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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1565, Fri Sep 15 14:02:48 2006 UTC
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1    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/other-pkgs.R (graph): small extenion in "graph" checks.
4    
5            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
6            (Tsp2grNEL): other fixes needed
7    
8    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
11                    Matrices, since "lMatrix", also "lsparseM" can have NA
12            * R/ndenseMatrix.R, etc: new source files
13            * man/nsparseMatrix-classes.Rd, etc: new help files
14            * tests/: adaptions
15            * src/chm_common.c (chm_dense_to_SEXP): and others:
16                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
17            * src/Csparse.c, etc: dito
18    
19    2006-09-11  Douglas Bates  <bates@R-project.org>
20    
21            * src/Mutils.[ch],init.c inst/include/*.h: Move the
22            alloc_d**Matrix functions to the lme4 package.
23    
24    2006-09-09  Douglas Bates  <bates@R-project.org>
25    
26            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
27            fixed
28    
29    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lMatrix.R: new
32    
33            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
34    
35            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
36            * man/tcrossprod.Rd: dito
37    
38    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
41            for exported functions
42            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
43            Remove partitioning algorithms for sparse matrix reordering.  The
44            copyright on the Metis code was problematic and the methods were
45            rarely used.
46            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
47            operations are now done entirely in CHOLMOD code.
48    
49    2006-09-06  Douglas Bates  <bates@R-project.org>
50    
51            * src/Mutils.h: Remove functions that are no longer used.
52    
53    2006-09-04  Douglas Bates  <bates@R-project.org>
54    
55            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
56            * src/DEPS.mkf: update
57    
58    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * created branches/Matrix-for-R-2.3.x;  on trunk: do
61            * DESCRIPTION (Version): 0.9975-0
62            (Depends): R (>= 2.4.0)
63    
64    2006-09-01  Douglas Bates  <bates@R-project.org>
65    
66            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
67    
68    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
71            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
72    
73            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
78            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
79            * R/dsparseMatrix.R: dito
80            * R/Csparse.R: dito
81    
82    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Compare): improve availability of "<", etc
85            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
86    
87    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
90            of a 0-index which was used as 1-index (..hmm)
91    
92            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
93    
94            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
95            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
96            (.is.diagonal): dito
97    
98            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
99    
100            * R/Matrix.R (Matrix): also work for NA data
101    
102    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
105            in all cases.
106    
107    2006-08-27  Douglas Bates  <bates@R-project.org>
108    
109            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
110            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
111    
112    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
115            subclasses of "ddenseMatrix"
116            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
117            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
118            instead of half dozen specialized ones.
119    
120    2006-08-25  Douglas Bates  <bates@R-project.org>
121    
122            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
123            <tillard@cirad.fr> - ordering standard errors to match effects.
124    
125    2006-08-24  Douglas Bates  <bates@R-project.org>
126    
127            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
128            on R_ldl.
129            * R/lCholCMatrix.R,
130            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
131            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
132            * many files in ./R and ./src: Use more general version of
133            dup_mMatrix_as_dgeMatrix to simplify method definitions.
134            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
135            dtpMatrix, dspMatrix and dppMatrix conversions.
136    
137    
138    2006-08-23  Douglas Bates  <bates@R-project.org>
139    
140            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
141            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
142            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
143            dgeMatrix_crossprod (may need to do this in other places).
144            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
145            generic and method for dsCMatrix.  Use CHOLMOD for chol().
146    
147    2006-08-22  Douglas Bates  <bates@R-project.org>
148    
149            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
150            types of classed Matrices, matrices or numeric or logical vectors.
151            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
152            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
153            to Mutils.h (as an inline) and change name to Matrix_check_class;
154            fixes in as_cholmod_factor and chm_factor_to_SEXP.
155            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
156            dsCMatrix_matrix_solve.  Comment out vestigial functions.
157            * src/Csparse.c: use diag_P and uplo_P macros.
158    
159    2006-08-21  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
162            valgrind.
163            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
164            inverses.
165            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
166            -Wall warnings.
167            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
168            Use dup_mMatrix_as_dgeMatrix.
169    
170    2006-08-20  Douglas Bates  <bates@R-project.org>
171    
172            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
173            * tests/sparseQR.R: Added
174            * man/sparseQR-class.Rd: Document methods for qr.* generics
175            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
176    
177    2006-08-19  Douglas Bates  <bates@R-project.org>
178    
179            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
180            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
181            and qr.fitted.
182            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
183            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
184    
185    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
188            the base version has no "..." argument.
189    
190            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
191    
192            * R/Matrix.R: define and
193            * NAMESPACE: export as.numeric() and as.logical() methods.
194                    Let's hope these do not badly slow down something...
195            Finally export the zapsmall() method.
196    
197    2006-08-17  Douglas Bates  <bates@R-project.org>
198    
199            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
200            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
201            * src/dtCMatrix.c :Remove code that is no longer used
202            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
207            Csparse_to_logical and Csparse_symmetric_to_general.
208            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
209            coercion methods between CsparseMatrix and TsparseMatrix.
210    
211    2006-08-14  Douglas Bates  <bates@R-project.org>
212    
213            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
214            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
215            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
216            possible.
217    
218    2006-08-12  Douglas Bates  <bates@R-project.org>
219    
220            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
221              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
222              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
223              generalize conversions between TsparseMatrix, CsparseMatrix,
224              denseMatrix and matrix.  Preserve triangularity property and
225              propagate Dimnames in the easy cases.
226    
227    2006-08-10  Douglas Bates  <bates@R-project.org>
228    
229            * src/lmer.c: adjust checks in glmer_init for S4SXP
230            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
231            before S4SXP but for the wrong reasons.
232    
233    2006-08-08  Douglas Bates  <bates@R-project.org>
234    
235            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
236            Later modified to return the upper triangle only.
237            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
238    
239    2006-08-07  Douglas Bates  <bates@R-project.org>
240    
241            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
242            R-level conversion to a sparse symmetric class.
243            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
244            Remove conversion to sparse symmetric classes (now done in C code).
245    
246    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
249            * man/band.Rd:  adapt the \dontshow{} unit test.
250    
251    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * DESCRIPTION (Version): 0.995-14  for CRAN
254    
255            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
256    
257            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
258            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
259    
260            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
261            * R/Tsparse.R (tril, triu, band): methods
262            * R/dgRMatrix.R (tril, ...):    ditto
263            * man/band.Rd:                  ditto
264    
265    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Matrix.R (head, tail): directly use utils:::head.matrix
268                    to be up-to-date automatically.
269    
270    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
273    
274            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
275            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
276            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
277            such that the S4 objects are always created by the current version
278            of R and 'Matrix' class definitions.
279    
280    2006-08-01  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (LMEoptimize method), tests/lmer.R,
283            inst/external/test3comp.rda: Added warnings for convergence on
284            boundary and test cases.
285    
286            * src/lmer.c (mer_postVar): Modified to return the variances that
287            are marginal to the fixed effects, not conditional on them (which
288            is what the bVar slot contents represent).
289    
290    2006-07-31  Douglas Bates  <bates@R-project.org>
291    
292            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
293            function which calls the C function mer_hat_trace2.
294    
295            * man/ranef.Rd: Include description of "postVar" argument and
296            producing a caterpillar plot.
297    
298    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * NAMESPACE:    change  "correlation" to "corMatrix"
301            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
302            * R/dpoMatrix.R: ditto
303            * R/lmer.R:      ditto
304    
305    2006-07-28  Douglas Bates  <bates@R-project.org>
306    
307            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
308            RZXinv slot's contents into a separate internal function that can
309            be used in mer_hat_trace.
310    
311    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
314            via new smart
315            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
316            utility functions.
317    
318    
319    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Csparse.R (tril, triu, band): do return *triangular* classed
322            matrices when appropriate; band() even symmetric ones.
323            (replCmat): extend to potentially all "CsparseMatrix"
324            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
325            allow subassignment for special sparse matrices.
326    
327            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
328    
329            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
330            argument; in glmer_*(): print only if(verbose).
331    
332            speed-optimize a few places by moving REAL(.) out of loops.
333    
334            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
335    
336    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
339                    since that wrongly triggers also for M[ logi , ]
340    
341            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
342            a symmetric matrix that results in a non-symmetric one.
343            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
344    
345            * R/dMatrix.R: make round(M) work as round(M, 0)
346    
347            * R/dgTMatrix.R (image): coordinate system and axis now use
348            1-based indices, not 0-based ones.
349    
350            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
351            * tests/indexing.R: test it.
352    
353            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
354            * man/isSymmetric-methods.Rd: and document it.
355    
356            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
357            * man/SparseM-conv.Rd: docu them
358    
359            * tests/other-pkgs.R: renamed from tests/graph.R and add example
360                    for 'SparseM' conversions
361    
362    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
363    
364            * R/Matrix.R (head): added head() and tail() methods.
365    
366    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version): 0.995-12 released to CRAN
369    
370    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * tests/simple.R: add check for correct dsT -> dgT coercion;
373                    add check for correct printing of symmetric sparse matrices.
374    
375            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
376            for sparse symmetric matrices.
377    
378            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
379            diagonal twice.
380    
381    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
382    
383            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
384            being applied to the x slot (detected by Brian Ripley).
385    
386    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
389    
390            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
391    
392    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/lgCMatrix.c (lgCMatrix_diag): new function
395            * R/lgCMatrix.R (diag): for new method
396    
397            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
398                 ==> construction of illegal "*gTMatrix" via new() should
399                 now be much less easy:
400            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
401    
402            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
403                    directly.
404            * man/Matrix.Rd: documents it.
405    
406    2006-07-06  Douglas Bates  <bates@R-project.org>
407    
408            * src/pedigree.c (pedigree_inbreeding): Correction in
409            initialization.  This function is not currently being used and is
410            not fully tested.
411    
412            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
413            Introduced the glmer class.  Added code for mcmcmsamp on glmer
414            objects.  Modified validity check on pedigree objects to account
415            for nonparallel patterns of missingness of parents.
416    
417            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
418            class.
419    
420    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/pMatrix.R: coercion pMatrix -> Tsparse
423    
424    2006-06-12  Douglas Bates  <bates@R-project.org>
425    
426            * DESCRIPTION (Version): 0.995-11 released to CRAN
427    
428            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
429            the output from mcmcsamp.
430    
431    2006-06-10  Douglas Bates  <bates@R-project.org>
432    
433            * R/lmer.R (simulestimate): added C code for calculating the trace
434            of the hat matrix.
435    
436    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
439            classes.
440            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
441    
442    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dgTMatrix.R (colSums): etc. All four of
445            colSums(), rowSums(), colMeans(), rowMeans() now should work for
446            all "Matrices".
447    
448    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/lmer.R (panel.ci): Add a reference line at zero and a
451            background grid to the qqmath plot of ranef.lmer.
452    
453    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
456            grouping factors to be specified in the formula as (1|foo/bar).
457    
458    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
459    
460            * R/lmer.R (findbars and others): Change check of is.numeric to
461            !is.language to resolve the bug reported by Jacob Wegelin.
462    
463            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
464            code to evaluate inbreeding coefficients without calculating T,
465            based on code in Sargolzaei and Iwaisaki's paper.
466    
467    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
470            generic and mer methods for isNested and denomDF. This denomDF was
471            an attempt to emulate that in lme but I don't think that makes
472            sense.  Use the trace of the hat matrix instead.
473    
474    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
477            the C code depending on a slot structure that's no longer valid.
478            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
479    
480    
481    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
482    
483            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
484            of lowerTriMatrix generic and methods to tril (also upper to triu)
485            and added a general band extractor.
486    
487    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
488    
489            * R/pedigree.R (pedigree): Replace sire and dam values outside the
490            allowable range with NAs. Added a corresponding check in the
491            validity check for the pedigree class.
492    
493            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
494            crossprod methods now inherits from symmetricMatrix.
495    
496    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
497    
498            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
499            generics lowerTriMatrix and upperTriMatrix along with methods for
500            the Csparse virtual class.  Also added a C function Csparse_band
501            that implements these methods by calling cholmod_band.
502    
503    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
506            erased when it was NULL.  This led to invalid subselections!
507    
508    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
509    
510            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
511            in method for "t" so as not to lose the unit diagonal property.
512    
513    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
516            and methods.  This is now an option to the ranef method for the
517            mer class.
518    
519            * src/cs_utils.c: Ensure that the nz component is -1 for a
520            compressed column-oriented matrix.  Minor formatting cleanup.
521    
522            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
523            objects.
524    
525    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
528            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
529    
530    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
533            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
534    
535            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
536            for the dtCMatrix class.
537    
538    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
539    
540            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
541            and methods for it.
542    
543    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
546            arguments, such that M %*% 1:6 now works
547            * Tests/matprod.R: test the above
548    
549    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
552            the ranef.lmer class.
553    
554            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
555            methods to extract the posterior variances from the bVar slot.
556    
557    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
560            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
561    
562            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
563            * tests/simple: (extended)
564    
565            * R/sparseMatrix.R (isTriangular): now using much improved
566            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
567    
568    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
569    
570            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
571            (problem report from Franklin Parlamis).  This should be done
572            generally.
573    
574    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
575    
576            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
577            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
578            update the plot methods.
579    
580    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/lmer.R (resid and ranef methods):  Added methods for the
583            "residuals" and "resid" generic but only for linear mixed model
584            fits.  Changed the ranef method to return a list of data frames so
585            that the plot methods now work.
586    
587    2006-03-16  Douglas Bates  <bates@bates2>
588    
589            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
590            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
591    
592            * DESCRIPTION (Date): New release
593    
594    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
597    
598            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
599            * man/KNex.Rd: and other help files
600            * tests/*.R: several ones needed adaption
601            * inst/doc/Comparisons.Rnw: ditto
602    
603    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
606    
607            * tests/indexing.R: tests for new [<- methods for sparse matrices.
608    
609    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
612    
613            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
614    
615    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/dMatrix.R: enable things like  M [ M < 10 ]
618            * R/dgeMatrix.R: implement it
619    
620    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/AllClass.R: define "summary.mer" and "*.lmer"
623            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
624            * R/lmer.R (show): now works with summary()
625    
626    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
629            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
630                    support the above
631    
632    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
633    
634            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
635            Use glmFit$prior.weights for weights in a glmm.
636            Allow an option usePQL = FALSE to skip the PQL steps for the
637            Laplace method (and, in time, the AGQ method).
638    
639            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
640            into a separate function internal_mer_Xfactor to be able to call
641            it from internal_bhat.
642    
643    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * tests/Class+Meth.R (tstMatrixClass): function for much better
646            testing; now again of all actual classes.
647    
648            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
649                    use macros and define make_d_matrix_* and make_i_matrix_*
650                    where _i_ is for the ldense routines:
651    
652            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
653            * src/ldense.c (lsyMatrix_as_lgeMatrix):
654    
655            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
656    
657    
658    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
661                    many different kinds of matrices.
662            * R/*.R: quite a few new methods were needed for R CMD check with
663                    new Matrix().  Very good for users playing around.
664    
665    
666    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/dgeMatrix.c (dMatrix_validate): new
669            * src/Mutils.c (dense_nonpacked_validate): new
670    
671            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
672    
673    
674    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
675    
676            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
677    
678    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
679    
680            * DESCRIPTION (Version): 0.99-6 released to CRAN
681    
682            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
683            segfault in cases with multiple non-nested grouping factors.
684    
685    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
688                    (Depends): also on 'utils'
689    
690            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
691            * R/diagMatrix.R (Diagonal): constructor and methods for
692            diagonal matrices
693    
694            * R/ltTMatrix.R: new "minimal methods"
695    
696    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
699            all methods (and help files).
700    
701    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
704                    for case (dimn.  op  no_dimn.)
705    
706    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * DESCRIPTION (Version): 0.99-2  released to CRAN
709    
710    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
713            by Julian Faraway.
714    
715    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Auxiliaries.R (try_as): new utility
718            * R/sparseMatrix.R: use try_as() in coercion to original class
719    
720    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
723    
724    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * R/Auxiliaries.R (dimNamesCheck): added
727    
728            * R/Matrix.R (as.array), (as.vector): new
729    
730    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
733                    default.
734            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
735                    "pMatrix" now contains "sparseMatrix"
736    
737    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * tests/Class+Meth.R: new tests; t(t(m)) == m
740    
741            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
742    
743            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
744            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
745    
746            * R/dspMatrix.R: typo in "t" method
747    
748    2005-09-18  Douglas Bates  <bates@wisc.edu>
749    
750            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
751            * R/Tsparse.R: instead of R/gTMatrix.R
752            * R/Csparse.R: new
753            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
754            * src/Tsparse.c: new; many trivial methods calling cholmod_()
755            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
756                            via cholmod
757    
758    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Auxiliaries.R (non0ind): new function using new C code
761            * src/dgCMatrix.c (compressed_non_0_ij): new utility
762    
763    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
764    
765            * src/chm_common.h: header file required by all C sources that
766            call CHOLMOD functions.  It defines a cholmod_common structure
767            called 'c' whose address is passed as the last argument to
768            (virtually) every CHOLMOD function.
769    
770            * src/Pattern.c: Simple example of the use of CHOLMOD.
771    
772            * src/init.c: initialize and finalize the cholmod_common structure.
773    
774            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
775            LDL and CCOLAMD from the U. of Florida sparse matrix library.
776    
777    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * inst/test-tools.R: new file collecting the utility functions used
780                    in ./tests/*.R
781    
782            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
783            * R/Matrix.R (cbind2): methods for NULL and missing
784    
785    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/AllClass.R: new "index" class for "[" and "[<-":
788                    First cut at "symmetricMatrix" and "triangularMatrix"
789            * R/gTMatrix.R (.ind.prep): new function;
790                    Logical and character indexing now work too.
791            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
792            * tests/indexing.R: new, including *.Rout.save
793            * tests/dgTMatrix.R: new
794    
795  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
796    
797          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 802 
802  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
805          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
806          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
807    
808  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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