented matrix.  Minor formatting cleanup.
276    
277            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
278            objects.
279    
280    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
283            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
284    
285    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
288            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
289    
290            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
291            for the dtCMatrix class.
292    
293    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
296            and methods for it.
297    
298    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
301            arguments, such that M %*% 1:6 now works
302            * Tests/matprod.R: test the above
303    
304    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
305    
306            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
307            the ranef.lmer class.
308    
309            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
310            methods to extract the posterior variances from the bVar slot.
311    
312    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
315            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
316    
317            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
318            * tests/simple: (extended)
319    
320            * R/sparseMatrix.R (isTriangular): now using much improved
321            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
322    
323    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
326            (problem report from Franklin Parlamis).  This should be done
327            generally.
328    
329    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
332            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
333            update the plot methods.
334    
335    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/lmer.R (resid and ranef methods):  Added methods for the
338            "residuals" and "resid" generic but only for linear mixed model
339            fits.  Changed the ranef method to return a list of data frames so
340            that the plot methods now work.
341    
342    2006-03-16  Douglas Bates  <bates@bates2>
343    
344            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
345            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
346    
347            * DESCRIPTION (Date): New release
348    
349    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
352    
353            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
354            * man/KNex.Rd: and other help files
355            * tests/*.R: several ones needed adaption
356            * inst/doc/Comparisons.Rnw: dito
357    
358    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
361    
362            * tests/indexing.R: tests for new [<- methods for sparse matrices.
363    
364    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
367    
368            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
369    
370    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/dMatrix.R: enable things like  M [ M < 10 ]
373            * R/dgeMatrix.R: implement it
374    
375    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/AllClass.R: define "summary.mer" and "*.lmer"
378            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
379            * R/lmer.R (show): now works with summary()
380    
381    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
384            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
385                    support the above
386    
387    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
388    
389            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
390            Use glmFit$prior.weights for weights in a glmm.
391            Allow an option usePQL = FALSE to skip the PQL steps for the
392            Laplace method (and, in time, the AGQ method).
393    
394            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
395            into a separate function internal_mer_Xfactor to be able to call
396            it from internal_bhat.
397    
398    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * tests/Class+Meth.R (tstMatrixClass): function for much better
401            testing; now again of all actual classes.
402    
403            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
404                    use macros and define make_d_matrix_* and make_i_matrix_*
405                    where _i_ is for the ldense routines:
406    
407            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
408            * src/ldense.c (lsyMatrix_as_lgeMatrix):
409    
410            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
411    
412    
413    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
416                    many different kinds of matrices.
417            * R/*.R: quite a few new methods were needed for R CMD check with
418                    new Matrix().  Very good for users playing around.
419    
420    
421    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * src/dgeMatrix.c (dMatrix_validate): new
424            * src/Mutils.c (dense_nonpacked_validate): new
425    
426            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
427    
428    
429    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
432    
433    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * DESCRIPTION (Version): 0.99-6 released to CRAN
436    
437            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
438            segfault in cases with multiple non-nested grouping factors.
439    
440    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
443                    (Depends): also on 'utils'
444    
445            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
446            * R/diagMatrix.R (Diagonal): constructor and methods for
447            diagonal matrices
448    
449            * R/ltTMatrix.R: new "minimal methods"
450    
451    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
454            all methods (and help files).
455    
456    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
459                    for case (dimn.  op  no_dimn.)
460    
461    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * DESCRIPTION (Version): 0.99-2  released to CRAN
464    
465    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
468            by Julian Faraway.
469    
470    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Auxiliaries.R (try_as): new utility
473            * R/sparseMatrix.R: use try_as() in coercion to original class
474    
475    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
478    
479    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/Auxiliaries.R (dimNamesCheck): added
482    
483            * R/Matrix.R (as.array), (as.vector): new
484    
485    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
488                    default.
489            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
490                    "pMatrix" now contains "sparseMatrix"
491    
492    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * tests/Class+Meth.R: new tests; t(t(m)) == m
495    
496            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
497    
498            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
499            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
500    
501            * R/dspMatrix.R: typo in "t" method
502    
503    2005-09-18  Douglas Bates  <bates@wisc.edu>
504    
505            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
506            * R/Tsparse.R: instead of R/gTMatrix.R
507            * R/Csparse.R: new
508            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
509            * src/Tsparse.c: new; many trivial methods calling cholmod_()
510            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
511                            via cholmod
512    
513    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/Auxiliaries.R (non0ind): new function using new C code
516            * src/dgCMatrix.c (compressed_non_0_ij): new utility
517    
518    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
519    
520            * src/chm_common.h: header file required by all C sources that
521            call CHOLMOD functions.  It defines a cholmod_common structure
522            called 'c' whose address is passed as the last argument to
523            (virtually) every CHOLMOD function.
524    
525            * src/Pattern.c: Simple example of the use of CHOLMOD.
526    
527            * src/init.c: initialize and finalize the cholmod_common structure.
528    
529            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
530            LDL and CCOLAMD from the U. of Florida sparse matrix library.
531    
532    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * inst/test-tools.R: new file collecting the utility functions used
535                    in ./tests/*.R
536    
537            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
538            * R/Matrix.R (cbind2): methods for NULL and missing
539    
540    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/AllClass.R: new "index" class for "[" and "[<-":
543                    First cut at "symmetricMatrix" and "triangularMatrix"
544            * R/gTMatrix.R (.ind.prep): new function;
545                    Logical and character indexing now work too.
546            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
547            * tests/indexing.R: new, including *.Rout.save
548            * tests/dgTMatrix.R: new
549    
550    2005-08-29  Douglas Bates  <bates@wisc.edu>
551    
552            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
553            indicator pos not being updated.  Also enforced upper triangular
554            for symmetric case.  Need to coerce edges component of elements of
555            edge list - grr! (Why don't they define their classes cleanly?)
556    
557    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Matrix.R:  added first "[<-" methods; not yet functional
560            * R/denseMatrix.R: dito
561            * man/Subassign-methods.Rd: new help file for these
562    
563    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * DESCRIPTION (Version): 0.98-6
566    
567            * R/denseMatrix.R: new file for "[" fallback methods for all dense
568            matrices.
569    
570    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
573                    as( <logical>, "matrix")
574    
575            * R/pMatrix.R: coercion to "lgTMatrix"
576    
577            * R/gTMatrix.R: new virtual class to define "[" methods for.
578            * man/gTMatrix-class.Rd:
579            * General slight re-organization of where "[" methods are defined.
580              more to come.
581    
582    2005-08-18  Douglas Bates  <bates@wisc.edu>
583    
584            * DESCRIPTION (Version): 0.98-5  released to CRAN
585    
586            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
587            * .....
588    
589    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
590    
591            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
592            or glmer objects.
593    
594    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
597    
598    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
599    
600            * R/HBMM.R: finish re-writing R-only code.
601    
602    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
603    
604            * man/externalFormats.Rd: move documentation for writeHB and
605            writeMM here.
606    
607            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
608            (suggested by Paul Roecker).
609    
610            * tests/validObj.R (assertError): Comment out test that is failing
611            after recent changes in r-devel.
612    
613    
614    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/AllClass.R: intermediate virtual class "denseMatrix"
617            * man/denseMatrix-class.Rd
618            * NAMESPACE: export it, and also export
619            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
620    
621    2005-08-10  Douglas Bates  <bates@wisc.edu>
622    
623            * DESCRIPTION (Version): 0.98-3 to CRAN
624    
625            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
626            matrix_solve code (which was really, really wrong).
627    
628    2005-08-07  Douglas Bates  <bates@wisc.edu>
629    
630            * DESCRIPTION (Version): 0.98-2
631    
632            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
633    
634            * R/lmer.R (abbrvNms): new
635            * R/lmer.R (mcmcsamp): allow transformed parameters
636            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
637            for the Harwell-Boeing and the MatrixMarket formats.
638    
639    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * man/dtrMatrix-class.Rd: add examples
642            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
643    
644            * TODO: note the dtpMatrix (docu) bug
645    
646            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
647            in order to ensure that new as.matrix() is used by old functions,
648            e.g., svd(), qr(), eigen(), dist(),..;
649                  apply(), also matplot() or pairs().
650    
651    
652    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
655              add comments about 'control' / lmerControl() arguments
656    
657    2005-07-27  Douglas Bates  <bates@wisc.edu>
658    
659            * man/sleepstudy.Rd: Added the sleep data set.
660            * DESCRIPTION (Version): 0.98-1  released to CRAN
661    
662    2005-07-12  Douglas Bates  <bates@wisc.edu>
663            * man/sleepstudy.Rd: Added the sleep data set.
664    
665            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
666            .Call calls that were producing spurious output.
667    
668    2005-07-05  Douglas Bates  <bates@wisc.edu>
669    
670            * R/lmer.R (lmer): stored updated variance component estimates in
671            mer object for the generalized model.  (Bug reported by Renaud
672            Lancelot).
673    
674    2005-07-03  Douglas Bates  <bates@wisc.edu>
675    
676            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
677            unidimensional case.
678    
679    2005-06-08  Douglas Bates  <bates@wisc.edu>
680    
681            * DESCRIPTION (Version): 0.96-1
682    
683            * moved  lmer-class' R and C code moved from lme4 to here
684    
685    2005-06-04  Douglas Bates  <bates@wisc.edu>
686    
687            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
688            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
689    
690    2005-06-02  Douglas Bates  <bates@wisc.edu>
691    
692            * src/Makefile.win: Forgot to update this when Makefile changed.
693    
694    2005-05-11  Douglas Bates  <bates@wisc.edu>
695    
696            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
697            bug reported by Kurt Hornik and Michael Hahsler.
698    
699    2005-05-10  Douglas Bates  <bates@wisc.edu>
700    
701            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
702            logical sparse matrices.  These will also be used in the symbolic
703            analysis for lmer objects.
704    
705            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
706            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
707    
708    2005-05-06  Douglas Bates  <bates@wisc.edu>
709    
710            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
711            colMeans, colSums, rowMeans and rowSums.
712    
713    2005-04-18  Douglas Bates  <bates@wisc.edu>
714    
715            * src/lgCMatrix.[ch]: code for _validate method and stub for
716            multiplication operation.
717    
718            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
719            to dgetrs.
720    
721            * src/init.c: Fix cut-and-paste error in definition of
722            dgeMatrix_matrix_solve
723    
724            * src/{many files}: Tighten code by using ALLOC_SLOT.
725    
726    2005-04-15  Douglas Bates  <bates@wisc.edu>
727    
728            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
729    
730            * DESCRIPTION: Eliminate import of stats.
731    
732    
733    2005-04-06  Douglas Bates  <bates@wisc.edu>
734    
735            * R/AllClass.R : add logical sparse matrix classes
736    
737    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/dgTMatrix.R: add "[" method for triplet matrices
740            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
741    
742    2005-03-31  Douglas Bates  <bates@wisc.edu>
743    
744            * DESCRIPTION (Version): release 0.95-5 to CRAN
745    
746            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
747            * R/sparseMatrix.R: %*%, crossprod()
748            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
749            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
750            * src/lmer.c (lmer_fitted): fix thinko
751    
752    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/AllClass.R: add two virtual sparse classes ``on top''
755    
756    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
759                    correspondingly fix examples and tests/ since new()
760                    doesn't work for virtual classes.
761    
762    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/Matrix.R (as.matrix): method and one for unname()
765            * tests/dpoMatrix.R: tests should now be less platform dependent;
766              also run for R 2.1.0; using as.matrix()
767    
768    2005-03-15  Douglas Bates  <bates@wisc.edu>
769    
770            * R/pMatrix.R: "pMatrix" class added
771            * ....
772    
773    2005-03-14  Douglas Bates  <bates@wisc.edu>
774    
775            * R/dtpMatrix.R: Add unpack method and an example.
776    
777            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
778            of general symmetric matrices and associated S4 methods.
779    
780    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
781            +
782    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/dgeMatrix.R (setAs): and many other files: more coercion,
785              crossprod() and "%*%" methods added; tests, too.
786            * tests/matprod.R: new, for testing these
787    
788    2005-03-03  Douglas Bates  <bates@wisc.edu>
789    
790            * src/lmer.c (lmer_fitted): Added.
791    
792    2005-03-02  Douglas Bates  <bates@wisc.edu>
793    
794            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
795    
796    2005-02-28  Douglas Bates  <bates@wisc.edu>
797    
798            * src/*.c,po/,inst/po: Internationalization and localization of
799            the package.
800    
801            * src/ldl.[ch]: Removed these as their contents are referenced in the
802            R_ldl.c file.
803    
804            * src/flame.[ch]: Removed these source files.
805    
806            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
807    
808            * src/LU.[ch],src/init.c: absorb in factorizations
809    
810            * src/Mutils.h: prepare for internationalization
811    
812            * src/cblas.h: move the enum definitions to Mutils.h and remove
813            this file
814    
815    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
818    
819            * R/dtrMatrix.R: fix t() method
820    
821            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
822            * NAMESPACE: export them (and import generics from "methods")
823            * tests/group-methods.R : and test them.
824    
825            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
826            border case
827    
828    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
829    
830            * DESCRIPTION (Version): 0.95-2  released to CRAN
831    
832            * src/dgBCMatrix.c:
833            * src/lmer.c: many changes
834            * ...
835    
836    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/Matrix.R: add more sophisticated show() method.
839    
840    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
841    
842            * */* : almost complete reorganization of classes.
843    
844    2005-01-26  Douglas Bates  <bates@wisc.edu>
845    
846            * R/AllGeneric.R: Added matrix exponential generic expm and a method
847            for the geMatrix class.
848    
849    2005-01-24  Douglas Bates  <bates@wisc.edu>
850    
851            * src/Makefile (clean): Remove *.a and *.so
852    
853            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
854    
855    2005-01-23  Douglas Bates  <bates@wisc.edu>
856    
857            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
858            had an effect in cases with more than 2 grouping factors.
859    
860    2005-01-03  Douglas Bates  <bates@wisc.edu>
861    
862            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
863    
864    2004-12-23  Douglas Bates  <bates@wisc.edu>
865    
866            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
867            and R_useDynamicSymbols (suggested by B.D.Ripley).
868    
869    2004-12-14  Douglas Bates  <bates@wisc.edu>
870    
871          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
872    
873          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
874          for tripletMatrix to matrix.          for tripletMatrix to matrix.
875    
876  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
877    
878          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
879          no longer used.          no longer used.
# Line 17  Line 885 
885          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
886          Fixes part but not all of #15.          Fixes part but not all of #15.
887    
888  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
889    
890          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
891          scalar grouping factors corrected.          scalar grouping factors corrected.
892    
893  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
894    
895          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
896    
897  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
898    
899          * 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
900          .h file can be included.          .h file can be included.
901    
902  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
903    
904          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
905          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
906    
907          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
908    
909  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
910    
911          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
912    
913  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
914    
915          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
916    
917  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
918    
919          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
920    
921  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
922    
923          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
924    
925  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
926    
927          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
928          routines.          routines.
929    
930  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
931    
932          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
933    
934  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
935    
936          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
937    

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