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revision 676, Sat Mar 26 15:59:18 2005 UTC revision 1368, Sat Aug 12 17:34:00 2006 UTC
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1    2006-08-12  Douglas Bates  <bates@R-project.org>
2    
3            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
4              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
5              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
6              generalize conversions between TsparseMatrix, CsparseMatrix,
7              denseMatrix and matrix.  Preserve triangularity property and
8              propagate Dimnames in the easy cases.
9    
10    2006-08-10  Douglas Bates  <bates@R-project.org>
11    
12            * src/lmer.c: adjust checks in glmer_init for S4SXP
13            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
14            before S4SXP but for the wrong reasons.
15    
16    2006-08-08  Douglas Bates  <bates@R-project.org>
17    
18            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
19            Later modified to return the upper triangle only.
20            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
21    
22    2006-08-07  Douglas Bates  <bates@R-project.org>
23    
24            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
25            R-level conversion to a sparse symmetric class.
26            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
27            Remove conversion to sparse symmetric classes (now done in C code).
28    
29    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
32            * man/band.Rd:  adapt the \dontshow{} unit test.
33    
34    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.995-14  for CRAN
37    
38            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
39    
40            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
41            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
42    
43            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
44            * R/Tsparse.R (tril, triu, band): methods
45            * R/dgRMatrix.R (tril, ...):    ditto
46            * man/band.Rd:                  ditto
47    
48    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Matrix.R (head, tail): directly use utils:::head.matrix
51                    to be up-to-date automatically.
52    
53    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
56    
57            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
58            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
59            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
60            such that the S4 objects are always created by the current version
61            of R and 'Matrix' class definitions.
62    
63    2006-08-01  Douglas Bates  <bates@R-project.org>
64    
65            * R/lmer.R (LMEoptimize method), tests/lmer.R,
66            inst/external/test3comp.rda: Added warnings for convergence on
67            boundary and test cases.
68    
69            * src/lmer.c (mer_postVar): Modified to return the variances that
70            are marginal to the fixed effects, not conditional on them (which
71            is what the bVar slot contents represent).
72    
73    2006-07-31  Douglas Bates  <bates@R-project.org>
74    
75            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
76            function which calls the C function mer_hat_trace2.
77    
78            * man/ranef.Rd: Include description of "postVar" argument and
79            producing a caterpillar plot.
80    
81    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * NAMESPACE:    change  "correlation" to "corMatrix"
84            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
85            * R/dpoMatrix.R: ditto
86            * R/lmer.R:      ditto
87    
88    2006-07-28  Douglas Bates  <bates@R-project.org>
89    
90            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
91            RZXinv slot's contents into a separate internal function that can
92            be used in mer_hat_trace.
93    
94    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
97            via new smart
98            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
99            utility functions.
100    
101    
102    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Csparse.R (tril, triu, band): do return *triangular* classed
105            matrices when appropriate; band() even symmetric ones.
106            (replCmat): extend to potentially all "CsparseMatrix"
107            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
108            allow subassignment for special sparse matrices.
109    
110            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
111    
112            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
113            argument; in glmer_*(): print only if(verbose).
114    
115            speed-optimize a few places by moving REAL(.) out of loops.
116    
117            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
118    
119    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
122                    since that wrongly triggers also for M[ logi , ]
123    
124            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
125            a symmetric matrix that results in a non-symmetric one.
126            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
127    
128            * R/dMatrix.R: make round(M) work as round(M, 0)
129    
130            * R/dgTMatrix.R (image): coordinate system and axis now use
131            1-based indices, not 0-based ones.
132    
133            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
134            * tests/indexing.R: test it.
135    
136            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
137            * man/isSymmetric-methods.Rd: and document it.
138    
139            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
140            * man/SparseM-conv.Rd: docu them
141    
142            * tests/other-pkgs.R: renamed from tests/graph.R and add example
143                    for 'SparseM' conversions
144    
145    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
146    
147            * R/Matrix.R (head): added head() and tail() methods.
148    
149    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * DESCRIPTION (Version): 0.995-12 released to CRAN
152    
153    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * tests/simple.R: add check for correct dsT -> dgT coercion;
156                    add check for correct printing of symmetric sparse matrices.
157    
158            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
159            for sparse symmetric matrices.
160    
161            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
162            diagonal twice.
163    
164    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
165    
166            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
167            being applied to the x slot (detected by Brian Ripley).
168    
169    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
172    
173            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
174    
175    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * src/lgCMatrix.c (lgCMatrix_diag): new function
178            * R/lgCMatrix.R (diag): for new method
179    
180            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
181                 ==> construction of illegal "*gTMatrix" via new() should
182                 now be much less easy:
183            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
184    
185            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
186                    directly.
187            * man/Matrix.Rd: documents it.
188    
189    2006-07-06  Douglas Bates  <bates@R-project.org>
190    
191            * src/pedigree.c (pedigree_inbreeding): Correction in
192            initialization.  This function is not currently being used and is
193            not fully tested.
194    
195            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
196            Introduced the glmer class.  Added code for mcmcmsamp on glmer
197            objects.  Modified validity check on pedigree objects to account
198            for nonparallel patterns of missingness of parents.
199    
200            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
201            class.
202    
203    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/pMatrix.R: coercion pMatrix -> Tsparse
206    
207    2006-06-12  Douglas Bates  <bates@R-project.org>
208    
209            * DESCRIPTION (Version): 0.995-11 released to CRAN
210    
211            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
212            the output from mcmcsamp.
213    
214    2006-06-10  Douglas Bates  <bates@R-project.org>
215    
216            * R/lmer.R (simulestimate): added C code for calculating the trace
217            of the hat matrix.
218    
219    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
222            classes.
223            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
224    
225    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgTMatrix.R (colSums): etc. All four of
228            colSums(), rowSums(), colMeans(), rowMeans() now should work for
229            all "Matrices".
230    
231    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
232    
233            * R/lmer.R (panel.ci): Add a reference line at zero and a
234            background grid to the qqmath plot of ranef.lmer.
235    
236    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
237    
238            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
239            grouping factors to be specified in the formula as (1|foo/bar).
240    
241    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
242    
243            * R/lmer.R (findbars and others): Change check of is.numeric to
244            !is.language to resolve the bug reported by Jacob Wegelin.
245    
246            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
247            code to evaluate inbreeding coefficients without calculating T,
248            based on code in Sargolzaei and Iwaisaki's paper.
249    
250    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
253            generic and mer methods for isNested and denomDF. This denomDF was
254            an attempt to emulate that in lme but I don't think that makes
255            sense.  Use the trace of the hat matrix instead.
256    
257    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
260            the C code depending on a slot structure that's no longer valid.
261            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
262    
263    
264    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
265    
266            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
267            of lowerTriMatrix generic and methods to tril (also upper to triu)
268            and added a general band extractor.
269    
270    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/pedigree.R (pedigree): Replace sire and dam values outside the
273            allowable range with NAs. Added a corresponding check in the
274            validity check for the pedigree class.
275    
276            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
277            crossprod methods now inherits from symmetricMatrix.
278    
279    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
282            generics lowerTriMatrix and upperTriMatrix along with methods for
283            the Csparse virtual class.  Also added a C function Csparse_band
284            that implements these methods by calling cholmod_band.
285    
286    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
289            erased when it was NULL.  This led to invalid subselections!
290    
291    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
294            in method for "t" so as not to lose the unit diagonal property.
295    
296    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
297    
298            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
299            and methods.  This is now an option to the ranef method for the
300            mer class.
301    
302            * src/cs_utils.c: Ensure that the nz component is -1 for a
303            compressed column-oriented matrix.  Minor formatting cleanup.
304    
305            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
306            objects.
307    
308    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
311            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
312    
313    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
314    
315            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
316            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
317    
318            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
319            for the dtCMatrix class.
320    
321    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
322    
323            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
324            and methods for it.
325    
326    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
329            arguments, such that M %*% 1:6 now works
330            * Tests/matprod.R: test the above
331    
332    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
333    
334            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
335            the ranef.lmer class.
336    
337            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
338            methods to extract the posterior variances from the bVar slot.
339    
340    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
343            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
344    
345            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
346            * tests/simple: (extended)
347    
348            * R/sparseMatrix.R (isTriangular): now using much improved
349            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
350    
351    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
352    
353            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
354            (problem report from Franklin Parlamis).  This should be done
355            generally.
356    
357    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
360            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
361            update the plot methods.
362    
363    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/lmer.R (resid and ranef methods):  Added methods for the
366            "residuals" and "resid" generic but only for linear mixed model
367            fits.  Changed the ranef method to return a list of data frames so
368            that the plot methods now work.
369    
370    2006-03-16  Douglas Bates  <bates@bates2>
371    
372            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
373            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
374    
375            * DESCRIPTION (Date): New release
376    
377    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
380    
381            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
382            * man/KNex.Rd: and other help files
383            * tests/*.R: several ones needed adaption
384            * inst/doc/Comparisons.Rnw: ditto
385    
386    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
389    
390            * tests/indexing.R: tests for new [<- methods for sparse matrices.
391    
392    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
395    
396            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
397    
398    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/dMatrix.R: enable things like  M [ M < 10 ]
401            * R/dgeMatrix.R: implement it
402    
403    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/AllClass.R: define "summary.mer" and "*.lmer"
406            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
407            * R/lmer.R (show): now works with summary()
408    
409    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
412            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
413                    support the above
414    
415    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
416    
417            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
418            Use glmFit$prior.weights for weights in a glmm.
419            Allow an option usePQL = FALSE to skip the PQL steps for the
420            Laplace method (and, in time, the AGQ method).
421    
422            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
423            into a separate function internal_mer_Xfactor to be able to call
424            it from internal_bhat.
425    
426    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * tests/Class+Meth.R (tstMatrixClass): function for much better
429            testing; now again of all actual classes.
430    
431            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
432                    use macros and define make_d_matrix_* and make_i_matrix_*
433                    where _i_ is for the ldense routines:
434    
435            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
436            * src/ldense.c (lsyMatrix_as_lgeMatrix):
437    
438            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
439    
440    
441    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
444                    many different kinds of matrices.
445            * R/*.R: quite a few new methods were needed for R CMD check with
446                    new Matrix().  Very good for users playing around.
447    
448    
449    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * src/dgeMatrix.c (dMatrix_validate): new
452            * src/Mutils.c (dense_nonpacked_validate): new
453    
454            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
455    
456    
457    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
458    
459            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
460    
461    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * DESCRIPTION (Version): 0.99-6 released to CRAN
464    
465            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
466            segfault in cases with multiple non-nested grouping factors.
467    
468    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
471                    (Depends): also on 'utils'
472    
473            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
474            * R/diagMatrix.R (Diagonal): constructor and methods for
475            diagonal matrices
476    
477            * R/ltTMatrix.R: new "minimal methods"
478    
479    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
482            all methods (and help files).
483    
484    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
487                    for case (dimn.  op  no_dimn.)
488    
489    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
490    
491            * DESCRIPTION (Version): 0.99-2  released to CRAN
492    
493    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
496            by Julian Faraway.
497    
498    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Auxiliaries.R (try_as): new utility
501            * R/sparseMatrix.R: use try_as() in coercion to original class
502    
503    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
506    
507    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/Auxiliaries.R (dimNamesCheck): added
510    
511            * R/Matrix.R (as.array), (as.vector): new
512    
513    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
516                    default.
517            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
518                    "pMatrix" now contains "sparseMatrix"
519    
520    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * tests/Class+Meth.R: new tests; t(t(m)) == m
523    
524            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
525    
526            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
527            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
528    
529            * R/dspMatrix.R: typo in "t" method
530    
531    2005-09-18  Douglas Bates  <bates@wisc.edu>
532    
533            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
534            * R/Tsparse.R: instead of R/gTMatrix.R
535            * R/Csparse.R: new
536            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
537            * src/Tsparse.c: new; many trivial methods calling cholmod_()
538            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
539                            via cholmod
540    
541    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/Auxiliaries.R (non0ind): new function using new C code
544            * src/dgCMatrix.c (compressed_non_0_ij): new utility
545    
546    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
547    
548            * src/chm_common.h: header file required by all C sources that
549            call CHOLMOD functions.  It defines a cholmod_common structure
550            called 'c' whose address is passed as the last argument to
551            (virtually) every CHOLMOD function.
552    
553            * src/Pattern.c: Simple example of the use of CHOLMOD.
554    
555            * src/init.c: initialize and finalize the cholmod_common structure.
556    
557            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
558            LDL and CCOLAMD from the U. of Florida sparse matrix library.
559    
560    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * inst/test-tools.R: new file collecting the utility functions used
563                    in ./tests/*.R
564    
565            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
566            * R/Matrix.R (cbind2): methods for NULL and missing
567    
568    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/AllClass.R: new "index" class for "[" and "[<-":
571                    First cut at "symmetricMatrix" and "triangularMatrix"
572            * R/gTMatrix.R (.ind.prep): new function;
573                    Logical and character indexing now work too.
574            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
575            * tests/indexing.R: new, including *.Rout.save
576            * tests/dgTMatrix.R: new
577    
578    2005-08-29  Douglas Bates  <bates@wisc.edu>
579    
580            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
581            indicator pos not being updated.  Also enforced upper triangular
582            for symmetric case.  Need to coerce edges component of elements of
583            edge list - grr! (Why don't they define their classes cleanly?)
584    
585    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Matrix.R:  added first "[<-" methods; not yet functional
588            * R/denseMatrix.R: ditto
589            * man/Subassign-methods.Rd: new help file for these
590    
591    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * DESCRIPTION (Version): 0.98-6
594    
595            * R/denseMatrix.R: new file for "[" fallback methods for all dense
596            matrices.
597    
598    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
601                    as( <logical>, "matrix")
602    
603            * R/pMatrix.R: coercion to "lgTMatrix"
604    
605            * R/gTMatrix.R: new virtual class to define "[" methods for.
606            * man/gTMatrix-class.Rd:
607            * General slight re-organization of where "[" methods are defined.
608              more to come.
609    
610    2005-08-18  Douglas Bates  <bates@wisc.edu>
611    
612            * DESCRIPTION (Version): 0.98-5  released to CRAN
613    
614            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
615            * .....
616    
617    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
618    
619            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
620            or glmer objects.
621    
622    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
625    
626    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
627    
628            * R/HBMM.R: finish re-writing R-only code.
629    
630    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
631    
632            * man/externalFormats.Rd: move documentation for writeHB and
633            writeMM here.
634    
635            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
636            (suggested by Paul Roecker).
637    
638            * tests/validObj.R (assertError): Comment out test that is failing
639            after recent changes in r-devel.
640    
641    
642    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/AllClass.R: intermediate virtual class "denseMatrix"
645            * man/denseMatrix-class.Rd
646            * NAMESPACE: export it, and also export
647            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
648    
649    2005-08-10  Douglas Bates  <bates@wisc.edu>
650    
651            * DESCRIPTION (Version): 0.98-3 to CRAN
652    
653            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
654            matrix_solve code (which was really, really wrong).
655    
656    2005-08-07  Douglas Bates  <bates@wisc.edu>
657    
658            * DESCRIPTION (Version): 0.98-2
659    
660            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
661    
662            * R/lmer.R (abbrvNms): new
663            * R/lmer.R (mcmcsamp): allow transformed parameters
664            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
665            for the Harwell-Boeing and the MatrixMarket formats.
666    
667    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * man/dtrMatrix-class.Rd: add examples
670            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
671    
672            * TODO: note the dtpMatrix (docu) bug
673    
674            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
675            in order to ensure that new as.matrix() is used by old functions,
676            e.g., svd(), qr(), eigen(), dist(),..;
677                  apply(), also matplot() or pairs().
678    
679    
680    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
683              add comments about 'control' / lmerControl() arguments
684    
685    2005-07-27  Douglas Bates  <bates@wisc.edu>
686    
687            * man/sleepstudy.Rd: Added the sleep data set.
688            * DESCRIPTION (Version): 0.98-1  released to CRAN
689    
690    2005-07-12  Douglas Bates  <bates@wisc.edu>
691            * man/sleepstudy.Rd: Added the sleep data set.
692    
693            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
694            .Call calls that were producing spurious output.
695    
696    2005-07-05  Douglas Bates  <bates@wisc.edu>
697    
698            * R/lmer.R (lmer): stored updated variance component estimates in
699            mer object for the generalized model.  (Bug reported by Renaud
700            Lancelot).
701    
702    2005-07-03  Douglas Bates  <bates@wisc.edu>
703    
704            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
705            unidimensional case.
706    
707    2005-06-08  Douglas Bates  <bates@wisc.edu>
708    
709            * DESCRIPTION (Version): 0.96-1
710    
711            * moved  lmer-class' R and C code moved from lme4 to here
712    
713    2005-06-04  Douglas Bates  <bates@wisc.edu>
714    
715            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
716            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
717    
718    2005-06-02  Douglas Bates  <bates@wisc.edu>
719    
720            * src/Makefile.win: Forgot to update this when Makefile changed.
721    
722    2005-05-11  Douglas Bates  <bates@wisc.edu>
723    
724            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
725            bug reported by Kurt Hornik and Michael Hahsler.
726    
727    2005-05-10  Douglas Bates  <bates@wisc.edu>
728    
729            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
730            logical sparse matrices.  These will also be used in the symbolic
731            analysis for lmer objects.
732    
733            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
734            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
735    
736    2005-05-06  Douglas Bates  <bates@wisc.edu>
737    
738            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
739            colMeans, colSums, rowMeans and rowSums.
740    
741    2005-04-18  Douglas Bates  <bates@wisc.edu>
742    
743            * src/lgCMatrix.[ch]: code for _validate method and stub for
744            multiplication operation.
745    
746            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
747            to dgetrs.
748    
749            * src/init.c: Fix cut-and-paste error in definition of
750            dgeMatrix_matrix_solve
751    
752            * src/{many files}: Tighten code by using ALLOC_SLOT.
753    
754    2005-04-15  Douglas Bates  <bates@wisc.edu>
755    
756            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
757    
758            * DESCRIPTION: Eliminate import of stats.
759    
760    
761    2005-04-06  Douglas Bates  <bates@wisc.edu>
762    
763            * R/AllClass.R : add logical sparse matrix classes
764    
765    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/dgTMatrix.R: add "[" method for triplet matrices
768            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
769    
770    2005-03-31  Douglas Bates  <bates@wisc.edu>
771    
772            * DESCRIPTION (Version): release 0.95-5 to CRAN
773    
774            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
775            * R/sparseMatrix.R: %*%, crossprod()
776            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
777            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
778            * src/lmer.c (lmer_fitted): fix thinko
779    
780  2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782          * R/AllClass.R: add two virtual sparse classes ``on top''          * R/AllClass.R: add two virtual sparse classes ``on top''
# Line 14  Line 793 
793          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
794            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
795    
796  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
797    
798          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
799          * ....          * ....
800    
801  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
802    
803          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
804    
# Line 34  Line 813 
813            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
814          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
815    
816  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
817    
818          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
819    
820  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
821    
822          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
823    
824  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
825    
826          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
827          the package.          the package.
# Line 90  Line 869 
869    
870          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
871    
872  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
873    
874          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
875          for the geMatrix class.          for the geMatrix class.
876    
877  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
878    
879          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
880    
881          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
882    
883  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
884    
885          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
886          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
887    
888  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
889    
890          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
891    
892  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
893    
894          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
895          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
896    
897  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
898    
899          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
900    
901          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
902          for tripletMatrix to matrix.          for tripletMatrix to matrix.
903    
904  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
905    
906          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
907          no longer used.          no longer used.
# Line 134  Line 913 
913          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
914          Fixes part but not all of #15.          Fixes part but not all of #15.
915    
916  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
917    
918          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
919          scalar grouping factors corrected.          scalar grouping factors corrected.
920    
921  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
922    
923          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
924    
925  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
926    
927          * 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
928          .h file can be included.          .h file can be included.
929    
930  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
931    
932          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
933          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
934    
935          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
936    
937  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
938    
939          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
940    
941  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
942    
943          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
944    
945  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
946    
947          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
948    
949  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
950    
951          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
952    
953  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
954    
955          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
956          routines.          routines.
957    
958  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
959    
960          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
961    
962  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
963    
964          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
965    

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