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revision 726, Thu May 12 14:59:04 2005 UTC revision 1613, Wed Oct 4 22:41:49 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): 0.9975-2
4    
5            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
6    
7    2006-10-02  Douglas Bates  <bates@R-project.org>
8    
9            * tests/dg_Matrix.R: Simplify test taking into account new code.
10    
11    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
14    
15            * R/lsTMatrix.R: new files w/ missing methods
16            * R/nsTMatrix.R:  "  'for completeness'
17    
18            * tests/Class+Meth.R: a bit less 'not.ok.classes'
19    
20            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
21    
22    
23    2006-09-28  Douglas Bates  <bates@R-project.org>
24    
25            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
26            included.
27    
28            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
29            Export C-callable functions used in Zt_create in lme4.
30    
31    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.9975-1
34    
35            * tests/simple.R: less checks fail; using NA, found that our
36                    kronecker() is not base-compatible with NA's.
37    
38            * R/dMatrix.R: "Compare" method now implemented for all cases
39    
40            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
41    
42            * man/dtpMatrix-class.Rd: mention length of 'x' slot
43    
44            * src/dtpMatrix.c (dtpMatrix_validate): fix check
45            * src/dspMatrix.c (dspMatrix_validate): ditto
46    
47            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
48              including coercion to [nl]tTMatrix.
49    
50            * R/diagMatrix.R (show): print a header line as for other classes.
51    
52    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/Makefile.win (SUBDIRS): fix typo
55    
56    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
59    
60    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
63            symmetric and y missing in R code using %*% (cholmod_aat doesn't
64            accept a symmetric matrix).
65            * tests/group-methods.R: Uncomment test of crossprod applied to
66            lsCMatrix objects.
67    
68    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllClass.R (symmetricMatrix): add validity method (available
71            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
72    
73            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
74    
75            * tests/indexing.Rout.save:
76            * tests/indexing.R: additions, mainly for 'lsparse'
77    
78            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
79            case.
80    
81            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
82    
83    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
86                    as 'N' (1-letter - Ok?)
87    
88            * tests/group-methods.R: add test for logical + NAs
89    
90            * R/dMatrix.R ("Compare"): fix to work with NA's
91    
92            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
93    
94            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
95                    which is implemented.
96    
97    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * src/chm_common.c: coerce logical <-> double instead of
100            typecasting;  needed for "l" matrix handling in cholmod.
101    
102            * tests/other-pkgs.R (graph): small extension in "graph" checks.
103    
104            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
105            (Tsp2grNEL): other fixes needed
106    
107    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
110                    Matrices, since "lMatrix", also "lsparseM" can have NA
111            * R/ndenseMatrix.R, etc: new source files
112            * man/nsparseMatrix-classes.Rd, etc: new help files
113            * tests/: adaptions
114            * src/chm_common.c (chm_dense_to_SEXP): and others:
115                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
116            * src/Csparse.c, etc: ditto
117    
118    2006-09-11  Douglas Bates  <bates@R-project.org>
119    
120            * src/Mutils.[ch],init.c inst/include/*.h: Move the
121            alloc_d**Matrix functions to the lme4 package.
122    
123    2006-09-09  Douglas Bates  <bates@R-project.org>
124    
125            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
126            fixed
127    
128    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/lMatrix.R: new
131    
132            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
133    
134            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
135            * man/tcrossprod.Rd: ditto
136    
137    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
140            for exported functions
141            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
142            Remove partitioning algorithms for sparse matrix reordering.  The
143            copyright on the Metis code was problematic and the methods were
144            rarely used.
145            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
146            operations are now done entirely in CHOLMOD code.
147    
148    2006-09-06  Douglas Bates  <bates@R-project.org>
149    
150            * src/Mutils.h: Remove functions that are no longer used.
151    
152    2006-09-04  Douglas Bates  <bates@R-project.org>
153    
154            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
155            * src/DEPS.mkf: update
156    
157    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * created branches/Matrix-for-R-2.3.x;  on trunk: do
160            * DESCRIPTION (Version): 0.9975-0
161            (Depends): R (>= 2.4.0)
162    
163    2006-09-01  Douglas Bates  <bates@R-project.org>
164    
165            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
166    
167    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
170            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
171    
172            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
173    
174    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
177            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
178            * R/dsparseMatrix.R: ditto
179            * R/Csparse.R: ditto
180    
181    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/dMatrix.R (Compare): improve availability of "<", etc
184            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
185    
186    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
189            of a 0-index which was used as 1-index (..hmm)
190    
191            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
192    
193            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
194            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
195            (.is.diagonal): ditto
196    
197            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
198    
199            * R/Matrix.R (Matrix): also work for NA data
200    
201    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
204            in all cases.
205    
206    2006-08-27  Douglas Bates  <bates@R-project.org>
207    
208            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
209            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
210    
211    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
214            subclasses of "ddenseMatrix"
215            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
216            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
217            instead of half dozen specialized ones.
218    
219    2006-08-25  Douglas Bates  <bates@R-project.org>
220    
221            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
222            <tillard@cirad.fr> - ordering standard errors to match effects.
223    
224    2006-08-24  Douglas Bates  <bates@R-project.org>
225    
226            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
227            on R_ldl.
228            * R/lCholCMatrix.R,
229            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
230            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
231            * many files in ./R and ./src: Use more general version of
232            dup_mMatrix_as_dgeMatrix to simplify method definitions.
233            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
234            dtpMatrix, dspMatrix and dppMatrix conversions.
235    
236    
237    2006-08-23  Douglas Bates  <bates@R-project.org>
238    
239            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
240            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
241            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
242            dgeMatrix_crossprod (may need to do this in other places).
243            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
244            generic and method for dsCMatrix.  Use CHOLMOD for chol().
245    
246    2006-08-22  Douglas Bates  <bates@R-project.org>
247    
248            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
249            types of classed Matrices, matrices or numeric or logical vectors.
250            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
251            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
252            to Mutils.h (as an inline) and change name to Matrix_check_class;
253            fixes in as_cholmod_factor and chm_factor_to_SEXP.
254            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
255            dsCMatrix_matrix_solve.  Comment out vestigial functions.
256            * src/Csparse.c: use diag_P and uplo_P macros.
257    
258    2006-08-21  Douglas Bates  <bates@R-project.org>
259    
260            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
261            valgrind.
262            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
263            inverses.
264            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
265            -Wall warnings.
266            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
267            Use dup_mMatrix_as_dgeMatrix.
268    
269    2006-08-20  Douglas Bates  <bates@R-project.org>
270    
271            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
272            * tests/sparseQR.R: Added
273            * man/sparseQR-class.Rd: Document methods for qr.* generics
274            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
275    
276    2006-08-19  Douglas Bates  <bates@R-project.org>
277    
278            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
279            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
280            and qr.fitted.
281            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
282            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
283    
284    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
287            the base version has no "..." argument.
288    
289            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
290    
291            * R/Matrix.R: define and
292            * NAMESPACE: export as.numeric() and as.logical() methods.
293                    Let's hope these do not badly slow down something...
294            Finally export the zapsmall() method.
295    
296    2006-08-17  Douglas Bates  <bates@R-project.org>
297    
298            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
299            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
300            * src/dtCMatrix.c :Remove code that is no longer used
301            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
302    
303    2006-08-14  Douglas Bates  <bates@R-project.org>
304    
305            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
306            Csparse_to_logical and Csparse_symmetric_to_general.
307            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
308            coercion methods between CsparseMatrix and TsparseMatrix.
309    
310    2006-08-14  Douglas Bates  <bates@R-project.org>
311    
312            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
313            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
314            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
315            possible.
316    
317    2006-08-12  Douglas Bates  <bates@R-project.org>
318    
319            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
320              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
321              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
322              generalize conversions between TsparseMatrix, CsparseMatrix,
323              denseMatrix and matrix.  Preserve triangularity property and
324              propagate Dimnames in the easy cases.
325    
326    2006-08-10  Douglas Bates  <bates@R-project.org>
327    
328            * src/lmer.c: adjust checks in glmer_init for S4SXP
329            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
330            before S4SXP but for the wrong reasons.
331    
332    2006-08-08  Douglas Bates  <bates@R-project.org>
333    
334            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
335            Later modified to return the upper triangle only.
336            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
337    
338    2006-08-07  Douglas Bates  <bates@R-project.org>
339    
340            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
341            R-level conversion to a sparse symmetric class.
342            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
343            Remove conversion to sparse symmetric classes (now done in C code).
344    
345    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
348            * man/band.Rd:  adapt the \dontshow{} unit test.
349    
350    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * DESCRIPTION (Version): 0.995-14  for CRAN
353    
354            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
355    
356            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
357            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
358    
359            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
360            * R/Tsparse.R (tril, triu, band): methods
361            * R/dgRMatrix.R (tril, ...):    ditto
362            * man/band.Rd:                  ditto
363    
364    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Matrix.R (head, tail): directly use utils:::head.matrix
367                    to be up-to-date automatically.
368    
369    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
372    
373            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
374            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
375            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
376            such that the S4 objects are always created by the current version
377            of R and 'Matrix' class definitions.
378    
379    2006-08-01  Douglas Bates  <bates@R-project.org>
380    
381            * R/lmer.R (LMEoptimize method), tests/lmer.R,
382            inst/external/test3comp.rda: Added warnings for convergence on
383            boundary and test cases.
384    
385            * src/lmer.c (mer_postVar): Modified to return the variances that
386            are marginal to the fixed effects, not conditional on them (which
387            is what the bVar slot contents represent).
388    
389    2006-07-31  Douglas Bates  <bates@R-project.org>
390    
391            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
392            function which calls the C function mer_hat_trace2.
393    
394            * man/ranef.Rd: Include description of "postVar" argument and
395            producing a caterpillar plot.
396    
397    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * NAMESPACE:    change  "correlation" to "corMatrix"
400            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
401            * R/dpoMatrix.R: ditto
402            * R/lmer.R:      ditto
403    
404    2006-07-28  Douglas Bates  <bates@R-project.org>
405    
406            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
407            RZXinv slot's contents into a separate internal function that can
408            be used in mer_hat_trace.
409    
410    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
413            via new smart
414            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
415            utility functions.
416    
417    
418    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/Csparse.R (tril, triu, band): do return *triangular* classed
421            matrices when appropriate; band() even symmetric ones.
422            (replCmat): extend to potentially all "CsparseMatrix"
423            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
424            allow subassignment for special sparse matrices.
425    
426            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
427    
428            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
429            argument; in glmer_*(): print only if(verbose).
430    
431            speed-optimize a few places by moving REAL(.) out of loops.
432    
433            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
434    
435    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
438                    since that wrongly triggers also for M[ logi , ]
439    
440            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
441            a symmetric matrix that results in a non-symmetric one.
442            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
443    
444            * R/dMatrix.R: make round(M) work as round(M, 0)
445    
446            * R/dgTMatrix.R (image): coordinate system and axis now use
447            1-based indices, not 0-based ones.
448    
449            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
450            * tests/indexing.R: test it.
451    
452            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
453            * man/isSymmetric-methods.Rd: and document it.
454    
455            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
456            * man/SparseM-conv.Rd: docu them
457    
458            * tests/other-pkgs.R: renamed from tests/graph.R and add example
459                    for 'SparseM' conversions
460    
461    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
462    
463            * R/Matrix.R (head): added head() and tail() methods.
464    
465    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * DESCRIPTION (Version): 0.995-12 released to CRAN
468    
469    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/simple.R: add check for correct dsT -> dgT coercion;
472                    add check for correct printing of symmetric sparse matrices.
473    
474            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
475            for sparse symmetric matrices.
476    
477            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
478            diagonal twice.
479    
480    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
481    
482            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
483            being applied to the x slot (detected by Brian Ripley).
484    
485    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
488    
489            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
490    
491    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * src/lgCMatrix.c (lgCMatrix_diag): new function
494            * R/lgCMatrix.R (diag): for new method
495    
496            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
497                 ==> construction of illegal "*gTMatrix" via new() should
498                 now be much less easy:
499            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
500    
501            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
502                    directly.
503            * man/Matrix.Rd: documents it.
504    
505    2006-07-06  Douglas Bates  <bates@R-project.org>
506    
507            * src/pedigree.c (pedigree_inbreeding): Correction in
508            initialization.  This function is not currently being used and is
509            not fully tested.
510    
511            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
512            Introduced the glmer class.  Added code for mcmcmsamp on glmer
513            objects.  Modified validity check on pedigree objects to account
514            for nonparallel patterns of missingness of parents.
515    
516            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
517            class.
518    
519    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/pMatrix.R: coercion pMatrix -> Tsparse
522    
523    2006-06-12  Douglas Bates  <bates@R-project.org>
524    
525            * DESCRIPTION (Version): 0.995-11 released to CRAN
526    
527            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
528            the output from mcmcsamp.
529    
530    2006-06-10  Douglas Bates  <bates@R-project.org>
531    
532            * R/lmer.R (simulestimate): added C code for calculating the trace
533            of the hat matrix.
534    
535    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
538            classes.
539            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
540    
541    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/dgTMatrix.R (colSums): etc. All four of
544            colSums(), rowSums(), colMeans(), rowMeans() now should work for
545            all "Matrices".
546    
547    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
548    
549            * R/lmer.R (panel.ci): Add a reference line at zero and a
550            background grid to the qqmath plot of ranef.lmer.
551    
552    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
553    
554            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
555            grouping factors to be specified in the formula as (1|foo/bar).
556    
557    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
558    
559            * R/lmer.R (findbars and others): Change check of is.numeric to
560            !is.language to resolve the bug reported by Jacob Wegelin.
561    
562            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
563            code to evaluate inbreeding coefficients without calculating T,
564            based on code in Sargolzaei and Iwaisaki's paper.
565    
566    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
567    
568            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
569            generic and mer methods for isNested and denomDF. This denomDF was
570            an attempt to emulate that in lme but I don't think that makes
571            sense.  Use the trace of the hat matrix instead.
572    
573    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
576            the C code depending on a slot structure that's no longer valid.
577            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
578    
579    
580    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
581    
582            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
583            of lowerTriMatrix generic and methods to tril (also upper to triu)
584            and added a general band extractor.
585    
586    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
587    
588            * R/pedigree.R (pedigree): Replace sire and dam values outside the
589            allowable range with NAs. Added a corresponding check in the
590            validity check for the pedigree class.
591    
592            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
593            crossprod methods now inherits from symmetricMatrix.
594    
595    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
596    
597            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
598            generics lowerTriMatrix and upperTriMatrix along with methods for
599            the Csparse virtual class.  Also added a C function Csparse_band
600            that implements these methods by calling cholmod_band.
601    
602    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
605            erased when it was NULL.  This led to invalid subselections!
606    
607    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
610            in method for "t" so as not to lose the unit diagonal property.
611    
612    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
613    
614            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
615            and methods.  This is now an option to the ranef method for the
616            mer class.
617    
618            * src/cs_utils.c: Ensure that the nz component is -1 for a
619            compressed column-oriented matrix.  Minor formatting cleanup.
620    
621            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
622            objects.
623    
624    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
627            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
628    
629    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
630    
631            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
632            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
633    
634            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
635            for the dtCMatrix class.
636    
637    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
638    
639            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
640            and methods for it.
641    
642    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
645            arguments, such that M %*% 1:6 now works
646            * Tests/matprod.R: test the above
647    
648    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
649    
650            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
651            the ranef.lmer class.
652    
653            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
654            methods to extract the posterior variances from the bVar slot.
655    
656    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
659            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
660    
661            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
662            * tests/simple: (extended)
663    
664            * R/sparseMatrix.R (isTriangular): now using much improved
665            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
666    
667    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
670            (problem report from Franklin Parlamis).  This should be done
671            generally.
672    
673    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
676            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
677            update the plot methods.
678    
679    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
680    
681            * R/lmer.R (resid and ranef methods):  Added methods for the
682            "residuals" and "resid" generic but only for linear mixed model
683            fits.  Changed the ranef method to return a list of data frames so
684            that the plot methods now work.
685    
686    2006-03-16  Douglas Bates  <bates@bates2>
687    
688            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
689            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
690    
691            * DESCRIPTION (Date): New release
692    
693    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
696    
697            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
698            * man/KNex.Rd: and other help files
699            * tests/*.R: several ones needed adaption
700            * inst/doc/Comparisons.Rnw: ditto
701    
702    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
705    
706            * tests/indexing.R: tests for new [<- methods for sparse matrices.
707    
708    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
711    
712            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
713    
714    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/dMatrix.R: enable things like  M [ M < 10 ]
717            * R/dgeMatrix.R: implement it
718    
719    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/AllClass.R: define "summary.mer" and "*.lmer"
722            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
723            * R/lmer.R (show): now works with summary()
724    
725    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
728            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
729                    support the above
730    
731    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
732    
733            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
734            Use glmFit$prior.weights for weights in a glmm.
735            Allow an option usePQL = FALSE to skip the PQL steps for the
736            Laplace method (and, in time, the AGQ method).
737    
738            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
739            into a separate function internal_mer_Xfactor to be able to call
740            it from internal_bhat.
741    
742    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * tests/Class+Meth.R (tstMatrixClass): function for much better
745            testing; now again of all actual classes.
746    
747            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
748                    use macros and define make_d_matrix_* and make_i_matrix_*
749                    where _i_ is for the ldense routines:
750    
751            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
752            * src/ldense.c (lsyMatrix_as_lgeMatrix):
753    
754            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
755    
756    
757    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
760                    many different kinds of matrices.
761            * R/*.R: quite a few new methods were needed for R CMD check with
762                    new Matrix().  Very good for users playing around.
763    
764    
765    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * src/dgeMatrix.c (dMatrix_validate): new
768            * src/Mutils.c (dense_nonpacked_validate): new
769    
770            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
771    
772    
773    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
776    
777    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
778    
779            * DESCRIPTION (Version): 0.99-6 released to CRAN
780    
781            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
782            segfault in cases with multiple non-nested grouping factors.
783    
784    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
787                    (Depends): also on 'utils'
788    
789            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
790            * R/diagMatrix.R (Diagonal): constructor and methods for
791            diagonal matrices
792    
793            * R/ltTMatrix.R: new "minimal methods"
794    
795    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
798            all methods (and help files).
799    
800    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
803                    for case (dimn.  op  no_dimn.)
804    
805    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
806    
807            * DESCRIPTION (Version): 0.99-2  released to CRAN
808    
809    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
810    
811            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
812            by Julian Faraway.
813    
814    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * R/Auxiliaries.R (try_as): new utility
817            * R/sparseMatrix.R: use try_as() in coercion to original class
818    
819    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
822    
823    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/Auxiliaries.R (dimNamesCheck): added
826    
827            * R/Matrix.R (as.array), (as.vector): new
828    
829    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
832                    default.
833            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
834                    "pMatrix" now contains "sparseMatrix"
835    
836    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * tests/Class+Meth.R: new tests; t(t(m)) == m
839    
840            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
841    
842            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
843            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
844    
845            * R/dspMatrix.R: typo in "t" method
846    
847    2005-09-18  Douglas Bates  <bates@wisc.edu>
848    
849            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
850            * R/Tsparse.R: instead of R/gTMatrix.R
851            * R/Csparse.R: new
852            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
853            * src/Tsparse.c: new; many trivial methods calling cholmod_()
854            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
855                            via cholmod
856    
857    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Auxiliaries.R (non0ind): new function using new C code
860            * src/dgCMatrix.c (compressed_non_0_ij): new utility
861    
862    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
863    
864            * src/chm_common.h: header file required by all C sources that
865            call CHOLMOD functions.  It defines a cholmod_common structure
866            called 'c' whose address is passed as the last argument to
867            (virtually) every CHOLMOD function.
868    
869            * src/Pattern.c: Simple example of the use of CHOLMOD.
870    
871            * src/init.c: initialize and finalize the cholmod_common structure.
872    
873            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
874            LDL and CCOLAMD from the U. of Florida sparse matrix library.
875    
876    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * inst/test-tools.R: new file collecting the utility functions used
879                    in ./tests/*.R
880    
881            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
882            * R/Matrix.R (cbind2): methods for NULL and missing
883    
884    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * R/AllClass.R: new "index" class for "[" and "[<-":
887                    First cut at "symmetricMatrix" and "triangularMatrix"
888            * R/gTMatrix.R (.ind.prep): new function;
889                    Logical and character indexing now work too.
890            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
891            * tests/indexing.R: new, including *.Rout.save
892            * tests/dgTMatrix.R: new
893    
894    2005-08-29  Douglas Bates  <bates@wisc.edu>
895    
896            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
897            indicator pos not being updated.  Also enforced upper triangular
898            for symmetric case.  Need to coerce edges component of elements of
899            edge list - grr! (Why don't they define their classes cleanly?)
900    
901    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * R/Matrix.R:  added first "[<-" methods; not yet functional
904            * R/denseMatrix.R: ditto
905            * man/Subassign-methods.Rd: new help file for these
906    
907    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * DESCRIPTION (Version): 0.98-6
910    
911            * R/denseMatrix.R: new file for "[" fallback methods for all dense
912            matrices.
913    
914    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
917                    as( <logical>, "matrix")
918    
919            * R/pMatrix.R: coercion to "lgTMatrix"
920    
921            * R/gTMatrix.R: new virtual class to define "[" methods for.
922            * man/gTMatrix-class.Rd:
923            * General slight re-organization of where "[" methods are defined.
924              more to come.
925    
926    2005-08-18  Douglas Bates  <bates@wisc.edu>
927    
928            * DESCRIPTION (Version): 0.98-5  released to CRAN
929    
930            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
931            * .....
932    
933    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
934    
935            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
936            or glmer objects.
937    
938    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
941    
942    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
943    
944            * R/HBMM.R: finish re-writing R-only code.
945    
946    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
947    
948            * man/externalFormats.Rd: move documentation for writeHB and
949            writeMM here.
950    
951            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
952            (suggested by Paul Roecker).
953    
954            * tests/validObj.R (assertError): Comment out test that is failing
955            after recent changes in r-devel.
956    
957    
958    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * R/AllClass.R: intermediate virtual class "denseMatrix"
961            * man/denseMatrix-class.Rd
962            * NAMESPACE: export it, and also export
963            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
964    
965    2005-08-10  Douglas Bates  <bates@wisc.edu>
966    
967            * DESCRIPTION (Version): 0.98-3 to CRAN
968    
969            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
970            matrix_solve code (which was really, really wrong).
971    
972    2005-08-07  Douglas Bates  <bates@wisc.edu>
973    
974            * DESCRIPTION (Version): 0.98-2
975    
976            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
977    
978            * R/lmer.R (abbrvNms): new
979            * R/lmer.R (mcmcsamp): allow transformed parameters
980            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
981            for the Harwell-Boeing and the MatrixMarket formats.
982    
983    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * man/dtrMatrix-class.Rd: add examples
986            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
987    
988            * TODO: note the dtpMatrix (docu) bug
989    
990            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
991            in order to ensure that new as.matrix() is used by old functions,
992            e.g., svd(), qr(), eigen(), dist(),..;
993                  apply(), also matplot() or pairs().
994    
995    
996    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
999              add comments about 'control' / lmerControl() arguments
1000    
1001    2005-07-27  Douglas Bates  <bates@wisc.edu>
1002    
1003            * man/sleepstudy.Rd: Added the sleep data set.
1004            * DESCRIPTION (Version): 0.98-1  released to CRAN
1005    
1006    2005-07-12  Douglas Bates  <bates@wisc.edu>
1007            * man/sleepstudy.Rd: Added the sleep data set.
1008    
1009            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1010            .Call calls that were producing spurious output.
1011    
1012    2005-07-05  Douglas Bates  <bates@wisc.edu>
1013    
1014            * R/lmer.R (lmer): stored updated variance component estimates in
1015            mer object for the generalized model.  (Bug reported by Renaud
1016            Lancelot).
1017    
1018    2005-07-03  Douglas Bates  <bates@wisc.edu>
1019    
1020            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1021            unidimensional case.
1022    
1023    2005-06-08  Douglas Bates  <bates@wisc.edu>
1024    
1025            * DESCRIPTION (Version): 0.96-1
1026    
1027            * moved  lmer-class' R and C code moved from lme4 to here
1028    
1029    2005-06-04  Douglas Bates  <bates@wisc.edu>
1030    
1031            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1032            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1033    
1034    2005-06-02  Douglas Bates  <bates@wisc.edu>
1035    
1036            * src/Makefile.win: Forgot to update this when Makefile changed.
1037    
1038    2005-05-11  Douglas Bates  <bates@wisc.edu>
1039    
1040          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1041          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1042    
1043  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1044    
1045          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1046          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1049 
1049          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1050          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1051    
1052  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1053    
1054          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1055          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1056    
1057  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1058    
1059          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1060          multiplication operation.          multiplication operation.
# Line 30  Line 1067 
1067    
1068          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1069    
1070  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1071    
1072          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1073    
1074          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1075    
1076    
1077  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1078    
1079          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1080    
# Line 46  Line 1083 
1083          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1084          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1085    
1086  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1087    
1088          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1089    
# Line 72  Line 1109 
1109          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1110            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1111    
1112  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1113    
1114          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1115          * ....          * ....
1116    
1117  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1118    
1119          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1120    
# Line 92  Line 1129 
1129            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1130          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1131    
1132  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1133    
1134          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1135    
1136  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1137    
1138          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1139    
1140  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1141    
1142          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1143          the package.          the package.
# Line 148  Line 1185 
1185    
1186          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1187    
1188  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1189    
1190          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1191          for the geMatrix class.          for the geMatrix class.
1192    
1193  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1194    
1195          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1196    
1197          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1198    
1199  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1200    
1201          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1202          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1203    
1204  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1205    
1206          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1207    
1208  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1209    
1210          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1211          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1212    
1213  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1214    
1215          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1216    
1217          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1218          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1219    
1220  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1221    
1222          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1223          no longer used.          no longer used.
# Line 192  Line 1229 
1229          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1230          Fixes part but not all of #15.          Fixes part but not all of #15.
1231    
1232  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1233    
1234          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1235          scalar grouping factors corrected.          scalar grouping factors corrected.
1236    
1237  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1238    
1239          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1240    
1241  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1242    
1243          * 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
1244          .h file can be included.          .h file can be included.
1245    
1246  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1247    
1248          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1249          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1250    
1251          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1252    
1253  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1254    
1255          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1256    
1257  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1258    
1259          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1260    
1261  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1262    
1263          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1264    
1265  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1266    
1267          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1268    
1269  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1270    
1271          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1272          routines.          routines.
1273    
1274  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1275    
1276          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1277    
1278  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1279    
1280          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1281    

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