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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1472, Fri Sep 1 15:31:04 2006 UTC
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1    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
4            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
5    
6            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
7    
8    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
11            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
12            * R/dsparseMatrix.R: dito
13            * R/Csparse.R: dito
14    
15    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/dMatrix.R (Compare): improve availability of "<", etc
18            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
19    
20    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
23            of a 0-index which was used as 1-index (..hmm)
24    
25            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
26    
27            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
28            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
29            (.is.diagonal): dito
30    
31            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
32    
33            * R/Matrix.R (Matrix): also work for NA data
34    
35    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
38            in all cases.
39    
40    2006-08-27  Douglas Bates  <bates@R-project.org>
41    
42            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
43            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
44    
45    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
48            subclasses of "ddenseMatrix"
49            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
50            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
51            instead of half dozen specialized ones.
52    
53    2006-08-25  Douglas Bates  <bates@R-project.org>
54    
55            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
56            <tillard@cirad.fr> - ordering standard errors to match effects.
57    
58    2006-08-24  Douglas Bates  <bates@R-project.org>
59    
60            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
61            on R_ldl.
62            * R/lCholCMatrix.R,
63            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
64            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
65            * many files in ./R and ./src: Use more general version of
66            dup_mMatrix_as_dgeMatrix to simplify method definitions.
67            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
68            dtpMatrix, dspMatrix and dppMatrix conversions.
69    
70    
71    2006-08-23  Douglas Bates  <bates@R-project.org>
72    
73            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
74            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
75            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
76            dgeMatrix_crossprod (may need to do this in other places).
77            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
78            generic and method for dsCMatrix.  Use CHOLMOD for chol().
79    
80    2006-08-22  Douglas Bates  <bates@R-project.org>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
83            types of classed Matrices, matrices or numeric or logical vectors.
84            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
85            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
86            to Mutils.h (as an inline) and change name to Matrix_check_class;
87            fixes in as_cholmod_factor and chm_factor_to_SEXP.
88            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
89            dsCMatrix_matrix_solve.  Comment out vestigial functions.
90            * src/Csparse.c: use diag_P and uplo_P macros.
91    
92    2006-08-21  Douglas Bates  <bates@R-project.org>
93    
94            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
95            valgrind.
96            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
97            inverses.
98            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
99            -Wall warnings.
100            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
101            Use dup_mMatrix_as_dgeMatrix.
102    
103    2006-08-20  Douglas Bates  <bates@R-project.org>
104    
105            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
106            * tests/sparseQR.R: Added
107            * man/sparseQR-class.Rd: Document methods for qr.* generics
108            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
109    
110    2006-08-19  Douglas Bates  <bates@R-project.org>
111    
112            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
113            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
114            and qr.fitted.
115            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
116            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
117    
118    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
121            the base version has no "..." argument.
122    
123            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
124    
125            * R/Matrix.R: define and
126            * NAMESPACE: export as.numeric() and as.logical() methods.
127                    Let's hope these do not badly slow down something...
128            Finally export the zapsmall() method.
129    
130    2006-08-17  Douglas Bates  <bates@R-project.org>
131    
132            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
133            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
134            * src/dtCMatrix.c :Remove code that is no longer used
135            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
136    
137    2006-08-14  Douglas Bates  <bates@R-project.org>
138    
139            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
140            Csparse_to_logical and Csparse_symmetric_to_general.
141            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
142            coercion methods between CsparseMatrix and TsparseMatrix.
143    
144    2006-08-14  Douglas Bates  <bates@R-project.org>
145    
146            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
147            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
148            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
149            possible.
150    
151    2006-08-12  Douglas Bates  <bates@R-project.org>
152    
153            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
154              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
155              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
156              generalize conversions between TsparseMatrix, CsparseMatrix,
157              denseMatrix and matrix.  Preserve triangularity property and
158              propagate Dimnames in the easy cases.
159    
160    2006-08-10  Douglas Bates  <bates@R-project.org>
161    
162            * src/lmer.c: adjust checks in glmer_init for S4SXP
163            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
164            before S4SXP but for the wrong reasons.
165    
166    2006-08-08  Douglas Bates  <bates@R-project.org>
167    
168            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
169            Later modified to return the upper triangle only.
170            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
171    
172    2006-08-07  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
175            R-level conversion to a sparse symmetric class.
176            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
177            Remove conversion to sparse symmetric classes (now done in C code).
178    
179    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
182            * man/band.Rd:  adapt the \dontshow{} unit test.
183    
184    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Version): 0.995-14  for CRAN
187    
188            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
189    
190            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
191            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
192    
193            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
194            * R/Tsparse.R (tril, triu, band): methods
195            * R/dgRMatrix.R (tril, ...):    ditto
196            * man/band.Rd:                  ditto
197    
198    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Matrix.R (head, tail): directly use utils:::head.matrix
201                    to be up-to-date automatically.
202    
203    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
206    
207            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
208            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
209            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
210            such that the S4 objects are always created by the current version
211            of R and 'Matrix' class definitions.
212    
213    2006-08-01  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (LMEoptimize method), tests/lmer.R,
216            inst/external/test3comp.rda: Added warnings for convergence on
217            boundary and test cases.
218    
219            * src/lmer.c (mer_postVar): Modified to return the variances that
220            are marginal to the fixed effects, not conditional on them (which
221            is what the bVar slot contents represent).
222    
223    2006-07-31  Douglas Bates  <bates@R-project.org>
224    
225            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
226            function which calls the C function mer_hat_trace2.
227    
228            * man/ranef.Rd: Include description of "postVar" argument and
229            producing a caterpillar plot.
230    
231    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * NAMESPACE:    change  "correlation" to "corMatrix"
234            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
235            * R/dpoMatrix.R: ditto
236            * R/lmer.R:      ditto
237    
238    2006-07-28  Douglas Bates  <bates@R-project.org>
239    
240            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
241            RZXinv slot's contents into a separate internal function that can
242            be used in mer_hat_trace.
243    
244    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
247            via new smart
248            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
249            utility functions.
250    
251    
252    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Csparse.R (tril, triu, band): do return *triangular* classed
255            matrices when appropriate; band() even symmetric ones.
256            (replCmat): extend to potentially all "CsparseMatrix"
257            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
258            allow subassignment for special sparse matrices.
259    
260            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
261    
262            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
263            argument; in glmer_*(): print only if(verbose).
264    
265            speed-optimize a few places by moving REAL(.) out of loops.
266    
267            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
268    
269    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
272                    since that wrongly triggers also for M[ logi , ]
273    
274            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
275            a symmetric matrix that results in a non-symmetric one.
276            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
277    
278            * R/dMatrix.R: make round(M) work as round(M, 0)
279    
280            * R/dgTMatrix.R (image): coordinate system and axis now use
281            1-based indices, not 0-based ones.
282    
283            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
284            * tests/indexing.R: test it.
285    
286            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
287            * man/isSymmetric-methods.Rd: and document it.
288    
289            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
290            * man/SparseM-conv.Rd: docu them
291    
292            * tests/other-pkgs.R: renamed from tests/graph.R and add example
293                    for 'SparseM' conversions
294    
295    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
296    
297            * R/Matrix.R (head): added head() and tail() methods.
298    
299    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * DESCRIPTION (Version): 0.995-12 released to CRAN
302    
303    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * tests/simple.R: add check for correct dsT -> dgT coercion;
306                    add check for correct printing of symmetric sparse matrices.
307    
308            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
309            for sparse symmetric matrices.
310    
311            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
312            diagonal twice.
313    
314    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
315    
316            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
317            being applied to the x slot (detected by Brian Ripley).
318    
319    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
322    
323            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
324    
325    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/lgCMatrix.c (lgCMatrix_diag): new function
328            * R/lgCMatrix.R (diag): for new method
329    
330            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
331                 ==> construction of illegal "*gTMatrix" via new() should
332                 now be much less easy:
333            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
334    
335            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
336                    directly.
337            * man/Matrix.Rd: documents it.
338    
339    2006-07-06  Douglas Bates  <bates@R-project.org>
340    
341            * src/pedigree.c (pedigree_inbreeding): Correction in
342            initialization.  This function is not currently being used and is
343            not fully tested.
344    
345            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
346            Introduced the glmer class.  Added code for mcmcmsamp on glmer
347            objects.  Modified validity check on pedigree objects to account
348            for nonparallel patterns of missingness of parents.
349    
350            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
351            class.
352    
353    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/pMatrix.R: coercion pMatrix -> Tsparse
356    
357    2006-06-12  Douglas Bates  <bates@R-project.org>
358    
359            * DESCRIPTION (Version): 0.995-11 released to CRAN
360    
361            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
362            the output from mcmcsamp.
363    
364    2006-06-10  Douglas Bates  <bates@R-project.org>
365    
366            * R/lmer.R (simulestimate): added C code for calculating the trace
367            of the hat matrix.
368    
369    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
372            classes.
373            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
374    
375    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/dgTMatrix.R (colSums): etc. All four of
378            colSums(), rowSums(), colMeans(), rowMeans() now should work for
379            all "Matrices".
380    
381    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * R/lmer.R (panel.ci): Add a reference line at zero and a
384            background grid to the qqmath plot of ranef.lmer.
385    
386    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
389            grouping factors to be specified in the formula as (1|foo/bar).
390    
391    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/lmer.R (findbars and others): Change check of is.numeric to
394            !is.language to resolve the bug reported by Jacob Wegelin.
395    
396            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
397            code to evaluate inbreeding coefficients without calculating T,
398            based on code in Sargolzaei and Iwaisaki's paper.
399    
400    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
401    
402            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
403            generic and mer methods for isNested and denomDF. This denomDF was
404            an attempt to emulate that in lme but I don't think that makes
405            sense.  Use the trace of the hat matrix instead.
406    
407    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
410            the C code depending on a slot structure that's no longer valid.
411            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
412    
413    
414    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
415    
416            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
417            of lowerTriMatrix generic and methods to tril (also upper to triu)
418            and added a general band extractor.
419    
420    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
421    
422            * R/pedigree.R (pedigree): Replace sire and dam values outside the
423            allowable range with NAs. Added a corresponding check in the
424            validity check for the pedigree class.
425    
426            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
427            crossprod methods now inherits from symmetricMatrix.
428    
429    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
432            generics lowerTriMatrix and upperTriMatrix along with methods for
433            the Csparse virtual class.  Also added a C function Csparse_band
434            that implements these methods by calling cholmod_band.
435    
436    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
439            erased when it was NULL.  This led to invalid subselections!
440    
441    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
442    
443            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
444            in method for "t" so as not to lose the unit diagonal property.
445    
446    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
449            and methods.  This is now an option to the ranef method for the
450            mer class.
451    
452            * src/cs_utils.c: Ensure that the nz component is -1 for a
453            compressed column-oriented matrix.  Minor formatting cleanup.
454    
455            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
456            objects.
457    
458    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
461            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
462    
463    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
466            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
467    
468            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
469            for the dtCMatrix class.
470    
471    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
474            and methods for it.
475    
476    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
479            arguments, such that M %*% 1:6 now works
480            * Tests/matprod.R: test the above
481    
482    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
485            the ranef.lmer class.
486    
487            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
488            methods to extract the posterior variances from the bVar slot.
489    
490    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
493            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
494    
495            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
496            * tests/simple: (extended)
497    
498            * R/sparseMatrix.R (isTriangular): now using much improved
499            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
500    
501    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
504            (problem report from Franklin Parlamis).  This should be done
505            generally.
506    
507    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
510            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
511            update the plot methods.
512    
513    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/lmer.R (resid and ranef methods):  Added methods for the
516            "residuals" and "resid" generic but only for linear mixed model
517            fits.  Changed the ranef method to return a list of data frames so
518            that the plot methods now work.
519    
520    2006-03-16  Douglas Bates  <bates@bates2>
521    
522            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
523            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
524    
525            * DESCRIPTION (Date): New release
526    
527    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
530    
531            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
532            * man/KNex.Rd: and other help files
533            * tests/*.R: several ones needed adaption
534            * inst/doc/Comparisons.Rnw: ditto
535    
536    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
539    
540            * tests/indexing.R: tests for new [<- methods for sparse matrices.
541    
542    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
545    
546            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
547    
548    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/dMatrix.R: enable things like  M [ M < 10 ]
551            * R/dgeMatrix.R: implement it
552    
553    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/AllClass.R: define "summary.mer" and "*.lmer"
556            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
557            * R/lmer.R (show): now works with summary()
558    
559    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
562            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
563                    support the above
564    
565    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
566    
567            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
568            Use glmFit$prior.weights for weights in a glmm.
569            Allow an option usePQL = FALSE to skip the PQL steps for the
570            Laplace method (and, in time, the AGQ method).
571    
572            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
573            into a separate function internal_mer_Xfactor to be able to call
574            it from internal_bhat.
575    
576    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * tests/Class+Meth.R (tstMatrixClass): function for much better
579            testing; now again of all actual classes.
580    
581            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
582                    use macros and define make_d_matrix_* and make_i_matrix_*
583                    where _i_ is for the ldense routines:
584    
585            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
586            * src/ldense.c (lsyMatrix_as_lgeMatrix):
587    
588            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
589    
590    
591    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
594                    many different kinds of matrices.
595            * R/*.R: quite a few new methods were needed for R CMD check with
596                    new Matrix().  Very good for users playing around.
597    
598    
599    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * src/dgeMatrix.c (dMatrix_validate): new
602            * src/Mutils.c (dense_nonpacked_validate): new
603    
604            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
605    
606    
607    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
610    
611    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * DESCRIPTION (Version): 0.99-6 released to CRAN
614    
615            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
616            segfault in cases with multiple non-nested grouping factors.
617    
618    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
621                    (Depends): also on 'utils'
622    
623            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
624            * R/diagMatrix.R (Diagonal): constructor and methods for
625            diagonal matrices
626    
627            * R/ltTMatrix.R: new "minimal methods"
628    
629    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
632            all methods (and help files).
633    
634    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
637                    for case (dimn.  op  no_dimn.)
638    
639    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * DESCRIPTION (Version): 0.99-2  released to CRAN
642    
643    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
644    
645            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
646            by Julian Faraway.
647    
648    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/Auxiliaries.R (try_as): new utility
651            * R/sparseMatrix.R: use try_as() in coercion to original class
652    
653    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
656    
657    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Auxiliaries.R (dimNamesCheck): added
660    
661            * R/Matrix.R (as.array), (as.vector): new
662    
663    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
666                    default.
667            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
668                    "pMatrix" now contains "sparseMatrix"
669    
670    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * tests/Class+Meth.R: new tests; t(t(m)) == m
673    
674            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
675    
676            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
677            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
678    
679            * R/dspMatrix.R: typo in "t" method
680    
681    2005-09-18  Douglas Bates  <bates@wisc.edu>
682    
683            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
684            * R/Tsparse.R: instead of R/gTMatrix.R
685            * R/Csparse.R: new
686            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
687            * src/Tsparse.c: new; many trivial methods calling cholmod_()
688            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
689                            via cholmod
690    
691    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/Auxiliaries.R (non0ind): new function using new C code
694            * src/dgCMatrix.c (compressed_non_0_ij): new utility
695    
696    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
697    
698            * src/chm_common.h: header file required by all C sources that
699            call CHOLMOD functions.  It defines a cholmod_common structure
700            called 'c' whose address is passed as the last argument to
701            (virtually) every CHOLMOD function.
702    
703            * src/Pattern.c: Simple example of the use of CHOLMOD.
704    
705            * src/init.c: initialize and finalize the cholmod_common structure.
706    
707            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
708            LDL and CCOLAMD from the U. of Florida sparse matrix library.
709    
710    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * inst/test-tools.R: new file collecting the utility functions used
713                    in ./tests/*.R
714    
715            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
716            * R/Matrix.R (cbind2): methods for NULL and missing
717    
718    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/AllClass.R: new "index" class for "[" and "[<-":
721                    First cut at "symmetricMatrix" and "triangularMatrix"
722            * R/gTMatrix.R (.ind.prep): new function;
723                    Logical and character indexing now work too.
724            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
725            * tests/indexing.R: new, including *.Rout.save
726            * tests/dgTMatrix.R: new
727    
728  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
729    
730          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 735 
735  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
738          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
739          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
740    
741  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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