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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1475, Fri Sep 1 22:35:59 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-09-01  Douglas Bates  <bates@R-project.org>
2    
3            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
4    
5    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
8            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
9    
10            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
11    
12    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
15            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
16            * R/dsparseMatrix.R: dito
17            * R/Csparse.R: dito
18    
19    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dMatrix.R (Compare): improve availability of "<", etc
22            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
23    
24    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
27            of a 0-index which was used as 1-index (..hmm)
28    
29            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
30    
31            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
32            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
33            (.is.diagonal): dito
34    
35            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
36    
37            * R/Matrix.R (Matrix): also work for NA data
38    
39    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
42            in all cases.
43    
44    2006-08-27  Douglas Bates  <bates@R-project.org>
45    
46            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
47            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
48    
49    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
52            subclasses of "ddenseMatrix"
53            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
54            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
55            instead of half dozen specialized ones.
56    
57    2006-08-25  Douglas Bates  <bates@R-project.org>
58    
59            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
60            <tillard@cirad.fr> - ordering standard errors to match effects.
61    
62    2006-08-24  Douglas Bates  <bates@R-project.org>
63    
64            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
65            on R_ldl.
66            * R/lCholCMatrix.R,
67            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
68            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
69            * many files in ./R and ./src: Use more general version of
70            dup_mMatrix_as_dgeMatrix to simplify method definitions.
71            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
72            dtpMatrix, dspMatrix and dppMatrix conversions.
73    
74    
75    2006-08-23  Douglas Bates  <bates@R-project.org>
76    
77            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
78            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
79            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
80            dgeMatrix_crossprod (may need to do this in other places).
81            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
82            generic and method for dsCMatrix.  Use CHOLMOD for chol().
83    
84    2006-08-22  Douglas Bates  <bates@R-project.org>
85    
86            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
87            types of classed Matrices, matrices or numeric or logical vectors.
88            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
89            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
90            to Mutils.h (as an inline) and change name to Matrix_check_class;
91            fixes in as_cholmod_factor and chm_factor_to_SEXP.
92            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
93            dsCMatrix_matrix_solve.  Comment out vestigial functions.
94            * src/Csparse.c: use diag_P and uplo_P macros.
95    
96    2006-08-21  Douglas Bates  <bates@R-project.org>
97    
98            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
99            valgrind.
100            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
101            inverses.
102            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
103            -Wall warnings.
104            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
105            Use dup_mMatrix_as_dgeMatrix.
106    
107    2006-08-20  Douglas Bates  <bates@R-project.org>
108    
109            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
110            * tests/sparseQR.R: Added
111            * man/sparseQR-class.Rd: Document methods for qr.* generics
112            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
113    
114    2006-08-19  Douglas Bates  <bates@R-project.org>
115    
116            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
117            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
118            and qr.fitted.
119            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
120            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
121    
122    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
125            the base version has no "..." argument.
126    
127            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
128    
129            * R/Matrix.R: define and
130            * NAMESPACE: export as.numeric() and as.logical() methods.
131                    Let's hope these do not badly slow down something...
132            Finally export the zapsmall() method.
133    
134    2006-08-17  Douglas Bates  <bates@R-project.org>
135    
136            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
137            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
138            * src/dtCMatrix.c :Remove code that is no longer used
139            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
140    
141    2006-08-14  Douglas Bates  <bates@R-project.org>
142    
143            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
144            Csparse_to_logical and Csparse_symmetric_to_general.
145            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
146            coercion methods between CsparseMatrix and TsparseMatrix.
147    
148    2006-08-14  Douglas Bates  <bates@R-project.org>
149    
150            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
151            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
152            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
153            possible.
154    
155    2006-08-12  Douglas Bates  <bates@R-project.org>
156    
157            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
158              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
159              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
160              generalize conversions between TsparseMatrix, CsparseMatrix,
161              denseMatrix and matrix.  Preserve triangularity property and
162              propagate Dimnames in the easy cases.
163    
164    2006-08-10  Douglas Bates  <bates@R-project.org>
165    
166            * src/lmer.c: adjust checks in glmer_init for S4SXP
167            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
168            before S4SXP but for the wrong reasons.
169    
170    2006-08-08  Douglas Bates  <bates@R-project.org>
171    
172            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
173            Later modified to return the upper triangle only.
174            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
175    
176    2006-08-07  Douglas Bates  <bates@R-project.org>
177    
178            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
179            R-level conversion to a sparse symmetric class.
180            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
181            Remove conversion to sparse symmetric classes (now done in C code).
182    
183    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
186            * man/band.Rd:  adapt the \dontshow{} unit test.
187    
188    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version): 0.995-14  for CRAN
191    
192            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
193    
194            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
195            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
196    
197            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
198            * R/Tsparse.R (tril, triu, band): methods
199            * R/dgRMatrix.R (tril, ...):    ditto
200            * man/band.Rd:                  ditto
201    
202    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Matrix.R (head, tail): directly use utils:::head.matrix
205                    to be up-to-date automatically.
206    
207    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
210    
211            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
212            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
213            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
214            such that the S4 objects are always created by the current version
215            of R and 'Matrix' class definitions.
216    
217    2006-08-01  Douglas Bates  <bates@R-project.org>
218    
219            * R/lmer.R (LMEoptimize method), tests/lmer.R,
220            inst/external/test3comp.rda: Added warnings for convergence on
221            boundary and test cases.
222    
223            * src/lmer.c (mer_postVar): Modified to return the variances that
224            are marginal to the fixed effects, not conditional on them (which
225            is what the bVar slot contents represent).
226    
227    2006-07-31  Douglas Bates  <bates@R-project.org>
228    
229            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
230            function which calls the C function mer_hat_trace2.
231    
232            * man/ranef.Rd: Include description of "postVar" argument and
233            producing a caterpillar plot.
234    
235    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * NAMESPACE:    change  "correlation" to "corMatrix"
238            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
239            * R/dpoMatrix.R: ditto
240            * R/lmer.R:      ditto
241    
242    2006-07-28  Douglas Bates  <bates@R-project.org>
243    
244            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
245            RZXinv slot's contents into a separate internal function that can
246            be used in mer_hat_trace.
247    
248    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
251            via new smart
252            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
253            utility functions.
254    
255    
256    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Csparse.R (tril, triu, band): do return *triangular* classed
259            matrices when appropriate; band() even symmetric ones.
260            (replCmat): extend to potentially all "CsparseMatrix"
261            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
262            allow subassignment for special sparse matrices.
263    
264            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
265    
266            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
267            argument; in glmer_*(): print only if(verbose).
268    
269            speed-optimize a few places by moving REAL(.) out of loops.
270    
271            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
272    
273    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
276                    since that wrongly triggers also for M[ logi , ]
277    
278            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
279            a symmetric matrix that results in a non-symmetric one.
280            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
281    
282            * R/dMatrix.R: make round(M) work as round(M, 0)
283    
284            * R/dgTMatrix.R (image): coordinate system and axis now use
285            1-based indices, not 0-based ones.
286    
287            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
288            * tests/indexing.R: test it.
289    
290            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
291            * man/isSymmetric-methods.Rd: and document it.
292    
293            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
294            * man/SparseM-conv.Rd: docu them
295    
296            * tests/other-pkgs.R: renamed from tests/graph.R and add example
297                    for 'SparseM' conversions
298    
299    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
300    
301            * R/Matrix.R (head): added head() and tail() methods.
302    
303    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * DESCRIPTION (Version): 0.995-12 released to CRAN
306    
307    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * tests/simple.R: add check for correct dsT -> dgT coercion;
310                    add check for correct printing of symmetric sparse matrices.
311    
312            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
313            for sparse symmetric matrices.
314    
315            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
316            diagonal twice.
317    
318    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
319    
320            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
321            being applied to the x slot (detected by Brian Ripley).
322    
323    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
326    
327            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
328    
329    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/lgCMatrix.c (lgCMatrix_diag): new function
332            * R/lgCMatrix.R (diag): for new method
333    
334            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
335                 ==> construction of illegal "*gTMatrix" via new() should
336                 now be much less easy:
337            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
338    
339            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
340                    directly.
341            * man/Matrix.Rd: documents it.
342    
343    2006-07-06  Douglas Bates  <bates@R-project.org>
344    
345            * src/pedigree.c (pedigree_inbreeding): Correction in
346            initialization.  This function is not currently being used and is
347            not fully tested.
348    
349            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
350            Introduced the glmer class.  Added code for mcmcmsamp on glmer
351            objects.  Modified validity check on pedigree objects to account
352            for nonparallel patterns of missingness of parents.
353    
354            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
355            class.
356    
357    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/pMatrix.R: coercion pMatrix -> Tsparse
360    
361    2006-06-12  Douglas Bates  <bates@R-project.org>
362    
363            * DESCRIPTION (Version): 0.995-11 released to CRAN
364    
365            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
366            the output from mcmcsamp.
367    
368    2006-06-10  Douglas Bates  <bates@R-project.org>
369    
370            * R/lmer.R (simulestimate): added C code for calculating the trace
371            of the hat matrix.
372    
373    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
376            classes.
377            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
378    
379    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/dgTMatrix.R (colSums): etc. All four of
382            colSums(), rowSums(), colMeans(), rowMeans() now should work for
383            all "Matrices".
384    
385    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * R/lmer.R (panel.ci): Add a reference line at zero and a
388            background grid to the qqmath plot of ranef.lmer.
389    
390    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
393            grouping factors to be specified in the formula as (1|foo/bar).
394    
395    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
396    
397            * R/lmer.R (findbars and others): Change check of is.numeric to
398            !is.language to resolve the bug reported by Jacob Wegelin.
399    
400            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
401            code to evaluate inbreeding coefficients without calculating T,
402            based on code in Sargolzaei and Iwaisaki's paper.
403    
404    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
405    
406            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
407            generic and mer methods for isNested and denomDF. This denomDF was
408            an attempt to emulate that in lme but I don't think that makes
409            sense.  Use the trace of the hat matrix instead.
410    
411    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
414            the C code depending on a slot structure that's no longer valid.
415            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
416    
417    
418    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
419    
420            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
421            of lowerTriMatrix generic and methods to tril (also upper to triu)
422            and added a general band extractor.
423    
424    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
425    
426            * R/pedigree.R (pedigree): Replace sire and dam values outside the
427            allowable range with NAs. Added a corresponding check in the
428            validity check for the pedigree class.
429    
430            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
431            crossprod methods now inherits from symmetricMatrix.
432    
433    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
436            generics lowerTriMatrix and upperTriMatrix along with methods for
437            the Csparse virtual class.  Also added a C function Csparse_band
438            that implements these methods by calling cholmod_band.
439    
440    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
443            erased when it was NULL.  This led to invalid subselections!
444    
445    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
446    
447            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
448            in method for "t" so as not to lose the unit diagonal property.
449    
450    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
453            and methods.  This is now an option to the ranef method for the
454            mer class.
455    
456            * src/cs_utils.c: Ensure that the nz component is -1 for a
457            compressed column-oriented matrix.  Minor formatting cleanup.
458    
459            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
460            objects.
461    
462    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
465            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
466    
467    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
470            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
471    
472            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
473            for the dtCMatrix class.
474    
475    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
476    
477            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
478            and methods for it.
479    
480    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
483            arguments, such that M %*% 1:6 now works
484            * Tests/matprod.R: test the above
485    
486    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
489            the ranef.lmer class.
490    
491            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
492            methods to extract the posterior variances from the bVar slot.
493    
494    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
497            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
498    
499            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
500            * tests/simple: (extended)
501    
502            * R/sparseMatrix.R (isTriangular): now using much improved
503            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
504    
505    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
506    
507            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
508            (problem report from Franklin Parlamis).  This should be done
509            generally.
510    
511    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
512    
513            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
514            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
515            update the plot methods.
516    
517    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * R/lmer.R (resid and ranef methods):  Added methods for the
520            "residuals" and "resid" generic but only for linear mixed model
521            fits.  Changed the ranef method to return a list of data frames so
522            that the plot methods now work.
523    
524    2006-03-16  Douglas Bates  <bates@bates2>
525    
526            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
527            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
528    
529            * DESCRIPTION (Date): New release
530    
531    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
534    
535            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
536            * man/KNex.Rd: and other help files
537            * tests/*.R: several ones needed adaption
538            * inst/doc/Comparisons.Rnw: ditto
539    
540    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
543    
544            * tests/indexing.R: tests for new [<- methods for sparse matrices.
545    
546    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
549    
550            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
551    
552    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/dMatrix.R: enable things like  M [ M < 10 ]
555            * R/dgeMatrix.R: implement it
556    
557    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/AllClass.R: define "summary.mer" and "*.lmer"
560            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
561            * R/lmer.R (show): now works with summary()
562    
563    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
566            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
567                    support the above
568    
569    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
570    
571            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
572            Use glmFit$prior.weights for weights in a glmm.
573            Allow an option usePQL = FALSE to skip the PQL steps for the
574            Laplace method (and, in time, the AGQ method).
575    
576            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
577            into a separate function internal_mer_Xfactor to be able to call
578            it from internal_bhat.
579    
580    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * tests/Class+Meth.R (tstMatrixClass): function for much better
583            testing; now again of all actual classes.
584    
585            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
586                    use macros and define make_d_matrix_* and make_i_matrix_*
587                    where _i_ is for the ldense routines:
588    
589            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
590            * src/ldense.c (lsyMatrix_as_lgeMatrix):
591    
592            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
593    
594    
595    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
598                    many different kinds of matrices.
599            * R/*.R: quite a few new methods were needed for R CMD check with
600                    new Matrix().  Very good for users playing around.
601    
602    
603    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * src/dgeMatrix.c (dMatrix_validate): new
606            * src/Mutils.c (dense_nonpacked_validate): new
607    
608            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
609    
610    
611    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
614    
615    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
616    
617            * DESCRIPTION (Version): 0.99-6 released to CRAN
618    
619            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
620            segfault in cases with multiple non-nested grouping factors.
621    
622    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
625                    (Depends): also on 'utils'
626    
627            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
628            * R/diagMatrix.R (Diagonal): constructor and methods for
629            diagonal matrices
630    
631            * R/ltTMatrix.R: new "minimal methods"
632    
633    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
636            all methods (and help files).
637    
638    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
641                    for case (dimn.  op  no_dimn.)
642    
643    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
644    
645            * DESCRIPTION (Version): 0.99-2  released to CRAN
646    
647    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
648    
649            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
650            by Julian Faraway.
651    
652    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/Auxiliaries.R (try_as): new utility
655            * R/sparseMatrix.R: use try_as() in coercion to original class
656    
657    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
660    
661    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Auxiliaries.R (dimNamesCheck): added
664    
665            * R/Matrix.R (as.array), (as.vector): new
666    
667    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
670                    default.
671            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
672                    "pMatrix" now contains "sparseMatrix"
673    
674    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * tests/Class+Meth.R: new tests; t(t(m)) == m
677    
678            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
679    
680            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
681            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
682    
683            * R/dspMatrix.R: typo in "t" method
684    
685    2005-09-18  Douglas Bates  <bates@wisc.edu>
686    
687            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
688            * R/Tsparse.R: instead of R/gTMatrix.R
689            * R/Csparse.R: new
690            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
691            * src/Tsparse.c: new; many trivial methods calling cholmod_()
692            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
693                            via cholmod
694    
695    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/Auxiliaries.R (non0ind): new function using new C code
698            * src/dgCMatrix.c (compressed_non_0_ij): new utility
699    
700    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
701    
702            * src/chm_common.h: header file required by all C sources that
703            call CHOLMOD functions.  It defines a cholmod_common structure
704            called 'c' whose address is passed as the last argument to
705            (virtually) every CHOLMOD function.
706    
707            * src/Pattern.c: Simple example of the use of CHOLMOD.
708    
709            * src/init.c: initialize and finalize the cholmod_common structure.
710    
711            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
712            LDL and CCOLAMD from the U. of Florida sparse matrix library.
713    
714    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * inst/test-tools.R: new file collecting the utility functions used
717                    in ./tests/*.R
718    
719            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
720            * R/Matrix.R (cbind2): methods for NULL and missing
721    
722    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/AllClass.R: new "index" class for "[" and "[<-":
725                    First cut at "symmetricMatrix" and "triangularMatrix"
726            * R/gTMatrix.R (.ind.prep): new function;
727                    Logical and character indexing now work too.
728            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
729            * tests/indexing.R: new, including *.Rout.save
730            * tests/dgTMatrix.R: new
731    
732    2005-08-29  Douglas Bates  <bates@wisc.edu>
733    
734            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
735            indicator pos not being updated.  Also enforced upper triangular
736            for symmetric case.  Need to coerce edges component of elements of
737            edge list - grr! (Why don't they define their classes cleanly?)
738    
739    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/Matrix.R:  added first "[<-" methods; not yet functional
742            * R/denseMatrix.R: ditto
743            * man/Subassign-methods.Rd: new help file for these
744    
745    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * DESCRIPTION (Version): 0.98-6
748    
749            * R/denseMatrix.R: new file for "[" fallback methods for all dense
750            matrices.
751    
752    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
755                    as( <logical>, "matrix")
756    
757            * R/pMatrix.R: coercion to "lgTMatrix"
758    
759            * R/gTMatrix.R: new virtual class to define "[" methods for.
760            * man/gTMatrix-class.Rd:
761            * General slight re-organization of where "[" methods are defined.
762              more to come.
763    
764    2005-08-18  Douglas Bates  <bates@wisc.edu>
765    
766            * DESCRIPTION (Version): 0.98-5  released to CRAN
767    
768            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
769            * .....
770    
771    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
772    
773            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
774            or glmer objects.
775    
776    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
779    
780    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
781    
782            * R/HBMM.R: finish re-writing R-only code.
783    
784    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
785    
786            * man/externalFormats.Rd: move documentation for writeHB and
787            writeMM here.
788    
789            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
790            (suggested by Paul Roecker).
791    
792            * tests/validObj.R (assertError): Comment out test that is failing
793            after recent changes in r-devel.
794    
795    
796    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/AllClass.R: intermediate virtual class "denseMatrix"
799            * man/denseMatrix-class.Rd
800            * NAMESPACE: export it, and also export
801            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
802    
803    2005-08-10  Douglas Bates  <bates@wisc.edu>
804    
805            * DESCRIPTION (Version): 0.98-3 to CRAN
806    
807            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
808            matrix_solve code (which was really, really wrong).
809    
810    2005-08-07  Douglas Bates  <bates@wisc.edu>
811    
812            * DESCRIPTION (Version): 0.98-2
813    
814            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
815    
816            * R/lmer.R (abbrvNms): new
817            * R/lmer.R (mcmcsamp): allow transformed parameters
818            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
819            for the Harwell-Boeing and the MatrixMarket formats.
820    
821    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * man/dtrMatrix-class.Rd: add examples
824            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
825    
826            * TODO: note the dtpMatrix (docu) bug
827    
828            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
829            in order to ensure that new as.matrix() is used by old functions,
830            e.g., svd(), qr(), eigen(), dist(),..;
831                  apply(), also matplot() or pairs().
832    
833    
834    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
837              add comments about 'control' / lmerControl() arguments
838    
839    2005-07-27  Douglas Bates  <bates@wisc.edu>
840    
841            * man/sleepstudy.Rd: Added the sleep data set.
842            * DESCRIPTION (Version): 0.98-1  released to CRAN
843    
844    2005-07-12  Douglas Bates  <bates@wisc.edu>
845            * man/sleepstudy.Rd: Added the sleep data set.
846    
847            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
848            .Call calls that were producing spurious output.
849    
850    2005-07-05  Douglas Bates  <bates@wisc.edu>
851    
852            * R/lmer.R (lmer): stored updated variance component estimates in
853            mer object for the generalized model.  (Bug reported by Renaud
854            Lancelot).
855    
856    2005-07-03  Douglas Bates  <bates@wisc.edu>
857    
858            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
859            unidimensional case.
860    
861    2005-06-08  Douglas Bates  <bates@wisc.edu>
862    
863            * DESCRIPTION (Version): 0.96-1
864    
865            * moved  lmer-class' R and C code moved from lme4 to here
866    
867    2005-06-04  Douglas Bates  <bates@wisc.edu>
868    
869            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
870            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
871    
872    2005-06-02  Douglas Bates  <bates@wisc.edu>
873    
874            * src/Makefile.win: Forgot to update this when Makefile changed.
875    
876    2005-05-11  Douglas Bates  <bates@wisc.edu>
877    
878            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
879            bug reported by Kurt Hornik and Michael Hahsler.
880    
881    2005-05-10  Douglas Bates  <bates@wisc.edu>
882    
883            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
884            logical sparse matrices.  These will also be used in the symbolic
885            analysis for lmer objects.
886    
887            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
888            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
889    
890    2005-05-06  Douglas Bates  <bates@wisc.edu>
891    
892            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
893            colMeans, colSums, rowMeans and rowSums.
894    
895    2005-04-18  Douglas Bates  <bates@wisc.edu>
896    
897            * src/lgCMatrix.[ch]: code for _validate method and stub for
898            multiplication operation.
899    
900            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
901            to dgetrs.
902    
903            * src/init.c: Fix cut-and-paste error in definition of
904            dgeMatrix_matrix_solve
905    
906            * src/{many files}: Tighten code by using ALLOC_SLOT.
907    
908    2005-04-15  Douglas Bates  <bates@wisc.edu>
909    
910            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
911    
912            * DESCRIPTION: Eliminate import of stats.
913    
914    
915    2005-04-06  Douglas Bates  <bates@wisc.edu>
916    
917            * R/AllClass.R : add logical sparse matrix classes
918    
919    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/dgTMatrix.R: add "[" method for triplet matrices
922            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
923    
924    2005-03-31  Douglas Bates  <bates@wisc.edu>
925    
926            * DESCRIPTION (Version): release 0.95-5 to CRAN
927    
928            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
929            * R/sparseMatrix.R: %*%, crossprod()
930            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
931            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
932            * src/lmer.c (lmer_fitted): fix thinko
933    
934    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/AllClass.R: add two virtual sparse classes ``on top''
937    
938    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
941                    correspondingly fix examples and tests/ since new()
942                    doesn't work for virtual classes.
943    
944    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/Matrix.R (as.matrix): method and one for unname()
947            * tests/dpoMatrix.R: tests should now be less platform dependent;
948              also run for R 2.1.0; using as.matrix()
949    
950    2005-03-15  Douglas Bates  <bates@wisc.edu>
951    
952            * R/pMatrix.R: "pMatrix" class added
953            * ....
954    
955    2005-03-14  Douglas Bates  <bates@wisc.edu>
956    
957            * R/dtpMatrix.R: Add unpack method and an example.
958    
959            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
960            of general symmetric matrices and associated S4 methods.
961    
962    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
963            +
964    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/dgeMatrix.R (setAs): and many other files: more coercion,
967              crossprod() and "%*%" methods added; tests, too.
968            * tests/matprod.R: new, for testing these
969    
970    2005-03-03  Douglas Bates  <bates@wisc.edu>
971    
972            * src/lmer.c (lmer_fitted): Added.
973    
974    2005-03-02  Douglas Bates  <bates@wisc.edu>
975    
976            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
977    
978    2005-02-28  Douglas Bates  <bates@wisc.edu>
979    
980            * src/*.c,po/,inst/po: Internationalization and localization of
981            the package.
982    
983            * src/ldl.[ch]: Removed these as their contents are referenced in the
984            R_ldl.c file.
985    
986            * src/flame.[ch]: Removed these source files.
987    
988            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
989    
990            * src/LU.[ch],src/init.c: absorb in factorizations
991    
992            * src/Mutils.h: prepare for internationalization
993    
994            * src/cblas.h: move the enum definitions to Mutils.h and remove
995            this file
996    
997    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1000    
1001            * R/dtrMatrix.R: fix t() method
1002    
1003            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1004            * NAMESPACE: export them (and import generics from "methods")
1005            * tests/group-methods.R : and test them.
1006    
1007            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1008            border case
1009    
1010    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1011    
1012            * DESCRIPTION (Version): 0.95-2  released to CRAN
1013    
1014            * src/dgBCMatrix.c:
1015            * src/lmer.c: many changes
1016            * ...
1017    
1018    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/Matrix.R: add more sophisticated show() method.
1021    
1022    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1023    
1024            * */* : almost complete reorganization of classes.
1025    
1026    2005-01-26  Douglas Bates  <bates@wisc.edu>
1027    
1028            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1029            for the geMatrix class.
1030    
1031    2005-01-24  Douglas Bates  <bates@wisc.edu>
1032    
1033            * src/Makefile (clean): Remove *.a and *.so
1034    
1035            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1036    
1037    2005-01-23  Douglas Bates  <bates@wisc.edu>
1038    
1039            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1040            had an effect in cases with more than 2 grouping factors.
1041    
1042    2005-01-03  Douglas Bates  <bates@wisc.edu>
1043    
1044            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1045    
1046    2004-12-23  Douglas Bates  <bates@wisc.edu>
1047    
1048            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1049            and R_useDynamicSymbols (suggested by B.D.Ripley).
1050    
1051    2004-12-14  Douglas Bates  <bates@wisc.edu>
1052    
1053            * R/sscMatrix.R: Add determinant methods
1054    
1055            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1056            for tripletMatrix to matrix.
1057    
1058    2004-12-13  Douglas Bates  <bates@wisc.edu>
1059    
1060            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1061            no longer used.
1062    
1063            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1064            with dynamic allocation of scratch arrays.
1065    
1066            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1067            for multivariate random effects with multiple grouping factors.
1068            Fixes part but not all of #15.
1069    
1070    2004-12-03  Douglas Bates  <bates@wisc.edu>
1071    
1072            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1073            scalar grouping factors corrected.
1074    
1075    2004-11-29  Douglas Bates  <bates@wisc.edu>
1076    
1077            * src/bCrosstab.c: remove diag_update which is no longer used
1078    
1079    2004-11-16  Douglas Bates  <bates@wisc.edu>
1080    
1081          * 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
1082          .h file can be included.          .h file can be included.
1083    
1084  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1085    
1086          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1087          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1088    
1089          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1090    
1091  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1092    
1093          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1094    
1095  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1096    
1097          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1098    
1099  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1100    
1101          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1102    
1103  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1104    
1105          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1106    
1107  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1108    
1109          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1110          routines.          routines.
1111    
1112  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1113    
1114          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1115    
1116  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1117    
1118          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1119    

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