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revision 10, Mon Mar 22 20:20:05 2004 UTC revision 1548, Mon Sep 11 22:13:07 2006 UTC
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1    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
4                    Matrices, since "lMatrix", also "lsparseM" can have NA
5            * R/ndenseMatrix.R, etc: new source files
6            * man/nsparseMatrix-classes.Rd, etc: new help files
7            * tests/: adaptions
8            * src/chm_common.c (chm_dense_to_SEXP): and others:
9                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
10            * src/Csparse.c, etc: dito
11    
12    2006-09-11  Douglas Bates  <bates@R-project.org>
13    
14            * src/Mutils.[ch],init.c inst/include/*.h: Move the
15            alloc_d**Matrix functions to the lme4 package.
16    
17    2006-09-09  Douglas Bates  <bates@R-project.org>
18    
19            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
20            fixed
21    
22    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/lMatrix.R: new
25    
26            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
27    
28            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
29            * man/tcrossprod.Rd: dito
30    
31    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
34            for exported functions
35            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
36            Remove partitioning algorithms for sparse matrix reordering.  The
37            copyright on the Metis code was problematic and the methods were
38            rarely used.
39            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
40            operations are now done entirely in CHOLMOD code.
41    
42    2006-09-06  Douglas Bates  <bates@R-project.org>
43    
44            * src/Mutils.h: Remove functions that are no longer used.
45    
46    2006-09-04  Douglas Bates  <bates@R-project.org>
47    
48            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
49            * src/DEPS.mkf: update
50    
51    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * created branches/Matrix-for-R-2.3.x;  on trunk: do
54            * DESCRIPTION (Version): 0.9975-0
55            (Depends): R (>= 2.4.0)
56    
57    2006-09-01  Douglas Bates  <bates@R-project.org>
58    
59            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
60    
61    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
64            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
65    
66            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
67    
68    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
71            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
72            * R/dsparseMatrix.R: dito
73            * R/Csparse.R: dito
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R (Compare): improve availability of "<", etc
78            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
79    
80    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
83            of a 0-index which was used as 1-index (..hmm)
84    
85            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
86    
87            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
88            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
89            (.is.diagonal): dito
90    
91            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
92    
93            * R/Matrix.R (Matrix): also work for NA data
94    
95    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
98            in all cases.
99    
100    2006-08-27  Douglas Bates  <bates@R-project.org>
101    
102            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
103            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
104    
105    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
108            subclasses of "ddenseMatrix"
109            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
110            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
111            instead of half dozen specialized ones.
112    
113    2006-08-25  Douglas Bates  <bates@R-project.org>
114    
115            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
116            <tillard@cirad.fr> - ordering standard errors to match effects.
117    
118    2006-08-24  Douglas Bates  <bates@R-project.org>
119    
120            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
121            on R_ldl.
122            * R/lCholCMatrix.R,
123            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
124            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
125            * many files in ./R and ./src: Use more general version of
126            dup_mMatrix_as_dgeMatrix to simplify method definitions.
127            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
128            dtpMatrix, dspMatrix and dppMatrix conversions.
129    
130    
131    2006-08-23  Douglas Bates  <bates@R-project.org>
132    
133            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
134            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
135            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
136            dgeMatrix_crossprod (may need to do this in other places).
137            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
138            generic and method for dsCMatrix.  Use CHOLMOD for chol().
139    
140    2006-08-22  Douglas Bates  <bates@R-project.org>
141    
142            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
143            types of classed Matrices, matrices or numeric or logical vectors.
144            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
145            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
146            to Mutils.h (as an inline) and change name to Matrix_check_class;
147            fixes in as_cholmod_factor and chm_factor_to_SEXP.
148            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
149            dsCMatrix_matrix_solve.  Comment out vestigial functions.
150            * src/Csparse.c: use diag_P and uplo_P macros.
151    
152    2006-08-21  Douglas Bates  <bates@R-project.org>
153    
154            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
155            valgrind.
156            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
157            inverses.
158            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
159            -Wall warnings.
160            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
161            Use dup_mMatrix_as_dgeMatrix.
162    
163    2006-08-20  Douglas Bates  <bates@R-project.org>
164    
165            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
166            * tests/sparseQR.R: Added
167            * man/sparseQR-class.Rd: Document methods for qr.* generics
168            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
169    
170    2006-08-19  Douglas Bates  <bates@R-project.org>
171    
172            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
173            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
174            and qr.fitted.
175            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
176            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
177    
178    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
181            the base version has no "..." argument.
182    
183            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
184    
185            * R/Matrix.R: define and
186            * NAMESPACE: export as.numeric() and as.logical() methods.
187                    Let's hope these do not badly slow down something...
188            Finally export the zapsmall() method.
189    
190    2006-08-17  Douglas Bates  <bates@R-project.org>
191    
192            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
193            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
194            * src/dtCMatrix.c :Remove code that is no longer used
195            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
196    
197    2006-08-14  Douglas Bates  <bates@R-project.org>
198    
199            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
200            Csparse_to_logical and Csparse_symmetric_to_general.
201            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
202            coercion methods between CsparseMatrix and TsparseMatrix.
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
207            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
208            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
209            possible.
210    
211    2006-08-12  Douglas Bates  <bates@R-project.org>
212    
213            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
214              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
215              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
216              generalize conversions between TsparseMatrix, CsparseMatrix,
217              denseMatrix and matrix.  Preserve triangularity property and
218              propagate Dimnames in the easy cases.
219    
220    2006-08-10  Douglas Bates  <bates@R-project.org>
221    
222            * src/lmer.c: adjust checks in glmer_init for S4SXP
223            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
224            before S4SXP but for the wrong reasons.
225    
226    2006-08-08  Douglas Bates  <bates@R-project.org>
227    
228            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
229            Later modified to return the upper triangle only.
230            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
231    
232    2006-08-07  Douglas Bates  <bates@R-project.org>
233    
234            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
235            R-level conversion to a sparse symmetric class.
236            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
237            Remove conversion to sparse symmetric classes (now done in C code).
238    
239    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
242            * man/band.Rd:  adapt the \dontshow{} unit test.
243    
244    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * DESCRIPTION (Version): 0.995-14  for CRAN
247    
248            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
249    
250            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
251            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
252    
253            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
254            * R/Tsparse.R (tril, triu, band): methods
255            * R/dgRMatrix.R (tril, ...):    ditto
256            * man/band.Rd:                  ditto
257    
258    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Matrix.R (head, tail): directly use utils:::head.matrix
261                    to be up-to-date automatically.
262    
263    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
266    
267            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
268            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
269            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
270            such that the S4 objects are always created by the current version
271            of R and 'Matrix' class definitions.
272    
273    2006-08-01  Douglas Bates  <bates@R-project.org>
274    
275            * R/lmer.R (LMEoptimize method), tests/lmer.R,
276            inst/external/test3comp.rda: Added warnings for convergence on
277            boundary and test cases.
278    
279            * src/lmer.c (mer_postVar): Modified to return the variances that
280            are marginal to the fixed effects, not conditional on them (which
281            is what the bVar slot contents represent).
282    
283    2006-07-31  Douglas Bates  <bates@R-project.org>
284    
285            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
286            function which calls the C function mer_hat_trace2.
287    
288            * man/ranef.Rd: Include description of "postVar" argument and
289            producing a caterpillar plot.
290    
291    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * NAMESPACE:    change  "correlation" to "corMatrix"
294            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
295            * R/dpoMatrix.R: ditto
296            * R/lmer.R:      ditto
297    
298    2006-07-28  Douglas Bates  <bates@R-project.org>
299    
300            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
301            RZXinv slot's contents into a separate internal function that can
302            be used in mer_hat_trace.
303    
304    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
307            via new smart
308            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
309            utility functions.
310    
311    
312    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Csparse.R (tril, triu, band): do return *triangular* classed
315            matrices when appropriate; band() even symmetric ones.
316            (replCmat): extend to potentially all "CsparseMatrix"
317            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
318            allow subassignment for special sparse matrices.
319    
320            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
321    
322            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
323            argument; in glmer_*(): print only if(verbose).
324    
325            speed-optimize a few places by moving REAL(.) out of loops.
326    
327            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
328    
329    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
332                    since that wrongly triggers also for M[ logi , ]
333    
334            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
335            a symmetric matrix that results in a non-symmetric one.
336            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
337    
338            * R/dMatrix.R: make round(M) work as round(M, 0)
339    
340            * R/dgTMatrix.R (image): coordinate system and axis now use
341            1-based indices, not 0-based ones.
342    
343            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
344            * tests/indexing.R: test it.
345    
346            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
347            * man/isSymmetric-methods.Rd: and document it.
348    
349            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
350            * man/SparseM-conv.Rd: docu them
351    
352            * tests/other-pkgs.R: renamed from tests/graph.R and add example
353                    for 'SparseM' conversions
354    
355    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
356    
357            * R/Matrix.R (head): added head() and tail() methods.
358    
359    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.995-12 released to CRAN
362    
363    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * tests/simple.R: add check for correct dsT -> dgT coercion;
366                    add check for correct printing of symmetric sparse matrices.
367    
368            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
369            for sparse symmetric matrices.
370    
371            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
372            diagonal twice.
373    
374    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
375    
376            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
377            being applied to the x slot (detected by Brian Ripley).
378    
379    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
382    
383            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
384    
385    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/lgCMatrix.c (lgCMatrix_diag): new function
388            * R/lgCMatrix.R (diag): for new method
389    
390            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
391                 ==> construction of illegal "*gTMatrix" via new() should
392                 now be much less easy:
393            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
394    
395            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
396                    directly.
397            * man/Matrix.Rd: documents it.
398    
399    2006-07-06  Douglas Bates  <bates@R-project.org>
400    
401            * src/pedigree.c (pedigree_inbreeding): Correction in
402            initialization.  This function is not currently being used and is
403            not fully tested.
404    
405            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
406            Introduced the glmer class.  Added code for mcmcmsamp on glmer
407            objects.  Modified validity check on pedigree objects to account
408            for nonparallel patterns of missingness of parents.
409    
410            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
411            class.
412    
413    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/pMatrix.R: coercion pMatrix -> Tsparse
416    
417    2006-06-12  Douglas Bates  <bates@R-project.org>
418    
419            * DESCRIPTION (Version): 0.995-11 released to CRAN
420    
421            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
422            the output from mcmcsamp.
423    
424    2006-06-10  Douglas Bates  <bates@R-project.org>
425    
426            * R/lmer.R (simulestimate): added C code for calculating the trace
427            of the hat matrix.
428    
429    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
432            classes.
433            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
434    
435    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgTMatrix.R (colSums): etc. All four of
438            colSums(), rowSums(), colMeans(), rowMeans() now should work for
439            all "Matrices".
440    
441    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
442    
443            * R/lmer.R (panel.ci): Add a reference line at zero and a
444            background grid to the qqmath plot of ranef.lmer.
445    
446    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
449            grouping factors to be specified in the formula as (1|foo/bar).
450    
451    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
452    
453            * R/lmer.R (findbars and others): Change check of is.numeric to
454            !is.language to resolve the bug reported by Jacob Wegelin.
455    
456            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
457            code to evaluate inbreeding coefficients without calculating T,
458            based on code in Sargolzaei and Iwaisaki's paper.
459    
460    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
461    
462            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
463            generic and mer methods for isNested and denomDF. This denomDF was
464            an attempt to emulate that in lme but I don't think that makes
465            sense.  Use the trace of the hat matrix instead.
466    
467    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
470            the C code depending on a slot structure that's no longer valid.
471            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
472    
473    
474    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
475    
476            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
477            of lowerTriMatrix generic and methods to tril (also upper to triu)
478            and added a general band extractor.
479    
480    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * R/pedigree.R (pedigree): Replace sire and dam values outside the
483            allowable range with NAs. Added a corresponding check in the
484            validity check for the pedigree class.
485    
486            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
487            crossprod methods now inherits from symmetricMatrix.
488    
489    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
490    
491            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
492            generics lowerTriMatrix and upperTriMatrix along with methods for
493            the Csparse virtual class.  Also added a C function Csparse_band
494            that implements these methods by calling cholmod_band.
495    
496    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
499            erased when it was NULL.  This led to invalid subselections!
500    
501    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
504            in method for "t" so as not to lose the unit diagonal property.
505    
506    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
507    
508            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
509            and methods.  This is now an option to the ranef method for the
510            mer class.
511    
512            * src/cs_utils.c: Ensure that the nz component is -1 for a
513            compressed column-oriented matrix.  Minor formatting cleanup.
514    
515            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
516            objects.
517    
518    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
521            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
522    
523    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
524    
525            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
526            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
527    
528            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
529            for the dtCMatrix class.
530    
531    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
532    
533            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
534            and methods for it.
535    
536    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
539            arguments, such that M %*% 1:6 now works
540            * Tests/matprod.R: test the above
541    
542    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
545            the ranef.lmer class.
546    
547            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
548            methods to extract the posterior variances from the bVar slot.
549    
550    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
553            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
554    
555            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
556            * tests/simple: (extended)
557    
558            * R/sparseMatrix.R (isTriangular): now using much improved
559            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
560    
561    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
564            (problem report from Franklin Parlamis).  This should be done
565            generally.
566    
567    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
568    
569            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
570            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
571            update the plot methods.
572    
573    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
574    
575            * R/lmer.R (resid and ranef methods):  Added methods for the
576            "residuals" and "resid" generic but only for linear mixed model
577            fits.  Changed the ranef method to return a list of data frames so
578            that the plot methods now work.
579    
580    2006-03-16  Douglas Bates  <bates@bates2>
581    
582            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
583            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
584    
585            * DESCRIPTION (Date): New release
586    
587    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
590    
591            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
592            * man/KNex.Rd: and other help files
593            * tests/*.R: several ones needed adaption
594            * inst/doc/Comparisons.Rnw: ditto
595    
596    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
599    
600            * tests/indexing.R: tests for new [<- methods for sparse matrices.
601    
602    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
605    
606            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
607    
608    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/dMatrix.R: enable things like  M [ M < 10 ]
611            * R/dgeMatrix.R: implement it
612    
613    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/AllClass.R: define "summary.mer" and "*.lmer"
616            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
617            * R/lmer.R (show): now works with summary()
618    
619    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
622            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
623                    support the above
624    
625    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
628            Use glmFit$prior.weights for weights in a glmm.
629            Allow an option usePQL = FALSE to skip the PQL steps for the
630            Laplace method (and, in time, the AGQ method).
631    
632            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
633            into a separate function internal_mer_Xfactor to be able to call
634            it from internal_bhat.
635    
636    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * tests/Class+Meth.R (tstMatrixClass): function for much better
639            testing; now again of all actual classes.
640    
641            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
642                    use macros and define make_d_matrix_* and make_i_matrix_*
643                    where _i_ is for the ldense routines:
644    
645            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
646            * src/ldense.c (lsyMatrix_as_lgeMatrix):
647    
648            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
649    
650    
651    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
654                    many different kinds of matrices.
655            * R/*.R: quite a few new methods were needed for R CMD check with
656                    new Matrix().  Very good for users playing around.
657    
658    
659    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * src/dgeMatrix.c (dMatrix_validate): new
662            * src/Mutils.c (dense_nonpacked_validate): new
663    
664            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
665    
666    
667    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
670    
671    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
672    
673            * DESCRIPTION (Version): 0.99-6 released to CRAN
674    
675            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
676            segfault in cases with multiple non-nested grouping factors.
677    
678    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
681                    (Depends): also on 'utils'
682    
683            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
684            * R/diagMatrix.R (Diagonal): constructor and methods for
685            diagonal matrices
686    
687            * R/ltTMatrix.R: new "minimal methods"
688    
689    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
692            all methods (and help files).
693    
694    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
697                    for case (dimn.  op  no_dimn.)
698    
699    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
700    
701            * DESCRIPTION (Version): 0.99-2  released to CRAN
702    
703    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
704    
705            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
706            by Julian Faraway.
707    
708    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Auxiliaries.R (try_as): new utility
711            * R/sparseMatrix.R: use try_as() in coercion to original class
712    
713    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
716    
717    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/Auxiliaries.R (dimNamesCheck): added
720    
721            * R/Matrix.R (as.array), (as.vector): new
722    
723    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
726                    default.
727            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
728                    "pMatrix" now contains "sparseMatrix"
729    
730    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * tests/Class+Meth.R: new tests; t(t(m)) == m
733    
734            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
735    
736            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
737            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
738    
739            * R/dspMatrix.R: typo in "t" method
740    
741    2005-09-18  Douglas Bates  <bates@wisc.edu>
742    
743            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
744            * R/Tsparse.R: instead of R/gTMatrix.R
745            * R/Csparse.R: new
746            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
747            * src/Tsparse.c: new; many trivial methods calling cholmod_()
748            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
749                            via cholmod
750    
751    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/Auxiliaries.R (non0ind): new function using new C code
754            * src/dgCMatrix.c (compressed_non_0_ij): new utility
755    
756    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
757    
758            * src/chm_common.h: header file required by all C sources that
759            call CHOLMOD functions.  It defines a cholmod_common structure
760            called 'c' whose address is passed as the last argument to
761            (virtually) every CHOLMOD function.
762    
763            * src/Pattern.c: Simple example of the use of CHOLMOD.
764    
765            * src/init.c: initialize and finalize the cholmod_common structure.
766    
767            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
768            LDL and CCOLAMD from the U. of Florida sparse matrix library.
769    
770    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * inst/test-tools.R: new file collecting the utility functions used
773                    in ./tests/*.R
774    
775            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
776            * R/Matrix.R (cbind2): methods for NULL and missing
777    
778    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/AllClass.R: new "index" class for "[" and "[<-":
781                    First cut at "symmetricMatrix" and "triangularMatrix"
782            * R/gTMatrix.R (.ind.prep): new function;
783                    Logical and character indexing now work too.
784            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
785            * tests/indexing.R: new, including *.Rout.save
786            * tests/dgTMatrix.R: new
787    
788    2005-08-29  Douglas Bates  <bates@wisc.edu>
789    
790            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
791            indicator pos not being updated.  Also enforced upper triangular
792            for symmetric case.  Need to coerce edges component of elements of
793            edge list - grr! (Why don't they define their classes cleanly?)
794    
795    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/Matrix.R:  added first "[<-" methods; not yet functional
798            * R/denseMatrix.R: ditto
799            * man/Subassign-methods.Rd: new help file for these
800    
801    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * DESCRIPTION (Version): 0.98-6
804    
805            * R/denseMatrix.R: new file for "[" fallback methods for all dense
806            matrices.
807    
808    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
811                    as( <logical>, "matrix")
812    
813            * R/pMatrix.R: coercion to "lgTMatrix"
814    
815            * R/gTMatrix.R: new virtual class to define "[" methods for.
816            * man/gTMatrix-class.Rd:
817            * General slight re-organization of where "[" methods are defined.
818              more to come.
819    
820    2005-08-18  Douglas Bates  <bates@wisc.edu>
821    
822            * DESCRIPTION (Version): 0.98-5  released to CRAN
823    
824            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
825            * .....
826    
827    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
828    
829            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
830            or glmer objects.
831    
832    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
835    
836    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
837    
838            * R/HBMM.R: finish re-writing R-only code.
839    
840    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
841    
842            * man/externalFormats.Rd: move documentation for writeHB and
843            writeMM here.
844    
845            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
846            (suggested by Paul Roecker).
847    
848            * tests/validObj.R (assertError): Comment out test that is failing
849            after recent changes in r-devel.
850    
851    
852    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/AllClass.R: intermediate virtual class "denseMatrix"
855            * man/denseMatrix-class.Rd
856            * NAMESPACE: export it, and also export
857            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
858    
859    2005-08-10  Douglas Bates  <bates@wisc.edu>
860    
861            * DESCRIPTION (Version): 0.98-3 to CRAN
862    
863            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
864            matrix_solve code (which was really, really wrong).
865    
866    2005-08-07  Douglas Bates  <bates@wisc.edu>
867    
868            * DESCRIPTION (Version): 0.98-2
869    
870            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
871    
872            * R/lmer.R (abbrvNms): new
873            * R/lmer.R (mcmcsamp): allow transformed parameters
874            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
875            for the Harwell-Boeing and the MatrixMarket formats.
876    
877    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * man/dtrMatrix-class.Rd: add examples
880            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
881    
882            * TODO: note the dtpMatrix (docu) bug
883    
884            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
885            in order to ensure that new as.matrix() is used by old functions,
886            e.g., svd(), qr(), eigen(), dist(),..;
887                  apply(), also matplot() or pairs().
888    
889    
890    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
893              add comments about 'control' / lmerControl() arguments
894    
895    2005-07-27  Douglas Bates  <bates@wisc.edu>
896    
897            * man/sleepstudy.Rd: Added the sleep data set.
898            * DESCRIPTION (Version): 0.98-1  released to CRAN
899    
900    2005-07-12  Douglas Bates  <bates@wisc.edu>
901            * man/sleepstudy.Rd: Added the sleep data set.
902    
903            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
904            .Call calls that were producing spurious output.
905    
906    2005-07-05  Douglas Bates  <bates@wisc.edu>
907    
908            * R/lmer.R (lmer): stored updated variance component estimates in
909            mer object for the generalized model.  (Bug reported by Renaud
910            Lancelot).
911    
912    2005-07-03  Douglas Bates  <bates@wisc.edu>
913    
914            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
915            unidimensional case.
916    
917    2005-06-08  Douglas Bates  <bates@wisc.edu>
918    
919            * DESCRIPTION (Version): 0.96-1
920    
921            * moved  lmer-class' R and C code moved from lme4 to here
922    
923    2005-06-04  Douglas Bates  <bates@wisc.edu>
924    
925            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
926            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
927    
928    2005-06-02  Douglas Bates  <bates@wisc.edu>
929    
930            * src/Makefile.win: Forgot to update this when Makefile changed.
931    
932    2005-05-11  Douglas Bates  <bates@wisc.edu>
933    
934            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
935            bug reported by Kurt Hornik and Michael Hahsler.
936    
937    2005-05-10  Douglas Bates  <bates@wisc.edu>
938    
939            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
940            logical sparse matrices.  These will also be used in the symbolic
941            analysis for lmer objects.
942    
943            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
944            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
945    
946    2005-05-06  Douglas Bates  <bates@wisc.edu>
947    
948            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
949            colMeans, colSums, rowMeans and rowSums.
950    
951    2005-04-18  Douglas Bates  <bates@wisc.edu>
952    
953            * src/lgCMatrix.[ch]: code for _validate method and stub for
954            multiplication operation.
955    
956            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
957            to dgetrs.
958    
959            * src/init.c: Fix cut-and-paste error in definition of
960            dgeMatrix_matrix_solve
961    
962            * src/{many files}: Tighten code by using ALLOC_SLOT.
963    
964    2005-04-15  Douglas Bates  <bates@wisc.edu>
965    
966            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
967    
968            * DESCRIPTION: Eliminate import of stats.
969    
970    
971    2005-04-06  Douglas Bates  <bates@wisc.edu>
972    
973            * R/AllClass.R : add logical sparse matrix classes
974    
975    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * R/dgTMatrix.R: add "[" method for triplet matrices
978            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
979    
980    2005-03-31  Douglas Bates  <bates@wisc.edu>
981    
982            * DESCRIPTION (Version): release 0.95-5 to CRAN
983    
984            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
985            * R/sparseMatrix.R: %*%, crossprod()
986            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
987            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
988            * src/lmer.c (lmer_fitted): fix thinko
989    
990    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/AllClass.R: add two virtual sparse classes ``on top''
993    
994    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
997                    correspondingly fix examples and tests/ since new()
998                    doesn't work for virtual classes.
999    
1000    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/Matrix.R (as.matrix): method and one for unname()
1003            * tests/dpoMatrix.R: tests should now be less platform dependent;
1004              also run for R 2.1.0; using as.matrix()
1005    
1006    2005-03-15  Douglas Bates  <bates@wisc.edu>
1007    
1008            * R/pMatrix.R: "pMatrix" class added
1009            * ....
1010    
1011    2005-03-14  Douglas Bates  <bates@wisc.edu>
1012    
1013            * R/dtpMatrix.R: Add unpack method and an example.
1014    
1015            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1016            of general symmetric matrices and associated S4 methods.
1017    
1018    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1019            +
1020    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1023              crossprod() and "%*%" methods added; tests, too.
1024            * tests/matprod.R: new, for testing these
1025    
1026    2005-03-03  Douglas Bates  <bates@wisc.edu>
1027    
1028            * src/lmer.c (lmer_fitted): Added.
1029    
1030    2005-03-02  Douglas Bates  <bates@wisc.edu>
1031    
1032            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1033    
1034    2005-02-28  Douglas Bates  <bates@wisc.edu>
1035    
1036            * src/*.c,po/,inst/po: Internationalization and localization of
1037            the package.
1038    
1039            * src/ldl.[ch]: Removed these as their contents are referenced in the
1040            R_ldl.c file.
1041    
1042            * src/flame.[ch]: Removed these source files.
1043    
1044            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1045    
1046            * src/LU.[ch],src/init.c: absorb in factorizations
1047    
1048            * src/Mutils.h: prepare for internationalization
1049    
1050            * src/cblas.h: move the enum definitions to Mutils.h and remove
1051            this file
1052    
1053    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1056    
1057            * R/dtrMatrix.R: fix t() method
1058    
1059            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1060            * NAMESPACE: export them (and import generics from "methods")
1061            * tests/group-methods.R : and test them.
1062    
1063            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1064            border case
1065    
1066    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1067    
1068            * DESCRIPTION (Version): 0.95-2  released to CRAN
1069    
1070            * src/dgBCMatrix.c:
1071            * src/lmer.c: many changes
1072            * ...
1073    
1074    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/Matrix.R: add more sophisticated show() method.
1077    
1078    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1079    
1080            * */* : almost complete reorganization of classes.
1081    
1082    2005-01-26  Douglas Bates  <bates@wisc.edu>
1083    
1084            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1085            for the geMatrix class.
1086    
1087    2005-01-24  Douglas Bates  <bates@wisc.edu>
1088    
1089            * src/Makefile (clean): Remove *.a and *.so
1090    
1091            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1092    
1093    2005-01-23  Douglas Bates  <bates@wisc.edu>
1094    
1095            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1096            had an effect in cases with more than 2 grouping factors.
1097    
1098    2005-01-03  Douglas Bates  <bates@wisc.edu>
1099    
1100            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1101    
1102    2004-12-23  Douglas Bates  <bates@wisc.edu>
1103    
1104            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1105            and R_useDynamicSymbols (suggested by B.D.Ripley).
1106    
1107    2004-12-14  Douglas Bates  <bates@wisc.edu>
1108    
1109            * R/sscMatrix.R: Add determinant methods
1110    
1111            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1112            for tripletMatrix to matrix.
1113    
1114    2004-12-13  Douglas Bates  <bates@wisc.edu>
1115    
1116            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1117            no longer used.
1118    
1119            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1120            with dynamic allocation of scratch arrays.
1121    
1122            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1123            for multivariate random effects with multiple grouping factors.
1124            Fixes part but not all of #15.
1125    
1126    2004-12-03  Douglas Bates  <bates@wisc.edu>
1127    
1128            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1129            scalar grouping factors corrected.
1130    
1131    2004-11-29  Douglas Bates  <bates@wisc.edu>
1132    
1133            * src/bCrosstab.c: remove diag_update which is no longer used
1134    
1135    2004-11-16  Douglas Bates  <bates@wisc.edu>
1136    
1137            * src/Metis_utils.c: Move metis.h include to C sources so that the
1138            .h file can be included.
1139    
1140    2004-11-12  Douglas Bates  <bates@wisc.edu>
1141    
1142            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1143            Complete allocation of slots in NEW_OBJECT.
1144    
1145            * src/Mutils.h: Moved list of symbols to an include file
1146    
1147    2004-11-11  Douglas Bates  <bates@wisc.edu>
1148    
1149            * src/geMutils.c (Matrix_init): remove unused function
1150    
1151    2004-11-10  Douglas Bates  <bates@wisc.edu>
1152    
1153            * src/cscMatrix.c (csc_to_imagemat): removed unused function
1154    
1155    2004-11-05  Douglas Bates  <bates@wisc.edu>
1156    
1157            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1158    
1159    2004-10-27  Douglas Bates  <bates@wisc.edu>
1160    
1161            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1162    
1163    2004-10-04  Douglas Bates  <bates@wisc.edu>
1164    
1165            * src/init.c: Created R_init_Matrix and added registration of C
1166            routines.
1167    
1168    2004-10-02  Douglas Bates  <bates@wisc.edu>
1169    
1170            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1171    
1172    2004-06-15  Douglas Bates  <bates@wisc.edu>
1173    
1174            * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1175    
1176    2004-04-20  Douglas Bates  <bates@stat.wisc.edu>
1177    
1178            * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1179    
1180    2004-04-19  Douglas Bates  <bates@stat.wisc.edu>
1181    
1182            * src/ssclme.c (ssclme_update_mm): fix logic error in
1183            ssclme_update_mm
1184    
1185    2004-04-18  Douglas Bates  <bates@stat.wisc.edu>
1186    
1187            * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1188            in the order of unconstrained and constrained parameters.
1189            (ssclme_gradient): Added the gradients (not yet correct for
1190            multidimensional, unconstrained case).
1191    
1192    2004-04-14  Douglas Bates  <bates@stat.wisc.edu>
1193    
1194            * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1195    
1196            * src/Makefile.win: Remove unneeded ranlib call
1197    
1198    2004-04-12  Douglas Bates  <bates@stat.wisc.edu>
1199    
1200            * DESCRIPTION (Version): New release
1201    
1202            * src/Makefile.win: Update Makefile.win to umfpack removal.
1203    
1204    2004-04-05  Douglas Bates  <bates@bates2_home>
1205    
1206            * src/triplet_to_col.c: Create triplet_to_col as a native
1207            function, not the version from umfpack.  There were problems with
1208            the configuration of UMFPACK for 64-bit processors and there was
1209            only one umfpack routine being used so I moved it here.
1210    
1211    2004-04-04  Douglas Bates  <bates@bates2_home>
1212    
1213            * src/ssclme.c (ssclme_variances): New function.
1214    
1215    2004-03-28  Douglas Bates  <bates@bates2_home>
1216    
1217            * src/ssclme.c (ssclme_fitted): Added function.
1218    
1219    2004-03-27  Douglas Bates  <bates@bates2_home>
1220    
1221            * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1222            store the dimnames in the XtX and bVar slots
1223            (ssclme_update_mm): Change the dimensions of the bVar slot
1224            components and the returned value from ssclme_ranef.
1225    
1226  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>  2004-03-18  Douglas Bates  <bates@stat.wisc.edu>
1227    
1228          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},          * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},

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