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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1370, Mon Aug 14 19:00:02 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-08-14  Douglas Bates  <bates@R-project.org>
2    
3            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
4            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
5            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
6            possible.
7    
8    2006-08-12  Douglas Bates  <bates@R-project.org>
9    
10            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
11              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
12              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
13              generalize conversions between TsparseMatrix, CsparseMatrix,
14              denseMatrix and matrix.  Preserve triangularity property and
15              propagate Dimnames in the easy cases.
16    
17    2006-08-10  Douglas Bates  <bates@R-project.org>
18    
19            * src/lmer.c: adjust checks in glmer_init for S4SXP
20            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
21            before S4SXP but for the wrong reasons.
22    
23    2006-08-08  Douglas Bates  <bates@R-project.org>
24    
25            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
26            Later modified to return the upper triangle only.
27            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
28    
29    2006-08-07  Douglas Bates  <bates@R-project.org>
30    
31            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
32            R-level conversion to a sparse symmetric class.
33            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
34            Remove conversion to sparse symmetric classes (now done in C code).
35    
36    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
39            * man/band.Rd:  adapt the \dontshow{} unit test.
40    
41    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * DESCRIPTION (Version): 0.995-14  for CRAN
44    
45            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
46    
47            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
48            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
49    
50            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
51            * R/Tsparse.R (tril, triu, band): methods
52            * R/dgRMatrix.R (tril, ...):    ditto
53            * man/band.Rd:                  ditto
54    
55    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (head, tail): directly use utils:::head.matrix
58                    to be up-to-date automatically.
59    
60    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
63    
64            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
65            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
66            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
67            such that the S4 objects are always created by the current version
68            of R and 'Matrix' class definitions.
69    
70    2006-08-01  Douglas Bates  <bates@R-project.org>
71    
72            * R/lmer.R (LMEoptimize method), tests/lmer.R,
73            inst/external/test3comp.rda: Added warnings for convergence on
74            boundary and test cases.
75    
76            * src/lmer.c (mer_postVar): Modified to return the variances that
77            are marginal to the fixed effects, not conditional on them (which
78            is what the bVar slot contents represent).
79    
80    2006-07-31  Douglas Bates  <bates@R-project.org>
81    
82            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
83            function which calls the C function mer_hat_trace2.
84    
85            * man/ranef.Rd: Include description of "postVar" argument and
86            producing a caterpillar plot.
87    
88    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * NAMESPACE:    change  "correlation" to "corMatrix"
91            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
92            * R/dpoMatrix.R: ditto
93            * R/lmer.R:      ditto
94    
95    2006-07-28  Douglas Bates  <bates@R-project.org>
96    
97            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
98            RZXinv slot's contents into a separate internal function that can
99            be used in mer_hat_trace.
100    
101    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
104            via new smart
105            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
106            utility functions.
107    
108    
109    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Csparse.R (tril, triu, band): do return *triangular* classed
112            matrices when appropriate; band() even symmetric ones.
113            (replCmat): extend to potentially all "CsparseMatrix"
114            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
115            allow subassignment for special sparse matrices.
116    
117            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
118    
119            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
120            argument; in glmer_*(): print only if(verbose).
121    
122            speed-optimize a few places by moving REAL(.) out of loops.
123    
124            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
125    
126    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
129                    since that wrongly triggers also for M[ logi , ]
130    
131            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
132            a symmetric matrix that results in a non-symmetric one.
133            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
134    
135            * R/dMatrix.R: make round(M) work as round(M, 0)
136    
137            * R/dgTMatrix.R (image): coordinate system and axis now use
138            1-based indices, not 0-based ones.
139    
140            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
141            * tests/indexing.R: test it.
142    
143            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
144            * man/isSymmetric-methods.Rd: and document it.
145    
146            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
147            * man/SparseM-conv.Rd: docu them
148    
149            * tests/other-pkgs.R: renamed from tests/graph.R and add example
150                    for 'SparseM' conversions
151    
152    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
153    
154            * R/Matrix.R (head): added head() and tail() methods.
155    
156    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * DESCRIPTION (Version): 0.995-12 released to CRAN
159    
160    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * tests/simple.R: add check for correct dsT -> dgT coercion;
163                    add check for correct printing of symmetric sparse matrices.
164    
165            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
166            for sparse symmetric matrices.
167    
168            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
169            diagonal twice.
170    
171    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
172    
173            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
174            being applied to the x slot (detected by Brian Ripley).
175    
176    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
179    
180            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
181    
182    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * src/lgCMatrix.c (lgCMatrix_diag): new function
185            * R/lgCMatrix.R (diag): for new method
186    
187            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
188                 ==> construction of illegal "*gTMatrix" via new() should
189                 now be much less easy:
190            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
191    
192            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
193                    directly.
194            * man/Matrix.Rd: documents it.
195    
196    2006-07-06  Douglas Bates  <bates@R-project.org>
197    
198            * src/pedigree.c (pedigree_inbreeding): Correction in
199            initialization.  This function is not currently being used and is
200            not fully tested.
201    
202            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
203            Introduced the glmer class.  Added code for mcmcmsamp on glmer
204            objects.  Modified validity check on pedigree objects to account
205            for nonparallel patterns of missingness of parents.
206    
207            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
208            class.
209    
210    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/pMatrix.R: coercion pMatrix -> Tsparse
213    
214    2006-06-12  Douglas Bates  <bates@R-project.org>
215    
216            * DESCRIPTION (Version): 0.995-11 released to CRAN
217    
218            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
219            the output from mcmcsamp.
220    
221    2006-06-10  Douglas Bates  <bates@R-project.org>
222    
223            * R/lmer.R (simulestimate): added C code for calculating the trace
224            of the hat matrix.
225    
226    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
229            classes.
230            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
231    
232    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dgTMatrix.R (colSums): etc. All four of
235            colSums(), rowSums(), colMeans(), rowMeans() now should work for
236            all "Matrices".
237    
238    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
239    
240            * R/lmer.R (panel.ci): Add a reference line at zero and a
241            background grid to the qqmath plot of ranef.lmer.
242    
243    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
244    
245            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
246            grouping factors to be specified in the formula as (1|foo/bar).
247    
248    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/lmer.R (findbars and others): Change check of is.numeric to
251            !is.language to resolve the bug reported by Jacob Wegelin.
252    
253            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
254            code to evaluate inbreeding coefficients without calculating T,
255            based on code in Sargolzaei and Iwaisaki's paper.
256    
257    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
260            generic and mer methods for isNested and denomDF. This denomDF was
261            an attempt to emulate that in lme but I don't think that makes
262            sense.  Use the trace of the hat matrix instead.
263    
264    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
267            the C code depending on a slot structure that's no longer valid.
268            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
269    
270    
271    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
272    
273            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
274            of lowerTriMatrix generic and methods to tril (also upper to triu)
275            and added a general band extractor.
276    
277    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
278    
279            * R/pedigree.R (pedigree): Replace sire and dam values outside the
280            allowable range with NAs. Added a corresponding check in the
281            validity check for the pedigree class.
282    
283            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
284            crossprod methods now inherits from symmetricMatrix.
285    
286    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
287    
288            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
289            generics lowerTriMatrix and upperTriMatrix along with methods for
290            the Csparse virtual class.  Also added a C function Csparse_band
291            that implements these methods by calling cholmod_band.
292    
293    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
296            erased when it was NULL.  This led to invalid subselections!
297    
298    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
299    
300            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
301            in method for "t" so as not to lose the unit diagonal property.
302    
303    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
304    
305            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
306            and methods.  This is now an option to the ranef method for the
307            mer class.
308    
309            * src/cs_utils.c: Ensure that the nz component is -1 for a
310            compressed column-oriented matrix.  Minor formatting cleanup.
311    
312            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
313            objects.
314    
315    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
318            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
319    
320    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
321    
322            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
323            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
324    
325            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
326            for the dtCMatrix class.
327    
328    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
329    
330            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
331            and methods for it.
332    
333    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
336            arguments, such that M %*% 1:6 now works
337            * Tests/matprod.R: test the above
338    
339    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
342            the ranef.lmer class.
343    
344            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
345            methods to extract the posterior variances from the bVar slot.
346    
347    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
350            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
351    
352            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
353            * tests/simple: (extended)
354    
355            * R/sparseMatrix.R (isTriangular): now using much improved
356            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
357    
358    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
359    
360            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
361            (problem report from Franklin Parlamis).  This should be done
362            generally.
363    
364    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
367            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
368            update the plot methods.
369    
370    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
371    
372            * R/lmer.R (resid and ranef methods):  Added methods for the
373            "residuals" and "resid" generic but only for linear mixed model
374            fits.  Changed the ranef method to return a list of data frames so
375            that the plot methods now work.
376    
377    2006-03-16  Douglas Bates  <bates@bates2>
378    
379            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
380            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
381    
382            * DESCRIPTION (Date): New release
383    
384    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
387    
388            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
389            * man/KNex.Rd: and other help files
390            * tests/*.R: several ones needed adaption
391            * inst/doc/Comparisons.Rnw: ditto
392    
393    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
396    
397            * tests/indexing.R: tests for new [<- methods for sparse matrices.
398    
399    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
402    
403            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
404    
405    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dMatrix.R: enable things like  M [ M < 10 ]
408            * R/dgeMatrix.R: implement it
409    
410    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/AllClass.R: define "summary.mer" and "*.lmer"
413            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
414            * R/lmer.R (show): now works with summary()
415    
416    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
419            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
420                    support the above
421    
422    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
425            Use glmFit$prior.weights for weights in a glmm.
426            Allow an option usePQL = FALSE to skip the PQL steps for the
427            Laplace method (and, in time, the AGQ method).
428    
429            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
430            into a separate function internal_mer_Xfactor to be able to call
431            it from internal_bhat.
432    
433    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * tests/Class+Meth.R (tstMatrixClass): function for much better
436            testing; now again of all actual classes.
437    
438            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
439                    use macros and define make_d_matrix_* and make_i_matrix_*
440                    where _i_ is for the ldense routines:
441    
442            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
443            * src/ldense.c (lsyMatrix_as_lgeMatrix):
444    
445            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
446    
447    
448    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
451                    many different kinds of matrices.
452            * R/*.R: quite a few new methods were needed for R CMD check with
453                    new Matrix().  Very good for users playing around.
454    
455    
456    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * src/dgeMatrix.c (dMatrix_validate): new
459            * src/Mutils.c (dense_nonpacked_validate): new
460    
461            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
462    
463    
464    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
465    
466            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
467    
468    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * DESCRIPTION (Version): 0.99-6 released to CRAN
471    
472            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
473            segfault in cases with multiple non-nested grouping factors.
474    
475    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
478                    (Depends): also on 'utils'
479    
480            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
481            * R/diagMatrix.R (Diagonal): constructor and methods for
482            diagonal matrices
483    
484            * R/ltTMatrix.R: new "minimal methods"
485    
486    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
489            all methods (and help files).
490    
491    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
494                    for case (dimn.  op  no_dimn.)
495    
496    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
497    
498            * DESCRIPTION (Version): 0.99-2  released to CRAN
499    
500    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
501    
502            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
503            by Julian Faraway.
504    
505    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Auxiliaries.R (try_as): new utility
508            * R/sparseMatrix.R: use try_as() in coercion to original class
509    
510    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
513    
514    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/Auxiliaries.R (dimNamesCheck): added
517    
518            * R/Matrix.R (as.array), (as.vector): new
519    
520    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
523                    default.
524            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
525                    "pMatrix" now contains "sparseMatrix"
526    
527    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * tests/Class+Meth.R: new tests; t(t(m)) == m
530    
531            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
532    
533            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
534            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
535    
536            * R/dspMatrix.R: typo in "t" method
537    
538    2005-09-18  Douglas Bates  <bates@wisc.edu>
539    
540            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
541            * R/Tsparse.R: instead of R/gTMatrix.R
542            * R/Csparse.R: new
543            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
544            * src/Tsparse.c: new; many trivial methods calling cholmod_()
545            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
546                            via cholmod
547    
548    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/Auxiliaries.R (non0ind): new function using new C code
551            * src/dgCMatrix.c (compressed_non_0_ij): new utility
552    
553    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
554    
555            * src/chm_common.h: header file required by all C sources that
556            call CHOLMOD functions.  It defines a cholmod_common structure
557            called 'c' whose address is passed as the last argument to
558            (virtually) every CHOLMOD function.
559    
560            * src/Pattern.c: Simple example of the use of CHOLMOD.
561    
562            * src/init.c: initialize and finalize the cholmod_common structure.
563    
564            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
565            LDL and CCOLAMD from the U. of Florida sparse matrix library.
566    
567    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * inst/test-tools.R: new file collecting the utility functions used
570                    in ./tests/*.R
571    
572            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
573            * R/Matrix.R (cbind2): methods for NULL and missing
574    
575    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/AllClass.R: new "index" class for "[" and "[<-":
578                    First cut at "symmetricMatrix" and "triangularMatrix"
579            * R/gTMatrix.R (.ind.prep): new function;
580                    Logical and character indexing now work too.
581            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
582            * tests/indexing.R: new, including *.Rout.save
583            * tests/dgTMatrix.R: new
584    
585    2005-08-29  Douglas Bates  <bates@wisc.edu>
586    
587            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
588            indicator pos not being updated.  Also enforced upper triangular
589            for symmetric case.  Need to coerce edges component of elements of
590            edge list - grr! (Why don't they define their classes cleanly?)
591    
592    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Matrix.R:  added first "[<-" methods; not yet functional
595            * R/denseMatrix.R: ditto
596            * man/Subassign-methods.Rd: new help file for these
597    
598    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * DESCRIPTION (Version): 0.98-6
601    
602            * R/denseMatrix.R: new file for "[" fallback methods for all dense
603            matrices.
604    
605    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
608                    as( <logical>, "matrix")
609    
610            * R/pMatrix.R: coercion to "lgTMatrix"
611    
612            * R/gTMatrix.R: new virtual class to define "[" methods for.
613            * man/gTMatrix-class.Rd:
614            * General slight re-organization of where "[" methods are defined.
615              more to come.
616    
617    2005-08-18  Douglas Bates  <bates@wisc.edu>
618    
619            * DESCRIPTION (Version): 0.98-5  released to CRAN
620    
621            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
622            * .....
623    
624    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
625    
626            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
627            or glmer objects.
628    
629    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
632    
633    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
634    
635            * R/HBMM.R: finish re-writing R-only code.
636    
637    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
638    
639            * man/externalFormats.Rd: move documentation for writeHB and
640            writeMM here.
641    
642            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
643            (suggested by Paul Roecker).
644    
645            * tests/validObj.R (assertError): Comment out test that is failing
646            after recent changes in r-devel.
647    
648    
649    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/AllClass.R: intermediate virtual class "denseMatrix"
652            * man/denseMatrix-class.Rd
653            * NAMESPACE: export it, and also export
654            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
655    
656    2005-08-10  Douglas Bates  <bates@wisc.edu>
657    
658            * DESCRIPTION (Version): 0.98-3 to CRAN
659    
660            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
661            matrix_solve code (which was really, really wrong).
662    
663    2005-08-07  Douglas Bates  <bates@wisc.edu>
664    
665            * DESCRIPTION (Version): 0.98-2
666    
667            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
668    
669            * R/lmer.R (abbrvNms): new
670            * R/lmer.R (mcmcsamp): allow transformed parameters
671            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
672            for the Harwell-Boeing and the MatrixMarket formats.
673    
674    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * man/dtrMatrix-class.Rd: add examples
677            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
678    
679            * TODO: note the dtpMatrix (docu) bug
680    
681            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
682            in order to ensure that new as.matrix() is used by old functions,
683            e.g., svd(), qr(), eigen(), dist(),..;
684                  apply(), also matplot() or pairs().
685    
686    
687    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
690              add comments about 'control' / lmerControl() arguments
691    
692    2005-07-27  Douglas Bates  <bates@wisc.edu>
693    
694            * man/sleepstudy.Rd: Added the sleep data set.
695            * DESCRIPTION (Version): 0.98-1  released to CRAN
696    
697    2005-07-12  Douglas Bates  <bates@wisc.edu>
698            * man/sleepstudy.Rd: Added the sleep data set.
699    
700            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
701            .Call calls that were producing spurious output.
702    
703    2005-07-05  Douglas Bates  <bates@wisc.edu>
704    
705            * R/lmer.R (lmer): stored updated variance component estimates in
706            mer object for the generalized model.  (Bug reported by Renaud
707            Lancelot).
708    
709    2005-07-03  Douglas Bates  <bates@wisc.edu>
710    
711            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
712            unidimensional case.
713    
714    2005-06-08  Douglas Bates  <bates@wisc.edu>
715    
716            * DESCRIPTION (Version): 0.96-1
717    
718            * moved  lmer-class' R and C code moved from lme4 to here
719    
720    2005-06-04  Douglas Bates  <bates@wisc.edu>
721    
722            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
723            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
724    
725    2005-06-02  Douglas Bates  <bates@wisc.edu>
726    
727            * src/Makefile.win: Forgot to update this when Makefile changed.
728    
729    2005-05-11  Douglas Bates  <bates@wisc.edu>
730    
731            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
732            bug reported by Kurt Hornik and Michael Hahsler.
733    
734    2005-05-10  Douglas Bates  <bates@wisc.edu>
735    
736            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
737            logical sparse matrices.  These will also be used in the symbolic
738            analysis for lmer objects.
739    
740            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
741            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
742    
743    2005-05-06  Douglas Bates  <bates@wisc.edu>
744    
745            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
746            colMeans, colSums, rowMeans and rowSums.
747    
748    2005-04-18  Douglas Bates  <bates@wisc.edu>
749    
750            * src/lgCMatrix.[ch]: code for _validate method and stub for
751            multiplication operation.
752    
753            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
754            to dgetrs.
755    
756            * src/init.c: Fix cut-and-paste error in definition of
757            dgeMatrix_matrix_solve
758    
759            * src/{many files}: Tighten code by using ALLOC_SLOT.
760    
761    2005-04-15  Douglas Bates  <bates@wisc.edu>
762    
763            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
764    
765            * DESCRIPTION: Eliminate import of stats.
766    
767    
768    2005-04-06  Douglas Bates  <bates@wisc.edu>
769    
770            * R/AllClass.R : add logical sparse matrix classes
771    
772    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/dgTMatrix.R: add "[" method for triplet matrices
775            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
776    
777    2005-03-31  Douglas Bates  <bates@wisc.edu>
778    
779            * DESCRIPTION (Version): release 0.95-5 to CRAN
780    
781            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
782            * R/sparseMatrix.R: %*%, crossprod()
783            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
784            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
785            * src/lmer.c (lmer_fitted): fix thinko
786    
787    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/AllClass.R: add two virtual sparse classes ``on top''
790    
791    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
794                    correspondingly fix examples and tests/ since new()
795                    doesn't work for virtual classes.
796    
797    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/Matrix.R (as.matrix): method and one for unname()
800            * tests/dpoMatrix.R: tests should now be less platform dependent;
801              also run for R 2.1.0; using as.matrix()
802    
803    2005-03-15  Douglas Bates  <bates@wisc.edu>
804    
805            * R/pMatrix.R: "pMatrix" class added
806            * ....
807    
808    2005-03-14  Douglas Bates  <bates@wisc.edu>
809    
810            * R/dtpMatrix.R: Add unpack method and an example.
811    
812            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
813            of general symmetric matrices and associated S4 methods.
814    
815    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
816            +
817    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/dgeMatrix.R (setAs): and many other files: more coercion,
820              crossprod() and "%*%" methods added; tests, too.
821            * tests/matprod.R: new, for testing these
822    
823    2005-03-03  Douglas Bates  <bates@wisc.edu>
824    
825            * src/lmer.c (lmer_fitted): Added.
826    
827    2005-03-02  Douglas Bates  <bates@wisc.edu>
828    
829            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
830    
831    2005-02-28  Douglas Bates  <bates@wisc.edu>
832    
833            * src/*.c,po/,inst/po: Internationalization and localization of
834            the package.
835    
836            * src/ldl.[ch]: Removed these as their contents are referenced in the
837            R_ldl.c file.
838    
839            * src/flame.[ch]: Removed these source files.
840    
841            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
842    
843            * src/LU.[ch],src/init.c: absorb in factorizations
844    
845            * src/Mutils.h: prepare for internationalization
846    
847            * src/cblas.h: move the enum definitions to Mutils.h and remove
848            this file
849    
850    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
853    
854            * R/dtrMatrix.R: fix t() method
855    
856            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
857            * NAMESPACE: export them (and import generics from "methods")
858            * tests/group-methods.R : and test them.
859    
860            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
861            border case
862    
863    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
864    
865            * DESCRIPTION (Version): 0.95-2  released to CRAN
866    
867            * src/dgBCMatrix.c:
868            * src/lmer.c: many changes
869            * ...
870    
871    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/Matrix.R: add more sophisticated show() method.
874    
875    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
876    
877            * */* : almost complete reorganization of classes.
878    
879    2005-01-26  Douglas Bates  <bates@wisc.edu>
880    
881            * R/AllGeneric.R: Added matrix exponential generic expm and a method
882            for the geMatrix class.
883    
884    2005-01-24  Douglas Bates  <bates@wisc.edu>
885    
886            * src/Makefile (clean): Remove *.a and *.so
887    
888            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
889    
890    2005-01-23  Douglas Bates  <bates@wisc.edu>
891    
892            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
893            had an effect in cases with more than 2 grouping factors.
894    
895    2005-01-03  Douglas Bates  <bates@wisc.edu>
896    
897            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
898    
899    2004-12-23  Douglas Bates  <bates@wisc.edu>
900    
901            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
902            and R_useDynamicSymbols (suggested by B.D.Ripley).
903    
904    2004-12-14  Douglas Bates  <bates@wisc.edu>
905    
906            * R/sscMatrix.R: Add determinant methods
907    
908            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
909            for tripletMatrix to matrix.
910    
911    2004-12-13  Douglas Bates  <bates@wisc.edu>
912    
913            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
914            no longer used.
915    
916          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
917          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 920 
920          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
921          Fixes part but not all of #15.          Fixes part but not all of #15.
922    
923  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
924    
925          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
926          scalar grouping factors corrected.          scalar grouping factors corrected.
927    
928  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
929    
930          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
931    
932  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
933    
934          * 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
935          .h file can be included.          .h file can be included.
936    
937  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
938    
939          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
940          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
941    
942          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
943    
944  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
945    
946          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
947    
948  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
949    
950          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
951    
952  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
953    
954          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
955    
956  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
957    
958          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
959    
960  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
961    
962          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
963          routines.          routines.
964    
965  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
966    
967          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
968    
969  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
970    
971          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
972    

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