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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1467, Wed Aug 30 21:35:09 2006 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
4            of a 0-index which was used as 1-index (..hmm)
5    
6            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
7    
8            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
9            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
10            (.is.diagonal): dito
11    
12            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
13    
14            * R/Matrix.R (Matrix): also work for NA data
15    
16    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
19            in all cases.
20    
21    2006-08-27  Douglas Bates  <bates@R-project.org>
22    
23            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
24            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
25    
26    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
29            subclasses of "ddenseMatrix"
30            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
31            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
32            instead of half dozen specialized ones.
33    
34    2006-08-25  Douglas Bates  <bates@R-project.org>
35    
36            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
37            <tillard@cirad.fr> - ordering standard errors to match effects.
38    
39    2006-08-24  Douglas Bates  <bates@R-project.org>
40    
41            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
42            on R_ldl.
43            * R/lCholCMatrix.R,
44            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
45            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
46            * many files in ./R and ./src: Use more general version of
47            dup_mMatrix_as_dgeMatrix to simplify method definitions.
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
49            dtpMatrix, dspMatrix and dppMatrix conversions.
50    
51    
52    2006-08-23  Douglas Bates  <bates@R-project.org>
53    
54            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
55            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
56            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
57            dgeMatrix_crossprod (may need to do this in other places).
58            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
59            generic and method for dsCMatrix.  Use CHOLMOD for chol().
60    
61    2006-08-22  Douglas Bates  <bates@R-project.org>
62    
63            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
64            types of classed Matrices, matrices or numeric or logical vectors.
65            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
66            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
67            to Mutils.h (as an inline) and change name to Matrix_check_class;
68            fixes in as_cholmod_factor and chm_factor_to_SEXP.
69            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
70            dsCMatrix_matrix_solve.  Comment out vestigial functions.
71            * src/Csparse.c: use diag_P and uplo_P macros.
72    
73    2006-08-21  Douglas Bates  <bates@R-project.org>
74    
75            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
76            valgrind.
77            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
78            inverses.
79            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
80            -Wall warnings.
81            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
82            Use dup_mMatrix_as_dgeMatrix.
83    
84    2006-08-20  Douglas Bates  <bates@R-project.org>
85    
86            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
87            * tests/sparseQR.R: Added
88            * man/sparseQR-class.Rd: Document methods for qr.* generics
89            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
90    
91    2006-08-19  Douglas Bates  <bates@R-project.org>
92    
93            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
94            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
95            and qr.fitted.
96            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
97            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
98    
99    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
102            the base version has no "..." argument.
103    
104            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
105    
106            * R/Matrix.R: define and
107            * NAMESPACE: export as.numeric() and as.logical() methods.
108                    Let's hope these do not badly slow down something...
109            Finally export the zapsmall() method.
110    
111    2006-08-17  Douglas Bates  <bates@R-project.org>
112    
113            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
114            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
115            * src/dtCMatrix.c :Remove code that is no longer used
116            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
117    
118    2006-08-14  Douglas Bates  <bates@R-project.org>
119    
120            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
121            Csparse_to_logical and Csparse_symmetric_to_general.
122            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
123            coercion methods between CsparseMatrix and TsparseMatrix.
124    
125    2006-08-14  Douglas Bates  <bates@R-project.org>
126    
127            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
128            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
129            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
130            possible.
131    
132    2006-08-12  Douglas Bates  <bates@R-project.org>
133    
134            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
135              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
136              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
137              generalize conversions between TsparseMatrix, CsparseMatrix,
138              denseMatrix and matrix.  Preserve triangularity property and
139              propagate Dimnames in the easy cases.
140    
141    2006-08-10  Douglas Bates  <bates@R-project.org>
142    
143            * src/lmer.c: adjust checks in glmer_init for S4SXP
144            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
145            before S4SXP but for the wrong reasons.
146    
147    2006-08-08  Douglas Bates  <bates@R-project.org>
148    
149            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
150            Later modified to return the upper triangle only.
151            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
152    
153    2006-08-07  Douglas Bates  <bates@R-project.org>
154    
155            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
156            R-level conversion to a sparse symmetric class.
157            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
158            Remove conversion to sparse symmetric classes (now done in C code).
159    
160    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
163            * man/band.Rd:  adapt the \dontshow{} unit test.
164    
165    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * DESCRIPTION (Version): 0.995-14  for CRAN
168    
169            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
170    
171            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
172            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
173    
174            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
175            * R/Tsparse.R (tril, triu, band): methods
176            * R/dgRMatrix.R (tril, ...):    ditto
177            * man/band.Rd:                  ditto
178    
179    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Matrix.R (head, tail): directly use utils:::head.matrix
182                    to be up-to-date automatically.
183    
184    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
187    
188            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
189            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
190            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
191            such that the S4 objects are always created by the current version
192            of R and 'Matrix' class definitions.
193    
194    2006-08-01  Douglas Bates  <bates@R-project.org>
195    
196            * R/lmer.R (LMEoptimize method), tests/lmer.R,
197            inst/external/test3comp.rda: Added warnings for convergence on
198            boundary and test cases.
199    
200            * src/lmer.c (mer_postVar): Modified to return the variances that
201            are marginal to the fixed effects, not conditional on them (which
202            is what the bVar slot contents represent).
203    
204    2006-07-31  Douglas Bates  <bates@R-project.org>
205    
206            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
207            function which calls the C function mer_hat_trace2.
208    
209            * man/ranef.Rd: Include description of "postVar" argument and
210            producing a caterpillar plot.
211    
212    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * NAMESPACE:    change  "correlation" to "corMatrix"
215            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
216            * R/dpoMatrix.R: ditto
217            * R/lmer.R:      ditto
218    
219    2006-07-28  Douglas Bates  <bates@R-project.org>
220    
221            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
222            RZXinv slot's contents into a separate internal function that can
223            be used in mer_hat_trace.
224    
225    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
228            via new smart
229            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
230            utility functions.
231    
232    
233    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Csparse.R (tril, triu, band): do return *triangular* classed
236            matrices when appropriate; band() even symmetric ones.
237            (replCmat): extend to potentially all "CsparseMatrix"
238            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
239            allow subassignment for special sparse matrices.
240    
241            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
242    
243            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
244            argument; in glmer_*(): print only if(verbose).
245    
246            speed-optimize a few places by moving REAL(.) out of loops.
247    
248            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
249    
250    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
253                    since that wrongly triggers also for M[ logi , ]
254    
255            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
256            a symmetric matrix that results in a non-symmetric one.
257            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
258    
259            * R/dMatrix.R: make round(M) work as round(M, 0)
260    
261            * R/dgTMatrix.R (image): coordinate system and axis now use
262            1-based indices, not 0-based ones.
263    
264            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
265            * tests/indexing.R: test it.
266    
267            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
268            * man/isSymmetric-methods.Rd: and document it.
269    
270            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
271            * man/SparseM-conv.Rd: docu them
272    
273            * tests/other-pkgs.R: renamed from tests/graph.R and add example
274                    for 'SparseM' conversions
275    
276    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
277    
278            * R/Matrix.R (head): added head() and tail() methods.
279    
280    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version): 0.995-12 released to CRAN
283    
284    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * tests/simple.R: add check for correct dsT -> dgT coercion;
287                    add check for correct printing of symmetric sparse matrices.
288    
289            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
290            for sparse symmetric matrices.
291    
292            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
293            diagonal twice.
294    
295    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
296    
297            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
298            being applied to the x slot (detected by Brian Ripley).
299    
300    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
303    
304            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
305    
306    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/lgCMatrix.c (lgCMatrix_diag): new function
309            * R/lgCMatrix.R (diag): for new method
310    
311            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
312                 ==> construction of illegal "*gTMatrix" via new() should
313                 now be much less easy:
314            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
315    
316            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
317                    directly.
318            * man/Matrix.Rd: documents it.
319    
320    2006-07-06  Douglas Bates  <bates@R-project.org>
321    
322            * src/pedigree.c (pedigree_inbreeding): Correction in
323            initialization.  This function is not currently being used and is
324            not fully tested.
325    
326            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
327            Introduced the glmer class.  Added code for mcmcmsamp on glmer
328            objects.  Modified validity check on pedigree objects to account
329            for nonparallel patterns of missingness of parents.
330    
331            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
332            class.
333    
334    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/pMatrix.R: coercion pMatrix -> Tsparse
337    
338    2006-06-12  Douglas Bates  <bates@R-project.org>
339    
340            * DESCRIPTION (Version): 0.995-11 released to CRAN
341    
342            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
343            the output from mcmcsamp.
344    
345    2006-06-10  Douglas Bates  <bates@R-project.org>
346    
347            * R/lmer.R (simulestimate): added C code for calculating the trace
348            of the hat matrix.
349    
350    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
353            classes.
354            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
355    
356    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/dgTMatrix.R (colSums): etc. All four of
359            colSums(), rowSums(), colMeans(), rowMeans() now should work for
360            all "Matrices".
361    
362    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
363    
364            * R/lmer.R (panel.ci): Add a reference line at zero and a
365            background grid to the qqmath plot of ranef.lmer.
366    
367    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
368    
369            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
370            grouping factors to be specified in the formula as (1|foo/bar).
371    
372    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * R/lmer.R (findbars and others): Change check of is.numeric to
375            !is.language to resolve the bug reported by Jacob Wegelin.
376    
377            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
378            code to evaluate inbreeding coefficients without calculating T,
379            based on code in Sargolzaei and Iwaisaki's paper.
380    
381    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
384            generic and mer methods for isNested and denomDF. This denomDF was
385            an attempt to emulate that in lme but I don't think that makes
386            sense.  Use the trace of the hat matrix instead.
387    
388    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
391            the C code depending on a slot structure that's no longer valid.
392            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
393    
394    
395    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
396    
397            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
398            of lowerTriMatrix generic and methods to tril (also upper to triu)
399            and added a general band extractor.
400    
401    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
402    
403            * R/pedigree.R (pedigree): Replace sire and dam values outside the
404            allowable range with NAs. Added a corresponding check in the
405            validity check for the pedigree class.
406    
407            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
408            crossprod methods now inherits from symmetricMatrix.
409    
410    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
413            generics lowerTriMatrix and upperTriMatrix along with methods for
414            the Csparse virtual class.  Also added a C function Csparse_band
415            that implements these methods by calling cholmod_band.
416    
417    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
420            erased when it was NULL.  This led to invalid subselections!
421    
422    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
425            in method for "t" so as not to lose the unit diagonal property.
426    
427    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
428    
429            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
430            and methods.  This is now an option to the ranef method for the
431            mer class.
432    
433            * src/cs_utils.c: Ensure that the nz component is -1 for a
434            compressed column-oriented matrix.  Minor formatting cleanup.
435    
436            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
437            objects.
438    
439    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
442            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
443    
444    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
445    
446            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
447            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
448    
449            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
450            for the dtCMatrix class.
451    
452    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
453    
454            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
455            and methods for it.
456    
457    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
460            arguments, such that M %*% 1:6 now works
461            * Tests/matprod.R: test the above
462    
463    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
466            the ranef.lmer class.
467    
468            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
469            methods to extract the posterior variances from the bVar slot.
470    
471    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
474            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
475    
476            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
477            * tests/simple: (extended)
478    
479            * R/sparseMatrix.R (isTriangular): now using much improved
480            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
481    
482    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
485            (problem report from Franklin Parlamis).  This should be done
486            generally.
487    
488    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
491            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
492            update the plot methods.
493    
494    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
495    
496            * R/lmer.R (resid and ranef methods):  Added methods for the
497            "residuals" and "resid" generic but only for linear mixed model
498            fits.  Changed the ranef method to return a list of data frames so
499            that the plot methods now work.
500    
501    2006-03-16  Douglas Bates  <bates@bates2>
502    
503            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
504            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
505    
506            * DESCRIPTION (Date): New release
507    
508    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
511    
512            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
513            * man/KNex.Rd: and other help files
514            * tests/*.R: several ones needed adaption
515            * inst/doc/Comparisons.Rnw: ditto
516    
517    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
520    
521            * tests/indexing.R: tests for new [<- methods for sparse matrices.
522    
523    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
526    
527            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
528    
529    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/dMatrix.R: enable things like  M [ M < 10 ]
532            * R/dgeMatrix.R: implement it
533    
534    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/AllClass.R: define "summary.mer" and "*.lmer"
537            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
538            * R/lmer.R (show): now works with summary()
539    
540    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
543            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
544                    support the above
545    
546    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
547    
548            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
549            Use glmFit$prior.weights for weights in a glmm.
550            Allow an option usePQL = FALSE to skip the PQL steps for the
551            Laplace method (and, in time, the AGQ method).
552    
553            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
554            into a separate function internal_mer_Xfactor to be able to call
555            it from internal_bhat.
556    
557    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * tests/Class+Meth.R (tstMatrixClass): function for much better
560            testing; now again of all actual classes.
561    
562            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
563                    use macros and define make_d_matrix_* and make_i_matrix_*
564                    where _i_ is for the ldense routines:
565    
566            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
567            * src/ldense.c (lsyMatrix_as_lgeMatrix):
568    
569            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
570    
571    
572    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
575                    many different kinds of matrices.
576            * R/*.R: quite a few new methods were needed for R CMD check with
577                    new Matrix().  Very good for users playing around.
578    
579    
580    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/dgeMatrix.c (dMatrix_validate): new
583            * src/Mutils.c (dense_nonpacked_validate): new
584    
585            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
586    
587    
588    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
591    
592    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
593    
594            * DESCRIPTION (Version): 0.99-6 released to CRAN
595    
596            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
597            segfault in cases with multiple non-nested grouping factors.
598    
599    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
602                    (Depends): also on 'utils'
603    
604            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
605            * R/diagMatrix.R (Diagonal): constructor and methods for
606            diagonal matrices
607    
608            * R/ltTMatrix.R: new "minimal methods"
609    
610    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
613            all methods (and help files).
614    
615    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
618                    for case (dimn.  op  no_dimn.)
619    
620    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * DESCRIPTION (Version): 0.99-2  released to CRAN
623    
624    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
627            by Julian Faraway.
628    
629    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Auxiliaries.R (try_as): new utility
632            * R/sparseMatrix.R: use try_as() in coercion to original class
633    
634    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
637    
638    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * R/Auxiliaries.R (dimNamesCheck): added
641    
642            * R/Matrix.R (as.array), (as.vector): new
643    
644    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
647                    default.
648            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
649                    "pMatrix" now contains "sparseMatrix"
650    
651    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * tests/Class+Meth.R: new tests; t(t(m)) == m
654    
655            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
656    
657            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
658            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
659    
660            * R/dspMatrix.R: typo in "t" method
661    
662    2005-09-18  Douglas Bates  <bates@wisc.edu>
663    
664            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
665            * R/Tsparse.R: instead of R/gTMatrix.R
666            * R/Csparse.R: new
667            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
668            * src/Tsparse.c: new; many trivial methods calling cholmod_()
669            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
670                            via cholmod
671    
672    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Auxiliaries.R (non0ind): new function using new C code
675            * src/dgCMatrix.c (compressed_non_0_ij): new utility
676    
677    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
678    
679            * src/chm_common.h: header file required by all C sources that
680            call CHOLMOD functions.  It defines a cholmod_common structure
681            called 'c' whose address is passed as the last argument to
682            (virtually) every CHOLMOD function.
683    
684            * src/Pattern.c: Simple example of the use of CHOLMOD.
685    
686            * src/init.c: initialize and finalize the cholmod_common structure.
687    
688            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
689            LDL and CCOLAMD from the U. of Florida sparse matrix library.
690    
691    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * inst/test-tools.R: new file collecting the utility functions used
694                    in ./tests/*.R
695    
696            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
697            * R/Matrix.R (cbind2): methods for NULL and missing
698    
699    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/AllClass.R: new "index" class for "[" and "[<-":
702                    First cut at "symmetricMatrix" and "triangularMatrix"
703            * R/gTMatrix.R (.ind.prep): new function;
704                    Logical and character indexing now work too.
705            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
706            * tests/indexing.R: new, including *.Rout.save
707            * tests/dgTMatrix.R: new
708    
709    2005-08-29  Douglas Bates  <bates@wisc.edu>
710    
711            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
712            indicator pos not being updated.  Also enforced upper triangular
713            for symmetric case.  Need to coerce edges component of elements of
714            edge list - grr! (Why don't they define their classes cleanly?)
715    
716    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Matrix.R:  added first "[<-" methods; not yet functional
719            * R/denseMatrix.R: ditto
720            * man/Subassign-methods.Rd: new help file for these
721    
722    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * DESCRIPTION (Version): 0.98-6
725    
726            * R/denseMatrix.R: new file for "[" fallback methods for all dense
727            matrices.
728    
729    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
732                    as( <logical>, "matrix")
733    
734            * R/pMatrix.R: coercion to "lgTMatrix"
735    
736            * R/gTMatrix.R: new virtual class to define "[" methods for.
737            * man/gTMatrix-class.Rd:
738            * General slight re-organization of where "[" methods are defined.
739              more to come.
740    
741    2005-08-18  Douglas Bates  <bates@wisc.edu>
742    
743            * DESCRIPTION (Version): 0.98-5  released to CRAN
744    
745            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
746            * .....
747    
748    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
749    
750            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
751            or glmer objects.
752    
753    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
756    
757    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
758    
759            * R/HBMM.R: finish re-writing R-only code.
760    
761    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
762    
763            * man/externalFormats.Rd: move documentation for writeHB and
764            writeMM here.
765    
766            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
767            (suggested by Paul Roecker).
768    
769            * tests/validObj.R (assertError): Comment out test that is failing
770            after recent changes in r-devel.
771    
772    
773    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/AllClass.R: intermediate virtual class "denseMatrix"
776            * man/denseMatrix-class.Rd
777            * NAMESPACE: export it, and also export
778            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
779    
780    2005-08-10  Douglas Bates  <bates@wisc.edu>
781    
782            * DESCRIPTION (Version): 0.98-3 to CRAN
783    
784            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
785            matrix_solve code (which was really, really wrong).
786    
787    2005-08-07  Douglas Bates  <bates@wisc.edu>
788    
789            * DESCRIPTION (Version): 0.98-2
790    
791            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
792    
793            * R/lmer.R (abbrvNms): new
794            * R/lmer.R (mcmcsamp): allow transformed parameters
795            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
796            for the Harwell-Boeing and the MatrixMarket formats.
797    
798    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * man/dtrMatrix-class.Rd: add examples
801            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
802    
803            * TODO: note the dtpMatrix (docu) bug
804    
805            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
806            in order to ensure that new as.matrix() is used by old functions,
807            e.g., svd(), qr(), eigen(), dist(),..;
808                  apply(), also matplot() or pairs().
809    
810    
811    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
814              add comments about 'control' / lmerControl() arguments
815    
816    2005-07-27  Douglas Bates  <bates@wisc.edu>
817    
818            * man/sleepstudy.Rd: Added the sleep data set.
819            * DESCRIPTION (Version): 0.98-1  released to CRAN
820    
821    2005-07-12  Douglas Bates  <bates@wisc.edu>
822            * man/sleepstudy.Rd: Added the sleep data set.
823    
824            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
825            .Call calls that were producing spurious output.
826    
827    2005-07-05  Douglas Bates  <bates@wisc.edu>
828    
829            * R/lmer.R (lmer): stored updated variance component estimates in
830            mer object for the generalized model.  (Bug reported by Renaud
831            Lancelot).
832    
833    2005-07-03  Douglas Bates  <bates@wisc.edu>
834    
835            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
836            unidimensional case.
837    
838    2005-06-08  Douglas Bates  <bates@wisc.edu>
839    
840            * DESCRIPTION (Version): 0.96-1
841    
842            * moved  lmer-class' R and C code moved from lme4 to here
843    
844    2005-06-04  Douglas Bates  <bates@wisc.edu>
845    
846            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
847            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
848    
849    2005-06-02  Douglas Bates  <bates@wisc.edu>
850    
851            * src/Makefile.win: Forgot to update this when Makefile changed.
852    
853    2005-05-11  Douglas Bates  <bates@wisc.edu>
854    
855            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
856            bug reported by Kurt Hornik and Michael Hahsler.
857    
858    2005-05-10  Douglas Bates  <bates@wisc.edu>
859    
860            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
861            logical sparse matrices.  These will also be used in the symbolic
862            analysis for lmer objects.
863    
864            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
865            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
866    
867    2005-05-06  Douglas Bates  <bates@wisc.edu>
868    
869            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
870            colMeans, colSums, rowMeans and rowSums.
871    
872    2005-04-18  Douglas Bates  <bates@wisc.edu>
873    
874            * src/lgCMatrix.[ch]: code for _validate method and stub for
875            multiplication operation.
876    
877            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
878            to dgetrs.
879    
880            * src/init.c: Fix cut-and-paste error in definition of
881            dgeMatrix_matrix_solve
882    
883            * src/{many files}: Tighten code by using ALLOC_SLOT.
884    
885    2005-04-15  Douglas Bates  <bates@wisc.edu>
886    
887            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
888    
889            * DESCRIPTION: Eliminate import of stats.
890    
891    
892    2005-04-06  Douglas Bates  <bates@wisc.edu>
893    
894            * R/AllClass.R : add logical sparse matrix classes
895    
896    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
897    
898            * R/dgTMatrix.R: add "[" method for triplet matrices
899            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
900    
901    2005-03-31  Douglas Bates  <bates@wisc.edu>
902    
903            * DESCRIPTION (Version): release 0.95-5 to CRAN
904    
905            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
906            * R/sparseMatrix.R: %*%, crossprod()
907            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
908            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
909            * src/lmer.c (lmer_fitted): fix thinko
910    
911    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/AllClass.R: add two virtual sparse classes ``on top''
914    
915    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
918                    correspondingly fix examples and tests/ since new()
919                    doesn't work for virtual classes.
920    
921    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * R/Matrix.R (as.matrix): method and one for unname()
924            * tests/dpoMatrix.R: tests should now be less platform dependent;
925              also run for R 2.1.0; using as.matrix()
926    
927    2005-03-15  Douglas Bates  <bates@wisc.edu>
928    
929            * R/pMatrix.R: "pMatrix" class added
930            * ....
931    
932    2005-03-14  Douglas Bates  <bates@wisc.edu>
933    
934            * R/dtpMatrix.R: Add unpack method and an example.
935    
936            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
937            of general symmetric matrices and associated S4 methods.
938    
939    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
940            +
941    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/dgeMatrix.R (setAs): and many other files: more coercion,
944              crossprod() and "%*%" methods added; tests, too.
945            * tests/matprod.R: new, for testing these
946    
947    2005-03-03  Douglas Bates  <bates@wisc.edu>
948    
949            * src/lmer.c (lmer_fitted): Added.
950    
951    2005-03-02  Douglas Bates  <bates@wisc.edu>
952    
953            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
954    
955    2005-02-28  Douglas Bates  <bates@wisc.edu>
956    
957            * src/*.c,po/,inst/po: Internationalization and localization of
958            the package.
959    
960            * src/ldl.[ch]: Removed these as their contents are referenced in the
961            R_ldl.c file.
962    
963            * src/flame.[ch]: Removed these source files.
964    
965            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
966    
967            * src/LU.[ch],src/init.c: absorb in factorizations
968    
969            * src/Mutils.h: prepare for internationalization
970    
971            * src/cblas.h: move the enum definitions to Mutils.h and remove
972            this file
973    
974    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
977    
978            * R/dtrMatrix.R: fix t() method
979    
980            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
981            * NAMESPACE: export them (and import generics from "methods")
982            * tests/group-methods.R : and test them.
983    
984            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
985            border case
986    
987    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
988    
989            * DESCRIPTION (Version): 0.95-2  released to CRAN
990    
991            * src/dgBCMatrix.c:
992            * src/lmer.c: many changes
993            * ...
994    
995    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Matrix.R: add more sophisticated show() method.
998    
999    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1000    
1001            * */* : almost complete reorganization of classes.
1002    
1003    2005-01-26  Douglas Bates  <bates@wisc.edu>
1004    
1005            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1006            for the geMatrix class.
1007    
1008    2005-01-24  Douglas Bates  <bates@wisc.edu>
1009    
1010            * src/Makefile (clean): Remove *.a and *.so
1011    
1012            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1013    
1014    2005-01-23  Douglas Bates  <bates@wisc.edu>
1015    
1016            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1017            had an effect in cases with more than 2 grouping factors.
1018    
1019    2005-01-03  Douglas Bates  <bates@wisc.edu>
1020    
1021            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1022    
1023    2004-12-23  Douglas Bates  <bates@wisc.edu>
1024    
1025            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1026            and R_useDynamicSymbols (suggested by B.D.Ripley).
1027    
1028    2004-12-14  Douglas Bates  <bates@wisc.edu>
1029    
1030            * R/sscMatrix.R: Add determinant methods
1031    
1032            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1033            for tripletMatrix to matrix.
1034    
1035    2004-12-13  Douglas Bates  <bates@wisc.edu>
1036    
1037            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1038            no longer used.
1039    
1040          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1041          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1044 
1044          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1045          Fixes part but not all of #15.          Fixes part but not all of #15.
1046    
1047  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1048    
1049          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1050          scalar grouping factors corrected.          scalar grouping factors corrected.
1051    
1052  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1053    
1054          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1055    
1056  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1057    
1058          * 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
1059          .h file can be included.          .h file can be included.
1060    
1061  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1062    
1063          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1064          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1065    
1066          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1067    
1068  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1069    
1070          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1071    
1072  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1073    
1074          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1075    
1076  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1077    
1078          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1079    
1080  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1081    
1082          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1083    
1084  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1085    
1086          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1087          routines.          routines.
1088    
1089  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1090    
1091          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1092    
1093  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1094    
1095          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1096    

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