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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1472, Fri Sep 1 15:31:04 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
4            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
5    
6            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
7    
8    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
11            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
12            * R/dsparseMatrix.R: dito
13            * R/Csparse.R: dito
14    
15    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/dMatrix.R (Compare): improve availability of "<", etc
18            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
19    
20    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
23            of a 0-index which was used as 1-index (..hmm)
24    
25            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
26    
27            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
28            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
29            (.is.diagonal): dito
30    
31            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
32    
33            * R/Matrix.R (Matrix): also work for NA data
34    
35    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
38            in all cases.
39    
40    2006-08-27  Douglas Bates  <bates@R-project.org>
41    
42            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
43            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
44    
45    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
48            subclasses of "ddenseMatrix"
49            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
50            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
51            instead of half dozen specialized ones.
52    
53    2006-08-25  Douglas Bates  <bates@R-project.org>
54    
55            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
56            <tillard@cirad.fr> - ordering standard errors to match effects.
57    
58    2006-08-24  Douglas Bates  <bates@R-project.org>
59    
60            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
61            on R_ldl.
62            * R/lCholCMatrix.R,
63            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
64            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
65            * many files in ./R and ./src: Use more general version of
66            dup_mMatrix_as_dgeMatrix to simplify method definitions.
67            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
68            dtpMatrix, dspMatrix and dppMatrix conversions.
69    
70    
71    2006-08-23  Douglas Bates  <bates@R-project.org>
72    
73            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
74            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
75            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
76            dgeMatrix_crossprod (may need to do this in other places).
77            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
78            generic and method for dsCMatrix.  Use CHOLMOD for chol().
79    
80    2006-08-22  Douglas Bates  <bates@R-project.org>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
83            types of classed Matrices, matrices or numeric or logical vectors.
84            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
85            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
86            to Mutils.h (as an inline) and change name to Matrix_check_class;
87            fixes in as_cholmod_factor and chm_factor_to_SEXP.
88            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
89            dsCMatrix_matrix_solve.  Comment out vestigial functions.
90            * src/Csparse.c: use diag_P and uplo_P macros.
91    
92    2006-08-21  Douglas Bates  <bates@R-project.org>
93    
94            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
95            valgrind.
96            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
97            inverses.
98            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
99            -Wall warnings.
100            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
101            Use dup_mMatrix_as_dgeMatrix.
102    
103    2006-08-20  Douglas Bates  <bates@R-project.org>
104    
105            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
106            * tests/sparseQR.R: Added
107            * man/sparseQR-class.Rd: Document methods for qr.* generics
108            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
109    
110    2006-08-19  Douglas Bates  <bates@R-project.org>
111    
112            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
113            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
114            and qr.fitted.
115            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
116            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
117    
118    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
121            the base version has no "..." argument.
122    
123            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
124    
125            * R/Matrix.R: define and
126            * NAMESPACE: export as.numeric() and as.logical() methods.
127                    Let's hope these do not badly slow down something...
128            Finally export the zapsmall() method.
129    
130    2006-08-17  Douglas Bates  <bates@R-project.org>
131    
132            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
133            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
134            * src/dtCMatrix.c :Remove code that is no longer used
135            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
136    
137    2006-08-14  Douglas Bates  <bates@R-project.org>
138    
139            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
140            Csparse_to_logical and Csparse_symmetric_to_general.
141            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
142            coercion methods between CsparseMatrix and TsparseMatrix.
143    
144    2006-08-14  Douglas Bates  <bates@R-project.org>
145    
146            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
147            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
148            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
149            possible.
150    
151    2006-08-12  Douglas Bates  <bates@R-project.org>
152    
153            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
154              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
155              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
156              generalize conversions between TsparseMatrix, CsparseMatrix,
157              denseMatrix and matrix.  Preserve triangularity property and
158              propagate Dimnames in the easy cases.
159    
160    2006-08-10  Douglas Bates  <bates@R-project.org>
161    
162            * src/lmer.c: adjust checks in glmer_init for S4SXP
163            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
164            before S4SXP but for the wrong reasons.
165    
166    2006-08-08  Douglas Bates  <bates@R-project.org>
167    
168            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
169            Later modified to return the upper triangle only.
170            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
171    
172    2006-08-07  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
175            R-level conversion to a sparse symmetric class.
176            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
177            Remove conversion to sparse symmetric classes (now done in C code).
178    
179    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
182            * man/band.Rd:  adapt the \dontshow{} unit test.
183    
184    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Version): 0.995-14  for CRAN
187    
188            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
189    
190            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
191            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
192    
193            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
194            * R/Tsparse.R (tril, triu, band): methods
195            * R/dgRMatrix.R (tril, ...):    ditto
196            * man/band.Rd:                  ditto
197    
198    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Matrix.R (head, tail): directly use utils:::head.matrix
201                    to be up-to-date automatically.
202    
203    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
206    
207            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
208            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
209            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
210            such that the S4 objects are always created by the current version
211            of R and 'Matrix' class definitions.
212    
213    2006-08-01  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (LMEoptimize method), tests/lmer.R,
216            inst/external/test3comp.rda: Added warnings for convergence on
217            boundary and test cases.
218    
219            * src/lmer.c (mer_postVar): Modified to return the variances that
220            are marginal to the fixed effects, not conditional on them (which
221            is what the bVar slot contents represent).
222    
223    2006-07-31  Douglas Bates  <bates@R-project.org>
224    
225            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
226            function which calls the C function mer_hat_trace2.
227    
228            * man/ranef.Rd: Include description of "postVar" argument and
229            producing a caterpillar plot.
230    
231    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * NAMESPACE:    change  "correlation" to "corMatrix"
234            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
235            * R/dpoMatrix.R: ditto
236            * R/lmer.R:      ditto
237    
238    2006-07-28  Douglas Bates  <bates@R-project.org>
239    
240            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
241            RZXinv slot's contents into a separate internal function that can
242            be used in mer_hat_trace.
243    
244    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
247            via new smart
248            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
249            utility functions.
250    
251    
252    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Csparse.R (tril, triu, band): do return *triangular* classed
255            matrices when appropriate; band() even symmetric ones.
256            (replCmat): extend to potentially all "CsparseMatrix"
257            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
258            allow subassignment for special sparse matrices.
259    
260            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
261    
262            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
263            argument; in glmer_*(): print only if(verbose).
264    
265            speed-optimize a few places by moving REAL(.) out of loops.
266    
267            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
268    
269    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
272                    since that wrongly triggers also for M[ logi , ]
273    
274            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
275            a symmetric matrix that results in a non-symmetric one.
276            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
277    
278            * R/dMatrix.R: make round(M) work as round(M, 0)
279    
280            * R/dgTMatrix.R (image): coordinate system and axis now use
281            1-based indices, not 0-based ones.
282    
283            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
284            * tests/indexing.R: test it.
285    
286            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
287            * man/isSymmetric-methods.Rd: and document it.
288    
289            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
290            * man/SparseM-conv.Rd: docu them
291    
292            * tests/other-pkgs.R: renamed from tests/graph.R and add example
293                    for 'SparseM' conversions
294    
295    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
296    
297            * R/Matrix.R (head): added head() and tail() methods.
298    
299    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * DESCRIPTION (Version): 0.995-12 released to CRAN
302    
303    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * tests/simple.R: add check for correct dsT -> dgT coercion;
306                    add check for correct printing of symmetric sparse matrices.
307    
308            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
309            for sparse symmetric matrices.
310    
311            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
312            diagonal twice.
313    
314    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
315    
316            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
317            being applied to the x slot (detected by Brian Ripley).
318    
319    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
322    
323            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
324    
325    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/lgCMatrix.c (lgCMatrix_diag): new function
328            * R/lgCMatrix.R (diag): for new method
329    
330            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
331                 ==> construction of illegal "*gTMatrix" via new() should
332                 now be much less easy:
333            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
334    
335            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
336                    directly.
337            * man/Matrix.Rd: documents it.
338    
339    2006-07-06  Douglas Bates  <bates@R-project.org>
340    
341            * src/pedigree.c (pedigree_inbreeding): Correction in
342            initialization.  This function is not currently being used and is
343            not fully tested.
344    
345            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
346            Introduced the glmer class.  Added code for mcmcmsamp on glmer
347            objects.  Modified validity check on pedigree objects to account
348            for nonparallel patterns of missingness of parents.
349    
350            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
351            class.
352    
353    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/pMatrix.R: coercion pMatrix -> Tsparse
356    
357    2006-06-12  Douglas Bates  <bates@R-project.org>
358    
359            * DESCRIPTION (Version): 0.995-11 released to CRAN
360    
361            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
362            the output from mcmcsamp.
363    
364    2006-06-10  Douglas Bates  <bates@R-project.org>
365    
366            * R/lmer.R (simulestimate): added C code for calculating the trace
367            of the hat matrix.
368    
369    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
372            classes.
373            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
374    
375    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/dgTMatrix.R (colSums): etc. All four of
378            colSums(), rowSums(), colMeans(), rowMeans() now should work for
379            all "Matrices".
380    
381    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * R/lmer.R (panel.ci): Add a reference line at zero and a
384            background grid to the qqmath plot of ranef.lmer.
385    
386    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
389            grouping factors to be specified in the formula as (1|foo/bar).
390    
391    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/lmer.R (findbars and others): Change check of is.numeric to
394            !is.language to resolve the bug reported by Jacob Wegelin.
395    
396            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
397            code to evaluate inbreeding coefficients without calculating T,
398            based on code in Sargolzaei and Iwaisaki's paper.
399    
400    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
401    
402            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
403            generic and mer methods for isNested and denomDF. This denomDF was
404            an attempt to emulate that in lme but I don't think that makes
405            sense.  Use the trace of the hat matrix instead.
406    
407    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
410            the C code depending on a slot structure that's no longer valid.
411            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
412    
413    
414    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
415    
416            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
417            of lowerTriMatrix generic and methods to tril (also upper to triu)
418            and added a general band extractor.
419    
420    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
421    
422            * R/pedigree.R (pedigree): Replace sire and dam values outside the
423            allowable range with NAs. Added a corresponding check in the
424            validity check for the pedigree class.
425    
426            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
427            crossprod methods now inherits from symmetricMatrix.
428    
429    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
430    
431            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
432            generics lowerTriMatrix and upperTriMatrix along with methods for
433            the Csparse virtual class.  Also added a C function Csparse_band
434            that implements these methods by calling cholmod_band.
435    
436    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
439            erased when it was NULL.  This led to invalid subselections!
440    
441    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
442    
443            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
444            in method for "t" so as not to lose the unit diagonal property.
445    
446    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
449            and methods.  This is now an option to the ranef method for the
450            mer class.
451    
452            * src/cs_utils.c: Ensure that the nz component is -1 for a
453            compressed column-oriented matrix.  Minor formatting cleanup.
454    
455            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
456            objects.
457    
458    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
461            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
462    
463    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
466            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
467    
468            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
469            for the dtCMatrix class.
470    
471    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
474            and methods for it.
475    
476    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
479            arguments, such that M %*% 1:6 now works
480            * Tests/matprod.R: test the above
481    
482    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
485            the ranef.lmer class.
486    
487            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
488            methods to extract the posterior variances from the bVar slot.
489    
490    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
493            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
494    
495            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
496            * tests/simple: (extended)
497    
498            * R/sparseMatrix.R (isTriangular): now using much improved
499            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
500    
501    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
504            (problem report from Franklin Parlamis).  This should be done
505            generally.
506    
507    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
510            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
511            update the plot methods.
512    
513    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/lmer.R (resid and ranef methods):  Added methods for the
516            "residuals" and "resid" generic but only for linear mixed model
517            fits.  Changed the ranef method to return a list of data frames so
518            that the plot methods now work.
519    
520    2006-03-16  Douglas Bates  <bates@bates2>
521    
522            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
523            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
524    
525            * DESCRIPTION (Date): New release
526    
527    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
530    
531            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
532            * man/KNex.Rd: and other help files
533            * tests/*.R: several ones needed adaption
534            * inst/doc/Comparisons.Rnw: ditto
535    
536    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
539    
540            * tests/indexing.R: tests for new [<- methods for sparse matrices.
541    
542    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
545    
546            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
547    
548    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/dMatrix.R: enable things like  M [ M < 10 ]
551            * R/dgeMatrix.R: implement it
552    
553    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/AllClass.R: define "summary.mer" and "*.lmer"
556            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
557            * R/lmer.R (show): now works with summary()
558    
559    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
562            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
563                    support the above
564    
565    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
566    
567            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
568            Use glmFit$prior.weights for weights in a glmm.
569            Allow an option usePQL = FALSE to skip the PQL steps for the
570            Laplace method (and, in time, the AGQ method).
571    
572            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
573            into a separate function internal_mer_Xfactor to be able to call
574            it from internal_bhat.
575    
576    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * tests/Class+Meth.R (tstMatrixClass): function for much better
579            testing; now again of all actual classes.
580    
581            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
582                    use macros and define make_d_matrix_* and make_i_matrix_*
583                    where _i_ is for the ldense routines:
584    
585            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
586            * src/ldense.c (lsyMatrix_as_lgeMatrix):
587    
588            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
589    
590    
591    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
594                    many different kinds of matrices.
595            * R/*.R: quite a few new methods were needed for R CMD check with
596                    new Matrix().  Very good for users playing around.
597    
598    
599    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * src/dgeMatrix.c (dMatrix_validate): new
602            * src/Mutils.c (dense_nonpacked_validate): new
603    
604            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
605    
606    
607    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
610    
611    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * DESCRIPTION (Version): 0.99-6 released to CRAN
614    
615            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
616            segfault in cases with multiple non-nested grouping factors.
617    
618    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
621                    (Depends): also on 'utils'
622    
623            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
624            * R/diagMatrix.R (Diagonal): constructor and methods for
625            diagonal matrices
626    
627            * R/ltTMatrix.R: new "minimal methods"
628    
629    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
632            all methods (and help files).
633    
634    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
637                    for case (dimn.  op  no_dimn.)
638    
639    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * DESCRIPTION (Version): 0.99-2  released to CRAN
642    
643    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
644    
645            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
646            by Julian Faraway.
647    
648    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/Auxiliaries.R (try_as): new utility
651            * R/sparseMatrix.R: use try_as() in coercion to original class
652    
653    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
656    
657    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Auxiliaries.R (dimNamesCheck): added
660    
661            * R/Matrix.R (as.array), (as.vector): new
662    
663    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
666                    default.
667            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
668                    "pMatrix" now contains "sparseMatrix"
669    
670    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * tests/Class+Meth.R: new tests; t(t(m)) == m
673    
674            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
675    
676            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
677            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
678    
679            * R/dspMatrix.R: typo in "t" method
680    
681    2005-09-18  Douglas Bates  <bates@wisc.edu>
682    
683            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
684            * R/Tsparse.R: instead of R/gTMatrix.R
685            * R/Csparse.R: new
686            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
687            * src/Tsparse.c: new; many trivial methods calling cholmod_()
688            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
689                            via cholmod
690    
691    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/Auxiliaries.R (non0ind): new function using new C code
694            * src/dgCMatrix.c (compressed_non_0_ij): new utility
695    
696    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
697    
698            * src/chm_common.h: header file required by all C sources that
699            call CHOLMOD functions.  It defines a cholmod_common structure
700            called 'c' whose address is passed as the last argument to
701            (virtually) every CHOLMOD function.
702    
703            * src/Pattern.c: Simple example of the use of CHOLMOD.
704    
705            * src/init.c: initialize and finalize the cholmod_common structure.
706    
707            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
708            LDL and CCOLAMD from the U. of Florida sparse matrix library.
709    
710    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * inst/test-tools.R: new file collecting the utility functions used
713                    in ./tests/*.R
714    
715            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
716            * R/Matrix.R (cbind2): methods for NULL and missing
717    
718    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/AllClass.R: new "index" class for "[" and "[<-":
721                    First cut at "symmetricMatrix" and "triangularMatrix"
722            * R/gTMatrix.R (.ind.prep): new function;
723                    Logical and character indexing now work too.
724            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
725            * tests/indexing.R: new, including *.Rout.save
726            * tests/dgTMatrix.R: new
727    
728    2005-08-29  Douglas Bates  <bates@wisc.edu>
729    
730            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
731            indicator pos not being updated.  Also enforced upper triangular
732            for symmetric case.  Need to coerce edges component of elements of
733            edge list - grr! (Why don't they define their classes cleanly?)
734    
735    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Matrix.R:  added first "[<-" methods; not yet functional
738            * R/denseMatrix.R: ditto
739            * man/Subassign-methods.Rd: new help file for these
740    
741    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * DESCRIPTION (Version): 0.98-6
744    
745            * R/denseMatrix.R: new file for "[" fallback methods for all dense
746            matrices.
747    
748    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
751                    as( <logical>, "matrix")
752    
753            * R/pMatrix.R: coercion to "lgTMatrix"
754    
755            * R/gTMatrix.R: new virtual class to define "[" methods for.
756            * man/gTMatrix-class.Rd:
757            * General slight re-organization of where "[" methods are defined.
758              more to come.
759    
760    2005-08-18  Douglas Bates  <bates@wisc.edu>
761    
762            * DESCRIPTION (Version): 0.98-5  released to CRAN
763    
764            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
765            * .....
766    
767    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
768    
769            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
770            or glmer objects.
771    
772    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
775    
776    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
777    
778            * R/HBMM.R: finish re-writing R-only code.
779    
780    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
781    
782            * man/externalFormats.Rd: move documentation for writeHB and
783            writeMM here.
784    
785            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
786            (suggested by Paul Roecker).
787    
788            * tests/validObj.R (assertError): Comment out test that is failing
789            after recent changes in r-devel.
790    
791    
792    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
793    
794            * R/AllClass.R: intermediate virtual class "denseMatrix"
795            * man/denseMatrix-class.Rd
796            * NAMESPACE: export it, and also export
797            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
798    
799    2005-08-10  Douglas Bates  <bates@wisc.edu>
800    
801            * DESCRIPTION (Version): 0.98-3 to CRAN
802    
803            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
804            matrix_solve code (which was really, really wrong).
805    
806    2005-08-07  Douglas Bates  <bates@wisc.edu>
807    
808            * DESCRIPTION (Version): 0.98-2
809    
810            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
811    
812            * R/lmer.R (abbrvNms): new
813            * R/lmer.R (mcmcsamp): allow transformed parameters
814            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
815            for the Harwell-Boeing and the MatrixMarket formats.
816    
817    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * man/dtrMatrix-class.Rd: add examples
820            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
821    
822            * TODO: note the dtpMatrix (docu) bug
823    
824            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
825            in order to ensure that new as.matrix() is used by old functions,
826            e.g., svd(), qr(), eigen(), dist(),..;
827                  apply(), also matplot() or pairs().
828    
829    
830    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
833              add comments about 'control' / lmerControl() arguments
834    
835    2005-07-27  Douglas Bates  <bates@wisc.edu>
836    
837            * man/sleepstudy.Rd: Added the sleep data set.
838            * DESCRIPTION (Version): 0.98-1  released to CRAN
839    
840    2005-07-12  Douglas Bates  <bates@wisc.edu>
841            * man/sleepstudy.Rd: Added the sleep data set.
842    
843            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
844            .Call calls that were producing spurious output.
845    
846    2005-07-05  Douglas Bates  <bates@wisc.edu>
847    
848            * R/lmer.R (lmer): stored updated variance component estimates in
849            mer object for the generalized model.  (Bug reported by Renaud
850            Lancelot).
851    
852    2005-07-03  Douglas Bates  <bates@wisc.edu>
853    
854            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
855            unidimensional case.
856    
857    2005-06-08  Douglas Bates  <bates@wisc.edu>
858    
859            * DESCRIPTION (Version): 0.96-1
860    
861            * moved  lmer-class' R and C code moved from lme4 to here
862    
863    2005-06-04  Douglas Bates  <bates@wisc.edu>
864    
865            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
866            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
867    
868    2005-06-02  Douglas Bates  <bates@wisc.edu>
869    
870            * src/Makefile.win: Forgot to update this when Makefile changed.
871    
872    2005-05-11  Douglas Bates  <bates@wisc.edu>
873    
874            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
875            bug reported by Kurt Hornik and Michael Hahsler.
876    
877    2005-05-10  Douglas Bates  <bates@wisc.edu>
878    
879            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
880            logical sparse matrices.  These will also be used in the symbolic
881            analysis for lmer objects.
882    
883            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
884            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
885    
886    2005-05-06  Douglas Bates  <bates@wisc.edu>
887    
888            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
889            colMeans, colSums, rowMeans and rowSums.
890    
891    2005-04-18  Douglas Bates  <bates@wisc.edu>
892    
893            * src/lgCMatrix.[ch]: code for _validate method and stub for
894            multiplication operation.
895    
896            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
897            to dgetrs.
898    
899            * src/init.c: Fix cut-and-paste error in definition of
900            dgeMatrix_matrix_solve
901    
902            * src/{many files}: Tighten code by using ALLOC_SLOT.
903    
904    2005-04-15  Douglas Bates  <bates@wisc.edu>
905    
906            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
907    
908            * DESCRIPTION: Eliminate import of stats.
909    
910    
911    2005-04-06  Douglas Bates  <bates@wisc.edu>
912    
913            * R/AllClass.R : add logical sparse matrix classes
914    
915    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/dgTMatrix.R: add "[" method for triplet matrices
918            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
919    
920    2005-03-31  Douglas Bates  <bates@wisc.edu>
921    
922            * DESCRIPTION (Version): release 0.95-5 to CRAN
923    
924            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
925            * R/sparseMatrix.R: %*%, crossprod()
926            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
927            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
928            * src/lmer.c (lmer_fitted): fix thinko
929    
930    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/AllClass.R: add two virtual sparse classes ``on top''
933    
934    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
937                    correspondingly fix examples and tests/ since new()
938                    doesn't work for virtual classes.
939    
940    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * R/Matrix.R (as.matrix): method and one for unname()
943            * tests/dpoMatrix.R: tests should now be less platform dependent;
944              also run for R 2.1.0; using as.matrix()
945    
946    2005-03-15  Douglas Bates  <bates@wisc.edu>
947    
948            * R/pMatrix.R: "pMatrix" class added
949            * ....
950    
951    2005-03-14  Douglas Bates  <bates@wisc.edu>
952    
953            * R/dtpMatrix.R: Add unpack method and an example.
954    
955            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
956            of general symmetric matrices and associated S4 methods.
957    
958    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
959            +
960    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * R/dgeMatrix.R (setAs): and many other files: more coercion,
963              crossprod() and "%*%" methods added; tests, too.
964            * tests/matprod.R: new, for testing these
965    
966    2005-03-03  Douglas Bates  <bates@wisc.edu>
967    
968            * src/lmer.c (lmer_fitted): Added.
969    
970    2005-03-02  Douglas Bates  <bates@wisc.edu>
971    
972            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
973    
974    2005-02-28  Douglas Bates  <bates@wisc.edu>
975    
976            * src/*.c,po/,inst/po: Internationalization and localization of
977            the package.
978    
979            * src/ldl.[ch]: Removed these as their contents are referenced in the
980            R_ldl.c file.
981    
982            * src/flame.[ch]: Removed these source files.
983    
984            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
985    
986            * src/LU.[ch],src/init.c: absorb in factorizations
987    
988            * src/Mutils.h: prepare for internationalization
989    
990            * src/cblas.h: move the enum definitions to Mutils.h and remove
991            this file
992    
993    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
996    
997            * R/dtrMatrix.R: fix t() method
998    
999            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1000            * NAMESPACE: export them (and import generics from "methods")
1001            * tests/group-methods.R : and test them.
1002    
1003            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1004            border case
1005    
1006    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1007    
1008            * DESCRIPTION (Version): 0.95-2  released to CRAN
1009    
1010            * src/dgBCMatrix.c:
1011            * src/lmer.c: many changes
1012            * ...
1013    
1014    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Matrix.R: add more sophisticated show() method.
1017    
1018    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1019    
1020            * */* : almost complete reorganization of classes.
1021    
1022    2005-01-26  Douglas Bates  <bates@wisc.edu>
1023    
1024            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1025            for the geMatrix class.
1026    
1027    2005-01-24  Douglas Bates  <bates@wisc.edu>
1028    
1029            * src/Makefile (clean): Remove *.a and *.so
1030    
1031            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1032    
1033    2005-01-23  Douglas Bates  <bates@wisc.edu>
1034    
1035            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1036            had an effect in cases with more than 2 grouping factors.
1037    
1038    2005-01-03  Douglas Bates  <bates@wisc.edu>
1039    
1040            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1041    
1042    2004-12-23  Douglas Bates  <bates@wisc.edu>
1043    
1044            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1045            and R_useDynamicSymbols (suggested by B.D.Ripley).
1046    
1047    2004-12-14  Douglas Bates  <bates@wisc.edu>
1048    
1049          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1050    
1051          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1052          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1053    
1054  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1055    
1056          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1057          no longer used.          no longer used.
# Line 17  Line 1063 
1063          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1064          Fixes part but not all of #15.          Fixes part but not all of #15.
1065    
1066  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1067    
1068          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1069          scalar grouping factors corrected.          scalar grouping factors corrected.
1070    
1071  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1072    
1073          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1074    
1075  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1076    
1077          * 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
1078          .h file can be included.          .h file can be included.
1079    
1080  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1081    
1082          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1083          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1084    
1085          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1086    
1087  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1088    
1089          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1090    
1091  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1092    
1093          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1094    
1095  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1096    
1097          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1098    
1099  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1100    
1101          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1102    
1103  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1104    
1105          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1106          routines.          routines.
1107    
1108  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1109    
1110          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1111    
1112  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1113    
1114          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1115    

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