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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1388, Thu Aug 17 22:37:19 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-08-17  Douglas Bates  <bates@R-project.org>
2    
3            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
4            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
5            * src/dtCMatrix.c :Remove code that is no longer used
6            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
7    
8    2006-08-14  Douglas Bates  <bates@R-project.org>
9    
10            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
11            Csparse_to_logical and Csparse_symmetric_to_general.
12            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
13            coercion methods between CsparseMatrix and TsparseMatrix.
14    
15    2006-08-14  Douglas Bates  <bates@R-project.org>
16    
17            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
18            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
19            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
20            possible.
21    
22    2006-08-12  Douglas Bates  <bates@R-project.org>
23    
24            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
25              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
26              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
27              generalize conversions between TsparseMatrix, CsparseMatrix,
28              denseMatrix and matrix.  Preserve triangularity property and
29              propagate Dimnames in the easy cases.
30    
31    2006-08-10  Douglas Bates  <bates@R-project.org>
32    
33            * src/lmer.c: adjust checks in glmer_init for S4SXP
34            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
35            before S4SXP but for the wrong reasons.
36    
37    2006-08-08  Douglas Bates  <bates@R-project.org>
38    
39            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
40            Later modified to return the upper triangle only.
41            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
42    
43    2006-08-07  Douglas Bates  <bates@R-project.org>
44    
45            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
46            R-level conversion to a sparse symmetric class.
47            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
48            Remove conversion to sparse symmetric classes (now done in C code).
49    
50    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
53            * man/band.Rd:  adapt the \dontshow{} unit test.
54    
55    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * DESCRIPTION (Version): 0.995-14  for CRAN
58    
59            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
60    
61            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
62            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
63    
64            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
65            * R/Tsparse.R (tril, triu, band): methods
66            * R/dgRMatrix.R (tril, ...):    ditto
67            * man/band.Rd:                  ditto
68    
69    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Matrix.R (head, tail): directly use utils:::head.matrix
72                    to be up-to-date automatically.
73    
74    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
77    
78            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
79            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
80            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
81            such that the S4 objects are always created by the current version
82            of R and 'Matrix' class definitions.
83    
84    2006-08-01  Douglas Bates  <bates@R-project.org>
85    
86            * R/lmer.R (LMEoptimize method), tests/lmer.R,
87            inst/external/test3comp.rda: Added warnings for convergence on
88            boundary and test cases.
89    
90            * src/lmer.c (mer_postVar): Modified to return the variances that
91            are marginal to the fixed effects, not conditional on them (which
92            is what the bVar slot contents represent).
93    
94    2006-07-31  Douglas Bates  <bates@R-project.org>
95    
96            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
97            function which calls the C function mer_hat_trace2.
98    
99            * man/ranef.Rd: Include description of "postVar" argument and
100            producing a caterpillar plot.
101    
102    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * NAMESPACE:    change  "correlation" to "corMatrix"
105            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
106            * R/dpoMatrix.R: ditto
107            * R/lmer.R:      ditto
108    
109    2006-07-28  Douglas Bates  <bates@R-project.org>
110    
111            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
112            RZXinv slot's contents into a separate internal function that can
113            be used in mer_hat_trace.
114    
115    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
118            via new smart
119            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
120            utility functions.
121    
122    
123    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Csparse.R (tril, triu, band): do return *triangular* classed
126            matrices when appropriate; band() even symmetric ones.
127            (replCmat): extend to potentially all "CsparseMatrix"
128            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
129            allow subassignment for special sparse matrices.
130    
131            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
132    
133            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
134            argument; in glmer_*(): print only if(verbose).
135    
136            speed-optimize a few places by moving REAL(.) out of loops.
137    
138            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
139    
140    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
143                    since that wrongly triggers also for M[ logi , ]
144    
145            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
146            a symmetric matrix that results in a non-symmetric one.
147            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
148    
149            * R/dMatrix.R: make round(M) work as round(M, 0)
150    
151            * R/dgTMatrix.R (image): coordinate system and axis now use
152            1-based indices, not 0-based ones.
153    
154            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
155            * tests/indexing.R: test it.
156    
157            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
158            * man/isSymmetric-methods.Rd: and document it.
159    
160            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
161            * man/SparseM-conv.Rd: docu them
162    
163            * tests/other-pkgs.R: renamed from tests/graph.R and add example
164                    for 'SparseM' conversions
165    
166    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
167    
168            * R/Matrix.R (head): added head() and tail() methods.
169    
170    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * DESCRIPTION (Version): 0.995-12 released to CRAN
173    
174    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * tests/simple.R: add check for correct dsT -> dgT coercion;
177                    add check for correct printing of symmetric sparse matrices.
178    
179            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
180            for sparse symmetric matrices.
181    
182            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
183            diagonal twice.
184    
185    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
186    
187            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
188            being applied to the x slot (detected by Brian Ripley).
189    
190    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
193    
194            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
195    
196    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * src/lgCMatrix.c (lgCMatrix_diag): new function
199            * R/lgCMatrix.R (diag): for new method
200    
201            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
202                 ==> construction of illegal "*gTMatrix" via new() should
203                 now be much less easy:
204            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
205    
206            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
207                    directly.
208            * man/Matrix.Rd: documents it.
209    
210    2006-07-06  Douglas Bates  <bates@R-project.org>
211    
212            * src/pedigree.c (pedigree_inbreeding): Correction in
213            initialization.  This function is not currently being used and is
214            not fully tested.
215    
216            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
217            Introduced the glmer class.  Added code for mcmcmsamp on glmer
218            objects.  Modified validity check on pedigree objects to account
219            for nonparallel patterns of missingness of parents.
220    
221            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
222            class.
223    
224    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/pMatrix.R: coercion pMatrix -> Tsparse
227    
228    2006-06-12  Douglas Bates  <bates@R-project.org>
229    
230            * DESCRIPTION (Version): 0.995-11 released to CRAN
231    
232            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
233            the output from mcmcsamp.
234    
235    2006-06-10  Douglas Bates  <bates@R-project.org>
236    
237            * R/lmer.R (simulestimate): added C code for calculating the trace
238            of the hat matrix.
239    
240    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
243            classes.
244            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
245    
246    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgTMatrix.R (colSums): etc. All four of
249            colSums(), rowSums(), colMeans(), rowMeans() now should work for
250            all "Matrices".
251    
252    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * R/lmer.R (panel.ci): Add a reference line at zero and a
255            background grid to the qqmath plot of ranef.lmer.
256    
257    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
260            grouping factors to be specified in the formula as (1|foo/bar).
261    
262    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * R/lmer.R (findbars and others): Change check of is.numeric to
265            !is.language to resolve the bug reported by Jacob Wegelin.
266    
267            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
268            code to evaluate inbreeding coefficients without calculating T,
269            based on code in Sargolzaei and Iwaisaki's paper.
270    
271    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
274            generic and mer methods for isNested and denomDF. This denomDF was
275            an attempt to emulate that in lme but I don't think that makes
276            sense.  Use the trace of the hat matrix instead.
277    
278    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
281            the C code depending on a slot structure that's no longer valid.
282            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
283    
284    
285    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
286    
287            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
288            of lowerTriMatrix generic and methods to tril (also upper to triu)
289            and added a general band extractor.
290    
291    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * R/pedigree.R (pedigree): Replace sire and dam values outside the
294            allowable range with NAs. Added a corresponding check in the
295            validity check for the pedigree class.
296    
297            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
298            crossprod methods now inherits from symmetricMatrix.
299    
300    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
303            generics lowerTriMatrix and upperTriMatrix along with methods for
304            the Csparse virtual class.  Also added a C function Csparse_band
305            that implements these methods by calling cholmod_band.
306    
307    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
310            erased when it was NULL.  This led to invalid subselections!
311    
312    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
313    
314            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
315            in method for "t" so as not to lose the unit diagonal property.
316    
317    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
318    
319            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
320            and methods.  This is now an option to the ranef method for the
321            mer class.
322    
323            * src/cs_utils.c: Ensure that the nz component is -1 for a
324            compressed column-oriented matrix.  Minor formatting cleanup.
325    
326            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
327            objects.
328    
329    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
332            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
333    
334    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
337            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
338    
339            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
340            for the dtCMatrix class.
341    
342    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
345            and methods for it.
346    
347    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
350            arguments, such that M %*% 1:6 now works
351            * Tests/matprod.R: test the above
352    
353    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
354    
355            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
356            the ranef.lmer class.
357    
358            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
359            methods to extract the posterior variances from the bVar slot.
360    
361    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
364            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
365    
366            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
367            * tests/simple: (extended)
368    
369            * R/sparseMatrix.R (isTriangular): now using much improved
370            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
371    
372    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
375            (problem report from Franklin Parlamis).  This should be done
376            generally.
377    
378    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
379    
380            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
381            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
382            update the plot methods.
383    
384    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * R/lmer.R (resid and ranef methods):  Added methods for the
387            "residuals" and "resid" generic but only for linear mixed model
388            fits.  Changed the ranef method to return a list of data frames so
389            that the plot methods now work.
390    
391    2006-03-16  Douglas Bates  <bates@bates2>
392    
393            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
394            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
395    
396            * DESCRIPTION (Date): New release
397    
398    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
401    
402            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
403            * man/KNex.Rd: and other help files
404            * tests/*.R: several ones needed adaption
405            * inst/doc/Comparisons.Rnw: ditto
406    
407    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
410    
411            * tests/indexing.R: tests for new [<- methods for sparse matrices.
412    
413    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
416    
417            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
418    
419    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/dMatrix.R: enable things like  M [ M < 10 ]
422            * R/dgeMatrix.R: implement it
423    
424    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/AllClass.R: define "summary.mer" and "*.lmer"
427            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
428            * R/lmer.R (show): now works with summary()
429    
430    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
433            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
434                    support the above
435    
436    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
437    
438            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
439            Use glmFit$prior.weights for weights in a glmm.
440            Allow an option usePQL = FALSE to skip the PQL steps for the
441            Laplace method (and, in time, the AGQ method).
442    
443            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
444            into a separate function internal_mer_Xfactor to be able to call
445            it from internal_bhat.
446    
447    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/Class+Meth.R (tstMatrixClass): function for much better
450            testing; now again of all actual classes.
451    
452            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
453                    use macros and define make_d_matrix_* and make_i_matrix_*
454                    where _i_ is for the ldense routines:
455    
456            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
457            * src/ldense.c (lsyMatrix_as_lgeMatrix):
458    
459            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
460    
461    
462    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
465                    many different kinds of matrices.
466            * R/*.R: quite a few new methods were needed for R CMD check with
467                    new Matrix().  Very good for users playing around.
468    
469    
470    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * src/dgeMatrix.c (dMatrix_validate): new
473            * src/Mutils.c (dense_nonpacked_validate): new
474    
475            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
476    
477    
478    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
481    
482    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * DESCRIPTION (Version): 0.99-6 released to CRAN
485    
486            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
487            segfault in cases with multiple non-nested grouping factors.
488    
489    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
492                    (Depends): also on 'utils'
493    
494            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
495            * R/diagMatrix.R (Diagonal): constructor and methods for
496            diagonal matrices
497    
498            * R/ltTMatrix.R: new "minimal methods"
499    
500    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
503            all methods (and help files).
504    
505    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
508                    for case (dimn.  op  no_dimn.)
509    
510    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
511    
512            * DESCRIPTION (Version): 0.99-2  released to CRAN
513    
514    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
517            by Julian Faraway.
518    
519    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/Auxiliaries.R (try_as): new utility
522            * R/sparseMatrix.R: use try_as() in coercion to original class
523    
524    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
527    
528    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/Auxiliaries.R (dimNamesCheck): added
531    
532            * R/Matrix.R (as.array), (as.vector): new
533    
534    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
537                    default.
538            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
539                    "pMatrix" now contains "sparseMatrix"
540    
541    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * tests/Class+Meth.R: new tests; t(t(m)) == m
544    
545            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
546    
547            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
548            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
549    
550            * R/dspMatrix.R: typo in "t" method
551    
552    2005-09-18  Douglas Bates  <bates@wisc.edu>
553    
554            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
555            * R/Tsparse.R: instead of R/gTMatrix.R
556            * R/Csparse.R: new
557            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
558            * src/Tsparse.c: new; many trivial methods calling cholmod_()
559            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
560                            via cholmod
561    
562    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/Auxiliaries.R (non0ind): new function using new C code
565            * src/dgCMatrix.c (compressed_non_0_ij): new utility
566    
567    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
568    
569            * src/chm_common.h: header file required by all C sources that
570            call CHOLMOD functions.  It defines a cholmod_common structure
571            called 'c' whose address is passed as the last argument to
572            (virtually) every CHOLMOD function.
573    
574            * src/Pattern.c: Simple example of the use of CHOLMOD.
575    
576            * src/init.c: initialize and finalize the cholmod_common structure.
577    
578            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
579            LDL and CCOLAMD from the U. of Florida sparse matrix library.
580    
581    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * inst/test-tools.R: new file collecting the utility functions used
584                    in ./tests/*.R
585    
586            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
587            * R/Matrix.R (cbind2): methods for NULL and missing
588    
589    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/AllClass.R: new "index" class for "[" and "[<-":
592                    First cut at "symmetricMatrix" and "triangularMatrix"
593            * R/gTMatrix.R (.ind.prep): new function;
594                    Logical and character indexing now work too.
595            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
596            * tests/indexing.R: new, including *.Rout.save
597            * tests/dgTMatrix.R: new
598    
599    2005-08-29  Douglas Bates  <bates@wisc.edu>
600    
601            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
602            indicator pos not being updated.  Also enforced upper triangular
603            for symmetric case.  Need to coerce edges component of elements of
604            edge list - grr! (Why don't they define their classes cleanly?)
605    
606    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R:  added first "[<-" methods; not yet functional
609            * R/denseMatrix.R: ditto
610            * man/Subassign-methods.Rd: new help file for these
611    
612    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * DESCRIPTION (Version): 0.98-6
615    
616            * R/denseMatrix.R: new file for "[" fallback methods for all dense
617            matrices.
618    
619    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
622                    as( <logical>, "matrix")
623    
624            * R/pMatrix.R: coercion to "lgTMatrix"
625    
626            * R/gTMatrix.R: new virtual class to define "[" methods for.
627            * man/gTMatrix-class.Rd:
628            * General slight re-organization of where "[" methods are defined.
629              more to come.
630    
631    2005-08-18  Douglas Bates  <bates@wisc.edu>
632    
633            * DESCRIPTION (Version): 0.98-5  released to CRAN
634    
635            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
636            * .....
637    
638    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
639    
640            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
641            or glmer objects.
642    
643    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
646    
647    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
648    
649            * R/HBMM.R: finish re-writing R-only code.
650    
651    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
652    
653            * man/externalFormats.Rd: move documentation for writeHB and
654            writeMM here.
655    
656            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
657            (suggested by Paul Roecker).
658    
659            * tests/validObj.R (assertError): Comment out test that is failing
660            after recent changes in r-devel.
661    
662    
663    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/AllClass.R: intermediate virtual class "denseMatrix"
666            * man/denseMatrix-class.Rd
667            * NAMESPACE: export it, and also export
668            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
669    
670    2005-08-10  Douglas Bates  <bates@wisc.edu>
671    
672            * DESCRIPTION (Version): 0.98-3 to CRAN
673    
674            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
675            matrix_solve code (which was really, really wrong).
676    
677    2005-08-07  Douglas Bates  <bates@wisc.edu>
678    
679            * DESCRIPTION (Version): 0.98-2
680    
681            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
682    
683            * R/lmer.R (abbrvNms): new
684            * R/lmer.R (mcmcsamp): allow transformed parameters
685            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
686            for the Harwell-Boeing and the MatrixMarket formats.
687    
688    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * man/dtrMatrix-class.Rd: add examples
691            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
692    
693            * TODO: note the dtpMatrix (docu) bug
694    
695            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
696            in order to ensure that new as.matrix() is used by old functions,
697            e.g., svd(), qr(), eigen(), dist(),..;
698                  apply(), also matplot() or pairs().
699    
700    
701    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
704              add comments about 'control' / lmerControl() arguments
705    
706    2005-07-27  Douglas Bates  <bates@wisc.edu>
707    
708            * man/sleepstudy.Rd: Added the sleep data set.
709            * DESCRIPTION (Version): 0.98-1  released to CRAN
710    
711    2005-07-12  Douglas Bates  <bates@wisc.edu>
712            * man/sleepstudy.Rd: Added the sleep data set.
713    
714            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
715            .Call calls that were producing spurious output.
716    
717    2005-07-05  Douglas Bates  <bates@wisc.edu>
718    
719            * R/lmer.R (lmer): stored updated variance component estimates in
720            mer object for the generalized model.  (Bug reported by Renaud
721            Lancelot).
722    
723    2005-07-03  Douglas Bates  <bates@wisc.edu>
724    
725            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
726            unidimensional case.
727    
728    2005-06-08  Douglas Bates  <bates@wisc.edu>
729    
730            * DESCRIPTION (Version): 0.96-1
731    
732            * moved  lmer-class' R and C code moved from lme4 to here
733    
734    2005-06-04  Douglas Bates  <bates@wisc.edu>
735    
736            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
737            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
738    
739    2005-06-02  Douglas Bates  <bates@wisc.edu>
740    
741            * src/Makefile.win: Forgot to update this when Makefile changed.
742    
743    2005-05-11  Douglas Bates  <bates@wisc.edu>
744    
745            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
746            bug reported by Kurt Hornik and Michael Hahsler.
747    
748    2005-05-10  Douglas Bates  <bates@wisc.edu>
749    
750            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
751            logical sparse matrices.  These will also be used in the symbolic
752            analysis for lmer objects.
753    
754            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
755            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
756    
757    2005-05-06  Douglas Bates  <bates@wisc.edu>
758    
759            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
760            colMeans, colSums, rowMeans and rowSums.
761    
762    2005-04-18  Douglas Bates  <bates@wisc.edu>
763    
764            * src/lgCMatrix.[ch]: code for _validate method and stub for
765            multiplication operation.
766    
767            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
768            to dgetrs.
769    
770            * src/init.c: Fix cut-and-paste error in definition of
771            dgeMatrix_matrix_solve
772    
773            * src/{many files}: Tighten code by using ALLOC_SLOT.
774    
775    2005-04-15  Douglas Bates  <bates@wisc.edu>
776    
777            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
778    
779            * DESCRIPTION: Eliminate import of stats.
780    
781    
782    2005-04-06  Douglas Bates  <bates@wisc.edu>
783    
784            * R/AllClass.R : add logical sparse matrix classes
785    
786    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * R/dgTMatrix.R: add "[" method for triplet matrices
789            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
790    
791    2005-03-31  Douglas Bates  <bates@wisc.edu>
792    
793            * DESCRIPTION (Version): release 0.95-5 to CRAN
794    
795            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
796            * R/sparseMatrix.R: %*%, crossprod()
797            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
798            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
799            * src/lmer.c (lmer_fitted): fix thinko
800    
801    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/AllClass.R: add two virtual sparse classes ``on top''
804    
805    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
808                    correspondingly fix examples and tests/ since new()
809                    doesn't work for virtual classes.
810    
811    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/Matrix.R (as.matrix): method and one for unname()
814            * tests/dpoMatrix.R: tests should now be less platform dependent;
815              also run for R 2.1.0; using as.matrix()
816    
817    2005-03-15  Douglas Bates  <bates@wisc.edu>
818    
819            * R/pMatrix.R: "pMatrix" class added
820            * ....
821    
822    2005-03-14  Douglas Bates  <bates@wisc.edu>
823    
824            * R/dtpMatrix.R: Add unpack method and an example.
825    
826            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
827            of general symmetric matrices and associated S4 methods.
828    
829    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
830            +
831    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/dgeMatrix.R (setAs): and many other files: more coercion,
834              crossprod() and "%*%" methods added; tests, too.
835            * tests/matprod.R: new, for testing these
836    
837    2005-03-03  Douglas Bates  <bates@wisc.edu>
838    
839            * src/lmer.c (lmer_fitted): Added.
840    
841    2005-03-02  Douglas Bates  <bates@wisc.edu>
842    
843            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
844    
845    2005-02-28  Douglas Bates  <bates@wisc.edu>
846    
847            * src/*.c,po/,inst/po: Internationalization and localization of
848            the package.
849    
850            * src/ldl.[ch]: Removed these as their contents are referenced in the
851            R_ldl.c file.
852    
853            * src/flame.[ch]: Removed these source files.
854    
855            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
856    
857            * src/LU.[ch],src/init.c: absorb in factorizations
858    
859            * src/Mutils.h: prepare for internationalization
860    
861            * src/cblas.h: move the enum definitions to Mutils.h and remove
862            this file
863    
864    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
867    
868            * R/dtrMatrix.R: fix t() method
869    
870            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
871            * NAMESPACE: export them (and import generics from "methods")
872            * tests/group-methods.R : and test them.
873    
874            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
875            border case
876    
877    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
878    
879            * DESCRIPTION (Version): 0.95-2  released to CRAN
880    
881            * src/dgBCMatrix.c:
882            * src/lmer.c: many changes
883            * ...
884    
885    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/Matrix.R: add more sophisticated show() method.
888    
889    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
890    
891            * */* : almost complete reorganization of classes.
892    
893    2005-01-26  Douglas Bates  <bates@wisc.edu>
894    
895            * R/AllGeneric.R: Added matrix exponential generic expm and a method
896            for the geMatrix class.
897    
898    2005-01-24  Douglas Bates  <bates@wisc.edu>
899    
900            * src/Makefile (clean): Remove *.a and *.so
901    
902            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
903    
904    2005-01-23  Douglas Bates  <bates@wisc.edu>
905    
906            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
907            had an effect in cases with more than 2 grouping factors.
908    
909    2005-01-03  Douglas Bates  <bates@wisc.edu>
910    
911            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
912    
913    2004-12-23  Douglas Bates  <bates@wisc.edu>
914    
915            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
916            and R_useDynamicSymbols (suggested by B.D.Ripley).
917    
918    2004-12-14  Douglas Bates  <bates@wisc.edu>
919    
920            * R/sscMatrix.R: Add determinant methods
921    
922            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
923            for tripletMatrix to matrix.
924    
925    2004-12-13  Douglas Bates  <bates@wisc.edu>
926    
927            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
928            no longer used.
929    
930            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
931            with dynamic allocation of scratch arrays.
932    
933            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
934            for multivariate random effects with multiple grouping factors.
935            Fixes part but not all of #15.
936    
937    2004-12-03  Douglas Bates  <bates@wisc.edu>
938    
939            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
940            scalar grouping factors corrected.
941    
942    2004-11-29  Douglas Bates  <bates@wisc.edu>
943    
944            * src/bCrosstab.c: remove diag_update which is no longer used
945    
946    2004-11-16  Douglas Bates  <bates@wisc.edu>
947    
948          * 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
949          .h file can be included.          .h file can be included.
950    
951  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
952    
953          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
954          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
955    
956          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
957    
958  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
959    
960          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
961    
962  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
963    
964          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
965    
966  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
967    
968          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
969    
970  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
971    
972          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
973    
974  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
975    
976          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
977          routines.          routines.
978    
979  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
980    
981          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
982    
983  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
984    
985          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
986    

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