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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1445, Fri Aug 25 14:54:54 2006 UTC
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1    2006-08-25  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
4            <tillard@cirad.fr> - ordering standard errors to match effects.
5    
6    2006-08-24  Douglas Bates  <bates@R-project.org>
7    
8            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
9            on R_ldl.
10            * R/lCholCMatrix.R,
11            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
12            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
13            * many files in ./R and ./src: Use more general version of
14            dup_mMatrix_as_dgeMatrix to simplify method definitions.
15            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
16            dtpMatrix, dspMatrix and dppMatrix conversions.
17    
18    
19    2006-08-23  Douglas Bates  <bates@R-project.org>
20    
21            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
22            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
23            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
24            dgeMatrix_crossprod (may need to do this in other places).
25            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
26            generic and method for dsCMatrix.  Use CHOLMOD for chol().
27    
28    2006-08-22  Douglas Bates  <bates@R-project.org>
29    
30            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
31            types of classed Matrices, matrices or numeric or logical vectors.
32            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
33            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
34            to Mutils.h (as an inline) and change name to Matrix_check_class;
35            fixes in as_cholmod_factor and chm_factor_to_SEXP.
36            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
37            dsCMatrix_matrix_solve.  Comment out vestigial functions.
38            * src/Csparse.c: use diag_P and uplo_P macros.
39    
40    2006-08-21  Douglas Bates  <bates@R-project.org>
41    
42            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
43            valgrind.
44            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
45            inverses.
46            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
47            -Wall warnings.
48            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
49            Use dup_mMatrix_as_dgeMatrix.
50    
51    2006-08-20  Douglas Bates  <bates@R-project.org>
52    
53            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
54            * tests/sparseQR.R: Added
55            * man/sparseQR-class.Rd: Document methods for qr.* generics
56            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
57    
58    2006-08-19  Douglas Bates  <bates@R-project.org>
59    
60            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
61            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
62            and qr.fitted.
63            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
64            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
65    
66    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
69            the base version has no "..." argument.
70    
71            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
72    
73            * R/Matrix.R: define and
74            * NAMESPACE: export as.numeric() and as.logical() methods.
75                    Let's hope these do not badly slow down something...
76            Finally export the zapsmall() method.
77    
78    2006-08-17  Douglas Bates  <bates@R-project.org>
79    
80            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
81            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
82            * src/dtCMatrix.c :Remove code that is no longer used
83            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
84    
85    2006-08-14  Douglas Bates  <bates@R-project.org>
86    
87            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
88            Csparse_to_logical and Csparse_symmetric_to_general.
89            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
90            coercion methods between CsparseMatrix and TsparseMatrix.
91    
92    2006-08-14  Douglas Bates  <bates@R-project.org>
93    
94            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
95            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
96            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
97            possible.
98    
99    2006-08-12  Douglas Bates  <bates@R-project.org>
100    
101            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
102              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
103              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
104              generalize conversions between TsparseMatrix, CsparseMatrix,
105              denseMatrix and matrix.  Preserve triangularity property and
106              propagate Dimnames in the easy cases.
107    
108    2006-08-10  Douglas Bates  <bates@R-project.org>
109    
110            * src/lmer.c: adjust checks in glmer_init for S4SXP
111            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
112            before S4SXP but for the wrong reasons.
113    
114    2006-08-08  Douglas Bates  <bates@R-project.org>
115    
116            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
117            Later modified to return the upper triangle only.
118            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
119    
120    2006-08-07  Douglas Bates  <bates@R-project.org>
121    
122            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
123            R-level conversion to a sparse symmetric class.
124            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
125            Remove conversion to sparse symmetric classes (now done in C code).
126    
127    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
130            * man/band.Rd:  adapt the \dontshow{} unit test.
131    
132    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.995-14  for CRAN
135    
136            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
137    
138            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
139            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
140    
141            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
142            * R/Tsparse.R (tril, triu, band): methods
143            * R/dgRMatrix.R (tril, ...):    ditto
144            * man/band.Rd:                  ditto
145    
146    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (head, tail): directly use utils:::head.matrix
149                    to be up-to-date automatically.
150    
151    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
154    
155            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
156            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
157            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
158            such that the S4 objects are always created by the current version
159            of R and 'Matrix' class definitions.
160    
161    2006-08-01  Douglas Bates  <bates@R-project.org>
162    
163            * R/lmer.R (LMEoptimize method), tests/lmer.R,
164            inst/external/test3comp.rda: Added warnings for convergence on
165            boundary and test cases.
166    
167            * src/lmer.c (mer_postVar): Modified to return the variances that
168            are marginal to the fixed effects, not conditional on them (which
169            is what the bVar slot contents represent).
170    
171    2006-07-31  Douglas Bates  <bates@R-project.org>
172    
173            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
174            function which calls the C function mer_hat_trace2.
175    
176            * man/ranef.Rd: Include description of "postVar" argument and
177            producing a caterpillar plot.
178    
179    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * NAMESPACE:    change  "correlation" to "corMatrix"
182            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
183            * R/dpoMatrix.R: ditto
184            * R/lmer.R:      ditto
185    
186    2006-07-28  Douglas Bates  <bates@R-project.org>
187    
188            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
189            RZXinv slot's contents into a separate internal function that can
190            be used in mer_hat_trace.
191    
192    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
195            via new smart
196            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
197            utility functions.
198    
199    
200    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Csparse.R (tril, triu, band): do return *triangular* classed
203            matrices when appropriate; band() even symmetric ones.
204            (replCmat): extend to potentially all "CsparseMatrix"
205            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
206            allow subassignment for special sparse matrices.
207    
208            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
209    
210            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
211            argument; in glmer_*(): print only if(verbose).
212    
213            speed-optimize a few places by moving REAL(.) out of loops.
214    
215            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
216    
217    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
220                    since that wrongly triggers also for M[ logi , ]
221    
222            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
223            a symmetric matrix that results in a non-symmetric one.
224            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
225    
226            * R/dMatrix.R: make round(M) work as round(M, 0)
227    
228            * R/dgTMatrix.R (image): coordinate system and axis now use
229            1-based indices, not 0-based ones.
230    
231            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
232            * tests/indexing.R: test it.
233    
234            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
235            * man/isSymmetric-methods.Rd: and document it.
236    
237            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
238            * man/SparseM-conv.Rd: docu them
239    
240            * tests/other-pkgs.R: renamed from tests/graph.R and add example
241                    for 'SparseM' conversions
242    
243    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
244    
245            * R/Matrix.R (head): added head() and tail() methods.
246    
247    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * DESCRIPTION (Version): 0.995-12 released to CRAN
250    
251    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * tests/simple.R: add check for correct dsT -> dgT coercion;
254                    add check for correct printing of symmetric sparse matrices.
255    
256            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
257            for sparse symmetric matrices.
258    
259            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
260            diagonal twice.
261    
262    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
263    
264            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
265            being applied to the x slot (detected by Brian Ripley).
266    
267    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
270    
271            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
272    
273    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/lgCMatrix.c (lgCMatrix_diag): new function
276            * R/lgCMatrix.R (diag): for new method
277    
278            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
279                 ==> construction of illegal "*gTMatrix" via new() should
280                 now be much less easy:
281            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
282    
283            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
284                    directly.
285            * man/Matrix.Rd: documents it.
286    
287    2006-07-06  Douglas Bates  <bates@R-project.org>
288    
289            * src/pedigree.c (pedigree_inbreeding): Correction in
290            initialization.  This function is not currently being used and is
291            not fully tested.
292    
293            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
294            Introduced the glmer class.  Added code for mcmcmsamp on glmer
295            objects.  Modified validity check on pedigree objects to account
296            for nonparallel patterns of missingness of parents.
297    
298            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
299            class.
300    
301    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/pMatrix.R: coercion pMatrix -> Tsparse
304    
305    2006-06-12  Douglas Bates  <bates@R-project.org>
306    
307            * DESCRIPTION (Version): 0.995-11 released to CRAN
308    
309            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
310            the output from mcmcsamp.
311    
312    2006-06-10  Douglas Bates  <bates@R-project.org>
313    
314            * R/lmer.R (simulestimate): added C code for calculating the trace
315            of the hat matrix.
316    
317    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
320            classes.
321            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
322    
323    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgTMatrix.R (colSums): etc. All four of
326            colSums(), rowSums(), colMeans(), rowMeans() now should work for
327            all "Matrices".
328    
329    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R (panel.ci): Add a reference line at zero and a
332            background grid to the qqmath plot of ranef.lmer.
333    
334    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
337            grouping factors to be specified in the formula as (1|foo/bar).
338    
339    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * R/lmer.R (findbars and others): Change check of is.numeric to
342            !is.language to resolve the bug reported by Jacob Wegelin.
343    
344            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
345            code to evaluate inbreeding coefficients without calculating T,
346            based on code in Sargolzaei and Iwaisaki's paper.
347    
348    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
351            generic and mer methods for isNested and denomDF. This denomDF was
352            an attempt to emulate that in lme but I don't think that makes
353            sense.  Use the trace of the hat matrix instead.
354    
355    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
358            the C code depending on a slot structure that's no longer valid.
359            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
360    
361    
362    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
363    
364            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
365            of lowerTriMatrix generic and methods to tril (also upper to triu)
366            and added a general band extractor.
367    
368    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
369    
370            * R/pedigree.R (pedigree): Replace sire and dam values outside the
371            allowable range with NAs. Added a corresponding check in the
372            validity check for the pedigree class.
373    
374            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
375            crossprod methods now inherits from symmetricMatrix.
376    
377    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
380            generics lowerTriMatrix and upperTriMatrix along with methods for
381            the Csparse virtual class.  Also added a C function Csparse_band
382            that implements these methods by calling cholmod_band.
383    
384    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
387            erased when it was NULL.  This led to invalid subselections!
388    
389    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
390    
391            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
392            in method for "t" so as not to lose the unit diagonal property.
393    
394    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
395    
396            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
397            and methods.  This is now an option to the ranef method for the
398            mer class.
399    
400            * src/cs_utils.c: Ensure that the nz component is -1 for a
401            compressed column-oriented matrix.  Minor formatting cleanup.
402    
403            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
404            objects.
405    
406    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
409            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
410    
411    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
412    
413            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
414            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
415    
416            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
417            for the dtCMatrix class.
418    
419    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
420    
421            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
422            and methods for it.
423    
424    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
427            arguments, such that M %*% 1:6 now works
428            * Tests/matprod.R: test the above
429    
430    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
431    
432            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
433            the ranef.lmer class.
434    
435            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
436            methods to extract the posterior variances from the bVar slot.
437    
438    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
441            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
442    
443            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
444            * tests/simple: (extended)
445    
446            * R/sparseMatrix.R (isTriangular): now using much improved
447            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
448    
449    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
450    
451            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
452            (problem report from Franklin Parlamis).  This should be done
453            generally.
454    
455    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
456    
457            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
458            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
459            update the plot methods.
460    
461    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * R/lmer.R (resid and ranef methods):  Added methods for the
464            "residuals" and "resid" generic but only for linear mixed model
465            fits.  Changed the ranef method to return a list of data frames so
466            that the plot methods now work.
467    
468    2006-03-16  Douglas Bates  <bates@bates2>
469    
470            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
471            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
472    
473            * DESCRIPTION (Date): New release
474    
475    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
478    
479            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
480            * man/KNex.Rd: and other help files
481            * tests/*.R: several ones needed adaption
482            * inst/doc/Comparisons.Rnw: ditto
483    
484    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
487    
488            * tests/indexing.R: tests for new [<- methods for sparse matrices.
489    
490    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
493    
494            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
495    
496    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/dMatrix.R: enable things like  M [ M < 10 ]
499            * R/dgeMatrix.R: implement it
500    
501    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/AllClass.R: define "summary.mer" and "*.lmer"
504            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
505            * R/lmer.R (show): now works with summary()
506    
507    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
510            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
511                    support the above
512    
513    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
516            Use glmFit$prior.weights for weights in a glmm.
517            Allow an option usePQL = FALSE to skip the PQL steps for the
518            Laplace method (and, in time, the AGQ method).
519    
520            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
521            into a separate function internal_mer_Xfactor to be able to call
522            it from internal_bhat.
523    
524    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * tests/Class+Meth.R (tstMatrixClass): function for much better
527            testing; now again of all actual classes.
528    
529            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
530                    use macros and define make_d_matrix_* and make_i_matrix_*
531                    where _i_ is for the ldense routines:
532    
533            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
534            * src/ldense.c (lsyMatrix_as_lgeMatrix):
535    
536            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
537    
538    
539    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
542                    many different kinds of matrices.
543            * R/*.R: quite a few new methods were needed for R CMD check with
544                    new Matrix().  Very good for users playing around.
545    
546    
547    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * src/dgeMatrix.c (dMatrix_validate): new
550            * src/Mutils.c (dense_nonpacked_validate): new
551    
552            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
553    
554    
555    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
556    
557            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
558    
559    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
560    
561            * DESCRIPTION (Version): 0.99-6 released to CRAN
562    
563            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
564            segfault in cases with multiple non-nested grouping factors.
565    
566    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
569                    (Depends): also on 'utils'
570    
571            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
572            * R/diagMatrix.R (Diagonal): constructor and methods for
573            diagonal matrices
574    
575            * R/ltTMatrix.R: new "minimal methods"
576    
577    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
580            all methods (and help files).
581    
582    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
585                    for case (dimn.  op  no_dimn.)
586    
587    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
588    
589            * DESCRIPTION (Version): 0.99-2  released to CRAN
590    
591    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
592    
593            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
594            by Julian Faraway.
595    
596    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Auxiliaries.R (try_as): new utility
599            * R/sparseMatrix.R: use try_as() in coercion to original class
600    
601    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
604    
605    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/Auxiliaries.R (dimNamesCheck): added
608    
609            * R/Matrix.R (as.array), (as.vector): new
610    
611    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
614                    default.
615            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
616                    "pMatrix" now contains "sparseMatrix"
617    
618    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * tests/Class+Meth.R: new tests; t(t(m)) == m
621    
622            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
623    
624            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
625            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
626    
627            * R/dspMatrix.R: typo in "t" method
628    
629    2005-09-18  Douglas Bates  <bates@wisc.edu>
630    
631            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
632            * R/Tsparse.R: instead of R/gTMatrix.R
633            * R/Csparse.R: new
634            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
635            * src/Tsparse.c: new; many trivial methods calling cholmod_()
636            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
637                            via cholmod
638    
639    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/Auxiliaries.R (non0ind): new function using new C code
642            * src/dgCMatrix.c (compressed_non_0_ij): new utility
643    
644    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
645    
646            * src/chm_common.h: header file required by all C sources that
647            call CHOLMOD functions.  It defines a cholmod_common structure
648            called 'c' whose address is passed as the last argument to
649            (virtually) every CHOLMOD function.
650    
651            * src/Pattern.c: Simple example of the use of CHOLMOD.
652    
653            * src/init.c: initialize and finalize the cholmod_common structure.
654    
655            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
656            LDL and CCOLAMD from the U. of Florida sparse matrix library.
657    
658    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * inst/test-tools.R: new file collecting the utility functions used
661                    in ./tests/*.R
662    
663            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
664            * R/Matrix.R (cbind2): methods for NULL and missing
665    
666    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/AllClass.R: new "index" class for "[" and "[<-":
669                    First cut at "symmetricMatrix" and "triangularMatrix"
670            * R/gTMatrix.R (.ind.prep): new function;
671                    Logical and character indexing now work too.
672            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
673            * tests/indexing.R: new, including *.Rout.save
674            * tests/dgTMatrix.R: new
675    
676  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
677    
678          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 683 
683  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
686          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
687          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
688    
689  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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