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revision 410, Tue Dec 28 14:51:42 2004 UTC revision 1507, Mon Sep 4 18:41:34 2006 UTC
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1  2004-12-23  Douglas Bates  <bates@bates1-home>  2006-09-04  Douglas Bates  <bates@R-project.org>
2    
3            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
4            * src/DEPS.mkf: update
5    
6    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * created branches/Matrix-for-R-2.3.x;  on trunk: do
9            * DESCRIPTION (Version): 0.9975-0
10            (Depends): R (>= 2.4.0)
11    
12    2006-09-01  Douglas Bates  <bates@R-project.org>
13    
14            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
15    
16    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
19            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
20    
21            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
22    
23    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
26            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
27            * R/dsparseMatrix.R: dito
28            * R/Csparse.R: dito
29    
30    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dMatrix.R (Compare): improve availability of "<", etc
33            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
34    
35    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
38            of a 0-index which was used as 1-index (..hmm)
39    
40            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
41    
42            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
43            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
44            (.is.diagonal): dito
45    
46            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
47    
48            * R/Matrix.R (Matrix): also work for NA data
49    
50    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
53            in all cases.
54    
55    2006-08-27  Douglas Bates  <bates@R-project.org>
56    
57            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
58            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
59    
60    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
63            subclasses of "ddenseMatrix"
64            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
65            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
66            instead of half dozen specialized ones.
67    
68    2006-08-25  Douglas Bates  <bates@R-project.org>
69    
70            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
71            <tillard@cirad.fr> - ordering standard errors to match effects.
72    
73    2006-08-24  Douglas Bates  <bates@R-project.org>
74    
75            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
76            on R_ldl.
77            * R/lCholCMatrix.R,
78            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
79            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
80            * many files in ./R and ./src: Use more general version of
81            dup_mMatrix_as_dgeMatrix to simplify method definitions.
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
83            dtpMatrix, dspMatrix and dppMatrix conversions.
84    
85    
86    2006-08-23  Douglas Bates  <bates@R-project.org>
87    
88            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
89            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
90            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
91            dgeMatrix_crossprod (may need to do this in other places).
92            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
93            generic and method for dsCMatrix.  Use CHOLMOD for chol().
94    
95    2006-08-22  Douglas Bates  <bates@R-project.org>
96    
97            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
98            types of classed Matrices, matrices or numeric or logical vectors.
99            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
100            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
101            to Mutils.h (as an inline) and change name to Matrix_check_class;
102            fixes in as_cholmod_factor and chm_factor_to_SEXP.
103            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
104            dsCMatrix_matrix_solve.  Comment out vestigial functions.
105            * src/Csparse.c: use diag_P and uplo_P macros.
106    
107    2006-08-21  Douglas Bates  <bates@R-project.org>
108    
109            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
110            valgrind.
111            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
112            inverses.
113            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
114            -Wall warnings.
115            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
116            Use dup_mMatrix_as_dgeMatrix.
117    
118    2006-08-20  Douglas Bates  <bates@R-project.org>
119    
120            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
121            * tests/sparseQR.R: Added
122            * man/sparseQR-class.Rd: Document methods for qr.* generics
123            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
124    
125    2006-08-19  Douglas Bates  <bates@R-project.org>
126    
127            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
128            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
129            and qr.fitted.
130            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
131            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
132    
133    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
136            the base version has no "..." argument.
137    
138            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
139    
140            * R/Matrix.R: define and
141            * NAMESPACE: export as.numeric() and as.logical() methods.
142                    Let's hope these do not badly slow down something...
143            Finally export the zapsmall() method.
144    
145    2006-08-17  Douglas Bates  <bates@R-project.org>
146    
147            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
148            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
149            * src/dtCMatrix.c :Remove code that is no longer used
150            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
151    
152    2006-08-14  Douglas Bates  <bates@R-project.org>
153    
154            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
155            Csparse_to_logical and Csparse_symmetric_to_general.
156            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
157            coercion methods between CsparseMatrix and TsparseMatrix.
158    
159    2006-08-14  Douglas Bates  <bates@R-project.org>
160    
161            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
162            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
163            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
164            possible.
165    
166    2006-08-12  Douglas Bates  <bates@R-project.org>
167    
168            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
169              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
170              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
171              generalize conversions between TsparseMatrix, CsparseMatrix,
172              denseMatrix and matrix.  Preserve triangularity property and
173              propagate Dimnames in the easy cases.
174    
175    2006-08-10  Douglas Bates  <bates@R-project.org>
176    
177            * src/lmer.c: adjust checks in glmer_init for S4SXP
178            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
179            before S4SXP but for the wrong reasons.
180    
181    2006-08-08  Douglas Bates  <bates@R-project.org>
182    
183            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
184            Later modified to return the upper triangle only.
185            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
186    
187    2006-08-07  Douglas Bates  <bates@R-project.org>
188    
189            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
190            R-level conversion to a sparse symmetric class.
191            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
192            Remove conversion to sparse symmetric classes (now done in C code).
193    
194    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
197            * man/band.Rd:  adapt the \dontshow{} unit test.
198    
199    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * DESCRIPTION (Version): 0.995-14  for CRAN
202    
203            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
204    
205            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
206            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
207    
208            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
209            * R/Tsparse.R (tril, triu, band): methods
210            * R/dgRMatrix.R (tril, ...):    ditto
211            * man/band.Rd:                  ditto
212    
213    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R (head, tail): directly use utils:::head.matrix
216                    to be up-to-date automatically.
217    
218    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
221    
222            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
223            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
224            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
225            such that the S4 objects are always created by the current version
226            of R and 'Matrix' class definitions.
227    
228    2006-08-01  Douglas Bates  <bates@R-project.org>
229    
230            * R/lmer.R (LMEoptimize method), tests/lmer.R,
231            inst/external/test3comp.rda: Added warnings for convergence on
232            boundary and test cases.
233    
234            * src/lmer.c (mer_postVar): Modified to return the variances that
235            are marginal to the fixed effects, not conditional on them (which
236            is what the bVar slot contents represent).
237    
238    2006-07-31  Douglas Bates  <bates@R-project.org>
239    
240            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
241            function which calls the C function mer_hat_trace2.
242    
243            * man/ranef.Rd: Include description of "postVar" argument and
244            producing a caterpillar plot.
245    
246    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * NAMESPACE:    change  "correlation" to "corMatrix"
249            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
250            * R/dpoMatrix.R: ditto
251            * R/lmer.R:      ditto
252    
253    2006-07-28  Douglas Bates  <bates@R-project.org>
254    
255            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
256            RZXinv slot's contents into a separate internal function that can
257            be used in mer_hat_trace.
258    
259    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
262            via new smart
263            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
264            utility functions.
265    
266    
267    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Csparse.R (tril, triu, band): do return *triangular* classed
270            matrices when appropriate; band() even symmetric ones.
271            (replCmat): extend to potentially all "CsparseMatrix"
272            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
273            allow subassignment for special sparse matrices.
274    
275            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
276    
277            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
278            argument; in glmer_*(): print only if(verbose).
279    
280            speed-optimize a few places by moving REAL(.) out of loops.
281    
282            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
283    
284    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
287                    since that wrongly triggers also for M[ logi , ]
288    
289            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
290            a symmetric matrix that results in a non-symmetric one.
291            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
292    
293            * R/dMatrix.R: make round(M) work as round(M, 0)
294    
295            * R/dgTMatrix.R (image): coordinate system and axis now use
296            1-based indices, not 0-based ones.
297    
298            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
299            * tests/indexing.R: test it.
300    
301            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
302            * man/isSymmetric-methods.Rd: and document it.
303    
304            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
305            * man/SparseM-conv.Rd: docu them
306    
307            * tests/other-pkgs.R: renamed from tests/graph.R and add example
308                    for 'SparseM' conversions
309    
310    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
311    
312            * R/Matrix.R (head): added head() and tail() methods.
313    
314    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * DESCRIPTION (Version): 0.995-12 released to CRAN
317    
318    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * tests/simple.R: add check for correct dsT -> dgT coercion;
321                    add check for correct printing of symmetric sparse matrices.
322    
323            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
324            for sparse symmetric matrices.
325    
326            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
327            diagonal twice.
328    
329    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
330    
331            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
332            being applied to the x slot (detected by Brian Ripley).
333    
334    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
337    
338            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
339    
340    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * src/lgCMatrix.c (lgCMatrix_diag): new function
343            * R/lgCMatrix.R (diag): for new method
344    
345            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
346                 ==> construction of illegal "*gTMatrix" via new() should
347                 now be much less easy:
348            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
349    
350            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
351                    directly.
352            * man/Matrix.Rd: documents it.
353    
354    2006-07-06  Douglas Bates  <bates@R-project.org>
355    
356            * src/pedigree.c (pedigree_inbreeding): Correction in
357            initialization.  This function is not currently being used and is
358            not fully tested.
359    
360            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
361            Introduced the glmer class.  Added code for mcmcmsamp on glmer
362            objects.  Modified validity check on pedigree objects to account
363            for nonparallel patterns of missingness of parents.
364    
365            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
366            class.
367    
368    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/pMatrix.R: coercion pMatrix -> Tsparse
371    
372    2006-06-12  Douglas Bates  <bates@R-project.org>
373    
374            * DESCRIPTION (Version): 0.995-11 released to CRAN
375    
376            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
377            the output from mcmcsamp.
378    
379    2006-06-10  Douglas Bates  <bates@R-project.org>
380    
381            * R/lmer.R (simulestimate): added C code for calculating the trace
382            of the hat matrix.
383    
384    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
387            classes.
388            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
389    
390    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/dgTMatrix.R (colSums): etc. All four of
393            colSums(), rowSums(), colMeans(), rowMeans() now should work for
394            all "Matrices".
395    
396    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
397    
398            * R/lmer.R (panel.ci): Add a reference line at zero and a
399            background grid to the qqmath plot of ranef.lmer.
400    
401    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
402    
403            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
404            grouping factors to be specified in the formula as (1|foo/bar).
405    
406    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
407    
408            * R/lmer.R (findbars and others): Change check of is.numeric to
409            !is.language to resolve the bug reported by Jacob Wegelin.
410    
411            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
412            code to evaluate inbreeding coefficients without calculating T,
413            based on code in Sargolzaei and Iwaisaki's paper.
414    
415    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
416    
417            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
418            generic and mer methods for isNested and denomDF. This denomDF was
419            an attempt to emulate that in lme but I don't think that makes
420            sense.  Use the trace of the hat matrix instead.
421    
422    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
425            the C code depending on a slot structure that's no longer valid.
426            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
427    
428    
429    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
430    
431            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
432            of lowerTriMatrix generic and methods to tril (also upper to triu)
433            and added a general band extractor.
434    
435    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * R/pedigree.R (pedigree): Replace sire and dam values outside the
438            allowable range with NAs. Added a corresponding check in the
439            validity check for the pedigree class.
440    
441            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
442            crossprod methods now inherits from symmetricMatrix.
443    
444    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
445    
446            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
447            generics lowerTriMatrix and upperTriMatrix along with methods for
448            the Csparse virtual class.  Also added a C function Csparse_band
449            that implements these methods by calling cholmod_band.
450    
451    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
454            erased when it was NULL.  This led to invalid subselections!
455    
456    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
457    
458            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
459            in method for "t" so as not to lose the unit diagonal property.
460    
461    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
464            and methods.  This is now an option to the ranef method for the
465            mer class.
466    
467            * src/cs_utils.c: Ensure that the nz component is -1 for a
468            compressed column-oriented matrix.  Minor formatting cleanup.
469    
470            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
471            objects.
472    
473    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
476            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
477    
478    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
481            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
482    
483            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
484            for the dtCMatrix class.
485    
486    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
489            and methods for it.
490    
491    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
494            arguments, such that M %*% 1:6 now works
495            * Tests/matprod.R: test the above
496    
497    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
498    
499            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
500            the ranef.lmer class.
501    
502            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
503            methods to extract the posterior variances from the bVar slot.
504    
505    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
508            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
509    
510            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
511            * tests/simple: (extended)
512    
513            * R/sparseMatrix.R (isTriangular): now using much improved
514            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
515    
516    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
517    
518            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
519            (problem report from Franklin Parlamis).  This should be done
520            generally.
521    
522    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
525            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
526            update the plot methods.
527    
528    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * R/lmer.R (resid and ranef methods):  Added methods for the
531            "residuals" and "resid" generic but only for linear mixed model
532            fits.  Changed the ranef method to return a list of data frames so
533            that the plot methods now work.
534    
535    2006-03-16  Douglas Bates  <bates@bates2>
536    
537            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
538            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
539    
540            * DESCRIPTION (Date): New release
541    
542    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
545    
546            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
547            * man/KNex.Rd: and other help files
548            * tests/*.R: several ones needed adaption
549            * inst/doc/Comparisons.Rnw: ditto
550    
551    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
554    
555            * tests/indexing.R: tests for new [<- methods for sparse matrices.
556    
557    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
560    
561            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
562    
563    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/dMatrix.R: enable things like  M [ M < 10 ]
566            * R/dgeMatrix.R: implement it
567    
568    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/AllClass.R: define "summary.mer" and "*.lmer"
571            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
572            * R/lmer.R (show): now works with summary()
573    
574    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
577            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
578                    support the above
579    
580    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
581    
582            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
583            Use glmFit$prior.weights for weights in a glmm.
584            Allow an option usePQL = FALSE to skip the PQL steps for the
585            Laplace method (and, in time, the AGQ method).
586    
587            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
588            into a separate function internal_mer_Xfactor to be able to call
589            it from internal_bhat.
590    
591    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * tests/Class+Meth.R (tstMatrixClass): function for much better
594            testing; now again of all actual classes.
595    
596            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
597                    use macros and define make_d_matrix_* and make_i_matrix_*
598                    where _i_ is for the ldense routines:
599    
600            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
601            * src/ldense.c (lsyMatrix_as_lgeMatrix):
602    
603            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
604    
605    
606    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
609                    many different kinds of matrices.
610            * R/*.R: quite a few new methods were needed for R CMD check with
611                    new Matrix().  Very good for users playing around.
612    
613    
614    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * src/dgeMatrix.c (dMatrix_validate): new
617            * src/Mutils.c (dense_nonpacked_validate): new
618    
619            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
620    
621    
622    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
623    
624            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
625    
626    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
627    
628            * DESCRIPTION (Version): 0.99-6 released to CRAN
629    
630            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
631            segfault in cases with multiple non-nested grouping factors.
632    
633    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
636                    (Depends): also on 'utils'
637    
638            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
639            * R/diagMatrix.R (Diagonal): constructor and methods for
640            diagonal matrices
641    
642            * R/ltTMatrix.R: new "minimal methods"
643    
644    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
647            all methods (and help files).
648    
649    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
652                    for case (dimn.  op  no_dimn.)
653    
654    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
655    
656            * DESCRIPTION (Version): 0.99-2  released to CRAN
657    
658    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
659    
660            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
661            by Julian Faraway.
662    
663    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Auxiliaries.R (try_as): new utility
666            * R/sparseMatrix.R: use try_as() in coercion to original class
667    
668    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
671    
672    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Auxiliaries.R (dimNamesCheck): added
675    
676            * R/Matrix.R (as.array), (as.vector): new
677    
678    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
681                    default.
682            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
683                    "pMatrix" now contains "sparseMatrix"
684    
685    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * tests/Class+Meth.R: new tests; t(t(m)) == m
688    
689            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
690    
691            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
692            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
693    
694            * R/dspMatrix.R: typo in "t" method
695    
696    2005-09-18  Douglas Bates  <bates@wisc.edu>
697    
698            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
699            * R/Tsparse.R: instead of R/gTMatrix.R
700            * R/Csparse.R: new
701            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
702            * src/Tsparse.c: new; many trivial methods calling cholmod_()
703            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
704                            via cholmod
705    
706    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
707    
708            * R/Auxiliaries.R (non0ind): new function using new C code
709            * src/dgCMatrix.c (compressed_non_0_ij): new utility
710    
711    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
712    
713            * src/chm_common.h: header file required by all C sources that
714            call CHOLMOD functions.  It defines a cholmod_common structure
715            called 'c' whose address is passed as the last argument to
716            (virtually) every CHOLMOD function.
717    
718            * src/Pattern.c: Simple example of the use of CHOLMOD.
719    
720            * src/init.c: initialize and finalize the cholmod_common structure.
721    
722            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
723            LDL and CCOLAMD from the U. of Florida sparse matrix library.
724    
725    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * inst/test-tools.R: new file collecting the utility functions used
728                    in ./tests/*.R
729    
730            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
731            * R/Matrix.R (cbind2): methods for NULL and missing
732    
733    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/AllClass.R: new "index" class for "[" and "[<-":
736                    First cut at "symmetricMatrix" and "triangularMatrix"
737            * R/gTMatrix.R (.ind.prep): new function;
738                    Logical and character indexing now work too.
739            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
740            * tests/indexing.R: new, including *.Rout.save
741            * tests/dgTMatrix.R: new
742    
743    2005-08-29  Douglas Bates  <bates@wisc.edu>
744    
745            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
746            indicator pos not being updated.  Also enforced upper triangular
747            for symmetric case.  Need to coerce edges component of elements of
748            edge list - grr! (Why don't they define their classes cleanly?)
749    
750    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/Matrix.R:  added first "[<-" methods; not yet functional
753            * R/denseMatrix.R: ditto
754            * man/Subassign-methods.Rd: new help file for these
755    
756    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * DESCRIPTION (Version): 0.98-6
759    
760            * R/denseMatrix.R: new file for "[" fallback methods for all dense
761            matrices.
762    
763    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
766                    as( <logical>, "matrix")
767    
768            * R/pMatrix.R: coercion to "lgTMatrix"
769    
770            * R/gTMatrix.R: new virtual class to define "[" methods for.
771            * man/gTMatrix-class.Rd:
772            * General slight re-organization of where "[" methods are defined.
773              more to come.
774    
775    2005-08-18  Douglas Bates  <bates@wisc.edu>
776    
777            * DESCRIPTION (Version): 0.98-5  released to CRAN
778    
779            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
780            * .....
781    
782    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
783    
784            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
785            or glmer objects.
786    
787    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
790    
791    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
792    
793            * R/HBMM.R: finish re-writing R-only code.
794    
795    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
796    
797            * man/externalFormats.Rd: move documentation for writeHB and
798            writeMM here.
799    
800            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
801            (suggested by Paul Roecker).
802    
803            * tests/validObj.R (assertError): Comment out test that is failing
804            after recent changes in r-devel.
805    
806    
807    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/AllClass.R: intermediate virtual class "denseMatrix"
810            * man/denseMatrix-class.Rd
811            * NAMESPACE: export it, and also export
812            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
813    
814    2005-08-10  Douglas Bates  <bates@wisc.edu>
815    
816            * DESCRIPTION (Version): 0.98-3 to CRAN
817    
818            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
819            matrix_solve code (which was really, really wrong).
820    
821    2005-08-07  Douglas Bates  <bates@wisc.edu>
822    
823            * DESCRIPTION (Version): 0.98-2
824    
825            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
826    
827            * R/lmer.R (abbrvNms): new
828            * R/lmer.R (mcmcsamp): allow transformed parameters
829            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
830            for the Harwell-Boeing and the MatrixMarket formats.
831    
832    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * man/dtrMatrix-class.Rd: add examples
835            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
836    
837            * TODO: note the dtpMatrix (docu) bug
838    
839            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
840            in order to ensure that new as.matrix() is used by old functions,
841            e.g., svd(), qr(), eigen(), dist(),..;
842                  apply(), also matplot() or pairs().
843    
844    
845    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
848              add comments about 'control' / lmerControl() arguments
849    
850    2005-07-27  Douglas Bates  <bates@wisc.edu>
851    
852            * man/sleepstudy.Rd: Added the sleep data set.
853            * DESCRIPTION (Version): 0.98-1  released to CRAN
854    
855    2005-07-12  Douglas Bates  <bates@wisc.edu>
856            * man/sleepstudy.Rd: Added the sleep data set.
857    
858            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
859            .Call calls that were producing spurious output.
860    
861    2005-07-05  Douglas Bates  <bates@wisc.edu>
862    
863            * R/lmer.R (lmer): stored updated variance component estimates in
864            mer object for the generalized model.  (Bug reported by Renaud
865            Lancelot).
866    
867    2005-07-03  Douglas Bates  <bates@wisc.edu>
868    
869            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
870            unidimensional case.
871    
872    2005-06-08  Douglas Bates  <bates@wisc.edu>
873    
874            * DESCRIPTION (Version): 0.96-1
875    
876            * moved  lmer-class' R and C code moved from lme4 to here
877    
878    2005-06-04  Douglas Bates  <bates@wisc.edu>
879    
880            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
881            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
882    
883    2005-06-02  Douglas Bates  <bates@wisc.edu>
884    
885            * src/Makefile.win: Forgot to update this when Makefile changed.
886    
887    2005-05-11  Douglas Bates  <bates@wisc.edu>
888    
889            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
890            bug reported by Kurt Hornik and Michael Hahsler.
891    
892    2005-05-10  Douglas Bates  <bates@wisc.edu>
893    
894            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
895            logical sparse matrices.  These will also be used in the symbolic
896            analysis for lmer objects.
897    
898            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
899            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
900    
901    2005-05-06  Douglas Bates  <bates@wisc.edu>
902    
903            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
904            colMeans, colSums, rowMeans and rowSums.
905    
906    2005-04-18  Douglas Bates  <bates@wisc.edu>
907    
908            * src/lgCMatrix.[ch]: code for _validate method and stub for
909            multiplication operation.
910    
911            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
912            to dgetrs.
913    
914            * src/init.c: Fix cut-and-paste error in definition of
915            dgeMatrix_matrix_solve
916    
917            * src/{many files}: Tighten code by using ALLOC_SLOT.
918    
919    2005-04-15  Douglas Bates  <bates@wisc.edu>
920    
921            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
922    
923            * DESCRIPTION: Eliminate import of stats.
924    
925    
926    2005-04-06  Douglas Bates  <bates@wisc.edu>
927    
928            * R/AllClass.R : add logical sparse matrix classes
929    
930    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/dgTMatrix.R: add "[" method for triplet matrices
933            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
934    
935    2005-03-31  Douglas Bates  <bates@wisc.edu>
936    
937            * DESCRIPTION (Version): release 0.95-5 to CRAN
938    
939            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
940            * R/sparseMatrix.R: %*%, crossprod()
941            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
942            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
943            * src/lmer.c (lmer_fitted): fix thinko
944    
945    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * R/AllClass.R: add two virtual sparse classes ``on top''
948    
949    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
952                    correspondingly fix examples and tests/ since new()
953                    doesn't work for virtual classes.
954    
955    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/Matrix.R (as.matrix): method and one for unname()
958            * tests/dpoMatrix.R: tests should now be less platform dependent;
959              also run for R 2.1.0; using as.matrix()
960    
961    2005-03-15  Douglas Bates  <bates@wisc.edu>
962    
963            * R/pMatrix.R: "pMatrix" class added
964            * ....
965    
966    2005-03-14  Douglas Bates  <bates@wisc.edu>
967    
968            * R/dtpMatrix.R: Add unpack method and an example.
969    
970            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
971            of general symmetric matrices and associated S4 methods.
972    
973    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
974            +
975    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * R/dgeMatrix.R (setAs): and many other files: more coercion,
978              crossprod() and "%*%" methods added; tests, too.
979            * tests/matprod.R: new, for testing these
980    
981    2005-03-03  Douglas Bates  <bates@wisc.edu>
982    
983            * src/lmer.c (lmer_fitted): Added.
984    
985    2005-03-02  Douglas Bates  <bates@wisc.edu>
986    
987            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
988    
989    2005-02-28  Douglas Bates  <bates@wisc.edu>
990    
991            * src/*.c,po/,inst/po: Internationalization and localization of
992            the package.
993    
994            * src/ldl.[ch]: Removed these as their contents are referenced in the
995            R_ldl.c file.
996    
997            * src/flame.[ch]: Removed these source files.
998    
999            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1000    
1001            * src/LU.[ch],src/init.c: absorb in factorizations
1002    
1003            * src/Mutils.h: prepare for internationalization
1004    
1005            * src/cblas.h: move the enum definitions to Mutils.h and remove
1006            this file
1007    
1008    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1009    
1010            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1011    
1012            * R/dtrMatrix.R: fix t() method
1013    
1014            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1015            * NAMESPACE: export them (and import generics from "methods")
1016            * tests/group-methods.R : and test them.
1017    
1018            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1019            border case
1020    
1021    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1022    
1023            * DESCRIPTION (Version): 0.95-2  released to CRAN
1024    
1025            * src/dgBCMatrix.c:
1026            * src/lmer.c: many changes
1027            * ...
1028    
1029    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * R/Matrix.R: add more sophisticated show() method.
1032    
1033    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1034    
1035            * */* : almost complete reorganization of classes.
1036    
1037    2005-01-26  Douglas Bates  <bates@wisc.edu>
1038    
1039            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1040            for the geMatrix class.
1041    
1042    2005-01-24  Douglas Bates  <bates@wisc.edu>
1043    
1044            * src/Makefile (clean): Remove *.a and *.so
1045    
1046            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1047    
1048    2005-01-23  Douglas Bates  <bates@wisc.edu>
1049    
1050            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1051            had an effect in cases with more than 2 grouping factors.
1052    
1053    2005-01-03  Douglas Bates  <bates@wisc.edu>
1054    
1055            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1056    
1057    2004-12-23  Douglas Bates  <bates@wisc.edu>
1058    
1059          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1060          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1061    
1062  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1063    
1064          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1065    
1066          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1067          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1068    
1069  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1070    
1071          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1072          no longer used.          no longer used.
# Line 22  Line 1078 
1078          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1079          Fixes part but not all of #15.          Fixes part but not all of #15.
1080    
1081  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1082    
1083          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1084          scalar grouping factors corrected.          scalar grouping factors corrected.
1085    
1086  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1087    
1088          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1089    
1090  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1091    
1092          * 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
1093          .h file can be included.          .h file can be included.
1094    
1095  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1096    
1097          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1098          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1099    
1100          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1101    
1102  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1103    
1104          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1105    
1106  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1107    
1108          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1109    
1110  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1111    
1112          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1113    
1114  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1115    
1116          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1117    
1118  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1119    
1120          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1121          routines.          routines.
1122    
1123  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1124    
1125          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1126    
1127  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1128    
1129          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1130    

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