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revision 303, Wed Oct 27 21:33:03 2004 UTC revision 1716, Sat Jan 6 02:01:24 2007 UTC
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1  2004-10-27  Douglas Bates  <bates@bates1-home>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/init.c (R_init_Matrix): export cholmod_scale
4    
5    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
8            file; start using "Logic", hence
9    
10            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
11            * NAMESPACE: import and export "Logic"
12    
13    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
16            only needed previously to R version 2.5.0.
17    
18    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
21    
22            * R/Tsparse.R (replTmat): fix subassignment of triangular
23            * R/Csparse.R (replCmat): ditto
24            * tests/indexing.R: more tests, incl the above fix
25    
26    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (drop0): extend for non CSparse
29            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
30    
31            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
32                    use uplo correctly (!); other places: use uplo_P() macro
33    
34            * R/Csparse.R (replCmat): call diagU2N() when needed
35            * R/Tsparse.R (replTmat): ditto
36    
37            * src/dtCMatrix.c (tCMatrix_validate): new
38            * src/dtTMatrix.c (tTMatrix_validate): new, used in
39            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
40    
41            * R/diagMatrix.R (replDiag): to use in [<-
42    
43    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
46                    also more general diagU2N().
47    
48    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
51            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
52    
53    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * tests/bind.R: a few more cases
56            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
57    
58            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
59            * R/ddenseMatrix.R (cbind2/rbind2)
60            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
61            * tests/indexing.R
62            * tests/indexing.Rout.save: updated
63    
64    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
67            * tests/indexing.R
68    
69    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
72            align with proper position of "0", i.e., right for integers.
73            argument 'align' by default is "fancy".
74    
75    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
78            * R/Csparse.R: and fix "Compare" for more cases.
79            * tests/Class+Meth.R: test some of these (m == m, m != m)
80    
81    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/lsparseMatrix.R: all() and any() methods
84            * R/ldenseMatrix.R:      ditto
85            * NAMESPACE, R/Matrix.R: ditto
86    
87            * man/all-methods.Rd: document them minimally
88    
89            * tests/simple.R: add a few examples for these
90    
91    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ([): fix long standing typo in symmetric case
94            * man/dsCMatrix-class.Rd: add example exhibiting the above case
95    
96    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
99            to LL before converting to a sparse matrix. (The LDL form can be
100            converted to a sparse matrix but it is implicitly a unit
101            triangular matrix and a diagonal matrix overwritten on the diagonal.)
102    
103    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
104    
105            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
106    
107    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * DESCRIPTION (Version): updated -> release 0.9975-7
110            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
111    
112    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
115    
116    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
119            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
120            is exactly singular.
121    
122    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * DESCRIPTION (Date): updated -> release 0.9975-6
125    
126    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
129            now returns symmetric.
130    
131            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
132    
133            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
134            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
135    
136            * R/Auxiliaries.R (.type.kind): added
137    
138    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
141            running src/CSparse_install.sh
142    
143            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
144    
145    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
148            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
149    
150            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
151    
152            * tests/Class+Meth.R (tstMatrixClass): now assure
153            the (important in method programming) property :
154    
155                    ###>>  Every "Matrix" is either
156                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
157    
158                    (where "*" stands for "Matrix")
159    
160            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
161    
162            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
163            * tests/validObj.R: checks for "comparison"
164    
165            * R/sparseMatrix.R ([): improved indexing for sparse;
166                    trying to keep <symmetric>[ n, n] symmmetric
167    
168            * tests/indexing.R: indexing for logical sparse now ok
169    
170    
171    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * src/Tsparse.c: use xTsparse_validate() , and hence remove
174    
175            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
176    
177    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
180    
181            * tests/simple.R: validObject() checking the above.
182    
183            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
184            replacing both dgCMatrix_validate and lgCM*.
185    
186            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
187            fix dimnames setting in other places.
188            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
189    
190    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
193    
194            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
195            symmetry test, via
196            * R/Auxiliaries.R (.as.dgC.0.factors):
197    
198    2006-11-01  Douglas Bates  <bates@r-project.org>
199    
200            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
201            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
202            <CsparseMatrix>) added
203    
204    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * tests/matprod.R: add a variation of Harri's example
207    
208            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
209            recursive infinitely.
210    
211            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
212    
213            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
214    
215    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
218            matrix if possible; test m+m == 2*m; now test dgRMatrix.
219            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
220            satisfy the above test.
221    
222    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
225    
226            * R/dgCMatrix.R: solve(a, b="missing") based on
227            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
228            RHS = NULL.
229    
230            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
231            add more (needed) [t]crossprod() methods.
232    
233            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
234    
235            * R/Auxiliaries.R (as_CspClass): cleanup
236            (drop0): internal utility for "Csparse_drop(*, 0)"
237            (.bail.out.2): encourage active feedback
238    
239    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dMatrix.R(Compare): new(), then slots [no validity check]
242    
243            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
244            non-valid or 'sorted' case).
245    
246            * R/dsparseMatrix.R: add "chol" method.
247            * R/ddenseMatrix.R: ditto
248    
249            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
250            * NAMESPACE (Ops)
251            * R/diagMatrix.R (diag2T): simple utility used "higher level"
252            coercion; deprecating direct lower level coercions.
253    
254            * R/*.R (seq): use seq_len() and seq_along() where possible.
255    
256    
257    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.9975-5 ready for release
260    
261    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
264    
265    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/AllClass.R (corMatrix): add 'validity' check;
268                    comment out unused "LDL" class definition
269            * NAMESPACE: mention, but do not export "LDL" class
270            * R/corMatrix.R: new (simple), needed for R-devel with
271            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
272              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
273    
274    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
277            use Rprintf and R's error handling.
278    
279    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
282            * tests/matprod.R: add tests for the bug fixed.
283    
284    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
287            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
288    
289    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
292    
293    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * DESCRIPTION (Version): 0.9975-3
296    
297            * R/diagMatrix.R (bdiag): new function constructing block diagonal
298            (sparse) matrices.
299            * man/bdiag.Rd: docu + examples
300    
301            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
302    
303            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
304            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
305    
306            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
307            that result is sparse or diagonal (and not dense).
308    
309            * man/Subassign-methods.Rd: fix examples
310    
311            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
312            should always return a sparse (and not sometimes a diagonal) matrix.
313    
314    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
317    
318    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): 0.9975-2
321    
322            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
323    
324    2006-10-02  Douglas Bates  <bates@R-project.org>
325    
326            * tests/dg_Matrix.R: Simplify test taking into account new code.
327    
328    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
331    
332            * R/lsTMatrix.R: new files w/ missing methods
333            * R/nsTMatrix.R:  "  'for completeness'
334    
335            * tests/Class+Meth.R: a bit less 'not.ok.classes'
336    
337            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
338    
339    
340    2006-09-28  Douglas Bates  <bates@R-project.org>
341    
342            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
343            included.
344    
345            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
346            Export C-callable functions used in Zt_create in lme4.
347    
348    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * DESCRIPTION (Version): 0.9975-1
351    
352            * tests/simple.R: less checks fail; using NA, found that our
353                    kronecker() is not base-compatible with NA's.
354    
355            * R/dMatrix.R: "Compare" method now implemented for all cases
356    
357            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
358    
359            * man/dtpMatrix-class.Rd: mention length of 'x' slot
360    
361            * src/dtpMatrix.c (dtpMatrix_validate): fix check
362            * src/dspMatrix.c (dspMatrix_validate): ditto
363    
364            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
365              including coercion to [nl]tTMatrix.
366    
367            * R/diagMatrix.R (show): print a header line as for other classes.
368    
369    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * src/Makefile.win (SUBDIRS): fix typo
372    
373    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
376    
377    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
380            symmetric and y missing in R code using %*% (cholmod_aat doesn't
381            accept a symmetric matrix).
382            * tests/group-methods.R: Uncomment test of crossprod applied to
383            lsCMatrix objects.
384    
385    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/AllClass.R (symmetricMatrix): add validity method (available
388            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
389    
390            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
391    
392            * tests/indexing.Rout.save:
393            * tests/indexing.R: additions, mainly for 'lsparse'
394    
395            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
396            case.
397    
398            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
399    
400    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
403                    as 'N' (1-letter - Ok?)
404    
405            * tests/group-methods.R: add test for logical + NAs
406    
407            * R/dMatrix.R ("Compare"): fix to work with NA's
408    
409            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
410    
411            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
412                    which is implemented.
413    
414    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/chm_common.c: coerce logical <-> double instead of
417            typecasting;  needed for "l" matrix handling in cholmod.
418    
419            * tests/other-pkgs.R (graph): small extension in "graph" checks.
420    
421            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
422            (Tsp2grNEL): other fixes needed
423    
424    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
427                    Matrices, since "lMatrix", also "lsparseM" can have NA
428            * R/ndenseMatrix.R, etc: new source files
429            * man/nsparseMatrix-classes.Rd, etc: new help files
430            * tests/: adaptions
431            * src/chm_common.c (chm_dense_to_SEXP): and others:
432                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
433            * src/Csparse.c, etc: ditto
434    
435    2006-09-11  Douglas Bates  <bates@R-project.org>
436    
437            * src/Mutils.[ch],init.c inst/include/*.h: Move the
438            alloc_d**Matrix functions to the lme4 package.
439    
440    2006-09-09  Douglas Bates  <bates@R-project.org>
441    
442            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
443            fixed
444    
445    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/lMatrix.R: new
448    
449            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
450    
451            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
452            * man/tcrossprod.Rd: ditto
453    
454    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
455    
456            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
457            for exported functions
458            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
459            Remove partitioning algorithms for sparse matrix reordering.  The
460            copyright on the Metis code was problematic and the methods were
461            rarely used.
462            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
463            operations are now done entirely in CHOLMOD code.
464    
465    2006-09-06  Douglas Bates  <bates@R-project.org>
466    
467            * src/Mutils.h: Remove functions that are no longer used.
468    
469    2006-09-04  Douglas Bates  <bates@R-project.org>
470    
471            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
472            * src/DEPS.mkf: update
473    
474    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * created branches/Matrix-for-R-2.3.x;  on trunk: do
477            * DESCRIPTION (Version): 0.9975-0
478            (Depends): R (>= 2.4.0)
479    
480    2006-09-01  Douglas Bates  <bates@R-project.org>
481    
482            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
483    
484    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
487            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
488    
489            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
490    
491    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
494            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
495            * R/dsparseMatrix.R: ditto
496            * R/Csparse.R: ditto
497    
498    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/dMatrix.R (Compare): improve availability of "<", etc
501            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
502    
503    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
506            of a 0-index which was used as 1-index (..hmm)
507    
508            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
509    
510            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
511            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
512            (.is.diagonal): ditto
513    
514            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
515    
516            * R/Matrix.R (Matrix): also work for NA data
517    
518    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
521            in all cases.
522    
523    2006-08-27  Douglas Bates  <bates@R-project.org>
524    
525            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
526            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
527    
528    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
531            subclasses of "ddenseMatrix"
532            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
533            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
534            instead of half dozen specialized ones.
535    
536    2006-08-25  Douglas Bates  <bates@R-project.org>
537    
538            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
539            <tillard@cirad.fr> - ordering standard errors to match effects.
540    
541    2006-08-24  Douglas Bates  <bates@R-project.org>
542    
543            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
544            on R_ldl.
545            * R/lCholCMatrix.R,
546            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
547            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
548            * many files in ./R and ./src: Use more general version of
549            dup_mMatrix_as_dgeMatrix to simplify method definitions.
550            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
551            dtpMatrix, dspMatrix and dppMatrix conversions.
552    
553    
554    2006-08-23  Douglas Bates  <bates@R-project.org>
555    
556            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
557            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
558            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
559            dgeMatrix_crossprod (may need to do this in other places).
560            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
561            generic and method for dsCMatrix.  Use CHOLMOD for chol().
562    
563    2006-08-22  Douglas Bates  <bates@R-project.org>
564    
565            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
566            types of classed Matrices, matrices or numeric or logical vectors.
567            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
568            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
569            to Mutils.h (as an inline) and change name to Matrix_check_class;
570            fixes in as_cholmod_factor and chm_factor_to_SEXP.
571            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
572            dsCMatrix_matrix_solve.  Comment out vestigial functions.
573            * src/Csparse.c: use diag_P and uplo_P macros.
574    
575    2006-08-21  Douglas Bates  <bates@R-project.org>
576    
577            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
578            valgrind.
579            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
580            inverses.
581            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
582            -Wall warnings.
583            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
584            Use dup_mMatrix_as_dgeMatrix.
585    
586    2006-08-20  Douglas Bates  <bates@R-project.org>
587    
588            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
589            * tests/sparseQR.R: Added
590            * man/sparseQR-class.Rd: Document methods for qr.* generics
591            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
592    
593    2006-08-19  Douglas Bates  <bates@R-project.org>
594    
595            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
596            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
597            and qr.fitted.
598            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
599            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
600    
601    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
604            the base version has no "..." argument.
605    
606            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
607    
608            * R/Matrix.R: define and
609            * NAMESPACE: export as.numeric() and as.logical() methods.
610                    Let's hope these do not badly slow down something...
611            Finally export the zapsmall() method.
612    
613    2006-08-17  Douglas Bates  <bates@R-project.org>
614    
615            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
616            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
617            * src/dtCMatrix.c :Remove code that is no longer used
618            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
619    
620    2006-08-14  Douglas Bates  <bates@R-project.org>
621    
622            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
623            Csparse_to_logical and Csparse_symmetric_to_general.
624            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
625            coercion methods between CsparseMatrix and TsparseMatrix.
626    
627    2006-08-14  Douglas Bates  <bates@R-project.org>
628    
629            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
630            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
631            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
632            possible.
633    
634    2006-08-12  Douglas Bates  <bates@R-project.org>
635    
636            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
637              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
638              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
639              generalize conversions between TsparseMatrix, CsparseMatrix,
640              denseMatrix and matrix.  Preserve triangularity property and
641              propagate Dimnames in the easy cases.
642    
643    2006-08-10  Douglas Bates  <bates@R-project.org>
644    
645            * src/lmer.c: adjust checks in glmer_init for S4SXP
646            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
647            before S4SXP but for the wrong reasons.
648    
649    2006-08-08  Douglas Bates  <bates@R-project.org>
650    
651            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
652            Later modified to return the upper triangle only.
653            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
654    
655    2006-08-07  Douglas Bates  <bates@R-project.org>
656    
657            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
658            R-level conversion to a sparse symmetric class.
659            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
660            Remove conversion to sparse symmetric classes (now done in C code).
661    
662    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
665            * man/band.Rd:  adapt the \dontshow{} unit test.
666    
667    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * DESCRIPTION (Version): 0.995-14  for CRAN
670    
671            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
672    
673            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
674            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
675    
676            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
677            * R/Tsparse.R (tril, triu, band): methods
678            * R/dgRMatrix.R (tril, ...):    ditto
679            * man/band.Rd:                  ditto
680    
681    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Matrix.R (head, tail): directly use utils:::head.matrix
684                    to be up-to-date automatically.
685    
686    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
689    
690            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
691            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
692            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
693            such that the S4 objects are always created by the current version
694            of R and 'Matrix' class definitions.
695    
696    2006-08-01  Douglas Bates  <bates@R-project.org>
697    
698            * R/lmer.R (LMEoptimize method), tests/lmer.R,
699            inst/external/test3comp.rda: Added warnings for convergence on
700            boundary and test cases.
701    
702            * src/lmer.c (mer_postVar): Modified to return the variances that
703            are marginal to the fixed effects, not conditional on them (which
704            is what the bVar slot contents represent).
705    
706    2006-07-31  Douglas Bates  <bates@R-project.org>
707    
708            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
709            function which calls the C function mer_hat_trace2.
710    
711            * man/ranef.Rd: Include description of "postVar" argument and
712            producing a caterpillar plot.
713    
714    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * NAMESPACE:    change  "correlation" to "corMatrix"
717            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
718            * R/dpoMatrix.R: ditto
719            * R/lmer.R:      ditto
720    
721    2006-07-28  Douglas Bates  <bates@R-project.org>
722    
723            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
724            RZXinv slot's contents into a separate internal function that can
725            be used in mer_hat_trace.
726    
727    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
730            via new smart
731            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
732            utility functions.
733    
734    
735    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Csparse.R (tril, triu, band): do return *triangular* classed
738            matrices when appropriate; band() even symmetric ones.
739            (replCmat): extend to potentially all "CsparseMatrix"
740            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
741            allow subassignment for special sparse matrices.
742    
743            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
744    
745            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
746            argument; in glmer_*(): print only if(verbose).
747    
748            speed-optimize a few places by moving REAL(.) out of loops.
749    
750            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
751    
752    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
755                    since that wrongly triggers also for M[ logi , ]
756    
757            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
758            a symmetric matrix that results in a non-symmetric one.
759            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
760    
761            * R/dMatrix.R: make round(M) work as round(M, 0)
762    
763            * R/dgTMatrix.R (image): coordinate system and axis now use
764            1-based indices, not 0-based ones.
765    
766            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
767            * tests/indexing.R: test it.
768    
769            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
770            * man/isSymmetric-methods.Rd: and document it.
771    
772            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
773            * man/SparseM-conv.Rd: docu them
774    
775            * tests/other-pkgs.R: renamed from tests/graph.R and add example
776                    for 'SparseM' conversions
777    
778    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
779    
780            * R/Matrix.R (head): added head() and tail() methods.
781    
782    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * DESCRIPTION (Version): 0.995-12 released to CRAN
785    
786    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * tests/simple.R: add check for correct dsT -> dgT coercion;
789                    add check for correct printing of symmetric sparse matrices.
790    
791            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
792            for sparse symmetric matrices.
793    
794            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
795            diagonal twice.
796    
797    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
798    
799            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
800            being applied to the x slot (detected by Brian Ripley).
801    
802    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
805    
806            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
807    
808    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * src/lgCMatrix.c (lgCMatrix_diag): new function
811            * R/lgCMatrix.R (diag): for new method
812    
813            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
814                 ==> construction of illegal "*gTMatrix" via new() should
815                 now be much less easy:
816            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
817    
818            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
819                    directly.
820            * man/Matrix.Rd: documents it.
821    
822    2006-07-06  Douglas Bates  <bates@R-project.org>
823    
824            * src/pedigree.c (pedigree_inbreeding): Correction in
825            initialization.  This function is not currently being used and is
826            not fully tested.
827    
828            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
829            Introduced the glmer class.  Added code for mcmcmsamp on glmer
830            objects.  Modified validity check on pedigree objects to account
831            for nonparallel patterns of missingness of parents.
832    
833            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
834            class.
835    
836    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/pMatrix.R: coercion pMatrix -> Tsparse
839    
840    2006-06-12  Douglas Bates  <bates@R-project.org>
841    
842            * DESCRIPTION (Version): 0.995-11 released to CRAN
843    
844            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
845            the output from mcmcsamp.
846    
847    2006-06-10  Douglas Bates  <bates@R-project.org>
848    
849            * R/lmer.R (simulestimate): added C code for calculating the trace
850            of the hat matrix.
851    
852    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
855            classes.
856            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
857    
858    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/dgTMatrix.R (colSums): etc. All four of
861            colSums(), rowSums(), colMeans(), rowMeans() now should work for
862            all "Matrices".
863    
864    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
865    
866            * R/lmer.R (panel.ci): Add a reference line at zero and a
867            background grid to the qqmath plot of ranef.lmer.
868    
869    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
870    
871            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
872            grouping factors to be specified in the formula as (1|foo/bar).
873    
874    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
875    
876            * R/lmer.R (findbars and others): Change check of is.numeric to
877            !is.language to resolve the bug reported by Jacob Wegelin.
878    
879            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
880            code to evaluate inbreeding coefficients without calculating T,
881            based on code in Sargolzaei and Iwaisaki's paper.
882    
883    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
884    
885            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
886            generic and mer methods for isNested and denomDF. This denomDF was
887            an attempt to emulate that in lme but I don't think that makes
888            sense.  Use the trace of the hat matrix instead.
889    
890    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
893            the C code depending on a slot structure that's no longer valid.
894            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
895    
896    
897    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
898    
899            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
900            of lowerTriMatrix generic and methods to tril (also upper to triu)
901            and added a general band extractor.
902    
903    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
904    
905            * R/pedigree.R (pedigree): Replace sire and dam values outside the
906            allowable range with NAs. Added a corresponding check in the
907            validity check for the pedigree class.
908    
909            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
910            crossprod methods now inherits from symmetricMatrix.
911    
912    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
913    
914            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
915            generics lowerTriMatrix and upperTriMatrix along with methods for
916            the Csparse virtual class.  Also added a C function Csparse_band
917            that implements these methods by calling cholmod_band.
918    
919    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
922            erased when it was NULL.  This led to invalid subselections!
923    
924    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
925    
926            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
927            in method for "t" so as not to lose the unit diagonal property.
928    
929    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
930    
931            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
932            and methods.  This is now an option to the ranef method for the
933            mer class.
934    
935            * src/cs_utils.c: Ensure that the nz component is -1 for a
936            compressed column-oriented matrix.  Minor formatting cleanup.
937    
938            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
939            objects.
940    
941    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
944            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
945    
946    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
947    
948            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
949            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
950    
951            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
952            for the dtCMatrix class.
953    
954    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
955    
956            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
957            and methods for it.
958    
959    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
960    
961            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
962            arguments, such that M %*% 1:6 now works
963            * Tests/matprod.R: test the above
964    
965    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
966    
967            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
968            the ranef.lmer class.
969    
970            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
971            methods to extract the posterior variances from the bVar slot.
972    
973    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
976            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
977    
978            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
979            * tests/simple: (extended)
980    
981            * R/sparseMatrix.R (isTriangular): now using much improved
982            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
983    
984    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
985    
986            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
987            (problem report from Franklin Parlamis).  This should be done
988            generally.
989    
990    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
991    
992            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
993            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
994            update the plot methods.
995    
996    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
997    
998            * R/lmer.R (resid and ranef methods):  Added methods for the
999            "residuals" and "resid" generic but only for linear mixed model
1000            fits.  Changed the ranef method to return a list of data frames so
1001            that the plot methods now work.
1002    
1003    2006-03-16  Douglas Bates  <bates@bates2>
1004    
1005            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1006            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1007    
1008            * DESCRIPTION (Date): New release
1009    
1010    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1013    
1014            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1015            * man/KNex.Rd: and other help files
1016            * tests/*.R: several ones needed adaption
1017            * inst/doc/Comparisons.Rnw: ditto
1018    
1019    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1022    
1023            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1024    
1025    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1028    
1029            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1030    
1031    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/dMatrix.R: enable things like  M [ M < 10 ]
1034            * R/dgeMatrix.R: implement it
1035    
1036    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/AllClass.R: define "summary.mer" and "*.lmer"
1039            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1040            * R/lmer.R (show): now works with summary()
1041    
1042    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1045            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1046                    support the above
1047    
1048    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1049    
1050            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1051            Use glmFit$prior.weights for weights in a glmm.
1052            Allow an option usePQL = FALSE to skip the PQL steps for the
1053            Laplace method (and, in time, the AGQ method).
1054    
1055            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1056            into a separate function internal_mer_Xfactor to be able to call
1057            it from internal_bhat.
1058    
1059    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1060    
1061            * tests/Class+Meth.R (tstMatrixClass): function for much better
1062            testing; now again of all actual classes.
1063    
1064            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1065                    use macros and define make_d_matrix_* and make_i_matrix_*
1066                    where _i_ is for the ldense routines:
1067    
1068            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1069            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1070    
1071            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1072    
1073    
1074    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1077                    many different kinds of matrices.
1078            * R/*.R: quite a few new methods were needed for R CMD check with
1079                    new Matrix().  Very good for users playing around.
1080    
1081    
1082    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * src/dgeMatrix.c (dMatrix_validate): new
1085            * src/Mutils.c (dense_nonpacked_validate): new
1086    
1087            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1088    
1089    
1090    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1091    
1092            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1093    
1094    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1095    
1096            * DESCRIPTION (Version): 0.99-6 released to CRAN
1097    
1098            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1099            segfault in cases with multiple non-nested grouping factors.
1100    
1101    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1104                    (Depends): also on 'utils'
1105    
1106            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1107            * R/diagMatrix.R (Diagonal): constructor and methods for
1108            diagonal matrices
1109    
1110            * R/ltTMatrix.R: new "minimal methods"
1111    
1112    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1115            all methods (and help files).
1116    
1117    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1120                    for case (dimn.  op  no_dimn.)
1121    
1122    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1123    
1124            * DESCRIPTION (Version): 0.99-2  released to CRAN
1125    
1126    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1127    
1128            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1129            by Julian Faraway.
1130    
1131    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/Auxiliaries.R (try_as): new utility
1134            * R/sparseMatrix.R: use try_as() in coercion to original class
1135    
1136    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1139    
1140    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/Auxiliaries.R (dimNamesCheck): added
1143    
1144            * R/Matrix.R (as.array), (as.vector): new
1145    
1146    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1149                    default.
1150            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1151                    "pMatrix" now contains "sparseMatrix"
1152    
1153    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * tests/Class+Meth.R: new tests; t(t(m)) == m
1156    
1157            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1158    
1159            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1160            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1161    
1162            * R/dspMatrix.R: typo in "t" method
1163    
1164    2005-09-18  Douglas Bates  <bates@wisc.edu>
1165    
1166            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1167            * R/Tsparse.R: instead of R/gTMatrix.R
1168            * R/Csparse.R: new
1169            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1170            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1171            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1172                            via cholmod
1173    
1174    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * R/Auxiliaries.R (non0ind): new function using new C code
1177            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1178    
1179    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1180    
1181            * src/chm_common.h: header file required by all C sources that
1182            call CHOLMOD functions.  It defines a cholmod_common structure
1183            called 'c' whose address is passed as the last argument to
1184            (virtually) every CHOLMOD function.
1185    
1186            * src/Pattern.c: Simple example of the use of CHOLMOD.
1187    
1188            * src/init.c: initialize and finalize the cholmod_common structure.
1189    
1190            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1191            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1192    
1193    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1194    
1195            * inst/test-tools.R: new file collecting the utility functions used
1196                    in ./tests/*.R
1197    
1198            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1199            * R/Matrix.R (cbind2): methods for NULL and missing
1200    
1201    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/AllClass.R: new "index" class for "[" and "[<-":
1204                    First cut at "symmetricMatrix" and "triangularMatrix"
1205            * R/gTMatrix.R (.ind.prep): new function;
1206                    Logical and character indexing now work too.
1207            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1208            * tests/indexing.R: new, including *.Rout.save
1209            * tests/dgTMatrix.R: new
1210    
1211    2005-08-29  Douglas Bates  <bates@wisc.edu>
1212    
1213            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1214            indicator pos not being updated.  Also enforced upper triangular
1215            for symmetric case.  Need to coerce edges component of elements of
1216            edge list - grr! (Why don't they define their classes cleanly?)
1217    
1218    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * R/Matrix.R:  added first "[<-" methods; not yet functional
1221            * R/denseMatrix.R: ditto
1222            * man/Subassign-methods.Rd: new help file for these
1223    
1224    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1225    
1226            * DESCRIPTION (Version): 0.98-6
1227    
1228            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1229            matrices.
1230    
1231    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1234                    as( <logical>, "matrix")
1235    
1236            * R/pMatrix.R: coercion to "lgTMatrix"
1237    
1238            * R/gTMatrix.R: new virtual class to define "[" methods for.
1239            * man/gTMatrix-class.Rd:
1240            * General slight re-organization of where "[" methods are defined.
1241              more to come.
1242    
1243    2005-08-18  Douglas Bates  <bates@wisc.edu>
1244    
1245            * DESCRIPTION (Version): 0.98-5  released to CRAN
1246    
1247            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1248            * .....
1249    
1250    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1251    
1252            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1253            or glmer objects.
1254    
1255    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1258    
1259    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1260    
1261            * R/HBMM.R: finish re-writing R-only code.
1262    
1263    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1264    
1265            * man/externalFormats.Rd: move documentation for writeHB and
1266            writeMM here.
1267    
1268            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1269            (suggested by Paul Roecker).
1270    
1271            * tests/validObj.R (assertError): Comment out test that is failing
1272            after recent changes in r-devel.
1273    
1274    
1275    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1276    
1277            * R/AllClass.R: intermediate virtual class "denseMatrix"
1278            * man/denseMatrix-class.Rd
1279            * NAMESPACE: export it, and also export
1280            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1281    
1282    2005-08-10  Douglas Bates  <bates@wisc.edu>
1283    
1284            * DESCRIPTION (Version): 0.98-3 to CRAN
1285    
1286            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1287            matrix_solve code (which was really, really wrong).
1288    
1289    2005-08-07  Douglas Bates  <bates@wisc.edu>
1290    
1291            * DESCRIPTION (Version): 0.98-2
1292    
1293            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1294    
1295            * R/lmer.R (abbrvNms): new
1296            * R/lmer.R (mcmcsamp): allow transformed parameters
1297            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1298            for the Harwell-Boeing and the MatrixMarket formats.
1299    
1300    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * man/dtrMatrix-class.Rd: add examples
1303            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1304    
1305            * TODO: note the dtpMatrix (docu) bug
1306    
1307            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1308            in order to ensure that new as.matrix() is used by old functions,
1309            e.g., svd(), qr(), eigen(), dist(),..;
1310                  apply(), also matplot() or pairs().
1311    
1312    
1313    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1314    
1315            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1316              add comments about 'control' / lmerControl() arguments
1317    
1318    2005-07-27  Douglas Bates  <bates@wisc.edu>
1319    
1320            * man/sleepstudy.Rd: Added the sleep data set.
1321            * DESCRIPTION (Version): 0.98-1  released to CRAN
1322    
1323    2005-07-12  Douglas Bates  <bates@wisc.edu>
1324            * man/sleepstudy.Rd: Added the sleep data set.
1325    
1326            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1327            .Call calls that were producing spurious output.
1328    
1329    2005-07-05  Douglas Bates  <bates@wisc.edu>
1330    
1331            * R/lmer.R (lmer): stored updated variance component estimates in
1332            mer object for the generalized model.  (Bug reported by Renaud
1333            Lancelot).
1334    
1335    2005-07-03  Douglas Bates  <bates@wisc.edu>
1336    
1337            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1338            unidimensional case.
1339    
1340    2005-06-08  Douglas Bates  <bates@wisc.edu>
1341    
1342            * DESCRIPTION (Version): 0.96-1
1343    
1344            * moved  lmer-class' R and C code moved from lme4 to here
1345    
1346    2005-06-04  Douglas Bates  <bates@wisc.edu>
1347    
1348            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1349            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1350    
1351    2005-06-02  Douglas Bates  <bates@wisc.edu>
1352    
1353            * src/Makefile.win: Forgot to update this when Makefile changed.
1354    
1355    2005-05-11  Douglas Bates  <bates@wisc.edu>
1356    
1357            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1358            bug reported by Kurt Hornik and Michael Hahsler.
1359    
1360    2005-05-10  Douglas Bates  <bates@wisc.edu>
1361    
1362            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1363            logical sparse matrices.  These will also be used in the symbolic
1364            analysis for lmer objects.
1365    
1366            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1367            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1368    
1369    2005-05-06  Douglas Bates  <bates@wisc.edu>
1370    
1371            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1372            colMeans, colSums, rowMeans and rowSums.
1373    
1374    2005-04-18  Douglas Bates  <bates@wisc.edu>
1375    
1376            * src/lgCMatrix.[ch]: code for _validate method and stub for
1377            multiplication operation.
1378    
1379            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1380            to dgetrs.
1381    
1382            * src/init.c: Fix cut-and-paste error in definition of
1383            dgeMatrix_matrix_solve
1384    
1385            * src/{many files}: Tighten code by using ALLOC_SLOT.
1386    
1387    2005-04-15  Douglas Bates  <bates@wisc.edu>
1388    
1389            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1390    
1391            * DESCRIPTION: Eliminate import of stats.
1392    
1393    
1394    2005-04-06  Douglas Bates  <bates@wisc.edu>
1395    
1396            * R/AllClass.R : add logical sparse matrix classes
1397    
1398    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1399    
1400            * R/dgTMatrix.R: add "[" method for triplet matrices
1401            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1402    
1403    2005-03-31  Douglas Bates  <bates@wisc.edu>
1404    
1405            * DESCRIPTION (Version): release 0.95-5 to CRAN
1406    
1407            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1408            * R/sparseMatrix.R: %*%, crossprod()
1409            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1410            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1411            * src/lmer.c (lmer_fitted): fix thinko
1412    
1413    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * R/AllClass.R: add two virtual sparse classes ``on top''
1416    
1417    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1420                    correspondingly fix examples and tests/ since new()
1421                    doesn't work for virtual classes.
1422    
1423    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1424    
1425            * R/Matrix.R (as.matrix): method and one for unname()
1426            * tests/dpoMatrix.R: tests should now be less platform dependent;
1427              also run for R 2.1.0; using as.matrix()
1428    
1429    2005-03-15  Douglas Bates  <bates@wisc.edu>
1430    
1431            * R/pMatrix.R: "pMatrix" class added
1432            * ....
1433    
1434    2005-03-14  Douglas Bates  <bates@wisc.edu>
1435    
1436            * R/dtpMatrix.R: Add unpack method and an example.
1437    
1438            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1439            of general symmetric matrices and associated S4 methods.
1440    
1441    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1442            +
1443    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1444    
1445            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1446              crossprod() and "%*%" methods added; tests, too.
1447            * tests/matprod.R: new, for testing these
1448    
1449    2005-03-03  Douglas Bates  <bates@wisc.edu>
1450    
1451            * src/lmer.c (lmer_fitted): Added.
1452    
1453    2005-03-02  Douglas Bates  <bates@wisc.edu>
1454    
1455            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1456    
1457    2005-02-28  Douglas Bates  <bates@wisc.edu>
1458    
1459            * src/*.c,po/,inst/po: Internationalization and localization of
1460            the package.
1461    
1462            * src/ldl.[ch]: Removed these as their contents are referenced in the
1463            R_ldl.c file.
1464    
1465            * src/flame.[ch]: Removed these source files.
1466    
1467            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1468    
1469            * src/LU.[ch],src/init.c: absorb in factorizations
1470    
1471            * src/Mutils.h: prepare for internationalization
1472    
1473            * src/cblas.h: move the enum definitions to Mutils.h and remove
1474            this file
1475    
1476    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1477    
1478            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1479    
1480            * R/dtrMatrix.R: fix t() method
1481    
1482            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1483            * NAMESPACE: export them (and import generics from "methods")
1484            * tests/group-methods.R : and test them.
1485    
1486            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1487            border case
1488    
1489    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1490    
1491            * DESCRIPTION (Version): 0.95-2  released to CRAN
1492    
1493            * src/dgBCMatrix.c:
1494            * src/lmer.c: many changes
1495            * ...
1496    
1497    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1498    
1499            * R/Matrix.R: add more sophisticated show() method.
1500    
1501    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1502    
1503            * */* : almost complete reorganization of classes.
1504    
1505    2005-01-26  Douglas Bates  <bates@wisc.edu>
1506    
1507            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1508            for the geMatrix class.
1509    
1510    2005-01-24  Douglas Bates  <bates@wisc.edu>
1511    
1512            * src/Makefile (clean): Remove *.a and *.so
1513    
1514            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1515    
1516    2005-01-23  Douglas Bates  <bates@wisc.edu>
1517    
1518            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1519            had an effect in cases with more than 2 grouping factors.
1520    
1521    2005-01-03  Douglas Bates  <bates@wisc.edu>
1522    
1523            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1524    
1525    2004-12-23  Douglas Bates  <bates@wisc.edu>
1526    
1527            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1528            and R_useDynamicSymbols (suggested by B.D.Ripley).
1529    
1530    2004-12-14  Douglas Bates  <bates@wisc.edu>
1531    
1532            * R/sscMatrix.R: Add determinant methods
1533    
1534            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1535            for tripletMatrix to matrix.
1536    
1537    2004-12-13  Douglas Bates  <bates@wisc.edu>
1538    
1539            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1540            no longer used.
1541    
1542            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1543            with dynamic allocation of scratch arrays.
1544    
1545            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1546            for multivariate random effects with multiple grouping factors.
1547            Fixes part but not all of #15.
1548    
1549    2004-12-03  Douglas Bates  <bates@wisc.edu>
1550    
1551            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1552            scalar grouping factors corrected.
1553    
1554    2004-11-29  Douglas Bates  <bates@wisc.edu>
1555    
1556            * src/bCrosstab.c: remove diag_update which is no longer used
1557    
1558    2004-11-16  Douglas Bates  <bates@wisc.edu>
1559    
1560            * src/Metis_utils.c: Move metis.h include to C sources so that the
1561            .h file can be included.
1562    
1563    2004-11-12  Douglas Bates  <bates@wisc.edu>
1564    
1565            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1566            Complete allocation of slots in NEW_OBJECT.
1567    
1568            * src/Mutils.h: Moved list of symbols to an include file
1569    
1570    2004-11-11  Douglas Bates  <bates@wisc.edu>
1571    
1572            * src/geMutils.c (Matrix_init): remove unused function
1573    
1574    2004-11-10  Douglas Bates  <bates@wisc.edu>
1575    
1576            * src/cscMatrix.c (csc_to_imagemat): removed unused function
1577    
1578    2004-11-05  Douglas Bates  <bates@wisc.edu>
1579    
1580            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1581    
1582    2004-10-27  Douglas Bates  <bates@wisc.edu>
1583    
1584          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1585    
1586  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1587    
1588          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1589          routines.          routines.
1590    
1591  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1592    
1593          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1594    
1595  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1596    
1597          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1598    

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