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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1615, Thu Oct 5 16:30:46 2006 UTC
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1    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
4    
5    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
6    
7            * DESCRIPTION (Version): 0.9975-2
8    
9            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
10    
11    2006-10-02  Douglas Bates  <bates@R-project.org>
12    
13            * tests/dg_Matrix.R: Simplify test taking into account new code.
14    
15    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
18    
19            * R/lsTMatrix.R: new files w/ missing methods
20            * R/nsTMatrix.R:  "  'for completeness'
21    
22            * tests/Class+Meth.R: a bit less 'not.ok.classes'
23    
24            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
25    
26    
27    2006-09-28  Douglas Bates  <bates@R-project.org>
28    
29            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
30            included.
31    
32            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
33            Export C-callable functions used in Zt_create in lme4.
34    
35    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * DESCRIPTION (Version): 0.9975-1
38    
39            * tests/simple.R: less checks fail; using NA, found that our
40                    kronecker() is not base-compatible with NA's.
41    
42            * R/dMatrix.R: "Compare" method now implemented for all cases
43    
44            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
45    
46            * man/dtpMatrix-class.Rd: mention length of 'x' slot
47    
48            * src/dtpMatrix.c (dtpMatrix_validate): fix check
49            * src/dspMatrix.c (dspMatrix_validate): ditto
50    
51            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
52              including coercion to [nl]tTMatrix.
53    
54            * R/diagMatrix.R (show): print a header line as for other classes.
55    
56    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/Makefile.win (SUBDIRS): fix typo
59    
60    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
63    
64    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
67            symmetric and y missing in R code using %*% (cholmod_aat doesn't
68            accept a symmetric matrix).
69            * tests/group-methods.R: Uncomment test of crossprod applied to
70            lsCMatrix objects.
71    
72    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/AllClass.R (symmetricMatrix): add validity method (available
75            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
76    
77            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
78    
79            * tests/indexing.Rout.save:
80            * tests/indexing.R: additions, mainly for 'lsparse'
81    
82            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
83            case.
84    
85            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
86    
87    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
90                    as 'N' (1-letter - Ok?)
91    
92            * tests/group-methods.R: add test for logical + NAs
93    
94            * R/dMatrix.R ("Compare"): fix to work with NA's
95    
96            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
97    
98            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
99                    which is implemented.
100    
101    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * src/chm_common.c: coerce logical <-> double instead of
104            typecasting;  needed for "l" matrix handling in cholmod.
105    
106            * tests/other-pkgs.R (graph): small extension in "graph" checks.
107    
108            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
109            (Tsp2grNEL): other fixes needed
110    
111    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
114                    Matrices, since "lMatrix", also "lsparseM" can have NA
115            * R/ndenseMatrix.R, etc: new source files
116            * man/nsparseMatrix-classes.Rd, etc: new help files
117            * tests/: adaptions
118            * src/chm_common.c (chm_dense_to_SEXP): and others:
119                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
120            * src/Csparse.c, etc: ditto
121    
122    2006-09-11  Douglas Bates  <bates@R-project.org>
123    
124            * src/Mutils.[ch],init.c inst/include/*.h: Move the
125            alloc_d**Matrix functions to the lme4 package.
126    
127    2006-09-09  Douglas Bates  <bates@R-project.org>
128    
129            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
130            fixed
131    
132    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/lMatrix.R: new
135    
136            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
137    
138            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
139            * man/tcrossprod.Rd: ditto
140    
141    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
144            for exported functions
145            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
146            Remove partitioning algorithms for sparse matrix reordering.  The
147            copyright on the Metis code was problematic and the methods were
148            rarely used.
149            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
150            operations are now done entirely in CHOLMOD code.
151    
152    2006-09-06  Douglas Bates  <bates@R-project.org>
153    
154            * src/Mutils.h: Remove functions that are no longer used.
155    
156    2006-09-04  Douglas Bates  <bates@R-project.org>
157    
158            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
159            * src/DEPS.mkf: update
160    
161    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * created branches/Matrix-for-R-2.3.x;  on trunk: do
164            * DESCRIPTION (Version): 0.9975-0
165            (Depends): R (>= 2.4.0)
166    
167    2006-09-01  Douglas Bates  <bates@R-project.org>
168    
169            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
170    
171    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
174            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
175    
176            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
177    
178    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
181            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
182            * R/dsparseMatrix.R: ditto
183            * R/Csparse.R: ditto
184    
185    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dMatrix.R (Compare): improve availability of "<", etc
188            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
189    
190    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
193            of a 0-index which was used as 1-index (..hmm)
194    
195            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
196    
197            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
198            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
199            (.is.diagonal): ditto
200    
201            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
202    
203            * R/Matrix.R (Matrix): also work for NA data
204    
205    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
208            in all cases.
209    
210    2006-08-27  Douglas Bates  <bates@R-project.org>
211    
212            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
213            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
214    
215    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
218            subclasses of "ddenseMatrix"
219            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
220            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
221            instead of half dozen specialized ones.
222    
223    2006-08-25  Douglas Bates  <bates@R-project.org>
224    
225            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
226            <tillard@cirad.fr> - ordering standard errors to match effects.
227    
228    2006-08-24  Douglas Bates  <bates@R-project.org>
229    
230            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
231            on R_ldl.
232            * R/lCholCMatrix.R,
233            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
234            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
235            * many files in ./R and ./src: Use more general version of
236            dup_mMatrix_as_dgeMatrix to simplify method definitions.
237            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
238            dtpMatrix, dspMatrix and dppMatrix conversions.
239    
240    
241    2006-08-23  Douglas Bates  <bates@R-project.org>
242    
243            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
244            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
245            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
246            dgeMatrix_crossprod (may need to do this in other places).
247            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
248            generic and method for dsCMatrix.  Use CHOLMOD for chol().
249    
250    2006-08-22  Douglas Bates  <bates@R-project.org>
251    
252            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
253            types of classed Matrices, matrices or numeric or logical vectors.
254            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
255            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
256            to Mutils.h (as an inline) and change name to Matrix_check_class;
257            fixes in as_cholmod_factor and chm_factor_to_SEXP.
258            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
259            dsCMatrix_matrix_solve.  Comment out vestigial functions.
260            * src/Csparse.c: use diag_P and uplo_P macros.
261    
262    2006-08-21  Douglas Bates  <bates@R-project.org>
263    
264            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
265            valgrind.
266            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
267            inverses.
268            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
269            -Wall warnings.
270            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
271            Use dup_mMatrix_as_dgeMatrix.
272    
273    2006-08-20  Douglas Bates  <bates@R-project.org>
274    
275            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
276            * tests/sparseQR.R: Added
277            * man/sparseQR-class.Rd: Document methods for qr.* generics
278            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
279    
280    2006-08-19  Douglas Bates  <bates@R-project.org>
281    
282            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
283            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
284            and qr.fitted.
285            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
286            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
287    
288    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
291            the base version has no "..." argument.
292    
293            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
294    
295            * R/Matrix.R: define and
296            * NAMESPACE: export as.numeric() and as.logical() methods.
297                    Let's hope these do not badly slow down something...
298            Finally export the zapsmall() method.
299    
300    2006-08-17  Douglas Bates  <bates@R-project.org>
301    
302            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
303            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
304            * src/dtCMatrix.c :Remove code that is no longer used
305            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
306    
307    2006-08-14  Douglas Bates  <bates@R-project.org>
308    
309            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
310            Csparse_to_logical and Csparse_symmetric_to_general.
311            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
312            coercion methods between CsparseMatrix and TsparseMatrix.
313    
314    2006-08-14  Douglas Bates  <bates@R-project.org>
315    
316            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
317            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
318            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
319            possible.
320    
321    2006-08-12  Douglas Bates  <bates@R-project.org>
322    
323            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
324              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
325              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
326              generalize conversions between TsparseMatrix, CsparseMatrix,
327              denseMatrix and matrix.  Preserve triangularity property and
328              propagate Dimnames in the easy cases.
329    
330    2006-08-10  Douglas Bates  <bates@R-project.org>
331    
332            * src/lmer.c: adjust checks in glmer_init for S4SXP
333            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
334            before S4SXP but for the wrong reasons.
335    
336    2006-08-08  Douglas Bates  <bates@R-project.org>
337    
338            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
339            Later modified to return the upper triangle only.
340            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
341    
342    2006-08-07  Douglas Bates  <bates@R-project.org>
343    
344            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
345            R-level conversion to a sparse symmetric class.
346            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
347            Remove conversion to sparse symmetric classes (now done in C code).
348    
349    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
352            * man/band.Rd:  adapt the \dontshow{} unit test.
353    
354    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.995-14  for CRAN
357    
358            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
359    
360            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
361            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
362    
363            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
364            * R/Tsparse.R (tril, triu, band): methods
365            * R/dgRMatrix.R (tril, ...):    ditto
366            * man/band.Rd:                  ditto
367    
368    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Matrix.R (head, tail): directly use utils:::head.matrix
371                    to be up-to-date automatically.
372    
373    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
376    
377            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
378            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
379            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
380            such that the S4 objects are always created by the current version
381            of R and 'Matrix' class definitions.
382    
383    2006-08-01  Douglas Bates  <bates@R-project.org>
384    
385            * R/lmer.R (LMEoptimize method), tests/lmer.R,
386            inst/external/test3comp.rda: Added warnings for convergence on
387            boundary and test cases.
388    
389            * src/lmer.c (mer_postVar): Modified to return the variances that
390            are marginal to the fixed effects, not conditional on them (which
391            is what the bVar slot contents represent).
392    
393    2006-07-31  Douglas Bates  <bates@R-project.org>
394    
395            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
396            function which calls the C function mer_hat_trace2.
397    
398            * man/ranef.Rd: Include description of "postVar" argument and
399            producing a caterpillar plot.
400    
401    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * NAMESPACE:    change  "correlation" to "corMatrix"
404            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
405            * R/dpoMatrix.R: ditto
406            * R/lmer.R:      ditto
407    
408    2006-07-28  Douglas Bates  <bates@R-project.org>
409    
410            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
411            RZXinv slot's contents into a separate internal function that can
412            be used in mer_hat_trace.
413    
414    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
417            via new smart
418            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
419            utility functions.
420    
421    
422    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/Csparse.R (tril, triu, band): do return *triangular* classed
425            matrices when appropriate; band() even symmetric ones.
426            (replCmat): extend to potentially all "CsparseMatrix"
427            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
428            allow subassignment for special sparse matrices.
429    
430            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
431    
432            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
433            argument; in glmer_*(): print only if(verbose).
434    
435            speed-optimize a few places by moving REAL(.) out of loops.
436    
437            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
438    
439    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
442                    since that wrongly triggers also for M[ logi , ]
443    
444            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
445            a symmetric matrix that results in a non-symmetric one.
446            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
447    
448            * R/dMatrix.R: make round(M) work as round(M, 0)
449    
450            * R/dgTMatrix.R (image): coordinate system and axis now use
451            1-based indices, not 0-based ones.
452    
453            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
454            * tests/indexing.R: test it.
455    
456            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
457            * man/isSymmetric-methods.Rd: and document it.
458    
459            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
460            * man/SparseM-conv.Rd: docu them
461    
462            * tests/other-pkgs.R: renamed from tests/graph.R and add example
463                    for 'SparseM' conversions
464    
465    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
466    
467            * R/Matrix.R (head): added head() and tail() methods.
468    
469    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Version): 0.995-12 released to CRAN
472    
473    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * tests/simple.R: add check for correct dsT -> dgT coercion;
476                    add check for correct printing of symmetric sparse matrices.
477    
478            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
479            for sparse symmetric matrices.
480    
481            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
482            diagonal twice.
483    
484    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
485    
486            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
487            being applied to the x slot (detected by Brian Ripley).
488    
489    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
492    
493            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
494    
495    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/lgCMatrix.c (lgCMatrix_diag): new function
498            * R/lgCMatrix.R (diag): for new method
499    
500            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
501                 ==> construction of illegal "*gTMatrix" via new() should
502                 now be much less easy:
503            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
504    
505            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
506                    directly.
507            * man/Matrix.Rd: documents it.
508    
509    2006-07-06  Douglas Bates  <bates@R-project.org>
510    
511            * src/pedigree.c (pedigree_inbreeding): Correction in
512            initialization.  This function is not currently being used and is
513            not fully tested.
514    
515            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
516            Introduced the glmer class.  Added code for mcmcmsamp on glmer
517            objects.  Modified validity check on pedigree objects to account
518            for nonparallel patterns of missingness of parents.
519    
520            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
521            class.
522    
523    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/pMatrix.R: coercion pMatrix -> Tsparse
526    
527    2006-06-12  Douglas Bates  <bates@R-project.org>
528    
529            * DESCRIPTION (Version): 0.995-11 released to CRAN
530    
531            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
532            the output from mcmcsamp.
533    
534    2006-06-10  Douglas Bates  <bates@R-project.org>
535    
536            * R/lmer.R (simulestimate): added C code for calculating the trace
537            of the hat matrix.
538    
539    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
542            classes.
543            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
544    
545    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/dgTMatrix.R (colSums): etc. All four of
548            colSums(), rowSums(), colMeans(), rowMeans() now should work for
549            all "Matrices".
550    
551    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
552    
553            * R/lmer.R (panel.ci): Add a reference line at zero and a
554            background grid to the qqmath plot of ranef.lmer.
555    
556    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
559            grouping factors to be specified in the formula as (1|foo/bar).
560    
561    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * R/lmer.R (findbars and others): Change check of is.numeric to
564            !is.language to resolve the bug reported by Jacob Wegelin.
565    
566            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
567            code to evaluate inbreeding coefficients without calculating T,
568            based on code in Sargolzaei and Iwaisaki's paper.
569    
570    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
571    
572            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
573            generic and mer methods for isNested and denomDF. This denomDF was
574            an attempt to emulate that in lme but I don't think that makes
575            sense.  Use the trace of the hat matrix instead.
576    
577    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
580            the C code depending on a slot structure that's no longer valid.
581            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
582    
583    
584    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
585    
586            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
587            of lowerTriMatrix generic and methods to tril (also upper to triu)
588            and added a general band extractor.
589    
590    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
591    
592            * R/pedigree.R (pedigree): Replace sire and dam values outside the
593            allowable range with NAs. Added a corresponding check in the
594            validity check for the pedigree class.
595    
596            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
597            crossprod methods now inherits from symmetricMatrix.
598    
599    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
600    
601            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
602            generics lowerTriMatrix and upperTriMatrix along with methods for
603            the Csparse virtual class.  Also added a C function Csparse_band
604            that implements these methods by calling cholmod_band.
605    
606    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
609            erased when it was NULL.  This led to invalid subselections!
610    
611    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
614            in method for "t" so as not to lose the unit diagonal property.
615    
616    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
617    
618            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
619            and methods.  This is now an option to the ranef method for the
620            mer class.
621    
622            * src/cs_utils.c: Ensure that the nz component is -1 for a
623            compressed column-oriented matrix.  Minor formatting cleanup.
624    
625            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
626            objects.
627    
628    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
631            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
632    
633    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
634    
635            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
636            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
637    
638            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
639            for the dtCMatrix class.
640    
641    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
642    
643            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
644            and methods for it.
645    
646    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
649            arguments, such that M %*% 1:6 now works
650            * Tests/matprod.R: test the above
651    
652    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
653    
654            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
655            the ranef.lmer class.
656    
657            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
658            methods to extract the posterior variances from the bVar slot.
659    
660    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
663            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
664    
665            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
666            * tests/simple: (extended)
667    
668            * R/sparseMatrix.R (isTriangular): now using much improved
669            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
670    
671    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
674            (problem report from Franklin Parlamis).  This should be done
675            generally.
676    
677    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
680            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
681            update the plot methods.
682    
683    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
684    
685            * R/lmer.R (resid and ranef methods):  Added methods for the
686            "residuals" and "resid" generic but only for linear mixed model
687            fits.  Changed the ranef method to return a list of data frames so
688            that the plot methods now work.
689    
690    2006-03-16  Douglas Bates  <bates@bates2>
691    
692            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
693            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
694    
695            * DESCRIPTION (Date): New release
696    
697    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
700    
701            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
702            * man/KNex.Rd: and other help files
703            * tests/*.R: several ones needed adaption
704            * inst/doc/Comparisons.Rnw: ditto
705    
706    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
709    
710            * tests/indexing.R: tests for new [<- methods for sparse matrices.
711    
712    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
715    
716            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
717    
718    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/dMatrix.R: enable things like  M [ M < 10 ]
721            * R/dgeMatrix.R: implement it
722    
723    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/AllClass.R: define "summary.mer" and "*.lmer"
726            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
727            * R/lmer.R (show): now works with summary()
728    
729    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
732            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
733                    support the above
734    
735    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
736    
737            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
738            Use glmFit$prior.weights for weights in a glmm.
739            Allow an option usePQL = FALSE to skip the PQL steps for the
740            Laplace method (and, in time, the AGQ method).
741    
742            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
743            into a separate function internal_mer_Xfactor to be able to call
744            it from internal_bhat.
745    
746    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * tests/Class+Meth.R (tstMatrixClass): function for much better
749            testing; now again of all actual classes.
750    
751            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
752                    use macros and define make_d_matrix_* and make_i_matrix_*
753                    where _i_ is for the ldense routines:
754    
755            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
756            * src/ldense.c (lsyMatrix_as_lgeMatrix):
757    
758            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
759    
760    
761    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
764                    many different kinds of matrices.
765            * R/*.R: quite a few new methods were needed for R CMD check with
766                    new Matrix().  Very good for users playing around.
767    
768    
769    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * src/dgeMatrix.c (dMatrix_validate): new
772            * src/Mutils.c (dense_nonpacked_validate): new
773    
774            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
775    
776    
777    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
778    
779            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
780    
781    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
782    
783            * DESCRIPTION (Version): 0.99-6 released to CRAN
784    
785            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
786            segfault in cases with multiple non-nested grouping factors.
787    
788    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
791                    (Depends): also on 'utils'
792    
793            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
794            * R/diagMatrix.R (Diagonal): constructor and methods for
795            diagonal matrices
796    
797            * R/ltTMatrix.R: new "minimal methods"
798    
799    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
802            all methods (and help files).
803    
804    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
807                    for case (dimn.  op  no_dimn.)
808    
809    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
810    
811            * DESCRIPTION (Version): 0.99-2  released to CRAN
812    
813    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
814    
815            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
816            by Julian Faraway.
817    
818    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/Auxiliaries.R (try_as): new utility
821            * R/sparseMatrix.R: use try_as() in coercion to original class
822    
823    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
826    
827    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Auxiliaries.R (dimNamesCheck): added
830    
831            * R/Matrix.R (as.array), (as.vector): new
832    
833    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
836                    default.
837            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
838                    "pMatrix" now contains "sparseMatrix"
839    
840    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * tests/Class+Meth.R: new tests; t(t(m)) == m
843    
844            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
845    
846            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
847            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
848    
849            * R/dspMatrix.R: typo in "t" method
850    
851    2005-09-18  Douglas Bates  <bates@wisc.edu>
852    
853            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
854            * R/Tsparse.R: instead of R/gTMatrix.R
855            * R/Csparse.R: new
856            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
857            * src/Tsparse.c: new; many trivial methods calling cholmod_()
858            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
859                            via cholmod
860    
861    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Auxiliaries.R (non0ind): new function using new C code
864            * src/dgCMatrix.c (compressed_non_0_ij): new utility
865    
866    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
867    
868            * src/chm_common.h: header file required by all C sources that
869            call CHOLMOD functions.  It defines a cholmod_common structure
870            called 'c' whose address is passed as the last argument to
871            (virtually) every CHOLMOD function.
872    
873            * src/Pattern.c: Simple example of the use of CHOLMOD.
874    
875            * src/init.c: initialize and finalize the cholmod_common structure.
876    
877            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
878            LDL and CCOLAMD from the U. of Florida sparse matrix library.
879    
880    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * inst/test-tools.R: new file collecting the utility functions used
883                    in ./tests/*.R
884    
885            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
886            * R/Matrix.R (cbind2): methods for NULL and missing
887    
888    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
889    
890            * R/AllClass.R: new "index" class for "[" and "[<-":
891                    First cut at "symmetricMatrix" and "triangularMatrix"
892            * R/gTMatrix.R (.ind.prep): new function;
893                    Logical and character indexing now work too.
894            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
895            * tests/indexing.R: new, including *.Rout.save
896            * tests/dgTMatrix.R: new
897    
898    2005-08-29  Douglas Bates  <bates@wisc.edu>
899    
900            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
901            indicator pos not being updated.  Also enforced upper triangular
902            for symmetric case.  Need to coerce edges component of elements of
903            edge list - grr! (Why don't they define their classes cleanly?)
904    
905    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/Matrix.R:  added first "[<-" methods; not yet functional
908            * R/denseMatrix.R: ditto
909            * man/Subassign-methods.Rd: new help file for these
910    
911    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * DESCRIPTION (Version): 0.98-6
914    
915            * R/denseMatrix.R: new file for "[" fallback methods for all dense
916            matrices.
917    
918    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
921                    as( <logical>, "matrix")
922    
923            * R/pMatrix.R: coercion to "lgTMatrix"
924    
925            * R/gTMatrix.R: new virtual class to define "[" methods for.
926            * man/gTMatrix-class.Rd:
927            * General slight re-organization of where "[" methods are defined.
928              more to come.
929    
930    2005-08-18  Douglas Bates  <bates@wisc.edu>
931    
932            * DESCRIPTION (Version): 0.98-5  released to CRAN
933    
934            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
935            * .....
936    
937    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
938    
939            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
940            or glmer objects.
941    
942    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
945    
946    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
947    
948            * R/HBMM.R: finish re-writing R-only code.
949    
950    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
951    
952            * man/externalFormats.Rd: move documentation for writeHB and
953            writeMM here.
954    
955            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
956            (suggested by Paul Roecker).
957    
958            * tests/validObj.R (assertError): Comment out test that is failing
959            after recent changes in r-devel.
960    
961    
962  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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