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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1481, Sat Sep 2 16:43:22 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * created branches/Matrix-for-R-2.3.x;  on trunk: do
4            * DESCRIPTION (Version): 0.9975-0
5            (Depends): R (>= 2.4.0)
6    
7    2006-09-01  Douglas Bates  <bates@R-project.org>
8    
9            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
10    
11    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
14            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
15    
16            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
17    
18    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
21            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
22            * R/dsparseMatrix.R: dito
23            * R/Csparse.R: dito
24    
25    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/dMatrix.R (Compare): improve availability of "<", etc
28            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
29    
30    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
33            of a 0-index which was used as 1-index (..hmm)
34    
35            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
36    
37            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
38            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
39            (.is.diagonal): dito
40    
41            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
42    
43            * R/Matrix.R (Matrix): also work for NA data
44    
45    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
48            in all cases.
49    
50    2006-08-27  Douglas Bates  <bates@R-project.org>
51    
52            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
53            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
54    
55    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
58            subclasses of "ddenseMatrix"
59            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
60            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
61            instead of half dozen specialized ones.
62    
63    2006-08-25  Douglas Bates  <bates@R-project.org>
64    
65            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
66            <tillard@cirad.fr> - ordering standard errors to match effects.
67    
68    2006-08-24  Douglas Bates  <bates@R-project.org>
69    
70            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
71            on R_ldl.
72            * R/lCholCMatrix.R,
73            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
74            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
75            * many files in ./R and ./src: Use more general version of
76            dup_mMatrix_as_dgeMatrix to simplify method definitions.
77            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
78            dtpMatrix, dspMatrix and dppMatrix conversions.
79    
80    
81    2006-08-23  Douglas Bates  <bates@R-project.org>
82    
83            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
84            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
85            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
86            dgeMatrix_crossprod (may need to do this in other places).
87            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
88            generic and method for dsCMatrix.  Use CHOLMOD for chol().
89    
90    2006-08-22  Douglas Bates  <bates@R-project.org>
91    
92            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
93            types of classed Matrices, matrices or numeric or logical vectors.
94            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
95            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
96            to Mutils.h (as an inline) and change name to Matrix_check_class;
97            fixes in as_cholmod_factor and chm_factor_to_SEXP.
98            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
99            dsCMatrix_matrix_solve.  Comment out vestigial functions.
100            * src/Csparse.c: use diag_P and uplo_P macros.
101    
102    2006-08-21  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
105            valgrind.
106            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
107            inverses.
108            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
109            -Wall warnings.
110            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
111            Use dup_mMatrix_as_dgeMatrix.
112    
113    2006-08-20  Douglas Bates  <bates@R-project.org>
114    
115            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
116            * tests/sparseQR.R: Added
117            * man/sparseQR-class.Rd: Document methods for qr.* generics
118            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
119    
120    2006-08-19  Douglas Bates  <bates@R-project.org>
121    
122            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
123            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
124            and qr.fitted.
125            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
126            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
127    
128    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
131            the base version has no "..." argument.
132    
133            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
134    
135            * R/Matrix.R: define and
136            * NAMESPACE: export as.numeric() and as.logical() methods.
137                    Let's hope these do not badly slow down something...
138            Finally export the zapsmall() method.
139    
140    2006-08-17  Douglas Bates  <bates@R-project.org>
141    
142            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
143            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
144            * src/dtCMatrix.c :Remove code that is no longer used
145            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
146    
147    2006-08-14  Douglas Bates  <bates@R-project.org>
148    
149            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
150            Csparse_to_logical and Csparse_symmetric_to_general.
151            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
152            coercion methods between CsparseMatrix and TsparseMatrix.
153    
154    2006-08-14  Douglas Bates  <bates@R-project.org>
155    
156            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
157            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
158            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
159            possible.
160    
161    2006-08-12  Douglas Bates  <bates@R-project.org>
162    
163            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
164              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
165              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
166              generalize conversions between TsparseMatrix, CsparseMatrix,
167              denseMatrix and matrix.  Preserve triangularity property and
168              propagate Dimnames in the easy cases.
169    
170    2006-08-10  Douglas Bates  <bates@R-project.org>
171    
172            * src/lmer.c: adjust checks in glmer_init for S4SXP
173            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
174            before S4SXP but for the wrong reasons.
175    
176    2006-08-08  Douglas Bates  <bates@R-project.org>
177    
178            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
179            Later modified to return the upper triangle only.
180            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
181    
182    2006-08-07  Douglas Bates  <bates@R-project.org>
183    
184            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
185            R-level conversion to a sparse symmetric class.
186            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
187            Remove conversion to sparse symmetric classes (now done in C code).
188    
189    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
192            * man/band.Rd:  adapt the \dontshow{} unit test.
193    
194    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Version): 0.995-14  for CRAN
197    
198            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
199    
200            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
201            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
202    
203            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
204            * R/Tsparse.R (tril, triu, band): methods
205            * R/dgRMatrix.R (tril, ...):    ditto
206            * man/band.Rd:                  ditto
207    
208    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R (head, tail): directly use utils:::head.matrix
211                    to be up-to-date automatically.
212    
213    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
216    
217            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
218            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
219            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
220            such that the S4 objects are always created by the current version
221            of R and 'Matrix' class definitions.
222    
223    2006-08-01  Douglas Bates  <bates@R-project.org>
224    
225            * R/lmer.R (LMEoptimize method), tests/lmer.R,
226            inst/external/test3comp.rda: Added warnings for convergence on
227            boundary and test cases.
228    
229            * src/lmer.c (mer_postVar): Modified to return the variances that
230            are marginal to the fixed effects, not conditional on them (which
231            is what the bVar slot contents represent).
232    
233    2006-07-31  Douglas Bates  <bates@R-project.org>
234    
235            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
236            function which calls the C function mer_hat_trace2.
237    
238            * man/ranef.Rd: Include description of "postVar" argument and
239            producing a caterpillar plot.
240    
241    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * NAMESPACE:    change  "correlation" to "corMatrix"
244            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
245            * R/dpoMatrix.R: ditto
246            * R/lmer.R:      ditto
247    
248    2006-07-28  Douglas Bates  <bates@R-project.org>
249    
250            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
251            RZXinv slot's contents into a separate internal function that can
252            be used in mer_hat_trace.
253    
254    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
257            via new smart
258            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
259            utility functions.
260    
261    
262    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Csparse.R (tril, triu, band): do return *triangular* classed
265            matrices when appropriate; band() even symmetric ones.
266            (replCmat): extend to potentially all "CsparseMatrix"
267            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
268            allow subassignment for special sparse matrices.
269    
270            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
271    
272            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
273            argument; in glmer_*(): print only if(verbose).
274    
275            speed-optimize a few places by moving REAL(.) out of loops.
276    
277            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
278    
279    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
282                    since that wrongly triggers also for M[ logi , ]
283    
284            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
285            a symmetric matrix that results in a non-symmetric one.
286            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
287    
288            * R/dMatrix.R: make round(M) work as round(M, 0)
289    
290            * R/dgTMatrix.R (image): coordinate system and axis now use
291            1-based indices, not 0-based ones.
292    
293            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
294            * tests/indexing.R: test it.
295    
296            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
297            * man/isSymmetric-methods.Rd: and document it.
298    
299            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
300            * man/SparseM-conv.Rd: docu them
301    
302            * tests/other-pkgs.R: renamed from tests/graph.R and add example
303                    for 'SparseM' conversions
304    
305    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
306    
307            * R/Matrix.R (head): added head() and tail() methods.
308    
309    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * DESCRIPTION (Version): 0.995-12 released to CRAN
312    
313    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * tests/simple.R: add check for correct dsT -> dgT coercion;
316                    add check for correct printing of symmetric sparse matrices.
317    
318            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
319            for sparse symmetric matrices.
320    
321            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
322            diagonal twice.
323    
324    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
325    
326            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
327            being applied to the x slot (detected by Brian Ripley).
328    
329    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
332    
333            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
334    
335    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * src/lgCMatrix.c (lgCMatrix_diag): new function
338            * R/lgCMatrix.R (diag): for new method
339    
340            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
341                 ==> construction of illegal "*gTMatrix" via new() should
342                 now be much less easy:
343            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
344    
345            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
346                    directly.
347            * man/Matrix.Rd: documents it.
348    
349    2006-07-06  Douglas Bates  <bates@R-project.org>
350    
351            * src/pedigree.c (pedigree_inbreeding): Correction in
352            initialization.  This function is not currently being used and is
353            not fully tested.
354    
355            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
356            Introduced the glmer class.  Added code for mcmcmsamp on glmer
357            objects.  Modified validity check on pedigree objects to account
358            for nonparallel patterns of missingness of parents.
359    
360            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
361            class.
362    
363    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/pMatrix.R: coercion pMatrix -> Tsparse
366    
367    2006-06-12  Douglas Bates  <bates@R-project.org>
368    
369            * DESCRIPTION (Version): 0.995-11 released to CRAN
370    
371            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
372            the output from mcmcsamp.
373    
374    2006-06-10  Douglas Bates  <bates@R-project.org>
375    
376            * R/lmer.R (simulestimate): added C code for calculating the trace
377            of the hat matrix.
378    
379    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
382            classes.
383            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
384    
385    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/dgTMatrix.R (colSums): etc. All four of
388            colSums(), rowSums(), colMeans(), rowMeans() now should work for
389            all "Matrices".
390    
391    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/lmer.R (panel.ci): Add a reference line at zero and a
394            background grid to the qqmath plot of ranef.lmer.
395    
396    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
397    
398            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
399            grouping factors to be specified in the formula as (1|foo/bar).
400    
401    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
402    
403            * R/lmer.R (findbars and others): Change check of is.numeric to
404            !is.language to resolve the bug reported by Jacob Wegelin.
405    
406            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
407            code to evaluate inbreeding coefficients without calculating T,
408            based on code in Sargolzaei and Iwaisaki's paper.
409    
410    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
413            generic and mer methods for isNested and denomDF. This denomDF was
414            an attempt to emulate that in lme but I don't think that makes
415            sense.  Use the trace of the hat matrix instead.
416    
417    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
420            the C code depending on a slot structure that's no longer valid.
421            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
422    
423    
424    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
425    
426            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
427            of lowerTriMatrix generic and methods to tril (also upper to triu)
428            and added a general band extractor.
429    
430    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
431    
432            * R/pedigree.R (pedigree): Replace sire and dam values outside the
433            allowable range with NAs. Added a corresponding check in the
434            validity check for the pedigree class.
435    
436            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
437            crossprod methods now inherits from symmetricMatrix.
438    
439    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
440    
441            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
442            generics lowerTriMatrix and upperTriMatrix along with methods for
443            the Csparse virtual class.  Also added a C function Csparse_band
444            that implements these methods by calling cholmod_band.
445    
446    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
449            erased when it was NULL.  This led to invalid subselections!
450    
451    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
452    
453            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
454            in method for "t" so as not to lose the unit diagonal property.
455    
456    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
457    
458            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
459            and methods.  This is now an option to the ranef method for the
460            mer class.
461    
462            * src/cs_utils.c: Ensure that the nz component is -1 for a
463            compressed column-oriented matrix.  Minor formatting cleanup.
464    
465            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
466            objects.
467    
468    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
471            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
472    
473    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
474    
475            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
476            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
477    
478            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
479            for the dtCMatrix class.
480    
481    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
482    
483            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
484            and methods for it.
485    
486    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
489            arguments, such that M %*% 1:6 now works
490            * Tests/matprod.R: test the above
491    
492    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
493    
494            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
495            the ranef.lmer class.
496    
497            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
498            methods to extract the posterior variances from the bVar slot.
499    
500    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
503            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
504    
505            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
506            * tests/simple: (extended)
507    
508            * R/sparseMatrix.R (isTriangular): now using much improved
509            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
510    
511    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
512    
513            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
514            (problem report from Franklin Parlamis).  This should be done
515            generally.
516    
517    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
520            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
521            update the plot methods.
522    
523    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
524    
525            * R/lmer.R (resid and ranef methods):  Added methods for the
526            "residuals" and "resid" generic but only for linear mixed model
527            fits.  Changed the ranef method to return a list of data frames so
528            that the plot methods now work.
529    
530    2006-03-16  Douglas Bates  <bates@bates2>
531    
532            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
533            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
534    
535            * DESCRIPTION (Date): New release
536    
537    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
540    
541            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
542            * man/KNex.Rd: and other help files
543            * tests/*.R: several ones needed adaption
544            * inst/doc/Comparisons.Rnw: ditto
545    
546    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
549    
550            * tests/indexing.R: tests for new [<- methods for sparse matrices.
551    
552    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
555    
556            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
557    
558    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/dMatrix.R: enable things like  M [ M < 10 ]
561            * R/dgeMatrix.R: implement it
562    
563    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/AllClass.R: define "summary.mer" and "*.lmer"
566            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
567            * R/lmer.R (show): now works with summary()
568    
569    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
572            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
573                    support the above
574    
575    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
576    
577            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
578            Use glmFit$prior.weights for weights in a glmm.
579            Allow an option usePQL = FALSE to skip the PQL steps for the
580            Laplace method (and, in time, the AGQ method).
581    
582            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
583            into a separate function internal_mer_Xfactor to be able to call
584            it from internal_bhat.
585    
586    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * tests/Class+Meth.R (tstMatrixClass): function for much better
589            testing; now again of all actual classes.
590    
591            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
592                    use macros and define make_d_matrix_* and make_i_matrix_*
593                    where _i_ is for the ldense routines:
594    
595            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
596            * src/ldense.c (lsyMatrix_as_lgeMatrix):
597    
598            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
599    
600    
601    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
604                    many different kinds of matrices.
605            * R/*.R: quite a few new methods were needed for R CMD check with
606                    new Matrix().  Very good for users playing around.
607    
608    
609    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * src/dgeMatrix.c (dMatrix_validate): new
612            * src/Mutils.c (dense_nonpacked_validate): new
613    
614            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
615    
616    
617    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
618    
619            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
620    
621    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
622    
623            * DESCRIPTION (Version): 0.99-6 released to CRAN
624    
625            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
626            segfault in cases with multiple non-nested grouping factors.
627    
628    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
631                    (Depends): also on 'utils'
632    
633            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
634            * R/diagMatrix.R (Diagonal): constructor and methods for
635            diagonal matrices
636    
637            * R/ltTMatrix.R: new "minimal methods"
638    
639    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
642            all methods (and help files).
643    
644    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
647                    for case (dimn.  op  no_dimn.)
648    
649    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * DESCRIPTION (Version): 0.99-2  released to CRAN
652    
653    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
654    
655            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
656            by Julian Faraway.
657    
658    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Auxiliaries.R (try_as): new utility
661            * R/sparseMatrix.R: use try_as() in coercion to original class
662    
663    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
666    
667    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/Auxiliaries.R (dimNamesCheck): added
670    
671            * R/Matrix.R (as.array), (as.vector): new
672    
673    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
674    
675            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
676                    default.
677            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
678                    "pMatrix" now contains "sparseMatrix"
679    
680    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * tests/Class+Meth.R: new tests; t(t(m)) == m
683    
684            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
685    
686            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
687            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
688    
689            * R/dspMatrix.R: typo in "t" method
690    
691    2005-09-18  Douglas Bates  <bates@wisc.edu>
692    
693            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
694            * R/Tsparse.R: instead of R/gTMatrix.R
695            * R/Csparse.R: new
696            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
697            * src/Tsparse.c: new; many trivial methods calling cholmod_()
698            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
699                            via cholmod
700    
701    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Auxiliaries.R (non0ind): new function using new C code
704            * src/dgCMatrix.c (compressed_non_0_ij): new utility
705    
706    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
707    
708            * src/chm_common.h: header file required by all C sources that
709            call CHOLMOD functions.  It defines a cholmod_common structure
710            called 'c' whose address is passed as the last argument to
711            (virtually) every CHOLMOD function.
712    
713            * src/Pattern.c: Simple example of the use of CHOLMOD.
714    
715            * src/init.c: initialize and finalize the cholmod_common structure.
716    
717            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
718            LDL and CCOLAMD from the U. of Florida sparse matrix library.
719    
720    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * inst/test-tools.R: new file collecting the utility functions used
723                    in ./tests/*.R
724    
725            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
726            * R/Matrix.R (cbind2): methods for NULL and missing
727    
728    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/AllClass.R: new "index" class for "[" and "[<-":
731                    First cut at "symmetricMatrix" and "triangularMatrix"
732            * R/gTMatrix.R (.ind.prep): new function;
733                    Logical and character indexing now work too.
734            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
735            * tests/indexing.R: new, including *.Rout.save
736            * tests/dgTMatrix.R: new
737    
738    2005-08-29  Douglas Bates  <bates@wisc.edu>
739    
740            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
741            indicator pos not being updated.  Also enforced upper triangular
742            for symmetric case.  Need to coerce edges component of elements of
743            edge list - grr! (Why don't they define their classes cleanly?)
744    
745    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Matrix.R:  added first "[<-" methods; not yet functional
748            * R/denseMatrix.R: ditto
749            * man/Subassign-methods.Rd: new help file for these
750    
751    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * DESCRIPTION (Version): 0.98-6
754    
755            * R/denseMatrix.R: new file for "[" fallback methods for all dense
756            matrices.
757    
758    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
761                    as( <logical>, "matrix")
762    
763            * R/pMatrix.R: coercion to "lgTMatrix"
764    
765            * R/gTMatrix.R: new virtual class to define "[" methods for.
766            * man/gTMatrix-class.Rd:
767            * General slight re-organization of where "[" methods are defined.
768              more to come.
769    
770    2005-08-18  Douglas Bates  <bates@wisc.edu>
771    
772            * DESCRIPTION (Version): 0.98-5  released to CRAN
773    
774            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
775            * .....
776    
777    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
778    
779            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
780            or glmer objects.
781    
782    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
785    
786    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
787    
788            * R/HBMM.R: finish re-writing R-only code.
789    
790    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
791    
792            * man/externalFormats.Rd: move documentation for writeHB and
793            writeMM here.
794    
795            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
796            (suggested by Paul Roecker).
797    
798            * tests/validObj.R (assertError): Comment out test that is failing
799            after recent changes in r-devel.
800    
801    
802    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * R/AllClass.R: intermediate virtual class "denseMatrix"
805            * man/denseMatrix-class.Rd
806            * NAMESPACE: export it, and also export
807            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
808    
809    2005-08-10  Douglas Bates  <bates@wisc.edu>
810    
811            * DESCRIPTION (Version): 0.98-3 to CRAN
812    
813            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
814            matrix_solve code (which was really, really wrong).
815    
816    2005-08-07  Douglas Bates  <bates@wisc.edu>
817    
818            * DESCRIPTION (Version): 0.98-2
819    
820            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
821    
822            * R/lmer.R (abbrvNms): new
823            * R/lmer.R (mcmcsamp): allow transformed parameters
824            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
825            for the Harwell-Boeing and the MatrixMarket formats.
826    
827    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * man/dtrMatrix-class.Rd: add examples
830            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
831    
832            * TODO: note the dtpMatrix (docu) bug
833    
834            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
835            in order to ensure that new as.matrix() is used by old functions,
836            e.g., svd(), qr(), eigen(), dist(),..;
837                  apply(), also matplot() or pairs().
838    
839    
840    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
843              add comments about 'control' / lmerControl() arguments
844    
845    2005-07-27  Douglas Bates  <bates@wisc.edu>
846    
847            * man/sleepstudy.Rd: Added the sleep data set.
848            * DESCRIPTION (Version): 0.98-1  released to CRAN
849    
850    2005-07-12  Douglas Bates  <bates@wisc.edu>
851            * man/sleepstudy.Rd: Added the sleep data set.
852    
853            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
854            .Call calls that were producing spurious output.
855    
856    2005-07-05  Douglas Bates  <bates@wisc.edu>
857    
858            * R/lmer.R (lmer): stored updated variance component estimates in
859            mer object for the generalized model.  (Bug reported by Renaud
860            Lancelot).
861    
862    2005-07-03  Douglas Bates  <bates@wisc.edu>
863    
864            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
865            unidimensional case.
866    
867    2005-06-08  Douglas Bates  <bates@wisc.edu>
868    
869            * DESCRIPTION (Version): 0.96-1
870    
871            * moved  lmer-class' R and C code moved from lme4 to here
872    
873    2005-06-04  Douglas Bates  <bates@wisc.edu>
874    
875            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
876            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
877    
878    2005-06-02  Douglas Bates  <bates@wisc.edu>
879    
880            * src/Makefile.win: Forgot to update this when Makefile changed.
881    
882    2005-05-11  Douglas Bates  <bates@wisc.edu>
883    
884            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
885            bug reported by Kurt Hornik and Michael Hahsler.
886    
887    2005-05-10  Douglas Bates  <bates@wisc.edu>
888    
889            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
890            logical sparse matrices.  These will also be used in the symbolic
891            analysis for lmer objects.
892    
893            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
894            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
895    
896    2005-05-06  Douglas Bates  <bates@wisc.edu>
897    
898            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
899            colMeans, colSums, rowMeans and rowSums.
900    
901    2005-04-18  Douglas Bates  <bates@wisc.edu>
902    
903            * src/lgCMatrix.[ch]: code for _validate method and stub for
904            multiplication operation.
905    
906            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
907            to dgetrs.
908    
909            * src/init.c: Fix cut-and-paste error in definition of
910            dgeMatrix_matrix_solve
911    
912            * src/{many files}: Tighten code by using ALLOC_SLOT.
913    
914    2005-04-15  Douglas Bates  <bates@wisc.edu>
915    
916            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
917    
918            * DESCRIPTION: Eliminate import of stats.
919    
920    
921    2005-04-06  Douglas Bates  <bates@wisc.edu>
922    
923            * R/AllClass.R : add logical sparse matrix classes
924    
925    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/dgTMatrix.R: add "[" method for triplet matrices
928            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
929    
930    2005-03-31  Douglas Bates  <bates@wisc.edu>
931    
932            * DESCRIPTION (Version): release 0.95-5 to CRAN
933    
934            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
935            * R/sparseMatrix.R: %*%, crossprod()
936            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
937            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
938            * src/lmer.c (lmer_fitted): fix thinko
939    
940    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * R/AllClass.R: add two virtual sparse classes ``on top''
943    
944    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
947                    correspondingly fix examples and tests/ since new()
948                    doesn't work for virtual classes.
949    
950    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/Matrix.R (as.matrix): method and one for unname()
953            * tests/dpoMatrix.R: tests should now be less platform dependent;
954              also run for R 2.1.0; using as.matrix()
955    
956    2005-03-15  Douglas Bates  <bates@wisc.edu>
957    
958            * R/pMatrix.R: "pMatrix" class added
959            * ....
960    
961    2005-03-14  Douglas Bates  <bates@wisc.edu>
962    
963            * R/dtpMatrix.R: Add unpack method and an example.
964    
965            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
966            of general symmetric matrices and associated S4 methods.
967    
968    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
969            +
970    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/dgeMatrix.R (setAs): and many other files: more coercion,
973              crossprod() and "%*%" methods added; tests, too.
974            * tests/matprod.R: new, for testing these
975    
976    2005-03-03  Douglas Bates  <bates@wisc.edu>
977    
978            * src/lmer.c (lmer_fitted): Added.
979    
980    2005-03-02  Douglas Bates  <bates@wisc.edu>
981    
982            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
983    
984    2005-02-28  Douglas Bates  <bates@wisc.edu>
985    
986            * src/*.c,po/,inst/po: Internationalization and localization of
987            the package.
988    
989            * src/ldl.[ch]: Removed these as their contents are referenced in the
990            R_ldl.c file.
991    
992            * src/flame.[ch]: Removed these source files.
993    
994            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
995    
996            * src/LU.[ch],src/init.c: absorb in factorizations
997    
998            * src/Mutils.h: prepare for internationalization
999    
1000            * src/cblas.h: move the enum definitions to Mutils.h and remove
1001            this file
1002    
1003    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1006    
1007            * R/dtrMatrix.R: fix t() method
1008    
1009            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1010            * NAMESPACE: export them (and import generics from "methods")
1011            * tests/group-methods.R : and test them.
1012    
1013            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1014            border case
1015    
1016    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1017    
1018            * DESCRIPTION (Version): 0.95-2  released to CRAN
1019    
1020            * src/dgBCMatrix.c:
1021            * src/lmer.c: many changes
1022            * ...
1023    
1024    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1025    
1026            * R/Matrix.R: add more sophisticated show() method.
1027    
1028    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1029    
1030            * */* : almost complete reorganization of classes.
1031    
1032    2005-01-26  Douglas Bates  <bates@wisc.edu>
1033    
1034            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1035            for the geMatrix class.
1036    
1037    2005-01-24  Douglas Bates  <bates@wisc.edu>
1038    
1039            * src/Makefile (clean): Remove *.a and *.so
1040    
1041            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1042    
1043    2005-01-23  Douglas Bates  <bates@wisc.edu>
1044    
1045            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1046            had an effect in cases with more than 2 grouping factors.
1047    
1048    2005-01-03  Douglas Bates  <bates@wisc.edu>
1049    
1050            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1051    
1052    2004-12-23  Douglas Bates  <bates@wisc.edu>
1053    
1054            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1055            and R_useDynamicSymbols (suggested by B.D.Ripley).
1056    
1057    2004-12-14  Douglas Bates  <bates@wisc.edu>
1058    
1059          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1060    
1061          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1062          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1063    
1064  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1065    
1066          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1067          no longer used.          no longer used.
# Line 17  Line 1073 
1073          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1074          Fixes part but not all of #15.          Fixes part but not all of #15.
1075    
1076  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1077    
1078          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1079          scalar grouping factors corrected.          scalar grouping factors corrected.
1080    
1081  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1082    
1083          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1084    
1085  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1086    
1087          * 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
1088          .h file can be included.          .h file can be included.
1089    
1090  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1091    
1092          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1093          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1094    
1095          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1096    
1097  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1098    
1099          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1100    
1101  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1102    
1103          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1104    
1105  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1106    
1107          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1108    
1109  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1110    
1111          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1112    
1113  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1114    
1115          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1116          routines.          routines.
1117    
1118  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1119    
1120          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1121    
1122  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1123    
1124          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1125    

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