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revision 1109, Tue Jan 3 16:42:31 2006 UTC revision 1548, Mon Sep 11 22:13:07 2006 UTC
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1    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
4                    Matrices, since "lMatrix", also "lsparseM" can have NA
5            * R/ndenseMatrix.R, etc: new source files
6            * man/nsparseMatrix-classes.Rd, etc: new help files
7            * tests/: adaptions
8            * src/chm_common.c (chm_dense_to_SEXP): and others:
9                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
10            * src/Csparse.c, etc: dito
11    
12    2006-09-11  Douglas Bates  <bates@R-project.org>
13    
14            * src/Mutils.[ch],init.c inst/include/*.h: Move the
15            alloc_d**Matrix functions to the lme4 package.
16    
17    2006-09-09  Douglas Bates  <bates@R-project.org>
18    
19            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
20            fixed
21    
22    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/lMatrix.R: new
25    
26            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
27    
28            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
29            * man/tcrossprod.Rd: dito
30    
31    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
34            for exported functions
35            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
36            Remove partitioning algorithms for sparse matrix reordering.  The
37            copyright on the Metis code was problematic and the methods were
38            rarely used.
39            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
40            operations are now done entirely in CHOLMOD code.
41    
42    2006-09-06  Douglas Bates  <bates@R-project.org>
43    
44            * src/Mutils.h: Remove functions that are no longer used.
45    
46    2006-09-04  Douglas Bates  <bates@R-project.org>
47    
48            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
49            * src/DEPS.mkf: update
50    
51    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * created branches/Matrix-for-R-2.3.x;  on trunk: do
54            * DESCRIPTION (Version): 0.9975-0
55            (Depends): R (>= 2.4.0)
56    
57    2006-09-01  Douglas Bates  <bates@R-project.org>
58    
59            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
60    
61    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
64            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
65    
66            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
67    
68    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
71            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
72            * R/dsparseMatrix.R: dito
73            * R/Csparse.R: dito
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R (Compare): improve availability of "<", etc
78            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
79    
80    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
83            of a 0-index which was used as 1-index (..hmm)
84    
85            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
86    
87            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
88            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
89            (.is.diagonal): dito
90    
91            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
92    
93            * R/Matrix.R (Matrix): also work for NA data
94    
95    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
98            in all cases.
99    
100    2006-08-27  Douglas Bates  <bates@R-project.org>
101    
102            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
103            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
104    
105    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
108            subclasses of "ddenseMatrix"
109            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
110            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
111            instead of half dozen specialized ones.
112    
113    2006-08-25  Douglas Bates  <bates@R-project.org>
114    
115            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
116            <tillard@cirad.fr> - ordering standard errors to match effects.
117    
118    2006-08-24  Douglas Bates  <bates@R-project.org>
119    
120            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
121            on R_ldl.
122            * R/lCholCMatrix.R,
123            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
124            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
125            * many files in ./R and ./src: Use more general version of
126            dup_mMatrix_as_dgeMatrix to simplify method definitions.
127            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
128            dtpMatrix, dspMatrix and dppMatrix conversions.
129    
130    
131    2006-08-23  Douglas Bates  <bates@R-project.org>
132    
133            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
134            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
135            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
136            dgeMatrix_crossprod (may need to do this in other places).
137            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
138            generic and method for dsCMatrix.  Use CHOLMOD for chol().
139    
140    2006-08-22  Douglas Bates  <bates@R-project.org>
141    
142            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
143            types of classed Matrices, matrices or numeric or logical vectors.
144            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
145            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
146            to Mutils.h (as an inline) and change name to Matrix_check_class;
147            fixes in as_cholmod_factor and chm_factor_to_SEXP.
148            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
149            dsCMatrix_matrix_solve.  Comment out vestigial functions.
150            * src/Csparse.c: use diag_P and uplo_P macros.
151    
152    2006-08-21  Douglas Bates  <bates@R-project.org>
153    
154            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
155            valgrind.
156            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
157            inverses.
158            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
159            -Wall warnings.
160            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
161            Use dup_mMatrix_as_dgeMatrix.
162    
163    2006-08-20  Douglas Bates  <bates@R-project.org>
164    
165            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
166            * tests/sparseQR.R: Added
167            * man/sparseQR-class.Rd: Document methods for qr.* generics
168            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
169    
170    2006-08-19  Douglas Bates  <bates@R-project.org>
171    
172            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
173            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
174            and qr.fitted.
175            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
176            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
177    
178    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
181            the base version has no "..." argument.
182    
183            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
184    
185            * R/Matrix.R: define and
186            * NAMESPACE: export as.numeric() and as.logical() methods.
187                    Let's hope these do not badly slow down something...
188            Finally export the zapsmall() method.
189    
190    2006-08-17  Douglas Bates  <bates@R-project.org>
191    
192            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
193            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
194            * src/dtCMatrix.c :Remove code that is no longer used
195            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
196    
197    2006-08-14  Douglas Bates  <bates@R-project.org>
198    
199            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
200            Csparse_to_logical and Csparse_symmetric_to_general.
201            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
202            coercion methods between CsparseMatrix and TsparseMatrix.
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
207            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
208            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
209            possible.
210    
211    2006-08-12  Douglas Bates  <bates@R-project.org>
212    
213            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
214              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
215              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
216              generalize conversions between TsparseMatrix, CsparseMatrix,
217              denseMatrix and matrix.  Preserve triangularity property and
218              propagate Dimnames in the easy cases.
219    
220    2006-08-10  Douglas Bates  <bates@R-project.org>
221    
222            * src/lmer.c: adjust checks in glmer_init for S4SXP
223            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
224            before S4SXP but for the wrong reasons.
225    
226    2006-08-08  Douglas Bates  <bates@R-project.org>
227    
228            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
229            Later modified to return the upper triangle only.
230            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
231    
232    2006-08-07  Douglas Bates  <bates@R-project.org>
233    
234            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
235            R-level conversion to a sparse symmetric class.
236            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
237            Remove conversion to sparse symmetric classes (now done in C code).
238    
239    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
242            * man/band.Rd:  adapt the \dontshow{} unit test.
243    
244    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * DESCRIPTION (Version): 0.995-14  for CRAN
247    
248            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
249    
250            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
251            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
252    
253            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
254            * R/Tsparse.R (tril, triu, band): methods
255            * R/dgRMatrix.R (tril, ...):    ditto
256            * man/band.Rd:                  ditto
257    
258    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Matrix.R (head, tail): directly use utils:::head.matrix
261                    to be up-to-date automatically.
262    
263    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
266    
267            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
268            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
269            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
270            such that the S4 objects are always created by the current version
271            of R and 'Matrix' class definitions.
272    
273    2006-08-01  Douglas Bates  <bates@R-project.org>
274    
275            * R/lmer.R (LMEoptimize method), tests/lmer.R,
276            inst/external/test3comp.rda: Added warnings for convergence on
277            boundary and test cases.
278    
279            * src/lmer.c (mer_postVar): Modified to return the variances that
280            are marginal to the fixed effects, not conditional on them (which
281            is what the bVar slot contents represent).
282    
283    2006-07-31  Douglas Bates  <bates@R-project.org>
284    
285            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
286            function which calls the C function mer_hat_trace2.
287    
288            * man/ranef.Rd: Include description of "postVar" argument and
289            producing a caterpillar plot.
290    
291    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * NAMESPACE:    change  "correlation" to "corMatrix"
294            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
295            * R/dpoMatrix.R: ditto
296            * R/lmer.R:      ditto
297    
298    2006-07-28  Douglas Bates  <bates@R-project.org>
299    
300            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
301            RZXinv slot's contents into a separate internal function that can
302            be used in mer_hat_trace.
303    
304    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
307            via new smart
308            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
309            utility functions.
310    
311    
312    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Csparse.R (tril, triu, band): do return *triangular* classed
315            matrices when appropriate; band() even symmetric ones.
316            (replCmat): extend to potentially all "CsparseMatrix"
317            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
318            allow subassignment for special sparse matrices.
319    
320            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
321    
322            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
323            argument; in glmer_*(): print only if(verbose).
324    
325            speed-optimize a few places by moving REAL(.) out of loops.
326    
327            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
328    
329    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
332                    since that wrongly triggers also for M[ logi , ]
333    
334            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
335            a symmetric matrix that results in a non-symmetric one.
336            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
337    
338            * R/dMatrix.R: make round(M) work as round(M, 0)
339    
340            * R/dgTMatrix.R (image): coordinate system and axis now use
341            1-based indices, not 0-based ones.
342    
343            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
344            * tests/indexing.R: test it.
345    
346            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
347            * man/isSymmetric-methods.Rd: and document it.
348    
349            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
350            * man/SparseM-conv.Rd: docu them
351    
352            * tests/other-pkgs.R: renamed from tests/graph.R and add example
353                    for 'SparseM' conversions
354    
355    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
356    
357            * R/Matrix.R (head): added head() and tail() methods.
358    
359    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.995-12 released to CRAN
362    
363    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * tests/simple.R: add check for correct dsT -> dgT coercion;
366                    add check for correct printing of symmetric sparse matrices.
367    
368            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
369            for sparse symmetric matrices.
370    
371            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
372            diagonal twice.
373    
374    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
375    
376            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
377            being applied to the x slot (detected by Brian Ripley).
378    
379    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
382    
383            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
384    
385    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/lgCMatrix.c (lgCMatrix_diag): new function
388            * R/lgCMatrix.R (diag): for new method
389    
390            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
391                 ==> construction of illegal "*gTMatrix" via new() should
392                 now be much less easy:
393            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
394    
395            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
396                    directly.
397            * man/Matrix.Rd: documents it.
398    
399    2006-07-06  Douglas Bates  <bates@R-project.org>
400    
401            * src/pedigree.c (pedigree_inbreeding): Correction in
402            initialization.  This function is not currently being used and is
403            not fully tested.
404    
405            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
406            Introduced the glmer class.  Added code for mcmcmsamp on glmer
407            objects.  Modified validity check on pedigree objects to account
408            for nonparallel patterns of missingness of parents.
409    
410            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
411            class.
412    
413    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/pMatrix.R: coercion pMatrix -> Tsparse
416    
417    2006-06-12  Douglas Bates  <bates@R-project.org>
418    
419            * DESCRIPTION (Version): 0.995-11 released to CRAN
420    
421            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
422            the output from mcmcsamp.
423    
424    2006-06-10  Douglas Bates  <bates@R-project.org>
425    
426            * R/lmer.R (simulestimate): added C code for calculating the trace
427            of the hat matrix.
428    
429    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
432            classes.
433            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
434    
435    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgTMatrix.R (colSums): etc. All four of
438            colSums(), rowSums(), colMeans(), rowMeans() now should work for
439            all "Matrices".
440    
441    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
442    
443            * R/lmer.R (panel.ci): Add a reference line at zero and a
444            background grid to the qqmath plot of ranef.lmer.
445    
446    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
449            grouping factors to be specified in the formula as (1|foo/bar).
450    
451    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
452    
453            * R/lmer.R (findbars and others): Change check of is.numeric to
454            !is.language to resolve the bug reported by Jacob Wegelin.
455    
456            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
457            code to evaluate inbreeding coefficients without calculating T,
458            based on code in Sargolzaei and Iwaisaki's paper.
459    
460    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
461    
462            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
463            generic and mer methods for isNested and denomDF. This denomDF was
464            an attempt to emulate that in lme but I don't think that makes
465            sense.  Use the trace of the hat matrix instead.
466    
467    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
470            the C code depending on a slot structure that's no longer valid.
471            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
472    
473    
474    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
475    
476            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
477            of lowerTriMatrix generic and methods to tril (also upper to triu)
478            and added a general band extractor.
479    
480    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * R/pedigree.R (pedigree): Replace sire and dam values outside the
483            allowable range with NAs. Added a corresponding check in the
484            validity check for the pedigree class.
485    
486            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
487            crossprod methods now inherits from symmetricMatrix.
488    
489    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
490    
491            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
492            generics lowerTriMatrix and upperTriMatrix along with methods for
493            the Csparse virtual class.  Also added a C function Csparse_band
494            that implements these methods by calling cholmod_band.
495    
496    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
499            erased when it was NULL.  This led to invalid subselections!
500    
501    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
504            in method for "t" so as not to lose the unit diagonal property.
505    
506    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
507    
508            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
509            and methods.  This is now an option to the ranef method for the
510            mer class.
511    
512            * src/cs_utils.c: Ensure that the nz component is -1 for a
513            compressed column-oriented matrix.  Minor formatting cleanup.
514    
515            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
516            objects.
517    
518    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
521            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
522    
523    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
524    
525            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
526            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
527    
528            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
529            for the dtCMatrix class.
530    
531    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
532    
533            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
534            and methods for it.
535    
536    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
539            arguments, such that M %*% 1:6 now works
540            * Tests/matprod.R: test the above
541    
542    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
545            the ranef.lmer class.
546    
547            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
548            methods to extract the posterior variances from the bVar slot.
549    
550    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
553            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
554    
555            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
556            * tests/simple: (extended)
557    
558            * R/sparseMatrix.R (isTriangular): now using much improved
559            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
560    
561    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
564            (problem report from Franklin Parlamis).  This should be done
565            generally.
566    
567    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
568    
569            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
570            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
571            update the plot methods.
572    
573    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
574    
575            * R/lmer.R (resid and ranef methods):  Added methods for the
576            "residuals" and "resid" generic but only for linear mixed model
577            fits.  Changed the ranef method to return a list of data frames so
578            that the plot methods now work.
579    
580    2006-03-16  Douglas Bates  <bates@bates2>
581    
582            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
583            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
584    
585            * DESCRIPTION (Date): New release
586    
587    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
590    
591            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
592            * man/KNex.Rd: and other help files
593            * tests/*.R: several ones needed adaption
594            * inst/doc/Comparisons.Rnw: ditto
595    
596    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
599    
600            * tests/indexing.R: tests for new [<- methods for sparse matrices.
601    
602    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
605    
606            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
607    
608    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/dMatrix.R: enable things like  M [ M < 10 ]
611            * R/dgeMatrix.R: implement it
612    
613    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/AllClass.R: define "summary.mer" and "*.lmer"
616            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
617            * R/lmer.R (show): now works with summary()
618    
619    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
622            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
623                    support the above
624    
625    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
628            Use glmFit$prior.weights for weights in a glmm.
629            Allow an option usePQL = FALSE to skip the PQL steps for the
630            Laplace method (and, in time, the AGQ method).
631    
632            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
633            into a separate function internal_mer_Xfactor to be able to call
634            it from internal_bhat.
635    
636    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * tests/Class+Meth.R (tstMatrixClass): function for much better
639            testing; now again of all actual classes.
640    
641            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
642                    use macros and define make_d_matrix_* and make_i_matrix_*
643                    where _i_ is for the ldense routines:
644    
645            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
646            * src/ldense.c (lsyMatrix_as_lgeMatrix):
647    
648            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
649    
650    
651    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
654                    many different kinds of matrices.
655            * R/*.R: quite a few new methods were needed for R CMD check with
656                    new Matrix().  Very good for users playing around.
657    
658    
659    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * src/dgeMatrix.c (dMatrix_validate): new
662            * src/Mutils.c (dense_nonpacked_validate): new
663    
664            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
665    
666    
667    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
670    
671    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * DESCRIPTION (Version): 0.99-6 released to CRAN
674    
675            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
676            segfault in cases with multiple non-nested grouping factors.
677    
678  2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680          * DESCRIPTION (Version): 0.99-4 to be released to CRAN          * DESCRIPTION (Version): 0.99-4 to be released to CRAN
# Line 118  Line 795 
795  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
798          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
799          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
800    
801  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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