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revision 726, Thu May 12 14:59:04 2005 UTC revision 1411, Tue Aug 22 01:01:23 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-08-21  Douglas Bates  <bates@R-project.org>
2    
3            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
4            valgrind.
5            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
6            inverses.
7            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
8            -Wall warnings.
9            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
10            Use dup_mMatrix_as_dgeMatrix.
11    
12    2006-08-20  Douglas Bates  <bates@R-project.org>
13    
14            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
15            * tests/sparseQR.R: Added
16            * man/sparseQR-class.Rd: Document methods for qr.* generics
17            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
18    
19    2006-08-19  Douglas Bates  <bates@R-project.org>
20    
21            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
22            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
23            and qr.fitted.
24            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
25            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
26    
27    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
30            the base version has no "..." argument.
31    
32            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
33    
34            * R/Matrix.R: define and
35            * NAMESPACE: export as.numeric() and as.logical() methods.
36                    Let's hope these do not badly slow down something...
37            Finally export the zapsmall() method.
38    
39    2006-08-17  Douglas Bates  <bates@R-project.org>
40    
41            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
42            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
43            * src/dtCMatrix.c :Remove code that is no longer used
44            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
45    
46    2006-08-14  Douglas Bates  <bates@R-project.org>
47    
48            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
49            Csparse_to_logical and Csparse_symmetric_to_general.
50            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
51            coercion methods between CsparseMatrix and TsparseMatrix.
52    
53    2006-08-14  Douglas Bates  <bates@R-project.org>
54    
55            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
56            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
57            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
58            possible.
59    
60    2006-08-12  Douglas Bates  <bates@R-project.org>
61    
62            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
63              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
64              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
65              generalize conversions between TsparseMatrix, CsparseMatrix,
66              denseMatrix and matrix.  Preserve triangularity property and
67              propagate Dimnames in the easy cases.
68    
69    2006-08-10  Douglas Bates  <bates@R-project.org>
70    
71            * src/lmer.c: adjust checks in glmer_init for S4SXP
72            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
73            before S4SXP but for the wrong reasons.
74    
75    2006-08-08  Douglas Bates  <bates@R-project.org>
76    
77            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
78            Later modified to return the upper triangle only.
79            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
80    
81    2006-08-07  Douglas Bates  <bates@R-project.org>
82    
83            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
84            R-level conversion to a sparse symmetric class.
85            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
86            Remove conversion to sparse symmetric classes (now done in C code).
87    
88    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
91            * man/band.Rd:  adapt the \dontshow{} unit test.
92    
93    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version): 0.995-14  for CRAN
96    
97            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
98    
99            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
100            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
101    
102            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
103            * R/Tsparse.R (tril, triu, band): methods
104            * R/dgRMatrix.R (tril, ...):    ditto
105            * man/band.Rd:                  ditto
106    
107    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R (head, tail): directly use utils:::head.matrix
110                    to be up-to-date automatically.
111    
112    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
115    
116            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
117            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
118            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
119            such that the S4 objects are always created by the current version
120            of R and 'Matrix' class definitions.
121    
122    2006-08-01  Douglas Bates  <bates@R-project.org>
123    
124            * R/lmer.R (LMEoptimize method), tests/lmer.R,
125            inst/external/test3comp.rda: Added warnings for convergence on
126            boundary and test cases.
127    
128            * src/lmer.c (mer_postVar): Modified to return the variances that
129            are marginal to the fixed effects, not conditional on them (which
130            is what the bVar slot contents represent).
131    
132    2006-07-31  Douglas Bates  <bates@R-project.org>
133    
134            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
135            function which calls the C function mer_hat_trace2.
136    
137            * man/ranef.Rd: Include description of "postVar" argument and
138            producing a caterpillar plot.
139    
140    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * NAMESPACE:    change  "correlation" to "corMatrix"
143            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
144            * R/dpoMatrix.R: ditto
145            * R/lmer.R:      ditto
146    
147    2006-07-28  Douglas Bates  <bates@R-project.org>
148    
149            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
150            RZXinv slot's contents into a separate internal function that can
151            be used in mer_hat_trace.
152    
153    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
156            via new smart
157            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
158            utility functions.
159    
160    
161    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Csparse.R (tril, triu, band): do return *triangular* classed
164            matrices when appropriate; band() even symmetric ones.
165            (replCmat): extend to potentially all "CsparseMatrix"
166            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
167            allow subassignment for special sparse matrices.
168    
169            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
170    
171            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
172            argument; in glmer_*(): print only if(verbose).
173    
174            speed-optimize a few places by moving REAL(.) out of loops.
175    
176            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
177    
178    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
181                    since that wrongly triggers also for M[ logi , ]
182    
183            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
184            a symmetric matrix that results in a non-symmetric one.
185            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
186    
187            * R/dMatrix.R: make round(M) work as round(M, 0)
188    
189            * R/dgTMatrix.R (image): coordinate system and axis now use
190            1-based indices, not 0-based ones.
191    
192            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
193            * tests/indexing.R: test it.
194    
195            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
196            * man/isSymmetric-methods.Rd: and document it.
197    
198            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
199            * man/SparseM-conv.Rd: docu them
200    
201            * tests/other-pkgs.R: renamed from tests/graph.R and add example
202                    for 'SparseM' conversions
203    
204    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
205    
206            * R/Matrix.R (head): added head() and tail() methods.
207    
208    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.995-12 released to CRAN
211    
212    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * tests/simple.R: add check for correct dsT -> dgT coercion;
215                    add check for correct printing of symmetric sparse matrices.
216    
217            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
218            for sparse symmetric matrices.
219    
220            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
221            diagonal twice.
222    
223    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
224    
225            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
226            being applied to the x slot (detected by Brian Ripley).
227    
228    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
231    
232            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
233    
234    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/lgCMatrix.c (lgCMatrix_diag): new function
237            * R/lgCMatrix.R (diag): for new method
238    
239            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
240                 ==> construction of illegal "*gTMatrix" via new() should
241                 now be much less easy:
242            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
243    
244            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
245                    directly.
246            * man/Matrix.Rd: documents it.
247    
248    2006-07-06  Douglas Bates  <bates@R-project.org>
249    
250            * src/pedigree.c (pedigree_inbreeding): Correction in
251            initialization.  This function is not currently being used and is
252            not fully tested.
253    
254            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
255            Introduced the glmer class.  Added code for mcmcmsamp on glmer
256            objects.  Modified validity check on pedigree objects to account
257            for nonparallel patterns of missingness of parents.
258    
259            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
260            class.
261    
262    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/pMatrix.R: coercion pMatrix -> Tsparse
265    
266    2006-06-12  Douglas Bates  <bates@R-project.org>
267    
268            * DESCRIPTION (Version): 0.995-11 released to CRAN
269    
270            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
271            the output from mcmcsamp.
272    
273    2006-06-10  Douglas Bates  <bates@R-project.org>
274    
275            * R/lmer.R (simulestimate): added C code for calculating the trace
276            of the hat matrix.
277    
278    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
281            classes.
282            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
283    
284    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/dgTMatrix.R (colSums): etc. All four of
287            colSums(), rowSums(), colMeans(), rowMeans() now should work for
288            all "Matrices".
289    
290    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/lmer.R (panel.ci): Add a reference line at zero and a
293            background grid to the qqmath plot of ranef.lmer.
294    
295    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
298            grouping factors to be specified in the formula as (1|foo/bar).
299    
300    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/lmer.R (findbars and others): Change check of is.numeric to
303            !is.language to resolve the bug reported by Jacob Wegelin.
304    
305            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
306            code to evaluate inbreeding coefficients without calculating T,
307            based on code in Sargolzaei and Iwaisaki's paper.
308    
309    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
312            generic and mer methods for isNested and denomDF. This denomDF was
313            an attempt to emulate that in lme but I don't think that makes
314            sense.  Use the trace of the hat matrix instead.
315    
316    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
319            the C code depending on a slot structure that's no longer valid.
320            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
321    
322    
323    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
324    
325            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
326            of lowerTriMatrix generic and methods to tril (also upper to triu)
327            and added a general band extractor.
328    
329    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/pedigree.R (pedigree): Replace sire and dam values outside the
332            allowable range with NAs. Added a corresponding check in the
333            validity check for the pedigree class.
334    
335            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
336            crossprod methods now inherits from symmetricMatrix.
337    
338    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
341            generics lowerTriMatrix and upperTriMatrix along with methods for
342            the Csparse virtual class.  Also added a C function Csparse_band
343            that implements these methods by calling cholmod_band.
344    
345    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
348            erased when it was NULL.  This led to invalid subselections!
349    
350    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
353            in method for "t" so as not to lose the unit diagonal property.
354    
355    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
356    
357            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
358            and methods.  This is now an option to the ranef method for the
359            mer class.
360    
361            * src/cs_utils.c: Ensure that the nz component is -1 for a
362            compressed column-oriented matrix.  Minor formatting cleanup.
363    
364            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
365            objects.
366    
367    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
370            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
371    
372    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
375            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
376    
377            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
378            for the dtCMatrix class.
379    
380    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
381    
382            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
383            and methods for it.
384    
385    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
388            arguments, such that M %*% 1:6 now works
389            * Tests/matprod.R: test the above
390    
391    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
394            the ranef.lmer class.
395    
396            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
397            methods to extract the posterior variances from the bVar slot.
398    
399    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
402            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
403    
404            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
405            * tests/simple: (extended)
406    
407            * R/sparseMatrix.R (isTriangular): now using much improved
408            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
409    
410    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
413            (problem report from Franklin Parlamis).  This should be done
414            generally.
415    
416    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
419            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
420            update the plot methods.
421    
422    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/lmer.R (resid and ranef methods):  Added methods for the
425            "residuals" and "resid" generic but only for linear mixed model
426            fits.  Changed the ranef method to return a list of data frames so
427            that the plot methods now work.
428    
429    2006-03-16  Douglas Bates  <bates@bates2>
430    
431            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
432            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
433    
434            * DESCRIPTION (Date): New release
435    
436    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
439    
440            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
441            * man/KNex.Rd: and other help files
442            * tests/*.R: several ones needed adaption
443            * inst/doc/Comparisons.Rnw: ditto
444    
445    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
448    
449            * tests/indexing.R: tests for new [<- methods for sparse matrices.
450    
451    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
454    
455            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
456    
457    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dMatrix.R: enable things like  M [ M < 10 ]
460            * R/dgeMatrix.R: implement it
461    
462    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/AllClass.R: define "summary.mer" and "*.lmer"
465            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
466            * R/lmer.R (show): now works with summary()
467    
468    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
471            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
472                    support the above
473    
474    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
475    
476            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
477            Use glmFit$prior.weights for weights in a glmm.
478            Allow an option usePQL = FALSE to skip the PQL steps for the
479            Laplace method (and, in time, the AGQ method).
480    
481            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
482            into a separate function internal_mer_Xfactor to be able to call
483            it from internal_bhat.
484    
485    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * tests/Class+Meth.R (tstMatrixClass): function for much better
488            testing; now again of all actual classes.
489    
490            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
491                    use macros and define make_d_matrix_* and make_i_matrix_*
492                    where _i_ is for the ldense routines:
493    
494            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
495            * src/ldense.c (lsyMatrix_as_lgeMatrix):
496    
497            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
498    
499    
500    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
503                    many different kinds of matrices.
504            * R/*.R: quite a few new methods were needed for R CMD check with
505                    new Matrix().  Very good for users playing around.
506    
507    
508    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * src/dgeMatrix.c (dMatrix_validate): new
511            * src/Mutils.c (dense_nonpacked_validate): new
512    
513            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
514    
515    
516    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
517    
518            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
519    
520    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
521    
522            * DESCRIPTION (Version): 0.99-6 released to CRAN
523    
524            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
525            segfault in cases with multiple non-nested grouping factors.
526    
527    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
530                    (Depends): also on 'utils'
531    
532            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
533            * R/diagMatrix.R (Diagonal): constructor and methods for
534            diagonal matrices
535    
536            * R/ltTMatrix.R: new "minimal methods"
537    
538    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
541            all methods (and help files).
542    
543    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
546                    for case (dimn.  op  no_dimn.)
547    
548    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * DESCRIPTION (Version): 0.99-2  released to CRAN
551    
552    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
553    
554            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
555            by Julian Faraway.
556    
557    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Auxiliaries.R (try_as): new utility
560            * R/sparseMatrix.R: use try_as() in coercion to original class
561    
562    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
565    
566    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/Auxiliaries.R (dimNamesCheck): added
569    
570            * R/Matrix.R (as.array), (as.vector): new
571    
572    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
575                    default.
576            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
577                    "pMatrix" now contains "sparseMatrix"
578    
579    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * tests/Class+Meth.R: new tests; t(t(m)) == m
582    
583            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
584    
585            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
586            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
587    
588            * R/dspMatrix.R: typo in "t" method
589    
590    2005-09-18  Douglas Bates  <bates@wisc.edu>
591    
592            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
593            * R/Tsparse.R: instead of R/gTMatrix.R
594            * R/Csparse.R: new
595            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
596            * src/Tsparse.c: new; many trivial methods calling cholmod_()
597            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
598                            via cholmod
599    
600    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Auxiliaries.R (non0ind): new function using new C code
603            * src/dgCMatrix.c (compressed_non_0_ij): new utility
604    
605    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
606    
607            * src/chm_common.h: header file required by all C sources that
608            call CHOLMOD functions.  It defines a cholmod_common structure
609            called 'c' whose address is passed as the last argument to
610            (virtually) every CHOLMOD function.
611    
612            * src/Pattern.c: Simple example of the use of CHOLMOD.
613    
614            * src/init.c: initialize and finalize the cholmod_common structure.
615    
616            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
617            LDL and CCOLAMD from the U. of Florida sparse matrix library.
618    
619    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * inst/test-tools.R: new file collecting the utility functions used
622                    in ./tests/*.R
623    
624            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
625            * R/Matrix.R (cbind2): methods for NULL and missing
626    
627    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/AllClass.R: new "index" class for "[" and "[<-":
630                    First cut at "symmetricMatrix" and "triangularMatrix"
631            * R/gTMatrix.R (.ind.prep): new function;
632                    Logical and character indexing now work too.
633            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
634            * tests/indexing.R: new, including *.Rout.save
635            * tests/dgTMatrix.R: new
636    
637    2005-08-29  Douglas Bates  <bates@wisc.edu>
638    
639            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
640            indicator pos not being updated.  Also enforced upper triangular
641            for symmetric case.  Need to coerce edges component of elements of
642            edge list - grr! (Why don't they define their classes cleanly?)
643    
644    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Matrix.R:  added first "[<-" methods; not yet functional
647            * R/denseMatrix.R: ditto
648            * man/Subassign-methods.Rd: new help file for these
649    
650    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * DESCRIPTION (Version): 0.98-6
653    
654            * R/denseMatrix.R: new file for "[" fallback methods for all dense
655            matrices.
656    
657    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
660                    as( <logical>, "matrix")
661    
662            * R/pMatrix.R: coercion to "lgTMatrix"
663    
664            * R/gTMatrix.R: new virtual class to define "[" methods for.
665            * man/gTMatrix-class.Rd:
666            * General slight re-organization of where "[" methods are defined.
667              more to come.
668    
669    2005-08-18  Douglas Bates  <bates@wisc.edu>
670    
671            * DESCRIPTION (Version): 0.98-5  released to CRAN
672    
673            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
674            * .....
675    
676    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
677    
678            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
679            or glmer objects.
680    
681    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
684    
685    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
686    
687            * R/HBMM.R: finish re-writing R-only code.
688    
689    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
690    
691            * man/externalFormats.Rd: move documentation for writeHB and
692            writeMM here.
693    
694            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
695            (suggested by Paul Roecker).
696    
697            * tests/validObj.R (assertError): Comment out test that is failing
698            after recent changes in r-devel.
699    
700    
701    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/AllClass.R: intermediate virtual class "denseMatrix"
704            * man/denseMatrix-class.Rd
705            * NAMESPACE: export it, and also export
706            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
707    
708    2005-08-10  Douglas Bates  <bates@wisc.edu>
709    
710            * DESCRIPTION (Version): 0.98-3 to CRAN
711    
712            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
713            matrix_solve code (which was really, really wrong).
714    
715    2005-08-07  Douglas Bates  <bates@wisc.edu>
716    
717            * DESCRIPTION (Version): 0.98-2
718    
719            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
720    
721            * R/lmer.R (abbrvNms): new
722            * R/lmer.R (mcmcsamp): allow transformed parameters
723            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
724            for the Harwell-Boeing and the MatrixMarket formats.
725    
726    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * man/dtrMatrix-class.Rd: add examples
729            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
730    
731            * TODO: note the dtpMatrix (docu) bug
732    
733            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
734            in order to ensure that new as.matrix() is used by old functions,
735            e.g., svd(), qr(), eigen(), dist(),..;
736                  apply(), also matplot() or pairs().
737    
738    
739    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
742              add comments about 'control' / lmerControl() arguments
743    
744    2005-07-27  Douglas Bates  <bates@wisc.edu>
745    
746            * man/sleepstudy.Rd: Added the sleep data set.
747            * DESCRIPTION (Version): 0.98-1  released to CRAN
748    
749    2005-07-12  Douglas Bates  <bates@wisc.edu>
750            * man/sleepstudy.Rd: Added the sleep data set.
751    
752            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
753            .Call calls that were producing spurious output.
754    
755    2005-07-05  Douglas Bates  <bates@wisc.edu>
756    
757            * R/lmer.R (lmer): stored updated variance component estimates in
758            mer object for the generalized model.  (Bug reported by Renaud
759            Lancelot).
760    
761    2005-07-03  Douglas Bates  <bates@wisc.edu>
762    
763            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
764            unidimensional case.
765    
766    2005-06-08  Douglas Bates  <bates@wisc.edu>
767    
768            * DESCRIPTION (Version): 0.96-1
769    
770            * moved  lmer-class' R and C code moved from lme4 to here
771    
772    2005-06-04  Douglas Bates  <bates@wisc.edu>
773    
774            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
775            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
776    
777    2005-06-02  Douglas Bates  <bates@wisc.edu>
778    
779            * src/Makefile.win: Forgot to update this when Makefile changed.
780    
781    2005-05-11  Douglas Bates  <bates@wisc.edu>
782    
783          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
784          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
785    
786  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
787    
788          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
789          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 792 
792          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
793          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
794    
795  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
796    
797          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
798          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
799    
800  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
801    
802          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
803          multiplication operation.          multiplication operation.
# Line 30  Line 810 
810    
811          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
812    
813  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
814    
815          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
816    
817          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
818    
819    
820  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
821    
822          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
823    
# Line 46  Line 826 
826          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
827          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
828    
829  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
830    
831          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
832    
# Line 72  Line 852 
852          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
853            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
854    
855  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
856    
857          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
858          * ....          * ....
859    
860  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
861    
862          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
863    
# Line 92  Line 872 
872            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
873          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
874    
875  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
876    
877          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
878    
879  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
880    
881          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
882    
883  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
884    
885          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
886          the package.          the package.
# Line 148  Line 928 
928    
929          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
930    
931  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
932    
933          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
934          for the geMatrix class.          for the geMatrix class.
935    
936  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
937    
938          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
939    
940          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
941    
942  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
943    
944          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
945          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
946    
947  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
948    
949          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
950    
951  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
952    
953          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
954          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
955    
956  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
957    
958          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
959    
960          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
961          for tripletMatrix to matrix.          for tripletMatrix to matrix.
962    
963  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
964    
965          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
966          no longer used.          no longer used.
# Line 192  Line 972 
972          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
973          Fixes part but not all of #15.          Fixes part but not all of #15.
974    
975  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
976    
977          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
978          scalar grouping factors corrected.          scalar grouping factors corrected.
979    
980  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
981    
982          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
983    
984  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
985    
986          * 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
987          .h file can be included.          .h file can be included.
988    
989  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
990    
991          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
992          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
993    
994          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
995    
996  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
997    
998          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
999    
1000  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1001    
1002          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1003    
1004  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1005    
1006          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1007    
1008  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1009    
1010          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1011    
1012  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1013    
1014          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1015          routines.          routines.
1016    
1017  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1018    
1019          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1020    
1021  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1022    
1023          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1024    

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