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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1373, Mon Aug 14 21:15:38 2006 UTC
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1    2006-08-14  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
4            Csparse_to_logical and Csparse_symmetric_to_general.
5            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
6            coercion methods between CsparseMatrix and TsparseMatrix.
7    
8    2006-08-14  Douglas Bates  <bates@R-project.org>
9    
10            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
11            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
12            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
13            possible.
14    
15    2006-08-12  Douglas Bates  <bates@R-project.org>
16    
17            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
18              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
19              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
20              generalize conversions between TsparseMatrix, CsparseMatrix,
21              denseMatrix and matrix.  Preserve triangularity property and
22              propagate Dimnames in the easy cases.
23    
24    2006-08-10  Douglas Bates  <bates@R-project.org>
25    
26            * src/lmer.c: adjust checks in glmer_init for S4SXP
27            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
28            before S4SXP but for the wrong reasons.
29    
30    2006-08-08  Douglas Bates  <bates@R-project.org>
31    
32            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
33            Later modified to return the upper triangle only.
34            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
35    
36    2006-08-07  Douglas Bates  <bates@R-project.org>
37    
38            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
39            R-level conversion to a sparse symmetric class.
40            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
41            Remove conversion to sparse symmetric classes (now done in C code).
42    
43    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
46            * man/band.Rd:  adapt the \dontshow{} unit test.
47    
48    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Version): 0.995-14  for CRAN
51    
52            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
53    
54            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
55            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
56    
57            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
58            * R/Tsparse.R (tril, triu, band): methods
59            * R/dgRMatrix.R (tril, ...):    ditto
60            * man/band.Rd:                  ditto
61    
62    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Matrix.R (head, tail): directly use utils:::head.matrix
65                    to be up-to-date automatically.
66    
67    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
70    
71            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
72            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
73            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
74            such that the S4 objects are always created by the current version
75            of R and 'Matrix' class definitions.
76    
77    2006-08-01  Douglas Bates  <bates@R-project.org>
78    
79            * R/lmer.R (LMEoptimize method), tests/lmer.R,
80            inst/external/test3comp.rda: Added warnings for convergence on
81            boundary and test cases.
82    
83            * src/lmer.c (mer_postVar): Modified to return the variances that
84            are marginal to the fixed effects, not conditional on them (which
85            is what the bVar slot contents represent).
86    
87    2006-07-31  Douglas Bates  <bates@R-project.org>
88    
89            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
90            function which calls the C function mer_hat_trace2.
91    
92            * man/ranef.Rd: Include description of "postVar" argument and
93            producing a caterpillar plot.
94    
95    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * NAMESPACE:    change  "correlation" to "corMatrix"
98            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
99            * R/dpoMatrix.R: ditto
100            * R/lmer.R:      ditto
101    
102    2006-07-28  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
105            RZXinv slot's contents into a separate internal function that can
106            be used in mer_hat_trace.
107    
108    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
111            via new smart
112            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
113            utility functions.
114    
115    
116    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Csparse.R (tril, triu, band): do return *triangular* classed
119            matrices when appropriate; band() even symmetric ones.
120            (replCmat): extend to potentially all "CsparseMatrix"
121            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
122            allow subassignment for special sparse matrices.
123    
124            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
125    
126            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
127            argument; in glmer_*(): print only if(verbose).
128    
129            speed-optimize a few places by moving REAL(.) out of loops.
130    
131            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
132    
133    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
136                    since that wrongly triggers also for M[ logi , ]
137    
138            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
139            a symmetric matrix that results in a non-symmetric one.
140            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
141    
142            * R/dMatrix.R: make round(M) work as round(M, 0)
143    
144            * R/dgTMatrix.R (image): coordinate system and axis now use
145            1-based indices, not 0-based ones.
146    
147            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
148            * tests/indexing.R: test it.
149    
150            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
151            * man/isSymmetric-methods.Rd: and document it.
152    
153            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
154            * man/SparseM-conv.Rd: docu them
155    
156            * tests/other-pkgs.R: renamed from tests/graph.R and add example
157                    for 'SparseM' conversions
158    
159    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
160    
161            * R/Matrix.R (head): added head() and tail() methods.
162    
163    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * DESCRIPTION (Version): 0.995-12 released to CRAN
166    
167    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * tests/simple.R: add check for correct dsT -> dgT coercion;
170                    add check for correct printing of symmetric sparse matrices.
171    
172            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
173            for sparse symmetric matrices.
174    
175            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
176            diagonal twice.
177    
178    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
179    
180            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
181            being applied to the x slot (detected by Brian Ripley).
182    
183    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
186    
187            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
188    
189    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/lgCMatrix.c (lgCMatrix_diag): new function
192            * R/lgCMatrix.R (diag): for new method
193    
194            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
195                 ==> construction of illegal "*gTMatrix" via new() should
196                 now be much less easy:
197            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
198    
199            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
200                    directly.
201            * man/Matrix.Rd: documents it.
202    
203    2006-07-06  Douglas Bates  <bates@R-project.org>
204    
205            * src/pedigree.c (pedigree_inbreeding): Correction in
206            initialization.  This function is not currently being used and is
207            not fully tested.
208    
209            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
210            Introduced the glmer class.  Added code for mcmcmsamp on glmer
211            objects.  Modified validity check on pedigree objects to account
212            for nonparallel patterns of missingness of parents.
213    
214            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
215            class.
216    
217    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/pMatrix.R: coercion pMatrix -> Tsparse
220    
221    2006-06-12  Douglas Bates  <bates@R-project.org>
222    
223            * DESCRIPTION (Version): 0.995-11 released to CRAN
224    
225            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
226            the output from mcmcsamp.
227    
228    2006-06-10  Douglas Bates  <bates@R-project.org>
229    
230            * R/lmer.R (simulestimate): added C code for calculating the trace
231            of the hat matrix.
232    
233    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
236            classes.
237            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
238    
239    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgTMatrix.R (colSums): etc. All four of
242            colSums(), rowSums(), colMeans(), rowMeans() now should work for
243            all "Matrices".
244    
245    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (panel.ci): Add a reference line at zero and a
248            background grid to the qqmath plot of ranef.lmer.
249    
250    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
253            grouping factors to be specified in the formula as (1|foo/bar).
254    
255    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
256    
257            * R/lmer.R (findbars and others): Change check of is.numeric to
258            !is.language to resolve the bug reported by Jacob Wegelin.
259    
260            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
261            code to evaluate inbreeding coefficients without calculating T,
262            based on code in Sargolzaei and Iwaisaki's paper.
263    
264    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
267            generic and mer methods for isNested and denomDF. This denomDF was
268            an attempt to emulate that in lme but I don't think that makes
269            sense.  Use the trace of the hat matrix instead.
270    
271    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
274            the C code depending on a slot structure that's no longer valid.
275            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
276    
277    
278    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
279    
280            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
281            of lowerTriMatrix generic and methods to tril (also upper to triu)
282            and added a general band extractor.
283    
284    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/pedigree.R (pedigree): Replace sire and dam values outside the
287            allowable range with NAs. Added a corresponding check in the
288            validity check for the pedigree class.
289    
290            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
291            crossprod methods now inherits from symmetricMatrix.
292    
293    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
296            generics lowerTriMatrix and upperTriMatrix along with methods for
297            the Csparse virtual class.  Also added a C function Csparse_band
298            that implements these methods by calling cholmod_band.
299    
300    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
303            erased when it was NULL.  This led to invalid subselections!
304    
305    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
308            in method for "t" so as not to lose the unit diagonal property.
309    
310    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
313            and methods.  This is now an option to the ranef method for the
314            mer class.
315    
316            * src/cs_utils.c: Ensure that the nz component is -1 for a
317            compressed column-oriented matrix.  Minor formatting cleanup.
318    
319            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
320            objects.
321    
322    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
325            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
326    
327    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
330            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
331    
332            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
333            for the dtCMatrix class.
334    
335    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
338            and methods for it.
339    
340    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
343            arguments, such that M %*% 1:6 now works
344            * Tests/matprod.R: test the above
345    
346    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
349            the ranef.lmer class.
350    
351            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
352            methods to extract the posterior variances from the bVar slot.
353    
354    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
357            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
358    
359            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
360            * tests/simple: (extended)
361    
362            * R/sparseMatrix.R (isTriangular): now using much improved
363            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
364    
365    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
368            (problem report from Franklin Parlamis).  This should be done
369            generally.
370    
371    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
374            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
375            update the plot methods.
376    
377    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/lmer.R (resid and ranef methods):  Added methods for the
380            "residuals" and "resid" generic but only for linear mixed model
381            fits.  Changed the ranef method to return a list of data frames so
382            that the plot methods now work.
383    
384    2006-03-16  Douglas Bates  <bates@bates2>
385    
386            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
387            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
388    
389            * DESCRIPTION (Date): New release
390    
391    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
394    
395            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
396            * man/KNex.Rd: and other help files
397            * tests/*.R: several ones needed adaption
398            * inst/doc/Comparisons.Rnw: ditto
399    
400    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
403    
404            * tests/indexing.R: tests for new [<- methods for sparse matrices.
405    
406    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
409    
410            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
411    
412    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/dMatrix.R: enable things like  M [ M < 10 ]
415            * R/dgeMatrix.R: implement it
416    
417    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/AllClass.R: define "summary.mer" and "*.lmer"
420            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
421            * R/lmer.R (show): now works with summary()
422    
423    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
426            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
427                    support the above
428    
429    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
432            Use glmFit$prior.weights for weights in a glmm.
433            Allow an option usePQL = FALSE to skip the PQL steps for the
434            Laplace method (and, in time, the AGQ method).
435    
436            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
437            into a separate function internal_mer_Xfactor to be able to call
438            it from internal_bhat.
439    
440    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * tests/Class+Meth.R (tstMatrixClass): function for much better
443            testing; now again of all actual classes.
444    
445            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
446                    use macros and define make_d_matrix_* and make_i_matrix_*
447                    where _i_ is for the ldense routines:
448    
449            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
450            * src/ldense.c (lsyMatrix_as_lgeMatrix):
451    
452            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
453    
454    
455    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
458                    many different kinds of matrices.
459            * R/*.R: quite a few new methods were needed for R CMD check with
460                    new Matrix().  Very good for users playing around.
461    
462    
463    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * src/dgeMatrix.c (dMatrix_validate): new
466            * src/Mutils.c (dense_nonpacked_validate): new
467    
468            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
469    
470    
471    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
474    
475    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
476    
477            * DESCRIPTION (Version): 0.99-6 released to CRAN
478    
479            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
480            segfault in cases with multiple non-nested grouping factors.
481    
482    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
485                    (Depends): also on 'utils'
486    
487            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
488            * R/diagMatrix.R (Diagonal): constructor and methods for
489            diagonal matrices
490    
491            * R/ltTMatrix.R: new "minimal methods"
492    
493    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
496            all methods (and help files).
497    
498    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
501                    for case (dimn.  op  no_dimn.)
502    
503    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
504    
505            * DESCRIPTION (Version): 0.99-2  released to CRAN
506    
507    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
510            by Julian Faraway.
511    
512    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Auxiliaries.R (try_as): new utility
515            * R/sparseMatrix.R: use try_as() in coercion to original class
516    
517    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
520    
521    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/Auxiliaries.R (dimNamesCheck): added
524    
525            * R/Matrix.R (as.array), (as.vector): new
526    
527    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
530                    default.
531            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
532                    "pMatrix" now contains "sparseMatrix"
533    
534    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * tests/Class+Meth.R: new tests; t(t(m)) == m
537    
538            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
539    
540            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
541            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
542    
543            * R/dspMatrix.R: typo in "t" method
544    
545    2005-09-18  Douglas Bates  <bates@wisc.edu>
546    
547            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
548            * R/Tsparse.R: instead of R/gTMatrix.R
549            * R/Csparse.R: new
550            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
551            * src/Tsparse.c: new; many trivial methods calling cholmod_()
552            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
553                            via cholmod
554    
555    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Auxiliaries.R (non0ind): new function using new C code
558            * src/dgCMatrix.c (compressed_non_0_ij): new utility
559    
560    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
561    
562            * src/chm_common.h: header file required by all C sources that
563            call CHOLMOD functions.  It defines a cholmod_common structure
564            called 'c' whose address is passed as the last argument to
565            (virtually) every CHOLMOD function.
566    
567            * src/Pattern.c: Simple example of the use of CHOLMOD.
568    
569            * src/init.c: initialize and finalize the cholmod_common structure.
570    
571            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
572            LDL and CCOLAMD from the U. of Florida sparse matrix library.
573    
574    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * inst/test-tools.R: new file collecting the utility functions used
577                    in ./tests/*.R
578    
579            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
580            * R/Matrix.R (cbind2): methods for NULL and missing
581    
582    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/AllClass.R: new "index" class for "[" and "[<-":
585                    First cut at "symmetricMatrix" and "triangularMatrix"
586            * R/gTMatrix.R (.ind.prep): new function;
587                    Logical and character indexing now work too.
588            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
589            * tests/indexing.R: new, including *.Rout.save
590            * tests/dgTMatrix.R: new
591    
592    2005-08-29  Douglas Bates  <bates@wisc.edu>
593    
594            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
595            indicator pos not being updated.  Also enforced upper triangular
596            for symmetric case.  Need to coerce edges component of elements of
597            edge list - grr! (Why don't they define their classes cleanly?)
598    
599    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/Matrix.R:  added first "[<-" methods; not yet functional
602            * R/denseMatrix.R: ditto
603            * man/Subassign-methods.Rd: new help file for these
604    
605    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.98-6
608    
609            * R/denseMatrix.R: new file for "[" fallback methods for all dense
610            matrices.
611    
612    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
615                    as( <logical>, "matrix")
616    
617            * R/pMatrix.R: coercion to "lgTMatrix"
618    
619            * R/gTMatrix.R: new virtual class to define "[" methods for.
620            * man/gTMatrix-class.Rd:
621            * General slight re-organization of where "[" methods are defined.
622              more to come.
623    
624    2005-08-18  Douglas Bates  <bates@wisc.edu>
625    
626            * DESCRIPTION (Version): 0.98-5  released to CRAN
627    
628            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
629            * .....
630    
631    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
632    
633            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
634            or glmer objects.
635    
636    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
639    
640    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
641    
642            * R/HBMM.R: finish re-writing R-only code.
643    
644    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
645    
646            * man/externalFormats.Rd: move documentation for writeHB and
647            writeMM here.
648    
649            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
650            (suggested by Paul Roecker).
651    
652            * tests/validObj.R (assertError): Comment out test that is failing
653            after recent changes in r-devel.
654    
655    
656    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/AllClass.R: intermediate virtual class "denseMatrix"
659            * man/denseMatrix-class.Rd
660            * NAMESPACE: export it, and also export
661            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
662    
663    2005-08-10  Douglas Bates  <bates@wisc.edu>
664    
665            * DESCRIPTION (Version): 0.98-3 to CRAN
666    
667            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
668            matrix_solve code (which was really, really wrong).
669    
670    2005-08-07  Douglas Bates  <bates@wisc.edu>
671    
672            * DESCRIPTION (Version): 0.98-2
673    
674            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
675    
676            * R/lmer.R (abbrvNms): new
677            * R/lmer.R (mcmcsamp): allow transformed parameters
678            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
679            for the Harwell-Boeing and the MatrixMarket formats.
680    
681    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * man/dtrMatrix-class.Rd: add examples
684            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
685    
686            * TODO: note the dtpMatrix (docu) bug
687    
688            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
689            in order to ensure that new as.matrix() is used by old functions,
690            e.g., svd(), qr(), eigen(), dist(),..;
691                  apply(), also matplot() or pairs().
692    
693    
694    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
697              add comments about 'control' / lmerControl() arguments
698    
699    2005-07-27  Douglas Bates  <bates@wisc.edu>
700    
701            * man/sleepstudy.Rd: Added the sleep data set.
702            * DESCRIPTION (Version): 0.98-1  released to CRAN
703    
704    2005-07-12  Douglas Bates  <bates@wisc.edu>
705            * man/sleepstudy.Rd: Added the sleep data set.
706    
707            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
708            .Call calls that were producing spurious output.
709    
710    2005-07-05  Douglas Bates  <bates@wisc.edu>
711    
712            * R/lmer.R (lmer): stored updated variance component estimates in
713            mer object for the generalized model.  (Bug reported by Renaud
714            Lancelot).
715    
716    2005-07-03  Douglas Bates  <bates@wisc.edu>
717    
718            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
719            unidimensional case.
720    
721    2005-06-08  Douglas Bates  <bates@wisc.edu>
722    
723            * DESCRIPTION (Version): 0.96-1
724    
725            * moved  lmer-class' R and C code moved from lme4 to here
726    
727    2005-06-04  Douglas Bates  <bates@wisc.edu>
728    
729            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
730            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
731    
732    2005-06-02  Douglas Bates  <bates@wisc.edu>
733    
734            * src/Makefile.win: Forgot to update this when Makefile changed.
735    
736    2005-05-11  Douglas Bates  <bates@wisc.edu>
737    
738            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
739            bug reported by Kurt Hornik and Michael Hahsler.
740    
741    2005-05-10  Douglas Bates  <bates@wisc.edu>
742    
743            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
744            logical sparse matrices.  These will also be used in the symbolic
745            analysis for lmer objects.
746    
747            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
748            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
749    
750    2005-05-06  Douglas Bates  <bates@wisc.edu>
751    
752            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
753            colMeans, colSums, rowMeans and rowSums.
754    
755    2005-04-18  Douglas Bates  <bates@wisc.edu>
756    
757            * src/lgCMatrix.[ch]: code for _validate method and stub for
758            multiplication operation.
759    
760            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
761            to dgetrs.
762    
763            * src/init.c: Fix cut-and-paste error in definition of
764            dgeMatrix_matrix_solve
765    
766            * src/{many files}: Tighten code by using ALLOC_SLOT.
767    
768    2005-04-15  Douglas Bates  <bates@wisc.edu>
769    
770            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
771    
772            * DESCRIPTION: Eliminate import of stats.
773    
774    
775    2005-04-06  Douglas Bates  <bates@wisc.edu>
776    
777            * R/AllClass.R : add logical sparse matrix classes
778    
779  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
782          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
783    
784  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
785    
786          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
787    
# Line 29  Line 807 
807          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
808            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
809    
810  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
811    
812          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
813          * ....          * ....
814    
815  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
816    
817          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
818    
# Line 49  Line 827 
827            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
828          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
829    
830  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
831    
832          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
833    
834  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
835    
836          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
837    
838  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
839    
840          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
841          the package.          the package.
# Line 105  Line 883 
883    
884          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
885    
886  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
887    
888          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
889          for the geMatrix class.          for the geMatrix class.
890    
891  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
892    
893          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
894    
895          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
896    
897  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
898    
899          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
900          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
901    
902  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
903    
904          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
905    
906  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
907    
908          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
909          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
910    
911  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
912    
913          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
914    
915          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
916          for tripletMatrix to matrix.          for tripletMatrix to matrix.
917    
918  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
919    
920          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
921          no longer used.          no longer used.
# Line 149  Line 927 
927          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
928          Fixes part but not all of #15.          Fixes part but not all of #15.
929    
930  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
931    
932          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
933          scalar grouping factors corrected.          scalar grouping factors corrected.
934    
935  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
936    
937          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
938    
939  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
940    
941          * 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
942          .h file can be included.          .h file can be included.
943    
944  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
945    
946          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
947          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
948    
949          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
950    
951  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
952    
953          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
954    
955  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
956    
957          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
958    
959  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
960    
961          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
962    
963  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
964    
965          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
966    
967  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
968    
969          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
970          routines.          routines.
971    
972  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
973    
974          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
975    
976  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
977    
978          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
979    

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