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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1447, Fri Aug 25 20:38:36 2006 UTC
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1    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
4            subclasses of "ddenseMatrix"
5            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
6            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
7            instead of half dozen specialized ones.
8    
9    2006-08-25  Douglas Bates  <bates@R-project.org>
10    
11            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
12            <tillard@cirad.fr> - ordering standard errors to match effects.
13    
14    2006-08-24  Douglas Bates  <bates@R-project.org>
15    
16            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
17            on R_ldl.
18            * R/lCholCMatrix.R,
19            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
20            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
21            * many files in ./R and ./src: Use more general version of
22            dup_mMatrix_as_dgeMatrix to simplify method definitions.
23            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
24            dtpMatrix, dspMatrix and dppMatrix conversions.
25    
26    
27    2006-08-23  Douglas Bates  <bates@R-project.org>
28    
29            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
30            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
31            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
32            dgeMatrix_crossprod (may need to do this in other places).
33            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
34            generic and method for dsCMatrix.  Use CHOLMOD for chol().
35    
36    2006-08-22  Douglas Bates  <bates@R-project.org>
37    
38            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
39            types of classed Matrices, matrices or numeric or logical vectors.
40            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
41            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
42            to Mutils.h (as an inline) and change name to Matrix_check_class;
43            fixes in as_cholmod_factor and chm_factor_to_SEXP.
44            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
45            dsCMatrix_matrix_solve.  Comment out vestigial functions.
46            * src/Csparse.c: use diag_P and uplo_P macros.
47    
48    2006-08-21  Douglas Bates  <bates@R-project.org>
49    
50            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
51            valgrind.
52            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
53            inverses.
54            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
55            -Wall warnings.
56            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
57            Use dup_mMatrix_as_dgeMatrix.
58    
59    2006-08-20  Douglas Bates  <bates@R-project.org>
60    
61            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
62            * tests/sparseQR.R: Added
63            * man/sparseQR-class.Rd: Document methods for qr.* generics
64            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
65    
66    2006-08-19  Douglas Bates  <bates@R-project.org>
67    
68            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
69            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
70            and qr.fitted.
71            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
72            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
73    
74    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
77            the base version has no "..." argument.
78    
79            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
80    
81            * R/Matrix.R: define and
82            * NAMESPACE: export as.numeric() and as.logical() methods.
83                    Let's hope these do not badly slow down something...
84            Finally export the zapsmall() method.
85    
86    2006-08-17  Douglas Bates  <bates@R-project.org>
87    
88            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
89            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
90            * src/dtCMatrix.c :Remove code that is no longer used
91            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
92    
93    2006-08-14  Douglas Bates  <bates@R-project.org>
94    
95            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
96            Csparse_to_logical and Csparse_symmetric_to_general.
97            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
98            coercion methods between CsparseMatrix and TsparseMatrix.
99    
100    2006-08-14  Douglas Bates  <bates@R-project.org>
101    
102            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
103            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
104            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
105            possible.
106    
107    2006-08-12  Douglas Bates  <bates@R-project.org>
108    
109            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
110              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
111              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
112              generalize conversions between TsparseMatrix, CsparseMatrix,
113              denseMatrix and matrix.  Preserve triangularity property and
114              propagate Dimnames in the easy cases.
115    
116    2006-08-10  Douglas Bates  <bates@R-project.org>
117    
118            * src/lmer.c: adjust checks in glmer_init for S4SXP
119            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
120            before S4SXP but for the wrong reasons.
121    
122    2006-08-08  Douglas Bates  <bates@R-project.org>
123    
124            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
125            Later modified to return the upper triangle only.
126            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
127    
128    2006-08-07  Douglas Bates  <bates@R-project.org>
129    
130            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
131            R-level conversion to a sparse symmetric class.
132            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
133            Remove conversion to sparse symmetric classes (now done in C code).
134    
135    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
138            * man/band.Rd:  adapt the \dontshow{} unit test.
139    
140    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.995-14  for CRAN
143    
144            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
145    
146            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
147            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
148    
149            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
150            * R/Tsparse.R (tril, triu, band): methods
151            * R/dgRMatrix.R (tril, ...):    ditto
152            * man/band.Rd:                  ditto
153    
154    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Matrix.R (head, tail): directly use utils:::head.matrix
157                    to be up-to-date automatically.
158    
159    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
162    
163            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
164            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
165            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
166            such that the S4 objects are always created by the current version
167            of R and 'Matrix' class definitions.
168    
169    2006-08-01  Douglas Bates  <bates@R-project.org>
170    
171            * R/lmer.R (LMEoptimize method), tests/lmer.R,
172            inst/external/test3comp.rda: Added warnings for convergence on
173            boundary and test cases.
174    
175            * src/lmer.c (mer_postVar): Modified to return the variances that
176            are marginal to the fixed effects, not conditional on them (which
177            is what the bVar slot contents represent).
178    
179    2006-07-31  Douglas Bates  <bates@R-project.org>
180    
181            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
182            function which calls the C function mer_hat_trace2.
183    
184            * man/ranef.Rd: Include description of "postVar" argument and
185            producing a caterpillar plot.
186    
187    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * NAMESPACE:    change  "correlation" to "corMatrix"
190            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
191            * R/dpoMatrix.R: ditto
192            * R/lmer.R:      ditto
193    
194    2006-07-28  Douglas Bates  <bates@R-project.org>
195    
196            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
197            RZXinv slot's contents into a separate internal function that can
198            be used in mer_hat_trace.
199    
200    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
203            via new smart
204            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
205            utility functions.
206    
207    
208    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Csparse.R (tril, triu, band): do return *triangular* classed
211            matrices when appropriate; band() even symmetric ones.
212            (replCmat): extend to potentially all "CsparseMatrix"
213            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
214            allow subassignment for special sparse matrices.
215    
216            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
217    
218            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
219            argument; in glmer_*(): print only if(verbose).
220    
221            speed-optimize a few places by moving REAL(.) out of loops.
222    
223            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
224    
225    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
228                    since that wrongly triggers also for M[ logi , ]
229    
230            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
231            a symmetric matrix that results in a non-symmetric one.
232            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
233    
234            * R/dMatrix.R: make round(M) work as round(M, 0)
235    
236            * R/dgTMatrix.R (image): coordinate system and axis now use
237            1-based indices, not 0-based ones.
238    
239            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
240            * tests/indexing.R: test it.
241    
242            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
243            * man/isSymmetric-methods.Rd: and document it.
244    
245            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
246            * man/SparseM-conv.Rd: docu them
247    
248            * tests/other-pkgs.R: renamed from tests/graph.R and add example
249                    for 'SparseM' conversions
250    
251    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
252    
253            * R/Matrix.R (head): added head() and tail() methods.
254    
255    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * DESCRIPTION (Version): 0.995-12 released to CRAN
258    
259    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * tests/simple.R: add check for correct dsT -> dgT coercion;
262                    add check for correct printing of symmetric sparse matrices.
263    
264            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
265            for sparse symmetric matrices.
266    
267            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
268            diagonal twice.
269    
270    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
271    
272            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
273            being applied to the x slot (detected by Brian Ripley).
274    
275    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
278    
279            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
280    
281    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * src/lgCMatrix.c (lgCMatrix_diag): new function
284            * R/lgCMatrix.R (diag): for new method
285    
286            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
287                 ==> construction of illegal "*gTMatrix" via new() should
288                 now be much less easy:
289            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
290    
291            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
292                    directly.
293            * man/Matrix.Rd: documents it.
294    
295    2006-07-06  Douglas Bates  <bates@R-project.org>
296    
297            * src/pedigree.c (pedigree_inbreeding): Correction in
298            initialization.  This function is not currently being used and is
299            not fully tested.
300    
301            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
302            Introduced the glmer class.  Added code for mcmcmsamp on glmer
303            objects.  Modified validity check on pedigree objects to account
304            for nonparallel patterns of missingness of parents.
305    
306            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
307            class.
308    
309    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/pMatrix.R: coercion pMatrix -> Tsparse
312    
313    2006-06-12  Douglas Bates  <bates@R-project.org>
314    
315            * DESCRIPTION (Version): 0.995-11 released to CRAN
316    
317            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
318            the output from mcmcsamp.
319    
320    2006-06-10  Douglas Bates  <bates@R-project.org>
321    
322            * R/lmer.R (simulestimate): added C code for calculating the trace
323            of the hat matrix.
324    
325    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
328            classes.
329            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
330    
331    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/dgTMatrix.R (colSums): etc. All four of
334            colSums(), rowSums(), colMeans(), rowMeans() now should work for
335            all "Matrices".
336    
337    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
338    
339            * R/lmer.R (panel.ci): Add a reference line at zero and a
340            background grid to the qqmath plot of ranef.lmer.
341    
342    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
345            grouping factors to be specified in the formula as (1|foo/bar).
346    
347    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
348    
349            * R/lmer.R (findbars and others): Change check of is.numeric to
350            !is.language to resolve the bug reported by Jacob Wegelin.
351    
352            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
353            code to evaluate inbreeding coefficients without calculating T,
354            based on code in Sargolzaei and Iwaisaki's paper.
355    
356    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
357    
358            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
359            generic and mer methods for isNested and denomDF. This denomDF was
360            an attempt to emulate that in lme but I don't think that makes
361            sense.  Use the trace of the hat matrix instead.
362    
363    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
366            the C code depending on a slot structure that's no longer valid.
367            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
368    
369    
370    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
371    
372            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
373            of lowerTriMatrix generic and methods to tril (also upper to triu)
374            and added a general band extractor.
375    
376    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * R/pedigree.R (pedigree): Replace sire and dam values outside the
379            allowable range with NAs. Added a corresponding check in the
380            validity check for the pedigree class.
381    
382            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
383            crossprod methods now inherits from symmetricMatrix.
384    
385    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
388            generics lowerTriMatrix and upperTriMatrix along with methods for
389            the Csparse virtual class.  Also added a C function Csparse_band
390            that implements these methods by calling cholmod_band.
391    
392    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
395            erased when it was NULL.  This led to invalid subselections!
396    
397    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
398    
399            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
400            in method for "t" so as not to lose the unit diagonal property.
401    
402    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
405            and methods.  This is now an option to the ranef method for the
406            mer class.
407    
408            * src/cs_utils.c: Ensure that the nz component is -1 for a
409            compressed column-oriented matrix.  Minor formatting cleanup.
410    
411            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
412            objects.
413    
414    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
417            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
418    
419    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
420    
421            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
422            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
423    
424            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
425            for the dtCMatrix class.
426    
427    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
428    
429            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
430            and methods for it.
431    
432    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
435            arguments, such that M %*% 1:6 now works
436            * Tests/matprod.R: test the above
437    
438    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
441            the ranef.lmer class.
442    
443            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
444            methods to extract the posterior variances from the bVar slot.
445    
446    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
449            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
450    
451            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
452            * tests/simple: (extended)
453    
454            * R/sparseMatrix.R (isTriangular): now using much improved
455            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
456    
457    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
458    
459            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
460            (problem report from Franklin Parlamis).  This should be done
461            generally.
462    
463    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
466            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
467            update the plot methods.
468    
469    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
470    
471            * R/lmer.R (resid and ranef methods):  Added methods for the
472            "residuals" and "resid" generic but only for linear mixed model
473            fits.  Changed the ranef method to return a list of data frames so
474            that the plot methods now work.
475    
476    2006-03-16  Douglas Bates  <bates@bates2>
477    
478            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
479            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
480    
481            * DESCRIPTION (Date): New release
482    
483    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
486    
487            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
488            * man/KNex.Rd: and other help files
489            * tests/*.R: several ones needed adaption
490            * inst/doc/Comparisons.Rnw: ditto
491    
492    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
495    
496            * tests/indexing.R: tests for new [<- methods for sparse matrices.
497    
498    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
501    
502            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
503    
504    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/dMatrix.R: enable things like  M [ M < 10 ]
507            * R/dgeMatrix.R: implement it
508    
509    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/AllClass.R: define "summary.mer" and "*.lmer"
512            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
513            * R/lmer.R (show): now works with summary()
514    
515    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
518            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
519                    support the above
520    
521    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
522    
523            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
524            Use glmFit$prior.weights for weights in a glmm.
525            Allow an option usePQL = FALSE to skip the PQL steps for the
526            Laplace method (and, in time, the AGQ method).
527    
528            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
529            into a separate function internal_mer_Xfactor to be able to call
530            it from internal_bhat.
531    
532    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * tests/Class+Meth.R (tstMatrixClass): function for much better
535            testing; now again of all actual classes.
536    
537            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
538                    use macros and define make_d_matrix_* and make_i_matrix_*
539                    where _i_ is for the ldense routines:
540    
541            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
542            * src/ldense.c (lsyMatrix_as_lgeMatrix):
543    
544            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
545    
546    
547    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
550                    many different kinds of matrices.
551            * R/*.R: quite a few new methods were needed for R CMD check with
552                    new Matrix().  Very good for users playing around.
553    
554    
555    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * src/dgeMatrix.c (dMatrix_validate): new
558            * src/Mutils.c (dense_nonpacked_validate): new
559    
560            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
561    
562    
563    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
564    
565            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
566    
567    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
568    
569            * DESCRIPTION (Version): 0.99-6 released to CRAN
570    
571            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
572            segfault in cases with multiple non-nested grouping factors.
573    
574    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
577                    (Depends): also on 'utils'
578    
579            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
580            * R/diagMatrix.R (Diagonal): constructor and methods for
581            diagonal matrices
582    
583            * R/ltTMatrix.R: new "minimal methods"
584    
585    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
588            all methods (and help files).
589    
590    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
593                    for case (dimn.  op  no_dimn.)
594    
595    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
596    
597            * DESCRIPTION (Version): 0.99-2  released to CRAN
598    
599    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
600    
601            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
602            by Julian Faraway.
603    
604    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/Auxiliaries.R (try_as): new utility
607            * R/sparseMatrix.R: use try_as() in coercion to original class
608    
609    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
612    
613    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Auxiliaries.R (dimNamesCheck): added
616    
617            * R/Matrix.R (as.array), (as.vector): new
618    
619    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
622                    default.
623            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
624                    "pMatrix" now contains "sparseMatrix"
625    
626    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * tests/Class+Meth.R: new tests; t(t(m)) == m
629    
630            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
631    
632            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
633            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
634    
635            * R/dspMatrix.R: typo in "t" method
636    
637    2005-09-18  Douglas Bates  <bates@wisc.edu>
638    
639            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
640            * R/Tsparse.R: instead of R/gTMatrix.R
641            * R/Csparse.R: new
642            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
643            * src/Tsparse.c: new; many trivial methods calling cholmod_()
644            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
645                            via cholmod
646    
647    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/Auxiliaries.R (non0ind): new function using new C code
650            * src/dgCMatrix.c (compressed_non_0_ij): new utility
651    
652    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
653    
654            * src/chm_common.h: header file required by all C sources that
655            call CHOLMOD functions.  It defines a cholmod_common structure
656            called 'c' whose address is passed as the last argument to
657            (virtually) every CHOLMOD function.
658    
659            * src/Pattern.c: Simple example of the use of CHOLMOD.
660    
661            * src/init.c: initialize and finalize the cholmod_common structure.
662    
663            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
664            LDL and CCOLAMD from the U. of Florida sparse matrix library.
665    
666    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * inst/test-tools.R: new file collecting the utility functions used
669                    in ./tests/*.R
670    
671            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
672            * R/Matrix.R (cbind2): methods for NULL and missing
673    
674    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/AllClass.R: new "index" class for "[" and "[<-":
677                    First cut at "symmetricMatrix" and "triangularMatrix"
678            * R/gTMatrix.R (.ind.prep): new function;
679                    Logical and character indexing now work too.
680            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
681            * tests/indexing.R: new, including *.Rout.save
682            * tests/dgTMatrix.R: new
683    
684  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
685    
686          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 691 
691  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
694          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
695          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
696    
697  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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