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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1611, Mon Oct 2 17:07:16 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-10-02  Douglas Bates  <bates@R-project.org>
2    
3            * tests/dg_Matrix.R: Simplify test taking into account new code.
4    
5    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
8    
9            * R/lsTMatrix.R: new files w/ missing methods
10            * R/nsTMatrix.R:  "  'for completeness'
11    
12            * tests/Class+Meth.R: a bit less 'not.ok.classes'
13    
14            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
15    
16    
17    2006-09-28  Douglas Bates  <bates@R-project.org>
18    
19            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
20            included.
21    
22            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
23            Export C-callable functions used in Zt_create in lme4.
24    
25    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.9975-1
28    
29            * tests/simple.R: less checks fail; using NA, found that our
30                    kronecker() is not base-compatible with NA's.
31    
32            * R/dMatrix.R: "Compare" method now implemented for all cases
33    
34            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
35    
36            * man/dtpMatrix-class.Rd: mention length of 'x' slot
37    
38            * src/dtpMatrix.c (dtpMatrix_validate): fix check
39            * src/dspMatrix.c (dspMatrix_validate): ditto
40    
41            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
42              including coercion to [nl]tTMatrix.
43    
44            * R/diagMatrix.R (show): print a header line as for other classes.
45    
46    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Makefile.win (SUBDIRS): fix typo
49    
50    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
53    
54    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
57            symmetric and y missing in R code using %*% (cholmod_aat doesn't
58            accept a symmetric matrix).
59            * tests/group-methods.R: Uncomment test of crossprod applied to
60            lsCMatrix objects.
61    
62    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/AllClass.R (symmetricMatrix): add validity method (available
65            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
66    
67            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
68    
69            * tests/indexing.Rout.save:
70            * tests/indexing.R: additions, mainly for 'lsparse'
71    
72            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
73            case.
74    
75            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
76    
77    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
80                    as 'N' (1-letter - Ok?)
81    
82            * tests/group-methods.R: add test for logical + NAs
83    
84            * R/dMatrix.R ("Compare"): fix to work with NA's
85    
86            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
87    
88            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
89                    which is implemented.
90    
91    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/chm_common.c: coerce logical <-> double instead of
94            typecasting;  needed for "l" matrix handling in cholmod.
95    
96            * tests/other-pkgs.R (graph): small extension in "graph" checks.
97    
98            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
99            (Tsp2grNEL): other fixes needed
100    
101    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
104                    Matrices, since "lMatrix", also "lsparseM" can have NA
105            * R/ndenseMatrix.R, etc: new source files
106            * man/nsparseMatrix-classes.Rd, etc: new help files
107            * tests/: adaptions
108            * src/chm_common.c (chm_dense_to_SEXP): and others:
109                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
110            * src/Csparse.c, etc: ditto
111    
112    2006-09-11  Douglas Bates  <bates@R-project.org>
113    
114            * src/Mutils.[ch],init.c inst/include/*.h: Move the
115            alloc_d**Matrix functions to the lme4 package.
116    
117    2006-09-09  Douglas Bates  <bates@R-project.org>
118    
119            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
120            fixed
121    
122    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/lMatrix.R: new
125    
126            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
127    
128            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
129            * man/tcrossprod.Rd: ditto
130    
131    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
134            for exported functions
135            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
136            Remove partitioning algorithms for sparse matrix reordering.  The
137            copyright on the Metis code was problematic and the methods were
138            rarely used.
139            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
140            operations are now done entirely in CHOLMOD code.
141    
142    2006-09-06  Douglas Bates  <bates@R-project.org>
143    
144            * src/Mutils.h: Remove functions that are no longer used.
145    
146    2006-09-04  Douglas Bates  <bates@R-project.org>
147    
148            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
149            * src/DEPS.mkf: update
150    
151    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * created branches/Matrix-for-R-2.3.x;  on trunk: do
154            * DESCRIPTION (Version): 0.9975-0
155            (Depends): R (>= 2.4.0)
156    
157    2006-09-01  Douglas Bates  <bates@R-project.org>
158    
159            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
160    
161    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
164            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
165    
166            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
167    
168    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
171            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
172            * R/dsparseMatrix.R: ditto
173            * R/Csparse.R: ditto
174    
175    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/dMatrix.R (Compare): improve availability of "<", etc
178            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
179    
180    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
183            of a 0-index which was used as 1-index (..hmm)
184    
185            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
186    
187            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
188            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
189            (.is.diagonal): ditto
190    
191            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
192    
193            * R/Matrix.R (Matrix): also work for NA data
194    
195    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
198            in all cases.
199    
200    2006-08-27  Douglas Bates  <bates@R-project.org>
201    
202            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
203            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
204    
205    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
208            subclasses of "ddenseMatrix"
209            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
210            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
211            instead of half dozen specialized ones.
212    
213    2006-08-25  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
216            <tillard@cirad.fr> - ordering standard errors to match effects.
217    
218    2006-08-24  Douglas Bates  <bates@R-project.org>
219    
220            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
221            on R_ldl.
222            * R/lCholCMatrix.R,
223            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
224            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
225            * many files in ./R and ./src: Use more general version of
226            dup_mMatrix_as_dgeMatrix to simplify method definitions.
227            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
228            dtpMatrix, dspMatrix and dppMatrix conversions.
229    
230    
231    2006-08-23  Douglas Bates  <bates@R-project.org>
232    
233            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
234            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
235            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
236            dgeMatrix_crossprod (may need to do this in other places).
237            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
238            generic and method for dsCMatrix.  Use CHOLMOD for chol().
239    
240    2006-08-22  Douglas Bates  <bates@R-project.org>
241    
242            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
243            types of classed Matrices, matrices or numeric or logical vectors.
244            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
245            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
246            to Mutils.h (as an inline) and change name to Matrix_check_class;
247            fixes in as_cholmod_factor and chm_factor_to_SEXP.
248            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
249            dsCMatrix_matrix_solve.  Comment out vestigial functions.
250            * src/Csparse.c: use diag_P and uplo_P macros.
251    
252    2006-08-21  Douglas Bates  <bates@R-project.org>
253    
254            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
255            valgrind.
256            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
257            inverses.
258            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
259            -Wall warnings.
260            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
261            Use dup_mMatrix_as_dgeMatrix.
262    
263    2006-08-20  Douglas Bates  <bates@R-project.org>
264    
265            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
266            * tests/sparseQR.R: Added
267            * man/sparseQR-class.Rd: Document methods for qr.* generics
268            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
269    
270    2006-08-19  Douglas Bates  <bates@R-project.org>
271    
272            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
273            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
274            and qr.fitted.
275            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
276            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
277    
278    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
281            the base version has no "..." argument.
282    
283            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
284    
285            * R/Matrix.R: define and
286            * NAMESPACE: export as.numeric() and as.logical() methods.
287                    Let's hope these do not badly slow down something...
288            Finally export the zapsmall() method.
289    
290    2006-08-17  Douglas Bates  <bates@R-project.org>
291    
292            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
293            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
294            * src/dtCMatrix.c :Remove code that is no longer used
295            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
296    
297    2006-08-14  Douglas Bates  <bates@R-project.org>
298    
299            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
300            Csparse_to_logical and Csparse_symmetric_to_general.
301            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
302            coercion methods between CsparseMatrix and TsparseMatrix.
303    
304    2006-08-14  Douglas Bates  <bates@R-project.org>
305    
306            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
307            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
308            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
309            possible.
310    
311    2006-08-12  Douglas Bates  <bates@R-project.org>
312    
313            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
314              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
315              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
316              generalize conversions between TsparseMatrix, CsparseMatrix,
317              denseMatrix and matrix.  Preserve triangularity property and
318              propagate Dimnames in the easy cases.
319    
320    2006-08-10  Douglas Bates  <bates@R-project.org>
321    
322            * src/lmer.c: adjust checks in glmer_init for S4SXP
323            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
324            before S4SXP but for the wrong reasons.
325    
326    2006-08-08  Douglas Bates  <bates@R-project.org>
327    
328            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
329            Later modified to return the upper triangle only.
330            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
331    
332    2006-08-07  Douglas Bates  <bates@R-project.org>
333    
334            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
335            R-level conversion to a sparse symmetric class.
336            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
337            Remove conversion to sparse symmetric classes (now done in C code).
338    
339    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
342            * man/band.Rd:  adapt the \dontshow{} unit test.
343    
344    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.995-14  for CRAN
347    
348            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
349    
350            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
351            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
352    
353            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
354            * R/Tsparse.R (tril, triu, band): methods
355            * R/dgRMatrix.R (tril, ...):    ditto
356            * man/band.Rd:                  ditto
357    
358    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Matrix.R (head, tail): directly use utils:::head.matrix
361                    to be up-to-date automatically.
362    
363    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
366    
367            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
368            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
369            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
370            such that the S4 objects are always created by the current version
371            of R and 'Matrix' class definitions.
372    
373    2006-08-01  Douglas Bates  <bates@R-project.org>
374    
375            * R/lmer.R (LMEoptimize method), tests/lmer.R,
376            inst/external/test3comp.rda: Added warnings for convergence on
377            boundary and test cases.
378    
379            * src/lmer.c (mer_postVar): Modified to return the variances that
380            are marginal to the fixed effects, not conditional on them (which
381            is what the bVar slot contents represent).
382    
383    2006-07-31  Douglas Bates  <bates@R-project.org>
384    
385            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
386            function which calls the C function mer_hat_trace2.
387    
388            * man/ranef.Rd: Include description of "postVar" argument and
389            producing a caterpillar plot.
390    
391    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * NAMESPACE:    change  "correlation" to "corMatrix"
394            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
395            * R/dpoMatrix.R: ditto
396            * R/lmer.R:      ditto
397    
398    2006-07-28  Douglas Bates  <bates@R-project.org>
399    
400            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
401            RZXinv slot's contents into a separate internal function that can
402            be used in mer_hat_trace.
403    
404    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
407            via new smart
408            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
409            utility functions.
410    
411    
412    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/Csparse.R (tril, triu, band): do return *triangular* classed
415            matrices when appropriate; band() even symmetric ones.
416            (replCmat): extend to potentially all "CsparseMatrix"
417            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
418            allow subassignment for special sparse matrices.
419    
420            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
421    
422            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
423            argument; in glmer_*(): print only if(verbose).
424    
425            speed-optimize a few places by moving REAL(.) out of loops.
426    
427            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
428    
429    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
432                    since that wrongly triggers also for M[ logi , ]
433    
434            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
435            a symmetric matrix that results in a non-symmetric one.
436            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
437    
438            * R/dMatrix.R: make round(M) work as round(M, 0)
439    
440            * R/dgTMatrix.R (image): coordinate system and axis now use
441            1-based indices, not 0-based ones.
442    
443            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
444            * tests/indexing.R: test it.
445    
446            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
447            * man/isSymmetric-methods.Rd: and document it.
448    
449            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
450            * man/SparseM-conv.Rd: docu them
451    
452            * tests/other-pkgs.R: renamed from tests/graph.R and add example
453                    for 'SparseM' conversions
454    
455    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
456    
457            * R/Matrix.R (head): added head() and tail() methods.
458    
459    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * DESCRIPTION (Version): 0.995-12 released to CRAN
462    
463    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * tests/simple.R: add check for correct dsT -> dgT coercion;
466                    add check for correct printing of symmetric sparse matrices.
467    
468            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
469            for sparse symmetric matrices.
470    
471            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
472            diagonal twice.
473    
474    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
475    
476            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
477            being applied to the x slot (detected by Brian Ripley).
478    
479    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
482    
483            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
484    
485    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * src/lgCMatrix.c (lgCMatrix_diag): new function
488            * R/lgCMatrix.R (diag): for new method
489    
490            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
491                 ==> construction of illegal "*gTMatrix" via new() should
492                 now be much less easy:
493            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
494    
495            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
496                    directly.
497            * man/Matrix.Rd: documents it.
498    
499    2006-07-06  Douglas Bates  <bates@R-project.org>
500    
501            * src/pedigree.c (pedigree_inbreeding): Correction in
502            initialization.  This function is not currently being used and is
503            not fully tested.
504    
505            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
506            Introduced the glmer class.  Added code for mcmcmsamp on glmer
507            objects.  Modified validity check on pedigree objects to account
508            for nonparallel patterns of missingness of parents.
509    
510            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
511            class.
512    
513    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/pMatrix.R: coercion pMatrix -> Tsparse
516    
517    2006-06-12  Douglas Bates  <bates@R-project.org>
518    
519            * DESCRIPTION (Version): 0.995-11 released to CRAN
520    
521            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
522            the output from mcmcsamp.
523    
524    2006-06-10  Douglas Bates  <bates@R-project.org>
525    
526            * R/lmer.R (simulestimate): added C code for calculating the trace
527            of the hat matrix.
528    
529    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
532            classes.
533            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
534    
535    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/dgTMatrix.R (colSums): etc. All four of
538            colSums(), rowSums(), colMeans(), rowMeans() now should work for
539            all "Matrices".
540    
541    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
542    
543            * R/lmer.R (panel.ci): Add a reference line at zero and a
544            background grid to the qqmath plot of ranef.lmer.
545    
546    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
547    
548            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
549            grouping factors to be specified in the formula as (1|foo/bar).
550    
551    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
552    
553            * R/lmer.R (findbars and others): Change check of is.numeric to
554            !is.language to resolve the bug reported by Jacob Wegelin.
555    
556            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
557            code to evaluate inbreeding coefficients without calculating T,
558            based on code in Sargolzaei and Iwaisaki's paper.
559    
560    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
561    
562            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
563            generic and mer methods for isNested and denomDF. This denomDF was
564            an attempt to emulate that in lme but I don't think that makes
565            sense.  Use the trace of the hat matrix instead.
566    
567    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
570            the C code depending on a slot structure that's no longer valid.
571            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
572    
573    
574    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
575    
576            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
577            of lowerTriMatrix generic and methods to tril (also upper to triu)
578            and added a general band extractor.
579    
580    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/pedigree.R (pedigree): Replace sire and dam values outside the
583            allowable range with NAs. Added a corresponding check in the
584            validity check for the pedigree class.
585    
586            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
587            crossprod methods now inherits from symmetricMatrix.
588    
589    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
590    
591            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
592            generics lowerTriMatrix and upperTriMatrix along with methods for
593            the Csparse virtual class.  Also added a C function Csparse_band
594            that implements these methods by calling cholmod_band.
595    
596    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
599            erased when it was NULL.  This led to invalid subselections!
600    
601    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
604            in method for "t" so as not to lose the unit diagonal property.
605    
606    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
607    
608            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
609            and methods.  This is now an option to the ranef method for the
610            mer class.
611    
612            * src/cs_utils.c: Ensure that the nz component is -1 for a
613            compressed column-oriented matrix.  Minor formatting cleanup.
614    
615            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
616            objects.
617    
618    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
621            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
622    
623    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
624    
625            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
626            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
627    
628            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
629            for the dtCMatrix class.
630    
631    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
632    
633            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
634            and methods for it.
635    
636    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
639            arguments, such that M %*% 1:6 now works
640            * Tests/matprod.R: test the above
641    
642    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
643    
644            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
645            the ranef.lmer class.
646    
647            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
648            methods to extract the posterior variances from the bVar slot.
649    
650    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
653            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
654    
655            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
656            * tests/simple: (extended)
657    
658            * R/sparseMatrix.R (isTriangular): now using much improved
659            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
660    
661    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
662    
663            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
664            (problem report from Franklin Parlamis).  This should be done
665            generally.
666    
667    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
670            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
671            update the plot methods.
672    
673    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * R/lmer.R (resid and ranef methods):  Added methods for the
676            "residuals" and "resid" generic but only for linear mixed model
677            fits.  Changed the ranef method to return a list of data frames so
678            that the plot methods now work.
679    
680    2006-03-16  Douglas Bates  <bates@bates2>
681    
682            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
683            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
684    
685            * DESCRIPTION (Date): New release
686    
687    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
690    
691            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
692            * man/KNex.Rd: and other help files
693            * tests/*.R: several ones needed adaption
694            * inst/doc/Comparisons.Rnw: ditto
695    
696    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
699    
700            * tests/indexing.R: tests for new [<- methods for sparse matrices.
701    
702    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
705    
706            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
707    
708    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/dMatrix.R: enable things like  M [ M < 10 ]
711            * R/dgeMatrix.R: implement it
712    
713    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/AllClass.R: define "summary.mer" and "*.lmer"
716            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
717            * R/lmer.R (show): now works with summary()
718    
719    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
722            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
723                    support the above
724    
725    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
726    
727            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
728            Use glmFit$prior.weights for weights in a glmm.
729            Allow an option usePQL = FALSE to skip the PQL steps for the
730            Laplace method (and, in time, the AGQ method).
731    
732            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
733            into a separate function internal_mer_Xfactor to be able to call
734            it from internal_bhat.
735    
736    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * tests/Class+Meth.R (tstMatrixClass): function for much better
739            testing; now again of all actual classes.
740    
741            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
742                    use macros and define make_d_matrix_* and make_i_matrix_*
743                    where _i_ is for the ldense routines:
744    
745            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
746            * src/ldense.c (lsyMatrix_as_lgeMatrix):
747    
748            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
749    
750    
751    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
754                    many different kinds of matrices.
755            * R/*.R: quite a few new methods were needed for R CMD check with
756                    new Matrix().  Very good for users playing around.
757    
758    
759    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * src/dgeMatrix.c (dMatrix_validate): new
762            * src/Mutils.c (dense_nonpacked_validate): new
763    
764            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
765    
766    
767    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
768    
769            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
770    
771    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
772    
773            * DESCRIPTION (Version): 0.99-6 released to CRAN
774    
775            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
776            segfault in cases with multiple non-nested grouping factors.
777    
778    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
781                    (Depends): also on 'utils'
782    
783            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
784            * R/diagMatrix.R (Diagonal): constructor and methods for
785            diagonal matrices
786    
787            * R/ltTMatrix.R: new "minimal methods"
788    
789    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
792            all methods (and help files).
793    
794    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
797                    for case (dimn.  op  no_dimn.)
798    
799    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
800    
801            * DESCRIPTION (Version): 0.99-2  released to CRAN
802    
803    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
804    
805            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
806            by Julian Faraway.
807    
808    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/Auxiliaries.R (try_as): new utility
811            * R/sparseMatrix.R: use try_as() in coercion to original class
812    
813    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
816    
817    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/Auxiliaries.R (dimNamesCheck): added
820    
821            * R/Matrix.R (as.array), (as.vector): new
822    
823    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
826                    default.
827            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
828                    "pMatrix" now contains "sparseMatrix"
829    
830    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * tests/Class+Meth.R: new tests; t(t(m)) == m
833    
834            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
835    
836            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
837            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
838    
839            * R/dspMatrix.R: typo in "t" method
840    
841    2005-09-18  Douglas Bates  <bates@wisc.edu>
842    
843            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
844            * R/Tsparse.R: instead of R/gTMatrix.R
845            * R/Csparse.R: new
846            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
847            * src/Tsparse.c: new; many trivial methods calling cholmod_()
848            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
849                            via cholmod
850    
851    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/Auxiliaries.R (non0ind): new function using new C code
854            * src/dgCMatrix.c (compressed_non_0_ij): new utility
855    
856    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
857    
858            * src/chm_common.h: header file required by all C sources that
859            call CHOLMOD functions.  It defines a cholmod_common structure
860            called 'c' whose address is passed as the last argument to
861            (virtually) every CHOLMOD function.
862    
863            * src/Pattern.c: Simple example of the use of CHOLMOD.
864    
865            * src/init.c: initialize and finalize the cholmod_common structure.
866    
867            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
868            LDL and CCOLAMD from the U. of Florida sparse matrix library.
869    
870    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * inst/test-tools.R: new file collecting the utility functions used
873                    in ./tests/*.R
874    
875            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
876            * R/Matrix.R (cbind2): methods for NULL and missing
877    
878    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/AllClass.R: new "index" class for "[" and "[<-":
881                    First cut at "symmetricMatrix" and "triangularMatrix"
882            * R/gTMatrix.R (.ind.prep): new function;
883                    Logical and character indexing now work too.
884            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
885            * tests/indexing.R: new, including *.Rout.save
886            * tests/dgTMatrix.R: new
887    
888    2005-08-29  Douglas Bates  <bates@wisc.edu>
889    
890            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
891            indicator pos not being updated.  Also enforced upper triangular
892            for symmetric case.  Need to coerce edges component of elements of
893            edge list - grr! (Why don't they define their classes cleanly?)
894    
895    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Matrix.R:  added first "[<-" methods; not yet functional
898            * R/denseMatrix.R: ditto
899            * man/Subassign-methods.Rd: new help file for these
900    
901    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * DESCRIPTION (Version): 0.98-6
904    
905            * R/denseMatrix.R: new file for "[" fallback methods for all dense
906            matrices.
907    
908    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
911                    as( <logical>, "matrix")
912    
913            * R/pMatrix.R: coercion to "lgTMatrix"
914    
915            * R/gTMatrix.R: new virtual class to define "[" methods for.
916            * man/gTMatrix-class.Rd:
917            * General slight re-organization of where "[" methods are defined.
918              more to come.
919    
920    2005-08-18  Douglas Bates  <bates@wisc.edu>
921    
922            * DESCRIPTION (Version): 0.98-5  released to CRAN
923    
924            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
925            * .....
926    
927    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
928    
929            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
930            or glmer objects.
931    
932    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
935    
936    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
937    
938            * R/HBMM.R: finish re-writing R-only code.
939    
940    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
941    
942            * man/externalFormats.Rd: move documentation for writeHB and
943            writeMM here.
944    
945            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
946            (suggested by Paul Roecker).
947    
948            * tests/validObj.R (assertError): Comment out test that is failing
949            after recent changes in r-devel.
950    
951    
952    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/AllClass.R: intermediate virtual class "denseMatrix"
955            * man/denseMatrix-class.Rd
956            * NAMESPACE: export it, and also export
957            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
958    
959    2005-08-10  Douglas Bates  <bates@wisc.edu>
960    
961            * DESCRIPTION (Version): 0.98-3 to CRAN
962    
963            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
964            matrix_solve code (which was really, really wrong).
965    
966    2005-08-07  Douglas Bates  <bates@wisc.edu>
967    
968            * DESCRIPTION (Version): 0.98-2
969    
970            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
971    
972            * R/lmer.R (abbrvNms): new
973            * R/lmer.R (mcmcsamp): allow transformed parameters
974            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
975            for the Harwell-Boeing and the MatrixMarket formats.
976    
977    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * man/dtrMatrix-class.Rd: add examples
980            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
981    
982            * TODO: note the dtpMatrix (docu) bug
983    
984            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
985            in order to ensure that new as.matrix() is used by old functions,
986            e.g., svd(), qr(), eigen(), dist(),..;
987                  apply(), also matplot() or pairs().
988    
989    
990    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
993              add comments about 'control' / lmerControl() arguments
994    
995    2005-07-27  Douglas Bates  <bates@wisc.edu>
996    
997            * man/sleepstudy.Rd: Added the sleep data set.
998            * DESCRIPTION (Version): 0.98-1  released to CRAN
999    
1000    2005-07-12  Douglas Bates  <bates@wisc.edu>
1001            * man/sleepstudy.Rd: Added the sleep data set.
1002    
1003            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1004            .Call calls that were producing spurious output.
1005    
1006    2005-07-05  Douglas Bates  <bates@wisc.edu>
1007    
1008            * R/lmer.R (lmer): stored updated variance component estimates in
1009            mer object for the generalized model.  (Bug reported by Renaud
1010            Lancelot).
1011    
1012    2005-07-03  Douglas Bates  <bates@wisc.edu>
1013    
1014            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1015            unidimensional case.
1016    
1017    2005-06-08  Douglas Bates  <bates@wisc.edu>
1018    
1019            * DESCRIPTION (Version): 0.96-1
1020    
1021            * moved  lmer-class' R and C code moved from lme4 to here
1022    
1023    2005-06-04  Douglas Bates  <bates@wisc.edu>
1024    
1025            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1026            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1027    
1028    2005-06-02  Douglas Bates  <bates@wisc.edu>
1029    
1030            * src/Makefile.win: Forgot to update this when Makefile changed.
1031    
1032    2005-05-11  Douglas Bates  <bates@wisc.edu>
1033    
1034            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1035            bug reported by Kurt Hornik and Michael Hahsler.
1036    
1037    2005-05-10  Douglas Bates  <bates@wisc.edu>
1038    
1039            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1040            logical sparse matrices.  These will also be used in the symbolic
1041            analysis for lmer objects.
1042    
1043            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1044            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1045    
1046    2005-05-06  Douglas Bates  <bates@wisc.edu>
1047    
1048            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1049            colMeans, colSums, rowMeans and rowSums.
1050    
1051    2005-04-18  Douglas Bates  <bates@wisc.edu>
1052    
1053            * src/lgCMatrix.[ch]: code for _validate method and stub for
1054            multiplication operation.
1055    
1056            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1057            to dgetrs.
1058    
1059            * src/init.c: Fix cut-and-paste error in definition of
1060            dgeMatrix_matrix_solve
1061    
1062            * src/{many files}: Tighten code by using ALLOC_SLOT.
1063    
1064    2005-04-15  Douglas Bates  <bates@wisc.edu>
1065    
1066            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1067    
1068            * DESCRIPTION: Eliminate import of stats.
1069    
1070    
1071    2005-04-06  Douglas Bates  <bates@wisc.edu>
1072    
1073            * R/AllClass.R : add logical sparse matrix classes
1074    
1075    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/dgTMatrix.R: add "[" method for triplet matrices
1078            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1079    
1080    2005-03-31  Douglas Bates  <bates@wisc.edu>
1081    
1082            * DESCRIPTION (Version): release 0.95-5 to CRAN
1083    
1084            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1085            * R/sparseMatrix.R: %*%, crossprod()
1086            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1087            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1088            * src/lmer.c (lmer_fitted): fix thinko
1089    
1090    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1091    
1092            * R/AllClass.R: add two virtual sparse classes ``on top''
1093    
1094    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1097                    correspondingly fix examples and tests/ since new()
1098                    doesn't work for virtual classes.
1099    
1100    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/Matrix.R (as.matrix): method and one for unname()
1103            * tests/dpoMatrix.R: tests should now be less platform dependent;
1104              also run for R 2.1.0; using as.matrix()
1105    
1106    2005-03-15  Douglas Bates  <bates@wisc.edu>
1107    
1108            * R/pMatrix.R: "pMatrix" class added
1109            * ....
1110    
1111    2005-03-14  Douglas Bates  <bates@wisc.edu>
1112    
1113            * R/dtpMatrix.R: Add unpack method and an example.
1114    
1115            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1116            of general symmetric matrices and associated S4 methods.
1117    
1118    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1119            +
1120    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1123              crossprod() and "%*%" methods added; tests, too.
1124            * tests/matprod.R: new, for testing these
1125    
1126    2005-03-03  Douglas Bates  <bates@wisc.edu>
1127    
1128            * src/lmer.c (lmer_fitted): Added.
1129    
1130    2005-03-02  Douglas Bates  <bates@wisc.edu>
1131    
1132            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1133    
1134    2005-02-28  Douglas Bates  <bates@wisc.edu>
1135    
1136            * src/*.c,po/,inst/po: Internationalization and localization of
1137            the package.
1138    
1139            * src/ldl.[ch]: Removed these as their contents are referenced in the
1140            R_ldl.c file.
1141    
1142            * src/flame.[ch]: Removed these source files.
1143    
1144            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1145    
1146            * src/LU.[ch],src/init.c: absorb in factorizations
1147    
1148            * src/Mutils.h: prepare for internationalization
1149    
1150            * src/cblas.h: move the enum definitions to Mutils.h and remove
1151            this file
1152    
1153    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1156    
1157            * R/dtrMatrix.R: fix t() method
1158    
1159            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1160            * NAMESPACE: export them (and import generics from "methods")
1161            * tests/group-methods.R : and test them.
1162    
1163            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1164            border case
1165    
1166    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1167    
1168            * DESCRIPTION (Version): 0.95-2  released to CRAN
1169    
1170            * src/dgBCMatrix.c:
1171            * src/lmer.c: many changes
1172            * ...
1173    
1174    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * R/Matrix.R: add more sophisticated show() method.
1177    
1178    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1179    
1180            * */* : almost complete reorganization of classes.
1181    
1182    2005-01-26  Douglas Bates  <bates@wisc.edu>
1183    
1184            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1185            for the geMatrix class.
1186    
1187    2005-01-24  Douglas Bates  <bates@wisc.edu>
1188    
1189            * src/Makefile (clean): Remove *.a and *.so
1190    
1191            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1192    
1193    2005-01-23  Douglas Bates  <bates@wisc.edu>
1194    
1195            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1196            had an effect in cases with more than 2 grouping factors.
1197    
1198    2005-01-03  Douglas Bates  <bates@wisc.edu>
1199    
1200            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1201    
1202    2004-12-23  Douglas Bates  <bates@wisc.edu>
1203    
1204            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1205            and R_useDynamicSymbols (suggested by B.D.Ripley).
1206    
1207    2004-12-14  Douglas Bates  <bates@wisc.edu>
1208    
1209          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1210    
1211          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1212          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1213    
1214  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1215    
1216          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1217          no longer used.          no longer used.
# Line 17  Line 1223 
1223          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1224          Fixes part but not all of #15.          Fixes part but not all of #15.
1225    
1226  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1227    
1228          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1229          scalar grouping factors corrected.          scalar grouping factors corrected.
1230    
1231  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1232    
1233          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1234    
1235  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1236    
1237          * 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
1238          .h file can be included.          .h file can be included.
1239    
1240  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1241    
1242          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1243          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1244    
1245          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1246    
1247  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1248    
1249          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1250    
1251  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1252    
1253          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1254    
1255  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1256    
1257          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1258    
1259  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1260    
1261          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1262    
1263  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1264    
1265          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1266          routines.          routines.
1267    
1268  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1269    
1270          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1271    
1272  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1273    
1274          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1275    

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