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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1389, Fri Aug 18 13:53:33 2006 UTC
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1    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
4            the base version has no "..." argument.
5    
6            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
7    
8            * R/Matrix.R: define and
9            * NAMESPACE: export as.numeric() and as.logical() methods.
10                    Let's hope these do not badly slow down something...
11            Finally export the zapsmall() method.
12    
13    2006-08-17  Douglas Bates  <bates@R-project.org>
14    
15            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
16            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
17            * src/dtCMatrix.c :Remove code that is no longer used
18            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
19    
20    2006-08-14  Douglas Bates  <bates@R-project.org>
21    
22            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
23            Csparse_to_logical and Csparse_symmetric_to_general.
24            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
25            coercion methods between CsparseMatrix and TsparseMatrix.
26    
27    2006-08-14  Douglas Bates  <bates@R-project.org>
28    
29            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
30            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
31            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
32            possible.
33    
34    2006-08-12  Douglas Bates  <bates@R-project.org>
35    
36            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
37              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
38              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
39              generalize conversions between TsparseMatrix, CsparseMatrix,
40              denseMatrix and matrix.  Preserve triangularity property and
41              propagate Dimnames in the easy cases.
42    
43    2006-08-10  Douglas Bates  <bates@R-project.org>
44    
45            * src/lmer.c: adjust checks in glmer_init for S4SXP
46            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
47            before S4SXP but for the wrong reasons.
48    
49    2006-08-08  Douglas Bates  <bates@R-project.org>
50    
51            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
52            Later modified to return the upper triangle only.
53            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
54    
55    2006-08-07  Douglas Bates  <bates@R-project.org>
56    
57            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
58            R-level conversion to a sparse symmetric class.
59            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
60            Remove conversion to sparse symmetric classes (now done in C code).
61    
62    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
65            * man/band.Rd:  adapt the \dontshow{} unit test.
66    
67    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.995-14  for CRAN
70    
71            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
72    
73            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
74            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
75    
76            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
77            * R/Tsparse.R (tril, triu, band): methods
78            * R/dgRMatrix.R (tril, ...):    ditto
79            * man/band.Rd:                  ditto
80    
81    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Matrix.R (head, tail): directly use utils:::head.matrix
84                    to be up-to-date automatically.
85    
86    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
89    
90            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
91            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
92            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
93            such that the S4 objects are always created by the current version
94            of R and 'Matrix' class definitions.
95    
96    2006-08-01  Douglas Bates  <bates@R-project.org>
97    
98            * R/lmer.R (LMEoptimize method), tests/lmer.R,
99            inst/external/test3comp.rda: Added warnings for convergence on
100            boundary and test cases.
101    
102            * src/lmer.c (mer_postVar): Modified to return the variances that
103            are marginal to the fixed effects, not conditional on them (which
104            is what the bVar slot contents represent).
105    
106    2006-07-31  Douglas Bates  <bates@R-project.org>
107    
108            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
109            function which calls the C function mer_hat_trace2.
110    
111            * man/ranef.Rd: Include description of "postVar" argument and
112            producing a caterpillar plot.
113    
114    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * NAMESPACE:    change  "correlation" to "corMatrix"
117            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
118            * R/dpoMatrix.R: ditto
119            * R/lmer.R:      ditto
120    
121    2006-07-28  Douglas Bates  <bates@R-project.org>
122    
123            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
124            RZXinv slot's contents into a separate internal function that can
125            be used in mer_hat_trace.
126    
127    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
130            via new smart
131            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
132            utility functions.
133    
134    
135    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Csparse.R (tril, triu, band): do return *triangular* classed
138            matrices when appropriate; band() even symmetric ones.
139            (replCmat): extend to potentially all "CsparseMatrix"
140            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
141            allow subassignment for special sparse matrices.
142    
143            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
144    
145            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
146            argument; in glmer_*(): print only if(verbose).
147    
148            speed-optimize a few places by moving REAL(.) out of loops.
149    
150            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
151    
152    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
155                    since that wrongly triggers also for M[ logi , ]
156    
157            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
158            a symmetric matrix that results in a non-symmetric one.
159            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
160    
161            * R/dMatrix.R: make round(M) work as round(M, 0)
162    
163            * R/dgTMatrix.R (image): coordinate system and axis now use
164            1-based indices, not 0-based ones.
165    
166            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
167            * tests/indexing.R: test it.
168    
169            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
170            * man/isSymmetric-methods.Rd: and document it.
171    
172            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
173            * man/SparseM-conv.Rd: docu them
174    
175            * tests/other-pkgs.R: renamed from tests/graph.R and add example
176                    for 'SparseM' conversions
177    
178    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
179    
180            * R/Matrix.R (head): added head() and tail() methods.
181    
182    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.995-12 released to CRAN
185    
186    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * tests/simple.R: add check for correct dsT -> dgT coercion;
189                    add check for correct printing of symmetric sparse matrices.
190    
191            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
192            for sparse symmetric matrices.
193    
194            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
195            diagonal twice.
196    
197    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
198    
199            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
200            being applied to the x slot (detected by Brian Ripley).
201    
202    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
205    
206            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
207    
208    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/lgCMatrix.c (lgCMatrix_diag): new function
211            * R/lgCMatrix.R (diag): for new method
212    
213            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
214                 ==> construction of illegal "*gTMatrix" via new() should
215                 now be much less easy:
216            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
217    
218            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
219                    directly.
220            * man/Matrix.Rd: documents it.
221    
222    2006-07-06  Douglas Bates  <bates@R-project.org>
223    
224            * src/pedigree.c (pedigree_inbreeding): Correction in
225            initialization.  This function is not currently being used and is
226            not fully tested.
227    
228            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
229            Introduced the glmer class.  Added code for mcmcmsamp on glmer
230            objects.  Modified validity check on pedigree objects to account
231            for nonparallel patterns of missingness of parents.
232    
233            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
234            class.
235    
236    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/pMatrix.R: coercion pMatrix -> Tsparse
239    
240    2006-06-12  Douglas Bates  <bates@R-project.org>
241    
242            * DESCRIPTION (Version): 0.995-11 released to CRAN
243    
244            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
245            the output from mcmcsamp.
246    
247    2006-06-10  Douglas Bates  <bates@R-project.org>
248    
249            * R/lmer.R (simulestimate): added C code for calculating the trace
250            of the hat matrix.
251    
252    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
255            classes.
256            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
257    
258    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/dgTMatrix.R (colSums): etc. All four of
261            colSums(), rowSums(), colMeans(), rowMeans() now should work for
262            all "Matrices".
263    
264    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * R/lmer.R (panel.ci): Add a reference line at zero and a
267            background grid to the qqmath plot of ranef.lmer.
268    
269    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
270    
271            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
272            grouping factors to be specified in the formula as (1|foo/bar).
273    
274    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * R/lmer.R (findbars and others): Change check of is.numeric to
277            !is.language to resolve the bug reported by Jacob Wegelin.
278    
279            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
280            code to evaluate inbreeding coefficients without calculating T,
281            based on code in Sargolzaei and Iwaisaki's paper.
282    
283    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
286            generic and mer methods for isNested and denomDF. This denomDF was
287            an attempt to emulate that in lme but I don't think that makes
288            sense.  Use the trace of the hat matrix instead.
289    
290    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
293            the C code depending on a slot structure that's no longer valid.
294            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
295    
296    
297    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
298    
299            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
300            of lowerTriMatrix generic and methods to tril (also upper to triu)
301            and added a general band extractor.
302    
303    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
304    
305            * R/pedigree.R (pedigree): Replace sire and dam values outside the
306            allowable range with NAs. Added a corresponding check in the
307            validity check for the pedigree class.
308    
309            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
310            crossprod methods now inherits from symmetricMatrix.
311    
312    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
313    
314            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
315            generics lowerTriMatrix and upperTriMatrix along with methods for
316            the Csparse virtual class.  Also added a C function Csparse_band
317            that implements these methods by calling cholmod_band.
318    
319    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
322            erased when it was NULL.  This led to invalid subselections!
323    
324    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
325    
326            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
327            in method for "t" so as not to lose the unit diagonal property.
328    
329    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
332            and methods.  This is now an option to the ranef method for the
333            mer class.
334    
335            * src/cs_utils.c: Ensure that the nz component is -1 for a
336            compressed column-oriented matrix.  Minor formatting cleanup.
337    
338            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
339            objects.
340    
341    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
344            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
345    
346    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
349            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
350    
351            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
352            for the dtCMatrix class.
353    
354    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
355    
356            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
357            and methods for it.
358    
359    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
362            arguments, such that M %*% 1:6 now works
363            * Tests/matprod.R: test the above
364    
365    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
368            the ranef.lmer class.
369    
370            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
371            methods to extract the posterior variances from the bVar slot.
372    
373    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
376            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
377    
378            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
379            * tests/simple: (extended)
380    
381            * R/sparseMatrix.R (isTriangular): now using much improved
382            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
383    
384    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
387            (problem report from Franklin Parlamis).  This should be done
388            generally.
389    
390    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
393            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
394            update the plot methods.
395    
396    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
397    
398            * R/lmer.R (resid and ranef methods):  Added methods for the
399            "residuals" and "resid" generic but only for linear mixed model
400            fits.  Changed the ranef method to return a list of data frames so
401            that the plot methods now work.
402    
403    2006-03-16  Douglas Bates  <bates@bates2>
404    
405            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
406            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
407    
408            * DESCRIPTION (Date): New release
409    
410    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
413    
414            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
415            * man/KNex.Rd: and other help files
416            * tests/*.R: several ones needed adaption
417            * inst/doc/Comparisons.Rnw: ditto
418    
419    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
422    
423            * tests/indexing.R: tests for new [<- methods for sparse matrices.
424    
425    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
428    
429            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
430    
431    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/dMatrix.R: enable things like  M [ M < 10 ]
434            * R/dgeMatrix.R: implement it
435    
436    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/AllClass.R: define "summary.mer" and "*.lmer"
439            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
440            * R/lmer.R (show): now works with summary()
441    
442    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
445            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
446                    support the above
447    
448    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
451            Use glmFit$prior.weights for weights in a glmm.
452            Allow an option usePQL = FALSE to skip the PQL steps for the
453            Laplace method (and, in time, the AGQ method).
454    
455            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
456            into a separate function internal_mer_Xfactor to be able to call
457            it from internal_bhat.
458    
459    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * tests/Class+Meth.R (tstMatrixClass): function for much better
462            testing; now again of all actual classes.
463    
464            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
465                    use macros and define make_d_matrix_* and make_i_matrix_*
466                    where _i_ is for the ldense routines:
467    
468            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
469            * src/ldense.c (lsyMatrix_as_lgeMatrix):
470    
471            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
472    
473    
474    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
477                    many different kinds of matrices.
478            * R/*.R: quite a few new methods were needed for R CMD check with
479                    new Matrix().  Very good for users playing around.
480    
481    
482    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * src/dgeMatrix.c (dMatrix_validate): new
485            * src/Mutils.c (dense_nonpacked_validate): new
486    
487            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
488    
489    
490    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
491    
492            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
493    
494    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
495    
496            * DESCRIPTION (Version): 0.99-6 released to CRAN
497    
498            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
499            segfault in cases with multiple non-nested grouping factors.
500    
501    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
504                    (Depends): also on 'utils'
505    
506            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
507            * R/diagMatrix.R (Diagonal): constructor and methods for
508            diagonal matrices
509    
510            * R/ltTMatrix.R: new "minimal methods"
511    
512    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
515            all methods (and help files).
516    
517    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
520                    for case (dimn.  op  no_dimn.)
521    
522    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * DESCRIPTION (Version): 0.99-2  released to CRAN
525    
526    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
527    
528            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
529            by Julian Faraway.
530    
531    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Auxiliaries.R (try_as): new utility
534            * R/sparseMatrix.R: use try_as() in coercion to original class
535    
536    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
539    
540    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Auxiliaries.R (dimNamesCheck): added
543    
544            * R/Matrix.R (as.array), (as.vector): new
545    
546    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
549                    default.
550            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
551                    "pMatrix" now contains "sparseMatrix"
552    
553    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * tests/Class+Meth.R: new tests; t(t(m)) == m
556    
557            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
558    
559            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
560            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
561    
562            * R/dspMatrix.R: typo in "t" method
563    
564    2005-09-18  Douglas Bates  <bates@wisc.edu>
565    
566            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
567            * R/Tsparse.R: instead of R/gTMatrix.R
568            * R/Csparse.R: new
569            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
570            * src/Tsparse.c: new; many trivial methods calling cholmod_()
571            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
572                            via cholmod
573    
574    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Auxiliaries.R (non0ind): new function using new C code
577            * src/dgCMatrix.c (compressed_non_0_ij): new utility
578    
579    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
580    
581            * src/chm_common.h: header file required by all C sources that
582            call CHOLMOD functions.  It defines a cholmod_common structure
583            called 'c' whose address is passed as the last argument to
584            (virtually) every CHOLMOD function.
585    
586            * src/Pattern.c: Simple example of the use of CHOLMOD.
587    
588            * src/init.c: initialize and finalize the cholmod_common structure.
589    
590            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
591            LDL and CCOLAMD from the U. of Florida sparse matrix library.
592    
593    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * inst/test-tools.R: new file collecting the utility functions used
596                    in ./tests/*.R
597    
598            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
599            * R/Matrix.R (cbind2): methods for NULL and missing
600    
601    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/AllClass.R: new "index" class for "[" and "[<-":
604                    First cut at "symmetricMatrix" and "triangularMatrix"
605            * R/gTMatrix.R (.ind.prep): new function;
606                    Logical and character indexing now work too.
607            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
608            * tests/indexing.R: new, including *.Rout.save
609            * tests/dgTMatrix.R: new
610    
611    2005-08-29  Douglas Bates  <bates@wisc.edu>
612    
613            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
614            indicator pos not being updated.  Also enforced upper triangular
615            for symmetric case.  Need to coerce edges component of elements of
616            edge list - grr! (Why don't they define their classes cleanly?)
617    
618    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Matrix.R:  added first "[<-" methods; not yet functional
621            * R/denseMatrix.R: ditto
622            * man/Subassign-methods.Rd: new help file for these
623    
624    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * DESCRIPTION (Version): 0.98-6
627    
628            * R/denseMatrix.R: new file for "[" fallback methods for all dense
629            matrices.
630    
631    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
634                    as( <logical>, "matrix")
635    
636            * R/pMatrix.R: coercion to "lgTMatrix"
637    
638            * R/gTMatrix.R: new virtual class to define "[" methods for.
639            * man/gTMatrix-class.Rd:
640            * General slight re-organization of where "[" methods are defined.
641              more to come.
642    
643    2005-08-18  Douglas Bates  <bates@wisc.edu>
644    
645            * DESCRIPTION (Version): 0.98-5  released to CRAN
646    
647            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
648            * .....
649    
650    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
651    
652            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
653            or glmer objects.
654    
655    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
658    
659    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
660    
661            * R/HBMM.R: finish re-writing R-only code.
662    
663    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
664    
665            * man/externalFormats.Rd: move documentation for writeHB and
666            writeMM here.
667    
668            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
669            (suggested by Paul Roecker).
670    
671            * tests/validObj.R (assertError): Comment out test that is failing
672            after recent changes in r-devel.
673    
674    
675    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/AllClass.R: intermediate virtual class "denseMatrix"
678            * man/denseMatrix-class.Rd
679            * NAMESPACE: export it, and also export
680            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
681    
682    2005-08-10  Douglas Bates  <bates@wisc.edu>
683    
684            * DESCRIPTION (Version): 0.98-3 to CRAN
685    
686            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
687            matrix_solve code (which was really, really wrong).
688    
689    2005-08-07  Douglas Bates  <bates@wisc.edu>
690    
691            * DESCRIPTION (Version): 0.98-2
692    
693            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
694    
695            * R/lmer.R (abbrvNms): new
696            * R/lmer.R (mcmcsamp): allow transformed parameters
697            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
698            for the Harwell-Boeing and the MatrixMarket formats.
699    
700    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * man/dtrMatrix-class.Rd: add examples
703            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
704    
705            * TODO: note the dtpMatrix (docu) bug
706    
707            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
708            in order to ensure that new as.matrix() is used by old functions,
709            e.g., svd(), qr(), eigen(), dist(),..;
710                  apply(), also matplot() or pairs().
711    
712    
713    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
716              add comments about 'control' / lmerControl() arguments
717    
718    2005-07-27  Douglas Bates  <bates@wisc.edu>
719    
720            * man/sleepstudy.Rd: Added the sleep data set.
721            * DESCRIPTION (Version): 0.98-1  released to CRAN
722    
723    2005-07-12  Douglas Bates  <bates@wisc.edu>
724            * man/sleepstudy.Rd: Added the sleep data set.
725    
726            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
727            .Call calls that were producing spurious output.
728    
729    2005-07-05  Douglas Bates  <bates@wisc.edu>
730    
731            * R/lmer.R (lmer): stored updated variance component estimates in
732            mer object for the generalized model.  (Bug reported by Renaud
733            Lancelot).
734    
735    2005-07-03  Douglas Bates  <bates@wisc.edu>
736    
737            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
738            unidimensional case.
739    
740    2005-06-08  Douglas Bates  <bates@wisc.edu>
741    
742            * DESCRIPTION (Version): 0.96-1
743    
744            * moved  lmer-class' R and C code moved from lme4 to here
745    
746    2005-06-04  Douglas Bates  <bates@wisc.edu>
747    
748            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
749            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
750    
751    2005-06-02  Douglas Bates  <bates@wisc.edu>
752    
753            * src/Makefile.win: Forgot to update this when Makefile changed.
754    
755    2005-05-11  Douglas Bates  <bates@wisc.edu>
756    
757            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
758            bug reported by Kurt Hornik and Michael Hahsler.
759    
760    2005-05-10  Douglas Bates  <bates@wisc.edu>
761    
762            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
763            logical sparse matrices.  These will also be used in the symbolic
764            analysis for lmer objects.
765    
766            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
767            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
768    
769    2005-05-06  Douglas Bates  <bates@wisc.edu>
770    
771            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
772            colMeans, colSums, rowMeans and rowSums.
773    
774    2005-04-18  Douglas Bates  <bates@wisc.edu>
775    
776            * src/lgCMatrix.[ch]: code for _validate method and stub for
777            multiplication operation.
778    
779            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
780            to dgetrs.
781    
782            * src/init.c: Fix cut-and-paste error in definition of
783            dgeMatrix_matrix_solve
784    
785            * src/{many files}: Tighten code by using ALLOC_SLOT.
786    
787    2005-04-15  Douglas Bates  <bates@wisc.edu>
788    
789            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
790    
791            * DESCRIPTION: Eliminate import of stats.
792    
793    
794    2005-04-06  Douglas Bates  <bates@wisc.edu>
795    
796            * R/AllClass.R : add logical sparse matrix classes
797    
798  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
801          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
802    
803  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
804    
805          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
806    
# Line 29  Line 826 
826          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
827            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
828    
829  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
830    
831          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
832          * ....          * ....
833    
834  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
835    
836          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
837    
# Line 49  Line 846 
846            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
847          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
848    
849  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
850    
851          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
852    
853  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
854    
855          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
856    
857  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
858    
859          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
860          the package.          the package.
# Line 105  Line 902 
902    
903          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
904    
905  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
906    
907          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
908          for the geMatrix class.          for the geMatrix class.
909    
910  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
911    
912          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
913    
914          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
915    
916  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
917    
918          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
919          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
920    
921  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
922    
923          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
924    
925  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
926    
927          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
928          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
929    
930  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
931    
932          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
933    
934          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
935          for tripletMatrix to matrix.          for tripletMatrix to matrix.
936    
937  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
938    
939          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
940          no longer used.          no longer used.
# Line 149  Line 946 
946          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
947          Fixes part but not all of #15.          Fixes part but not all of #15.
948    
949  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
950    
951          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
952          scalar grouping factors corrected.          scalar grouping factors corrected.
953    
954  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
955    
956          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
957    
958  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
959    
960          * 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
961          .h file can be included.          .h file can be included.
962    
963  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
964    
965          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
966          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
967    
968          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
969    
970  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
971    
972          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
973    
974  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
975    
976          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
977    
978  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
979    
980          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
981    
982  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
983    
984          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
985    
986  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
987    
988          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
989          routines.          routines.
990    
991  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
992    
993          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
994    
995  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
996    
997          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
998    

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