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revision 726, Thu May 12 14:59:04 2005 UTC revision 1354, Tue Aug 8 14:54:43 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-08-08  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1
4    
5    2006-08-07  Douglas Bates  <bates@R-project.org>
6    
7            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
8            R-level conversion to a sparse symmetric class.
9            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
10            Remove conversion to sparse symmetric classes (now done in C code).
11    
12    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
15            * man/band.Rd:  adapt the \dontshow{} unit test.
16    
17    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * DESCRIPTION (Version): 0.995-14  for CRAN
20    
21            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
22    
23            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
24            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
25    
26            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
27            * R/Tsparse.R (tril, triu, band): methods
28            * R/dgRMatrix.R (tril, ...):    ditto
29            * man/band.Rd:                  ditto
30    
31    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R (head, tail): directly use utils:::head.matrix
34                    to be up-to-date automatically.
35    
36    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
39    
40            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
41            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
42            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
43            such that the S4 objects are always created by the current version
44            of R and 'Matrix' class definitions.
45    
46    2006-08-01  Douglas Bates  <bates@R-project.org>
47    
48            * R/lmer.R (LMEoptimize method), tests/lmer.R,
49            inst/external/test3comp.rda: Added warnings for convergence on
50            boundary and test cases.
51    
52            * src/lmer.c (mer_postVar): Modified to return the variances that
53            are marginal to the fixed effects, not conditional on them (which
54            is what the bVar slot contents represent).
55    
56    2006-07-31  Douglas Bates  <bates@R-project.org>
57    
58            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
59            function which calls the C function mer_hat_trace2.
60    
61            * man/ranef.Rd: Include description of "postVar" argument and
62            producing a caterpillar plot.
63    
64    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * NAMESPACE:    change  "correlation" to "corMatrix"
67            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
68            * R/dpoMatrix.R: ditto
69            * R/lmer.R:      ditto
70    
71    2006-07-28  Douglas Bates  <bates@R-project.org>
72    
73            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
74            RZXinv slot's contents into a separate internal function that can
75            be used in mer_hat_trace.
76    
77    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
80            via new smart
81            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
82            utility functions.
83    
84    
85    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Csparse.R (tril, triu, band): do return *triangular* classed
88            matrices when appropriate; band() even symmetric ones.
89            (replCmat): extend to potentially all "CsparseMatrix"
90            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
91            allow subassignment for special sparse matrices.
92    
93            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
94    
95            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
96            argument; in glmer_*(): print only if(verbose).
97    
98            speed-optimize a few places by moving REAL(.) out of loops.
99    
100            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
101    
102    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
105                    since that wrongly triggers also for M[ logi , ]
106    
107            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
108            a symmetric matrix that results in a non-symmetric one.
109            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
110    
111            * R/dMatrix.R: make round(M) work as round(M, 0)
112    
113            * R/dgTMatrix.R (image): coordinate system and axis now use
114            1-based indices, not 0-based ones.
115    
116            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
117            * tests/indexing.R: test it.
118    
119            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
120            * man/isSymmetric-methods.Rd: and document it.
121    
122            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
123            * man/SparseM-conv.Rd: docu them
124    
125            * tests/other-pkgs.R: renamed from tests/graph.R and add example
126                    for 'SparseM' conversions
127    
128    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
129    
130            * R/Matrix.R (head): added head() and tail() methods.
131    
132    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.995-12 released to CRAN
135    
136    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/simple.R: add check for correct dsT -> dgT coercion;
139                    add check for correct printing of symmetric sparse matrices.
140    
141            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
142            for sparse symmetric matrices.
143    
144            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
145            diagonal twice.
146    
147    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
148    
149            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
150            being applied to the x slot (detected by Brian Ripley).
151    
152    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
155    
156            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
157    
158    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/lgCMatrix.c (lgCMatrix_diag): new function
161            * R/lgCMatrix.R (diag): for new method
162    
163            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
164                 ==> construction of illegal "*gTMatrix" via new() should
165                 now be much less easy:
166            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
167    
168            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
169                    directly.
170            * man/Matrix.Rd: documents it.
171    
172    2006-07-06  Douglas Bates  <bates@R-project.org>
173    
174            * src/pedigree.c (pedigree_inbreeding): Correction in
175            initialization.  This function is not currently being used and is
176            not fully tested.
177    
178            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
179            Introduced the glmer class.  Added code for mcmcmsamp on glmer
180            objects.  Modified validity check on pedigree objects to account
181            for nonparallel patterns of missingness of parents.
182    
183            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
184            class.
185    
186    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/pMatrix.R: coercion pMatrix -> Tsparse
189    
190    2006-06-12  Douglas Bates  <bates@R-project.org>
191    
192            * DESCRIPTION (Version): 0.995-11 released to CRAN
193    
194            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
195            the output from mcmcsamp.
196    
197    2006-06-10  Douglas Bates  <bates@R-project.org>
198    
199            * R/lmer.R (simulestimate): added C code for calculating the trace
200            of the hat matrix.
201    
202    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
205            classes.
206            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
207    
208    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/dgTMatrix.R (colSums): etc. All four of
211            colSums(), rowSums(), colMeans(), rowMeans() now should work for
212            all "Matrices".
213    
214    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
215    
216            * R/lmer.R (panel.ci): Add a reference line at zero and a
217            background grid to the qqmath plot of ranef.lmer.
218    
219    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
222            grouping factors to be specified in the formula as (1|foo/bar).
223    
224    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
225    
226            * R/lmer.R (findbars and others): Change check of is.numeric to
227            !is.language to resolve the bug reported by Jacob Wegelin.
228    
229            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
230            code to evaluate inbreeding coefficients without calculating T,
231            based on code in Sargolzaei and Iwaisaki's paper.
232    
233    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
236            generic and mer methods for isNested and denomDF. This denomDF was
237            an attempt to emulate that in lme but I don't think that makes
238            sense.  Use the trace of the hat matrix instead.
239    
240    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
243            the C code depending on a slot structure that's no longer valid.
244            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
245    
246    
247    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
248    
249            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
250            of lowerTriMatrix generic and methods to tril (also upper to triu)
251            and added a general band extractor.
252    
253    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
254    
255            * R/pedigree.R (pedigree): Replace sire and dam values outside the
256            allowable range with NAs. Added a corresponding check in the
257            validity check for the pedigree class.
258    
259            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
260            crossprod methods now inherits from symmetricMatrix.
261    
262    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
265            generics lowerTriMatrix and upperTriMatrix along with methods for
266            the Csparse virtual class.  Also added a C function Csparse_band
267            that implements these methods by calling cholmod_band.
268    
269    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
272            erased when it was NULL.  This led to invalid subselections!
273    
274    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
277            in method for "t" so as not to lose the unit diagonal property.
278    
279    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
282            and methods.  This is now an option to the ranef method for the
283            mer class.
284    
285            * src/cs_utils.c: Ensure that the nz component is -1 for a
286            compressed column-oriented matrix.  Minor formatting cleanup.
287    
288            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
289            objects.
290    
291    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
294            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
295    
296    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
297    
298            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
299            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
300    
301            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
302            for the dtCMatrix class.
303    
304    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
305    
306            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
307            and methods for it.
308    
309    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
312            arguments, such that M %*% 1:6 now works
313            * Tests/matprod.R: test the above
314    
315    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
316    
317            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
318            the ranef.lmer class.
319    
320            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
321            methods to extract the posterior variances from the bVar slot.
322    
323    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
326            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
327    
328            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
329            * tests/simple: (extended)
330    
331            * R/sparseMatrix.R (isTriangular): now using much improved
332            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
333    
334    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
337            (problem report from Franklin Parlamis).  This should be done
338            generally.
339    
340    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
341    
342            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
343            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
344            update the plot methods.
345    
346    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * R/lmer.R (resid and ranef methods):  Added methods for the
349            "residuals" and "resid" generic but only for linear mixed model
350            fits.  Changed the ranef method to return a list of data frames so
351            that the plot methods now work.
352    
353    2006-03-16  Douglas Bates  <bates@bates2>
354    
355            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
356            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
357    
358            * DESCRIPTION (Date): New release
359    
360    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
363    
364            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
365            * man/KNex.Rd: and other help files
366            * tests/*.R: several ones needed adaption
367            * inst/doc/Comparisons.Rnw: ditto
368    
369    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
372    
373            * tests/indexing.R: tests for new [<- methods for sparse matrices.
374    
375    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
378    
379            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
380    
381    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dMatrix.R: enable things like  M [ M < 10 ]
384            * R/dgeMatrix.R: implement it
385    
386    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/AllClass.R: define "summary.mer" and "*.lmer"
389            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
390            * R/lmer.R (show): now works with summary()
391    
392    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
395            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
396                    support the above
397    
398    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
401            Use glmFit$prior.weights for weights in a glmm.
402            Allow an option usePQL = FALSE to skip the PQL steps for the
403            Laplace method (and, in time, the AGQ method).
404    
405            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
406            into a separate function internal_mer_Xfactor to be able to call
407            it from internal_bhat.
408    
409    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * tests/Class+Meth.R (tstMatrixClass): function for much better
412            testing; now again of all actual classes.
413    
414            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
415                    use macros and define make_d_matrix_* and make_i_matrix_*
416                    where _i_ is for the ldense routines:
417    
418            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
419            * src/ldense.c (lsyMatrix_as_lgeMatrix):
420    
421            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
422    
423    
424    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
427                    many different kinds of matrices.
428            * R/*.R: quite a few new methods were needed for R CMD check with
429                    new Matrix().  Very good for users playing around.
430    
431    
432    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * src/dgeMatrix.c (dMatrix_validate): new
435            * src/Mutils.c (dense_nonpacked_validate): new
436    
437            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
438    
439    
440    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
441    
442            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
443    
444    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
445    
446            * DESCRIPTION (Version): 0.99-6 released to CRAN
447    
448            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
449            segfault in cases with multiple non-nested grouping factors.
450    
451    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
454                    (Depends): also on 'utils'
455    
456            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
457            * R/diagMatrix.R (Diagonal): constructor and methods for
458            diagonal matrices
459    
460            * R/ltTMatrix.R: new "minimal methods"
461    
462    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
465            all methods (and help files).
466    
467    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
470                    for case (dimn.  op  no_dimn.)
471    
472    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * DESCRIPTION (Version): 0.99-2  released to CRAN
475    
476    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
477    
478            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
479            by Julian Faraway.
480    
481    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/Auxiliaries.R (try_as): new utility
484            * R/sparseMatrix.R: use try_as() in coercion to original class
485    
486    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
489    
490    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/Auxiliaries.R (dimNamesCheck): added
493    
494            * R/Matrix.R (as.array), (as.vector): new
495    
496    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
499                    default.
500            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
501                    "pMatrix" now contains "sparseMatrix"
502    
503    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * tests/Class+Meth.R: new tests; t(t(m)) == m
506    
507            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
508    
509            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
510            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
511    
512            * R/dspMatrix.R: typo in "t" method
513    
514    2005-09-18  Douglas Bates  <bates@wisc.edu>
515    
516            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
517            * R/Tsparse.R: instead of R/gTMatrix.R
518            * R/Csparse.R: new
519            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
520            * src/Tsparse.c: new; many trivial methods calling cholmod_()
521            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
522                            via cholmod
523    
524    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (non0ind): new function using new C code
527            * src/dgCMatrix.c (compressed_non_0_ij): new utility
528    
529    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
530    
531            * src/chm_common.h: header file required by all C sources that
532            call CHOLMOD functions.  It defines a cholmod_common structure
533            called 'c' whose address is passed as the last argument to
534            (virtually) every CHOLMOD function.
535    
536            * src/Pattern.c: Simple example of the use of CHOLMOD.
537    
538            * src/init.c: initialize and finalize the cholmod_common structure.
539    
540            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
541            LDL and CCOLAMD from the U. of Florida sparse matrix library.
542    
543    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * inst/test-tools.R: new file collecting the utility functions used
546                    in ./tests/*.R
547    
548            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
549            * R/Matrix.R (cbind2): methods for NULL and missing
550    
551    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/AllClass.R: new "index" class for "[" and "[<-":
554                    First cut at "symmetricMatrix" and "triangularMatrix"
555            * R/gTMatrix.R (.ind.prep): new function;
556                    Logical and character indexing now work too.
557            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
558            * tests/indexing.R: new, including *.Rout.save
559            * tests/dgTMatrix.R: new
560    
561    2005-08-29  Douglas Bates  <bates@wisc.edu>
562    
563            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
564            indicator pos not being updated.  Also enforced upper triangular
565            for symmetric case.  Need to coerce edges component of elements of
566            edge list - grr! (Why don't they define their classes cleanly?)
567    
568    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/Matrix.R:  added first "[<-" methods; not yet functional
571            * R/denseMatrix.R: ditto
572            * man/Subassign-methods.Rd: new help file for these
573    
574    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * DESCRIPTION (Version): 0.98-6
577    
578            * R/denseMatrix.R: new file for "[" fallback methods for all dense
579            matrices.
580    
581    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
584                    as( <logical>, "matrix")
585    
586            * R/pMatrix.R: coercion to "lgTMatrix"
587    
588            * R/gTMatrix.R: new virtual class to define "[" methods for.
589            * man/gTMatrix-class.Rd:
590            * General slight re-organization of where "[" methods are defined.
591              more to come.
592    
593    2005-08-18  Douglas Bates  <bates@wisc.edu>
594    
595            * DESCRIPTION (Version): 0.98-5  released to CRAN
596    
597            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
598            * .....
599    
600    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
601    
602            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
603            or glmer objects.
604    
605    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
608    
609    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
610    
611            * R/HBMM.R: finish re-writing R-only code.
612    
613    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
614    
615            * man/externalFormats.Rd: move documentation for writeHB and
616            writeMM here.
617    
618            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
619            (suggested by Paul Roecker).
620    
621            * tests/validObj.R (assertError): Comment out test that is failing
622            after recent changes in r-devel.
623    
624    
625    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * R/AllClass.R: intermediate virtual class "denseMatrix"
628            * man/denseMatrix-class.Rd
629            * NAMESPACE: export it, and also export
630            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
631    
632    2005-08-10  Douglas Bates  <bates@wisc.edu>
633    
634            * DESCRIPTION (Version): 0.98-3 to CRAN
635    
636            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
637            matrix_solve code (which was really, really wrong).
638    
639    2005-08-07  Douglas Bates  <bates@wisc.edu>
640    
641            * DESCRIPTION (Version): 0.98-2
642    
643            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
644    
645            * R/lmer.R (abbrvNms): new
646            * R/lmer.R (mcmcsamp): allow transformed parameters
647            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
648            for the Harwell-Boeing and the MatrixMarket formats.
649    
650    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * man/dtrMatrix-class.Rd: add examples
653            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
654    
655            * TODO: note the dtpMatrix (docu) bug
656    
657            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
658            in order to ensure that new as.matrix() is used by old functions,
659            e.g., svd(), qr(), eigen(), dist(),..;
660                  apply(), also matplot() or pairs().
661    
662    
663    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
666              add comments about 'control' / lmerControl() arguments
667    
668    2005-07-27  Douglas Bates  <bates@wisc.edu>
669    
670            * man/sleepstudy.Rd: Added the sleep data set.
671            * DESCRIPTION (Version): 0.98-1  released to CRAN
672    
673    2005-07-12  Douglas Bates  <bates@wisc.edu>
674            * man/sleepstudy.Rd: Added the sleep data set.
675    
676            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
677            .Call calls that were producing spurious output.
678    
679    2005-07-05  Douglas Bates  <bates@wisc.edu>
680    
681            * R/lmer.R (lmer): stored updated variance component estimates in
682            mer object for the generalized model.  (Bug reported by Renaud
683            Lancelot).
684    
685    2005-07-03  Douglas Bates  <bates@wisc.edu>
686    
687            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
688            unidimensional case.
689    
690    2005-06-08  Douglas Bates  <bates@wisc.edu>
691    
692            * DESCRIPTION (Version): 0.96-1
693    
694            * moved  lmer-class' R and C code moved from lme4 to here
695    
696    2005-06-04  Douglas Bates  <bates@wisc.edu>
697    
698            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
699            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
700    
701    2005-06-02  Douglas Bates  <bates@wisc.edu>
702    
703            * src/Makefile.win: Forgot to update this when Makefile changed.
704    
705    2005-05-11  Douglas Bates  <bates@wisc.edu>
706    
707          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
708          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
709    
710  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
711    
712          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
713          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 716 
716          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
717          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
718    
719  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
720    
721          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
722          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
723    
724  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
725    
726          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
727          multiplication operation.          multiplication operation.
# Line 30  Line 734 
734    
735          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
736    
737  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
738    
739          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
740    
741          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
742    
743    
744  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
745    
746          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
747    
# Line 46  Line 750 
750          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
751          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
752    
753  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
754    
755          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
756    
# Line 72  Line 776 
776          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
777            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
778    
779  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
780    
781          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
782          * ....          * ....
783    
784  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
785    
786          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
787    
# Line 92  Line 796 
796            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
797          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
798    
799  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
800    
801          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
802    
803  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
804    
805          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
806    
807  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
808    
809          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
810          the package.          the package.
# Line 148  Line 852 
852    
853          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
854    
855  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
856    
857          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
858          for the geMatrix class.          for the geMatrix class.
859    
860  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
861    
862          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
863    
864          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
865    
866  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
867    
868          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
869          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
870    
871  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
872    
873          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
874    
875  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
876    
877          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
878          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
879    
880  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
881    
882          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
883    
884          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
885          for tripletMatrix to matrix.          for tripletMatrix to matrix.
886    
887  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
888    
889          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
890          no longer used.          no longer used.
# Line 192  Line 896 
896          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
897          Fixes part but not all of #15.          Fixes part but not all of #15.
898    
899  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
900    
901          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
902          scalar grouping factors corrected.          scalar grouping factors corrected.
903    
904  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
905    
906          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
907    
908  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
909    
910          * 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
911          .h file can be included.          .h file can be included.
912    
913  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
914    
915          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
916          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
917    
918          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
919    
920  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
921    
922          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
923    
924  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
925    
926          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
927    
928  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
929    
930          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
931    
932  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
933    
934          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
935    
936  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
937    
938          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
939          routines.          routines.
940    
941  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
942    
943          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
944    
945  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
946    
947          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
948    

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