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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1592, Thu Sep 28 15:31:17 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.9975-1
4    
5            * tests/simple.R: less checks fail; using NA, found that our
6                    kronecker() is not base-compatible with NA's.
7    
8            * R/dMatrix.R: "Compare" method now implemented for all cases
9    
10            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
11    
12            * man/dtpMatrix-class.Rd: mention length of 'x' slot
13    
14            * src/dtpMatrix.c (dtpMatrix_validate): fix check
15            * src/dspMatrix.c (dspMatrix_validate): ditto
16    
17            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
18              including coercion to [nl]tTMatrix.
19    
20            * R/diagMatrix.R (show): print a header line as for other classes.
21    
22    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/Makefile.win (SUBDIRS): fix typo
25    
26    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
29    
30    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
33            symmetric and y missing in R code using %*% (cholmod_aat doesn't
34            accept a symmetric matrix).
35            * tests/group-methods.R: Uncomment test of crossprod applied to
36            lsCMatrix objects.
37    
38    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/AllClass.R (symmetricMatrix): add validity method (available
41            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
42    
43            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
44    
45            * tests/indexing.Rout.save:
46            * tests/indexing.R: additions, mainly for 'lsparse'
47    
48            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
49            case.
50    
51            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
52    
53    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
56                    as 'N' (1-letter - Ok?)
57    
58            * tests/group-methods.R: add test for logical + NAs
59    
60            * R/dMatrix.R ("Compare"): fix to work with NA's
61    
62            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
63    
64            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
65                    which is implemented.
66    
67    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * src/chm_common.c: coerce logical <-> double instead of
70            typecasting;  needed for "l" matrix handling in cholmod.
71    
72            * tests/other-pkgs.R (graph): small extension in "graph" checks.
73    
74            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
75            (Tsp2grNEL): other fixes needed
76    
77    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
80                    Matrices, since "lMatrix", also "lsparseM" can have NA
81            * R/ndenseMatrix.R, etc: new source files
82            * man/nsparseMatrix-classes.Rd, etc: new help files
83            * tests/: adaptions
84            * src/chm_common.c (chm_dense_to_SEXP): and others:
85                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
86            * src/Csparse.c, etc: ditto
87    
88    2006-09-11  Douglas Bates  <bates@R-project.org>
89    
90            * src/Mutils.[ch],init.c inst/include/*.h: Move the
91            alloc_d**Matrix functions to the lme4 package.
92    
93    2006-09-09  Douglas Bates  <bates@R-project.org>
94    
95            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
96            fixed
97    
98    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/lMatrix.R: new
101    
102            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
103    
104            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
105            * man/tcrossprod.Rd: ditto
106    
107    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
110            for exported functions
111            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
112            Remove partitioning algorithms for sparse matrix reordering.  The
113            copyright on the Metis code was problematic and the methods were
114            rarely used.
115            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
116            operations are now done entirely in CHOLMOD code.
117    
118    2006-09-06  Douglas Bates  <bates@R-project.org>
119    
120            * src/Mutils.h: Remove functions that are no longer used.
121    
122    2006-09-04  Douglas Bates  <bates@R-project.org>
123    
124            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
125            * src/DEPS.mkf: update
126    
127    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * created branches/Matrix-for-R-2.3.x;  on trunk: do
130            * DESCRIPTION (Version): 0.9975-0
131            (Depends): R (>= 2.4.0)
132    
133    2006-09-01  Douglas Bates  <bates@R-project.org>
134    
135            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
136    
137    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
140            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
141    
142            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
143    
144    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
147            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
148            * R/dsparseMatrix.R: ditto
149            * R/Csparse.R: ditto
150    
151    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dMatrix.R (Compare): improve availability of "<", etc
154            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
155    
156    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
159            of a 0-index which was used as 1-index (..hmm)
160    
161            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
162    
163            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
164            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
165            (.is.diagonal): ditto
166    
167            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
168    
169            * R/Matrix.R (Matrix): also work for NA data
170    
171    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
174            in all cases.
175    
176    2006-08-27  Douglas Bates  <bates@R-project.org>
177    
178            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
179            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
180    
181    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
184            subclasses of "ddenseMatrix"
185            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
186            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
187            instead of half dozen specialized ones.
188    
189    2006-08-25  Douglas Bates  <bates@R-project.org>
190    
191            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
192            <tillard@cirad.fr> - ordering standard errors to match effects.
193    
194    2006-08-24  Douglas Bates  <bates@R-project.org>
195    
196            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
197            on R_ldl.
198            * R/lCholCMatrix.R,
199            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
200            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
201            * many files in ./R and ./src: Use more general version of
202            dup_mMatrix_as_dgeMatrix to simplify method definitions.
203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
204            dtpMatrix, dspMatrix and dppMatrix conversions.
205    
206    
207    2006-08-23  Douglas Bates  <bates@R-project.org>
208    
209            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
210            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
211            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
212            dgeMatrix_crossprod (may need to do this in other places).
213            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
214            generic and method for dsCMatrix.  Use CHOLMOD for chol().
215    
216    2006-08-22  Douglas Bates  <bates@R-project.org>
217    
218            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
219            types of classed Matrices, matrices or numeric or logical vectors.
220            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
221            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
222            to Mutils.h (as an inline) and change name to Matrix_check_class;
223            fixes in as_cholmod_factor and chm_factor_to_SEXP.
224            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
225            dsCMatrix_matrix_solve.  Comment out vestigial functions.
226            * src/Csparse.c: use diag_P and uplo_P macros.
227    
228    2006-08-21  Douglas Bates  <bates@R-project.org>
229    
230            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
231            valgrind.
232            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
233            inverses.
234            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
235            -Wall warnings.
236            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
237            Use dup_mMatrix_as_dgeMatrix.
238    
239    2006-08-20  Douglas Bates  <bates@R-project.org>
240    
241            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
242            * tests/sparseQR.R: Added
243            * man/sparseQR-class.Rd: Document methods for qr.* generics
244            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
245    
246    2006-08-19  Douglas Bates  <bates@R-project.org>
247    
248            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
249            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
250            and qr.fitted.
251            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
252            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
253    
254    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
257            the base version has no "..." argument.
258    
259            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
260    
261            * R/Matrix.R: define and
262            * NAMESPACE: export as.numeric() and as.logical() methods.
263                    Let's hope these do not badly slow down something...
264            Finally export the zapsmall() method.
265    
266    2006-08-17  Douglas Bates  <bates@R-project.org>
267    
268            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
269            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
270            * src/dtCMatrix.c :Remove code that is no longer used
271            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
272    
273    2006-08-14  Douglas Bates  <bates@R-project.org>
274    
275            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
276            Csparse_to_logical and Csparse_symmetric_to_general.
277            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
278            coercion methods between CsparseMatrix and TsparseMatrix.
279    
280    2006-08-14  Douglas Bates  <bates@R-project.org>
281    
282            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
283            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
284            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
285            possible.
286    
287    2006-08-12  Douglas Bates  <bates@R-project.org>
288    
289            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
290              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
291              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
292              generalize conversions between TsparseMatrix, CsparseMatrix,
293              denseMatrix and matrix.  Preserve triangularity property and
294              propagate Dimnames in the easy cases.
295    
296    2006-08-10  Douglas Bates  <bates@R-project.org>
297    
298            * src/lmer.c: adjust checks in glmer_init for S4SXP
299            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
300            before S4SXP but for the wrong reasons.
301    
302    2006-08-08  Douglas Bates  <bates@R-project.org>
303    
304            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
305            Later modified to return the upper triangle only.
306            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
307    
308    2006-08-07  Douglas Bates  <bates@R-project.org>
309    
310            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
311            R-level conversion to a sparse symmetric class.
312            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
313            Remove conversion to sparse symmetric classes (now done in C code).
314    
315    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
318            * man/band.Rd:  adapt the \dontshow{} unit test.
319    
320    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * DESCRIPTION (Version): 0.995-14  for CRAN
323    
324            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
325    
326            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
327            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
328    
329            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
330            * R/Tsparse.R (tril, triu, band): methods
331            * R/dgRMatrix.R (tril, ...):    ditto
332            * man/band.Rd:                  ditto
333    
334    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Matrix.R (head, tail): directly use utils:::head.matrix
337                    to be up-to-date automatically.
338    
339    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
342    
343            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
344            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
345            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
346            such that the S4 objects are always created by the current version
347            of R and 'Matrix' class definitions.
348    
349    2006-08-01  Douglas Bates  <bates@R-project.org>
350    
351            * R/lmer.R (LMEoptimize method), tests/lmer.R,
352            inst/external/test3comp.rda: Added warnings for convergence on
353            boundary and test cases.
354    
355            * src/lmer.c (mer_postVar): Modified to return the variances that
356            are marginal to the fixed effects, not conditional on them (which
357            is what the bVar slot contents represent).
358    
359    2006-07-31  Douglas Bates  <bates@R-project.org>
360    
361            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
362            function which calls the C function mer_hat_trace2.
363    
364            * man/ranef.Rd: Include description of "postVar" argument and
365            producing a caterpillar plot.
366    
367    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * NAMESPACE:    change  "correlation" to "corMatrix"
370            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
371            * R/dpoMatrix.R: ditto
372            * R/lmer.R:      ditto
373    
374    2006-07-28  Douglas Bates  <bates@R-project.org>
375    
376            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
377            RZXinv slot's contents into a separate internal function that can
378            be used in mer_hat_trace.
379    
380    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
383            via new smart
384            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
385            utility functions.
386    
387    
388    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Csparse.R (tril, triu, band): do return *triangular* classed
391            matrices when appropriate; band() even symmetric ones.
392            (replCmat): extend to potentially all "CsparseMatrix"
393            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
394            allow subassignment for special sparse matrices.
395    
396            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
397    
398            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
399            argument; in glmer_*(): print only if(verbose).
400    
401            speed-optimize a few places by moving REAL(.) out of loops.
402    
403            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
404    
405    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
408                    since that wrongly triggers also for M[ logi , ]
409    
410            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
411            a symmetric matrix that results in a non-symmetric one.
412            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
413    
414            * R/dMatrix.R: make round(M) work as round(M, 0)
415    
416            * R/dgTMatrix.R (image): coordinate system and axis now use
417            1-based indices, not 0-based ones.
418    
419            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
420            * tests/indexing.R: test it.
421    
422            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
423            * man/isSymmetric-methods.Rd: and document it.
424    
425            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
426            * man/SparseM-conv.Rd: docu them
427    
428            * tests/other-pkgs.R: renamed from tests/graph.R and add example
429                    for 'SparseM' conversions
430    
431    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
432    
433            * R/Matrix.R (head): added head() and tail() methods.
434    
435    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * DESCRIPTION (Version): 0.995-12 released to CRAN
438    
439    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * tests/simple.R: add check for correct dsT -> dgT coercion;
442                    add check for correct printing of symmetric sparse matrices.
443    
444            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
445            for sparse symmetric matrices.
446    
447            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
448            diagonal twice.
449    
450    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
451    
452            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
453            being applied to the x slot (detected by Brian Ripley).
454    
455    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
458    
459            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
460    
461    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/lgCMatrix.c (lgCMatrix_diag): new function
464            * R/lgCMatrix.R (diag): for new method
465    
466            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
467                 ==> construction of illegal "*gTMatrix" via new() should
468                 now be much less easy:
469            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
470    
471            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
472                    directly.
473            * man/Matrix.Rd: documents it.
474    
475    2006-07-06  Douglas Bates  <bates@R-project.org>
476    
477            * src/pedigree.c (pedigree_inbreeding): Correction in
478            initialization.  This function is not currently being used and is
479            not fully tested.
480    
481            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
482            Introduced the glmer class.  Added code for mcmcmsamp on glmer
483            objects.  Modified validity check on pedigree objects to account
484            for nonparallel patterns of missingness of parents.
485    
486            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
487            class.
488    
489    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/pMatrix.R: coercion pMatrix -> Tsparse
492    
493    2006-06-12  Douglas Bates  <bates@R-project.org>
494    
495            * DESCRIPTION (Version): 0.995-11 released to CRAN
496    
497            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
498            the output from mcmcsamp.
499    
500    2006-06-10  Douglas Bates  <bates@R-project.org>
501    
502            * R/lmer.R (simulestimate): added C code for calculating the trace
503            of the hat matrix.
504    
505    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
508            classes.
509            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
510    
511    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/dgTMatrix.R (colSums): etc. All four of
514            colSums(), rowSums(), colMeans(), rowMeans() now should work for
515            all "Matrices".
516    
517    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * R/lmer.R (panel.ci): Add a reference line at zero and a
520            background grid to the qqmath plot of ranef.lmer.
521    
522    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
525            grouping factors to be specified in the formula as (1|foo/bar).
526    
527    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
528    
529            * R/lmer.R (findbars and others): Change check of is.numeric to
530            !is.language to resolve the bug reported by Jacob Wegelin.
531    
532            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
533            code to evaluate inbreeding coefficients without calculating T,
534            based on code in Sargolzaei and Iwaisaki's paper.
535    
536    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
537    
538            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
539            generic and mer methods for isNested and denomDF. This denomDF was
540            an attempt to emulate that in lme but I don't think that makes
541            sense.  Use the trace of the hat matrix instead.
542    
543    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
546            the C code depending on a slot structure that's no longer valid.
547            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
548    
549    
550    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
551    
552            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
553            of lowerTriMatrix generic and methods to tril (also upper to triu)
554            and added a general band extractor.
555    
556    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * R/pedigree.R (pedigree): Replace sire and dam values outside the
559            allowable range with NAs. Added a corresponding check in the
560            validity check for the pedigree class.
561    
562            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
563            crossprod methods now inherits from symmetricMatrix.
564    
565    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
566    
567            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
568            generics lowerTriMatrix and upperTriMatrix along with methods for
569            the Csparse virtual class.  Also added a C function Csparse_band
570            that implements these methods by calling cholmod_band.
571    
572    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
575            erased when it was NULL.  This led to invalid subselections!
576    
577    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
578    
579            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
580            in method for "t" so as not to lose the unit diagonal property.
581    
582    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
583    
584            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
585            and methods.  This is now an option to the ranef method for the
586            mer class.
587    
588            * src/cs_utils.c: Ensure that the nz component is -1 for a
589            compressed column-oriented matrix.  Minor formatting cleanup.
590    
591            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
592            objects.
593    
594    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
597            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
598    
599    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
600    
601            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
602            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
603    
604            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
605            for the dtCMatrix class.
606    
607    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
610            and methods for it.
611    
612    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
615            arguments, such that M %*% 1:6 now works
616            * Tests/matprod.R: test the above
617    
618    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
621            the ranef.lmer class.
622    
623            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
624            methods to extract the posterior variances from the bVar slot.
625    
626    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
629            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
630    
631            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
632            * tests/simple: (extended)
633    
634            * R/sparseMatrix.R (isTriangular): now using much improved
635            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
636    
637    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
638    
639            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
640            (problem report from Franklin Parlamis).  This should be done
641            generally.
642    
643    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
644    
645            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
646            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
647            update the plot methods.
648    
649    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * R/lmer.R (resid and ranef methods):  Added methods for the
652            "residuals" and "resid" generic but only for linear mixed model
653            fits.  Changed the ranef method to return a list of data frames so
654            that the plot methods now work.
655    
656    2006-03-16  Douglas Bates  <bates@bates2>
657    
658            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
659            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
660    
661            * DESCRIPTION (Date): New release
662    
663    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
666    
667            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
668            * man/KNex.Rd: and other help files
669            * tests/*.R: several ones needed adaption
670            * inst/doc/Comparisons.Rnw: ditto
671    
672    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
675    
676            * tests/indexing.R: tests for new [<- methods for sparse matrices.
677    
678    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
681    
682            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
683    
684    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/dMatrix.R: enable things like  M [ M < 10 ]
687            * R/dgeMatrix.R: implement it
688    
689    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/AllClass.R: define "summary.mer" and "*.lmer"
692            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
693            * R/lmer.R (show): now works with summary()
694    
695    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
698            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
699                    support the above
700    
701    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
704            Use glmFit$prior.weights for weights in a glmm.
705            Allow an option usePQL = FALSE to skip the PQL steps for the
706            Laplace method (and, in time, the AGQ method).
707    
708            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
709            into a separate function internal_mer_Xfactor to be able to call
710            it from internal_bhat.
711    
712    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * tests/Class+Meth.R (tstMatrixClass): function for much better
715            testing; now again of all actual classes.
716    
717            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
718                    use macros and define make_d_matrix_* and make_i_matrix_*
719                    where _i_ is for the ldense routines:
720    
721            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
722            * src/ldense.c (lsyMatrix_as_lgeMatrix):
723    
724            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
725    
726    
727    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
730                    many different kinds of matrices.
731            * R/*.R: quite a few new methods were needed for R CMD check with
732                    new Matrix().  Very good for users playing around.
733    
734    
735    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * src/dgeMatrix.c (dMatrix_validate): new
738            * src/Mutils.c (dense_nonpacked_validate): new
739    
740            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
741    
742    
743    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
746    
747    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
748    
749            * DESCRIPTION (Version): 0.99-6 released to CRAN
750    
751            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
752            segfault in cases with multiple non-nested grouping factors.
753    
754    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
757                    (Depends): also on 'utils'
758    
759            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
760            * R/diagMatrix.R (Diagonal): constructor and methods for
761            diagonal matrices
762    
763            * R/ltTMatrix.R: new "minimal methods"
764    
765    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
768            all methods (and help files).
769    
770    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
773                    for case (dimn.  op  no_dimn.)
774    
775    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
776    
777            * DESCRIPTION (Version): 0.99-2  released to CRAN
778    
779    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
782            by Julian Faraway.
783    
784    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/Auxiliaries.R (try_as): new utility
787            * R/sparseMatrix.R: use try_as() in coercion to original class
788    
789    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
792    
793    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Auxiliaries.R (dimNamesCheck): added
796    
797            * R/Matrix.R (as.array), (as.vector): new
798    
799    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
802                    default.
803            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
804                    "pMatrix" now contains "sparseMatrix"
805    
806    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * tests/Class+Meth.R: new tests; t(t(m)) == m
809    
810            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
811    
812            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
813            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
814    
815            * R/dspMatrix.R: typo in "t" method
816    
817    2005-09-18  Douglas Bates  <bates@wisc.edu>
818    
819            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
820            * R/Tsparse.R: instead of R/gTMatrix.R
821            * R/Csparse.R: new
822            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
823            * src/Tsparse.c: new; many trivial methods calling cholmod_()
824            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
825                            via cholmod
826    
827    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Auxiliaries.R (non0ind): new function using new C code
830            * src/dgCMatrix.c (compressed_non_0_ij): new utility
831    
832    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
833    
834            * src/chm_common.h: header file required by all C sources that
835            call CHOLMOD functions.  It defines a cholmod_common structure
836            called 'c' whose address is passed as the last argument to
837            (virtually) every CHOLMOD function.
838    
839            * src/Pattern.c: Simple example of the use of CHOLMOD.
840    
841            * src/init.c: initialize and finalize the cholmod_common structure.
842    
843            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
844            LDL and CCOLAMD from the U. of Florida sparse matrix library.
845    
846    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * inst/test-tools.R: new file collecting the utility functions used
849                    in ./tests/*.R
850    
851            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
852            * R/Matrix.R (cbind2): methods for NULL and missing
853    
854    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/AllClass.R: new "index" class for "[" and "[<-":
857                    First cut at "symmetricMatrix" and "triangularMatrix"
858            * R/gTMatrix.R (.ind.prep): new function;
859                    Logical and character indexing now work too.
860            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
861            * tests/indexing.R: new, including *.Rout.save
862            * tests/dgTMatrix.R: new
863    
864    2005-08-29  Douglas Bates  <bates@wisc.edu>
865    
866            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
867            indicator pos not being updated.  Also enforced upper triangular
868            for symmetric case.  Need to coerce edges component of elements of
869            edge list - grr! (Why don't they define their classes cleanly?)
870    
871    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/Matrix.R:  added first "[<-" methods; not yet functional
874            * R/denseMatrix.R: ditto
875            * man/Subassign-methods.Rd: new help file for these
876    
877    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * DESCRIPTION (Version): 0.98-6
880    
881            * R/denseMatrix.R: new file for "[" fallback methods for all dense
882            matrices.
883    
884    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
887                    as( <logical>, "matrix")
888    
889            * R/pMatrix.R: coercion to "lgTMatrix"
890    
891            * R/gTMatrix.R: new virtual class to define "[" methods for.
892            * man/gTMatrix-class.Rd:
893            * General slight re-organization of where "[" methods are defined.
894              more to come.
895    
896    2005-08-18  Douglas Bates  <bates@wisc.edu>
897    
898            * DESCRIPTION (Version): 0.98-5  released to CRAN
899    
900            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
901            * .....
902    
903    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
904    
905            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
906            or glmer objects.
907    
908    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
911    
912    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
913    
914            * R/HBMM.R: finish re-writing R-only code.
915    
916    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
917    
918            * man/externalFormats.Rd: move documentation for writeHB and
919            writeMM here.
920    
921            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
922            (suggested by Paul Roecker).
923    
924            * tests/validObj.R (assertError): Comment out test that is failing
925            after recent changes in r-devel.
926    
927    
928    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/AllClass.R: intermediate virtual class "denseMatrix"
931            * man/denseMatrix-class.Rd
932            * NAMESPACE: export it, and also export
933            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
934    
935    2005-08-10  Douglas Bates  <bates@wisc.edu>
936    
937            * DESCRIPTION (Version): 0.98-3 to CRAN
938    
939            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
940            matrix_solve code (which was really, really wrong).
941    
942    2005-08-07  Douglas Bates  <bates@wisc.edu>
943    
944            * DESCRIPTION (Version): 0.98-2
945    
946            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
947    
948            * R/lmer.R (abbrvNms): new
949            * R/lmer.R (mcmcsamp): allow transformed parameters
950            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
951            for the Harwell-Boeing and the MatrixMarket formats.
952    
953    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * man/dtrMatrix-class.Rd: add examples
956            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
957    
958            * TODO: note the dtpMatrix (docu) bug
959    
960            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
961            in order to ensure that new as.matrix() is used by old functions,
962            e.g., svd(), qr(), eigen(), dist(),..;
963                  apply(), also matplot() or pairs().
964    
965    
966    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
969              add comments about 'control' / lmerControl() arguments
970    
971    2005-07-27  Douglas Bates  <bates@wisc.edu>
972    
973            * man/sleepstudy.Rd: Added the sleep data set.
974            * DESCRIPTION (Version): 0.98-1  released to CRAN
975    
976    2005-07-12  Douglas Bates  <bates@wisc.edu>
977            * man/sleepstudy.Rd: Added the sleep data set.
978    
979            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
980            .Call calls that were producing spurious output.
981    
982    2005-07-05  Douglas Bates  <bates@wisc.edu>
983    
984            * R/lmer.R (lmer): stored updated variance component estimates in
985            mer object for the generalized model.  (Bug reported by Renaud
986            Lancelot).
987    
988    2005-07-03  Douglas Bates  <bates@wisc.edu>
989    
990            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
991            unidimensional case.
992    
993    2005-06-08  Douglas Bates  <bates@wisc.edu>
994    
995            * DESCRIPTION (Version): 0.96-1
996    
997            * moved  lmer-class' R and C code moved from lme4 to here
998    
999    2005-06-04  Douglas Bates  <bates@wisc.edu>
1000    
1001            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1002            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1003    
1004    2005-06-02  Douglas Bates  <bates@wisc.edu>
1005    
1006            * src/Makefile.win: Forgot to update this when Makefile changed.
1007    
1008    2005-05-11  Douglas Bates  <bates@wisc.edu>
1009    
1010            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1011            bug reported by Kurt Hornik and Michael Hahsler.
1012    
1013    2005-05-10  Douglas Bates  <bates@wisc.edu>
1014    
1015            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1016            logical sparse matrices.  These will also be used in the symbolic
1017            analysis for lmer objects.
1018    
1019            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1020            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1021    
1022    2005-05-06  Douglas Bates  <bates@wisc.edu>
1023    
1024            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1025            colMeans, colSums, rowMeans and rowSums.
1026    
1027    2005-04-18  Douglas Bates  <bates@wisc.edu>
1028    
1029            * src/lgCMatrix.[ch]: code for _validate method and stub for
1030            multiplication operation.
1031    
1032            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1033            to dgetrs.
1034    
1035            * src/init.c: Fix cut-and-paste error in definition of
1036            dgeMatrix_matrix_solve
1037    
1038            * src/{many files}: Tighten code by using ALLOC_SLOT.
1039    
1040    2005-04-15  Douglas Bates  <bates@wisc.edu>
1041    
1042            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1043    
1044            * DESCRIPTION: Eliminate import of stats.
1045    
1046    
1047    2005-04-06  Douglas Bates  <bates@wisc.edu>
1048    
1049            * R/AllClass.R : add logical sparse matrix classes
1050    
1051    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * R/dgTMatrix.R: add "[" method for triplet matrices
1054            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1055    
1056    2005-03-31  Douglas Bates  <bates@wisc.edu>
1057    
1058            * DESCRIPTION (Version): release 0.95-5 to CRAN
1059    
1060            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1061            * R/sparseMatrix.R: %*%, crossprod()
1062            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1063            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1064            * src/lmer.c (lmer_fitted): fix thinko
1065    
1066    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * R/AllClass.R: add two virtual sparse classes ``on top''
1069    
1070    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1073                    correspondingly fix examples and tests/ since new()
1074                    doesn't work for virtual classes.
1075    
1076    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1077    
1078            * R/Matrix.R (as.matrix): method and one for unname()
1079            * tests/dpoMatrix.R: tests should now be less platform dependent;
1080              also run for R 2.1.0; using as.matrix()
1081    
1082    2005-03-15  Douglas Bates  <bates@wisc.edu>
1083    
1084            * R/pMatrix.R: "pMatrix" class added
1085            * ....
1086    
1087    2005-03-14  Douglas Bates  <bates@wisc.edu>
1088    
1089            * R/dtpMatrix.R: Add unpack method and an example.
1090    
1091            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1092            of general symmetric matrices and associated S4 methods.
1093    
1094    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1095            +
1096    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1099              crossprod() and "%*%" methods added; tests, too.
1100            * tests/matprod.R: new, for testing these
1101    
1102    2005-03-03  Douglas Bates  <bates@wisc.edu>
1103    
1104            * src/lmer.c (lmer_fitted): Added.
1105    
1106    2005-03-02  Douglas Bates  <bates@wisc.edu>
1107    
1108            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1109    
1110    2005-02-28  Douglas Bates  <bates@wisc.edu>
1111    
1112            * src/*.c,po/,inst/po: Internationalization and localization of
1113            the package.
1114    
1115            * src/ldl.[ch]: Removed these as their contents are referenced in the
1116            R_ldl.c file.
1117    
1118            * src/flame.[ch]: Removed these source files.
1119    
1120            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1121    
1122            * src/LU.[ch],src/init.c: absorb in factorizations
1123    
1124            * src/Mutils.h: prepare for internationalization
1125    
1126            * src/cblas.h: move the enum definitions to Mutils.h and remove
1127            this file
1128    
1129    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1132    
1133            * R/dtrMatrix.R: fix t() method
1134    
1135            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1136            * NAMESPACE: export them (and import generics from "methods")
1137            * tests/group-methods.R : and test them.
1138    
1139            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1140            border case
1141    
1142    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1143    
1144            * DESCRIPTION (Version): 0.95-2  released to CRAN
1145    
1146            * src/dgBCMatrix.c:
1147            * src/lmer.c: many changes
1148            * ...
1149    
1150    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/Matrix.R: add more sophisticated show() method.
1153    
1154    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1155    
1156            * */* : almost complete reorganization of classes.
1157    
1158    2005-01-26  Douglas Bates  <bates@wisc.edu>
1159    
1160            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1161            for the geMatrix class.
1162    
1163    2005-01-24  Douglas Bates  <bates@wisc.edu>
1164    
1165            * src/Makefile (clean): Remove *.a and *.so
1166    
1167            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1168    
1169    2005-01-23  Douglas Bates  <bates@wisc.edu>
1170    
1171            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1172            had an effect in cases with more than 2 grouping factors.
1173    
1174    2005-01-03  Douglas Bates  <bates@wisc.edu>
1175    
1176            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1177    
1178    2004-12-23  Douglas Bates  <bates@wisc.edu>
1179    
1180            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1181            and R_useDynamicSymbols (suggested by B.D.Ripley).
1182    
1183    2004-12-14  Douglas Bates  <bates@wisc.edu>
1184    
1185            * R/sscMatrix.R: Add determinant methods
1186    
1187            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1188            for tripletMatrix to matrix.
1189    
1190    2004-12-13  Douglas Bates  <bates@wisc.edu>
1191    
1192            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1193            no longer used.
1194    
1195            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1196            with dynamic allocation of scratch arrays.
1197    
1198            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1199            for multivariate random effects with multiple grouping factors.
1200            Fixes part but not all of #15.
1201    
1202    2004-12-03  Douglas Bates  <bates@wisc.edu>
1203    
1204            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1205            scalar grouping factors corrected.
1206    
1207    2004-11-29  Douglas Bates  <bates@wisc.edu>
1208    
1209            * src/bCrosstab.c: remove diag_update which is no longer used
1210    
1211    2004-11-16  Douglas Bates  <bates@wisc.edu>
1212    
1213          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1214          .h file can be included.          .h file can be included.
1215    
1216  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1217    
1218          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1219          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1220    
1221          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1222    
1223  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1224    
1225          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1226    
1227  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1228    
1229          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1230    
1231  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1232    
1233          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1234    
1235  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1236    
1237          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1238    
1239  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1240    
1241          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1242          routines.          routines.
1243    
1244  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1245    
1246          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1247    
1248  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1249    
1250          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1251    

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