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revision 726, Thu May 12 14:59:04 2005 UTC revision 1714, Thu Dec 28 22:11:32 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
4            file; start using "Logic", hence
5    
6            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
7            * NAMESPACE: import and export "Logic"
8    
9    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
12            only needed previously to R version 2.5.0.
13    
14    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
17    
18            * R/Tsparse.R (replTmat): fix subassignment of triangular
19            * R/Csparse.R (replCmat): ditto
20            * tests/indexing.R: more tests, incl the above fix
21    
22    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Auxiliaries.R (drop0): extend for non CSparse
25            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
26    
27            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
28                    use uplo correctly (!); other places: use uplo_P() macro
29    
30            * R/Csparse.R (replCmat): call diagU2N() when needed
31            * R/Tsparse.R (replTmat): ditto
32    
33            * src/dtCMatrix.c (tCMatrix_validate): new
34            * src/dtTMatrix.c (tTMatrix_validate): new, used in
35            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
36    
37            * R/diagMatrix.R (replDiag): to use in [<-
38    
39    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
42                    also more general diagU2N().
43    
44    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
47            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
48    
49    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * tests/bind.R: a few more cases
52            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
53    
54            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
55            * R/ddenseMatrix.R (cbind2/rbind2)
56            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
57            * tests/indexing.R
58            * tests/indexing.Rout.save: updated
59    
60    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
63            * tests/indexing.R
64    
65    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
68            align with proper position of "0", i.e., right for integers.
69            argument 'align' by default is "fancy".
70    
71    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
74            * R/Csparse.R: and fix "Compare" for more cases.
75            * tests/Class+Meth.R: test some of these (m == m, m != m)
76    
77    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/lsparseMatrix.R: all() and any() methods
80            * R/ldenseMatrix.R:      ditto
81            * NAMESPACE, R/Matrix.R: ditto
82    
83            * man/all-methods.Rd: document them minimally
84    
85            * tests/simple.R: add a few examples for these
86    
87    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Tsparse.R ([): fix long standing typo in symmetric case
90            * man/dsCMatrix-class.Rd: add example exhibiting the above case
91    
92    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
95            to LL before converting to a sparse matrix. (The LDL form can be
96            converted to a sparse matrix but it is implicitly a unit
97            triangular matrix and a diagonal matrix overwritten on the diagonal.)
98    
99    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
102    
103    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
104    
105            * DESCRIPTION (Version): updated -> release 0.9975-7
106            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
107    
108    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
111    
112    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
113    
114            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
115            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
116            is exactly singular.
117    
118    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Date): updated -> release 0.9975-6
121    
122    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
125            now returns symmetric.
126    
127            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
128    
129            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
130            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
131    
132            * R/Auxiliaries.R (.type.kind): added
133    
134    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
137            running src/CSparse_install.sh
138    
139            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
140    
141    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
144            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
145    
146            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
147    
148            * tests/Class+Meth.R (tstMatrixClass): now assure
149            the (important in method programming) property :
150    
151                    ###>>  Every "Matrix" is either
152                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
153    
154                    (where "*" stands for "Matrix")
155    
156            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
157    
158            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
159            * tests/validObj.R: checks for "comparison"
160    
161            * R/sparseMatrix.R ([): improved indexing for sparse;
162                    trying to keep <symmetric>[ n, n] symmmetric
163    
164            * tests/indexing.R: indexing for logical sparse now ok
165    
166    
167    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/Tsparse.c: use xTsparse_validate() , and hence remove
170    
171            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
172    
173    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
176    
177            * tests/simple.R: validObject() checking the above.
178    
179            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
180            replacing both dgCMatrix_validate and lgCM*.
181    
182            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
183            fix dimnames setting in other places.
184            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
185    
186    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
189    
190            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
191            symmetry test, via
192            * R/Auxiliaries.R (.as.dgC.0.factors):
193    
194    2006-11-01  Douglas Bates  <bates@r-project.org>
195    
196            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
197            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
198            <CsparseMatrix>) added
199    
200    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * tests/matprod.R: add a variation of Harri's example
203    
204            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
205            recursive infinitely.
206    
207            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
208    
209            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
210    
211    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
214            matrix if possible; test m+m == 2*m; now test dgRMatrix.
215            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
216            satisfy the above test.
217    
218    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
221    
222            * R/dgCMatrix.R: solve(a, b="missing") based on
223            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
224            RHS = NULL.
225    
226            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
227            add more (needed) [t]crossprod() methods.
228    
229            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
230    
231            * R/Auxiliaries.R (as_CspClass): cleanup
232            (drop0): internal utility for "Csparse_drop(*, 0)"
233            (.bail.out.2): encourage active feedback
234    
235    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/dMatrix.R(Compare): new(), then slots [no validity check]
238    
239            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
240            non-valid or 'sorted' case).
241    
242            * R/dsparseMatrix.R: add "chol" method.
243            * R/ddenseMatrix.R: ditto
244    
245            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
246            * NAMESPACE (Ops)
247            * R/diagMatrix.R (diag2T): simple utility used "higher level"
248            coercion; deprecating direct lower level coercions.
249    
250            * R/*.R (seq): use seq_len() and seq_along() where possible.
251    
252    
253    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * DESCRIPTION (Version): 0.9975-5 ready for release
256    
257    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
260    
261    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/AllClass.R (corMatrix): add 'validity' check;
264                    comment out unused "LDL" class definition
265            * NAMESPACE: mention, but do not export "LDL" class
266            * R/corMatrix.R: new (simple), needed for R-devel with
267            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
268              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
269    
270    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
273            use Rprintf and R's error handling.
274    
275    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
278            * tests/matprod.R: add tests for the bug fixed.
279    
280    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
283            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
284    
285    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
288    
289    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * DESCRIPTION (Version): 0.9975-3
292    
293            * R/diagMatrix.R (bdiag): new function constructing block diagonal
294            (sparse) matrices.
295            * man/bdiag.Rd: docu + examples
296    
297            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
298    
299            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
300            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
301    
302            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
303            that result is sparse or diagonal (and not dense).
304    
305            * man/Subassign-methods.Rd: fix examples
306    
307            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
308            should always return a sparse (and not sometimes a diagonal) matrix.
309    
310    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
313    
314    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * DESCRIPTION (Version): 0.9975-2
317    
318            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
319    
320    2006-10-02  Douglas Bates  <bates@R-project.org>
321    
322            * tests/dg_Matrix.R: Simplify test taking into account new code.
323    
324    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
327    
328            * R/lsTMatrix.R: new files w/ missing methods
329            * R/nsTMatrix.R:  "  'for completeness'
330    
331            * tests/Class+Meth.R: a bit less 'not.ok.classes'
332    
333            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
334    
335    
336    2006-09-28  Douglas Bates  <bates@R-project.org>
337    
338            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
339            included.
340    
341            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
342            Export C-callable functions used in Zt_create in lme4.
343    
344    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.9975-1
347    
348            * tests/simple.R: less checks fail; using NA, found that our
349                    kronecker() is not base-compatible with NA's.
350    
351            * R/dMatrix.R: "Compare" method now implemented for all cases
352    
353            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
354    
355            * man/dtpMatrix-class.Rd: mention length of 'x' slot
356    
357            * src/dtpMatrix.c (dtpMatrix_validate): fix check
358            * src/dspMatrix.c (dspMatrix_validate): ditto
359    
360            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
361              including coercion to [nl]tTMatrix.
362    
363            * R/diagMatrix.R (show): print a header line as for other classes.
364    
365    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * src/Makefile.win (SUBDIRS): fix typo
368    
369    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
372    
373    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
374    
375            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
376            symmetric and y missing in R code using %*% (cholmod_aat doesn't
377            accept a symmetric matrix).
378            * tests/group-methods.R: Uncomment test of crossprod applied to
379            lsCMatrix objects.
380    
381    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/AllClass.R (symmetricMatrix): add validity method (available
384            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
385    
386            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
387    
388            * tests/indexing.Rout.save:
389            * tests/indexing.R: additions, mainly for 'lsparse'
390    
391            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
392            case.
393    
394            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
395    
396    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
399                    as 'N' (1-letter - Ok?)
400    
401            * tests/group-methods.R: add test for logical + NAs
402    
403            * R/dMatrix.R ("Compare"): fix to work with NA's
404    
405            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
406    
407            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
408                    which is implemented.
409    
410    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/chm_common.c: coerce logical <-> double instead of
413            typecasting;  needed for "l" matrix handling in cholmod.
414    
415            * tests/other-pkgs.R (graph): small extension in "graph" checks.
416    
417            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
418            (Tsp2grNEL): other fixes needed
419    
420    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
423                    Matrices, since "lMatrix", also "lsparseM" can have NA
424            * R/ndenseMatrix.R, etc: new source files
425            * man/nsparseMatrix-classes.Rd, etc: new help files
426            * tests/: adaptions
427            * src/chm_common.c (chm_dense_to_SEXP): and others:
428                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
429            * src/Csparse.c, etc: ditto
430    
431    2006-09-11  Douglas Bates  <bates@R-project.org>
432    
433            * src/Mutils.[ch],init.c inst/include/*.h: Move the
434            alloc_d**Matrix functions to the lme4 package.
435    
436    2006-09-09  Douglas Bates  <bates@R-project.org>
437    
438            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
439            fixed
440    
441    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/lMatrix.R: new
444    
445            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
446    
447            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
448            * man/tcrossprod.Rd: ditto
449    
450    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
453            for exported functions
454            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
455            Remove partitioning algorithms for sparse matrix reordering.  The
456            copyright on the Metis code was problematic and the methods were
457            rarely used.
458            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
459            operations are now done entirely in CHOLMOD code.
460    
461    2006-09-06  Douglas Bates  <bates@R-project.org>
462    
463            * src/Mutils.h: Remove functions that are no longer used.
464    
465    2006-09-04  Douglas Bates  <bates@R-project.org>
466    
467            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
468            * src/DEPS.mkf: update
469    
470    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * created branches/Matrix-for-R-2.3.x;  on trunk: do
473            * DESCRIPTION (Version): 0.9975-0
474            (Depends): R (>= 2.4.0)
475    
476    2006-09-01  Douglas Bates  <bates@R-project.org>
477    
478            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
479    
480    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
483            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
484    
485            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
486    
487    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
490            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
491            * R/dsparseMatrix.R: ditto
492            * R/Csparse.R: ditto
493    
494    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/dMatrix.R (Compare): improve availability of "<", etc
497            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
498    
499    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
502            of a 0-index which was used as 1-index (..hmm)
503    
504            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
505    
506            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
507            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
508            (.is.diagonal): ditto
509    
510            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
511    
512            * R/Matrix.R (Matrix): also work for NA data
513    
514    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
517            in all cases.
518    
519    2006-08-27  Douglas Bates  <bates@R-project.org>
520    
521            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
522            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
523    
524    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
527            subclasses of "ddenseMatrix"
528            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
529            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
530            instead of half dozen specialized ones.
531    
532    2006-08-25  Douglas Bates  <bates@R-project.org>
533    
534            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
535            <tillard@cirad.fr> - ordering standard errors to match effects.
536    
537    2006-08-24  Douglas Bates  <bates@R-project.org>
538    
539            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
540            on R_ldl.
541            * R/lCholCMatrix.R,
542            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
543            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
544            * many files in ./R and ./src: Use more general version of
545            dup_mMatrix_as_dgeMatrix to simplify method definitions.
546            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
547            dtpMatrix, dspMatrix and dppMatrix conversions.
548    
549    
550    2006-08-23  Douglas Bates  <bates@R-project.org>
551    
552            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
553            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
554            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
555            dgeMatrix_crossprod (may need to do this in other places).
556            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
557            generic and method for dsCMatrix.  Use CHOLMOD for chol().
558    
559    2006-08-22  Douglas Bates  <bates@R-project.org>
560    
561            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
562            types of classed Matrices, matrices or numeric or logical vectors.
563            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
564            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
565            to Mutils.h (as an inline) and change name to Matrix_check_class;
566            fixes in as_cholmod_factor and chm_factor_to_SEXP.
567            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
568            dsCMatrix_matrix_solve.  Comment out vestigial functions.
569            * src/Csparse.c: use diag_P and uplo_P macros.
570    
571    2006-08-21  Douglas Bates  <bates@R-project.org>
572    
573            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
574            valgrind.
575            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
576            inverses.
577            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
578            -Wall warnings.
579            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
580            Use dup_mMatrix_as_dgeMatrix.
581    
582    2006-08-20  Douglas Bates  <bates@R-project.org>
583    
584            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
585            * tests/sparseQR.R: Added
586            * man/sparseQR-class.Rd: Document methods for qr.* generics
587            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
588    
589    2006-08-19  Douglas Bates  <bates@R-project.org>
590    
591            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
592            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
593            and qr.fitted.
594            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
595            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
596    
597    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
600            the base version has no "..." argument.
601    
602            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
603    
604            * R/Matrix.R: define and
605            * NAMESPACE: export as.numeric() and as.logical() methods.
606                    Let's hope these do not badly slow down something...
607            Finally export the zapsmall() method.
608    
609    2006-08-17  Douglas Bates  <bates@R-project.org>
610    
611            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
612            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
613            * src/dtCMatrix.c :Remove code that is no longer used
614            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
615    
616    2006-08-14  Douglas Bates  <bates@R-project.org>
617    
618            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
619            Csparse_to_logical and Csparse_symmetric_to_general.
620            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
621            coercion methods between CsparseMatrix and TsparseMatrix.
622    
623    2006-08-14  Douglas Bates  <bates@R-project.org>
624    
625            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
626            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
627            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
628            possible.
629    
630    2006-08-12  Douglas Bates  <bates@R-project.org>
631    
632            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
633              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
634              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
635              generalize conversions between TsparseMatrix, CsparseMatrix,
636              denseMatrix and matrix.  Preserve triangularity property and
637              propagate Dimnames in the easy cases.
638    
639    2006-08-10  Douglas Bates  <bates@R-project.org>
640    
641            * src/lmer.c: adjust checks in glmer_init for S4SXP
642            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
643            before S4SXP but for the wrong reasons.
644    
645    2006-08-08  Douglas Bates  <bates@R-project.org>
646    
647            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
648            Later modified to return the upper triangle only.
649            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
650    
651    2006-08-07  Douglas Bates  <bates@R-project.org>
652    
653            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
654            R-level conversion to a sparse symmetric class.
655            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
656            Remove conversion to sparse symmetric classes (now done in C code).
657    
658    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
661            * man/band.Rd:  adapt the \dontshow{} unit test.
662    
663    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * DESCRIPTION (Version): 0.995-14  for CRAN
666    
667            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
668    
669            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
670            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
671    
672            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
673            * R/Tsparse.R (tril, triu, band): methods
674            * R/dgRMatrix.R (tril, ...):    ditto
675            * man/band.Rd:                  ditto
676    
677    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/Matrix.R (head, tail): directly use utils:::head.matrix
680                    to be up-to-date automatically.
681    
682    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
685    
686            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
687            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
688            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
689            such that the S4 objects are always created by the current version
690            of R and 'Matrix' class definitions.
691    
692    2006-08-01  Douglas Bates  <bates@R-project.org>
693    
694            * R/lmer.R (LMEoptimize method), tests/lmer.R,
695            inst/external/test3comp.rda: Added warnings for convergence on
696            boundary and test cases.
697    
698            * src/lmer.c (mer_postVar): Modified to return the variances that
699            are marginal to the fixed effects, not conditional on them (which
700            is what the bVar slot contents represent).
701    
702    2006-07-31  Douglas Bates  <bates@R-project.org>
703    
704            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
705            function which calls the C function mer_hat_trace2.
706    
707            * man/ranef.Rd: Include description of "postVar" argument and
708            producing a caterpillar plot.
709    
710    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * NAMESPACE:    change  "correlation" to "corMatrix"
713            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
714            * R/dpoMatrix.R: ditto
715            * R/lmer.R:      ditto
716    
717    2006-07-28  Douglas Bates  <bates@R-project.org>
718    
719            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
720            RZXinv slot's contents into a separate internal function that can
721            be used in mer_hat_trace.
722    
723    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
726            via new smart
727            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
728            utility functions.
729    
730    
731    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/Csparse.R (tril, triu, band): do return *triangular* classed
734            matrices when appropriate; band() even symmetric ones.
735            (replCmat): extend to potentially all "CsparseMatrix"
736            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
737            allow subassignment for special sparse matrices.
738    
739            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
740    
741            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
742            argument; in glmer_*(): print only if(verbose).
743    
744            speed-optimize a few places by moving REAL(.) out of loops.
745    
746            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
747    
748    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
751                    since that wrongly triggers also for M[ logi , ]
752    
753            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
754            a symmetric matrix that results in a non-symmetric one.
755            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
756    
757            * R/dMatrix.R: make round(M) work as round(M, 0)
758    
759            * R/dgTMatrix.R (image): coordinate system and axis now use
760            1-based indices, not 0-based ones.
761    
762            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
763            * tests/indexing.R: test it.
764    
765            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
766            * man/isSymmetric-methods.Rd: and document it.
767    
768            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
769            * man/SparseM-conv.Rd: docu them
770    
771            * tests/other-pkgs.R: renamed from tests/graph.R and add example
772                    for 'SparseM' conversions
773    
774    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
775    
776            * R/Matrix.R (head): added head() and tail() methods.
777    
778    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * DESCRIPTION (Version): 0.995-12 released to CRAN
781    
782    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * tests/simple.R: add check for correct dsT -> dgT coercion;
785                    add check for correct printing of symmetric sparse matrices.
786    
787            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
788            for sparse symmetric matrices.
789    
790            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
791            diagonal twice.
792    
793    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
794    
795            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
796            being applied to the x slot (detected by Brian Ripley).
797    
798    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
801    
802            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
803    
804    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * src/lgCMatrix.c (lgCMatrix_diag): new function
807            * R/lgCMatrix.R (diag): for new method
808    
809            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
810                 ==> construction of illegal "*gTMatrix" via new() should
811                 now be much less easy:
812            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
813    
814            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
815                    directly.
816            * man/Matrix.Rd: documents it.
817    
818    2006-07-06  Douglas Bates  <bates@R-project.org>
819    
820            * src/pedigree.c (pedigree_inbreeding): Correction in
821            initialization.  This function is not currently being used and is
822            not fully tested.
823    
824            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
825            Introduced the glmer class.  Added code for mcmcmsamp on glmer
826            objects.  Modified validity check on pedigree objects to account
827            for nonparallel patterns of missingness of parents.
828    
829            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
830            class.
831    
832    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/pMatrix.R: coercion pMatrix -> Tsparse
835    
836    2006-06-12  Douglas Bates  <bates@R-project.org>
837    
838            * DESCRIPTION (Version): 0.995-11 released to CRAN
839    
840            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
841            the output from mcmcsamp.
842    
843    2006-06-10  Douglas Bates  <bates@R-project.org>
844    
845            * R/lmer.R (simulestimate): added C code for calculating the trace
846            of the hat matrix.
847    
848    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
851            classes.
852            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
853    
854    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/dgTMatrix.R (colSums): etc. All four of
857            colSums(), rowSums(), colMeans(), rowMeans() now should work for
858            all "Matrices".
859    
860    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
861    
862            * R/lmer.R (panel.ci): Add a reference line at zero and a
863            background grid to the qqmath plot of ranef.lmer.
864    
865    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
868            grouping factors to be specified in the formula as (1|foo/bar).
869    
870    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
871    
872            * R/lmer.R (findbars and others): Change check of is.numeric to
873            !is.language to resolve the bug reported by Jacob Wegelin.
874    
875            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
876            code to evaluate inbreeding coefficients without calculating T,
877            based on code in Sargolzaei and Iwaisaki's paper.
878    
879    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
880    
881            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
882            generic and mer methods for isNested and denomDF. This denomDF was
883            an attempt to emulate that in lme but I don't think that makes
884            sense.  Use the trace of the hat matrix instead.
885    
886    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
889            the C code depending on a slot structure that's no longer valid.
890            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
891    
892    
893    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
894    
895            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
896            of lowerTriMatrix generic and methods to tril (also upper to triu)
897            and added a general band extractor.
898    
899    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * R/pedigree.R (pedigree): Replace sire and dam values outside the
902            allowable range with NAs. Added a corresponding check in the
903            validity check for the pedigree class.
904    
905            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
906            crossprod methods now inherits from symmetricMatrix.
907    
908    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
909    
910            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
911            generics lowerTriMatrix and upperTriMatrix along with methods for
912            the Csparse virtual class.  Also added a C function Csparse_band
913            that implements these methods by calling cholmod_band.
914    
915    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
918            erased when it was NULL.  This led to invalid subselections!
919    
920    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
921    
922            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
923            in method for "t" so as not to lose the unit diagonal property.
924    
925    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
926    
927            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
928            and methods.  This is now an option to the ranef method for the
929            mer class.
930    
931            * src/cs_utils.c: Ensure that the nz component is -1 for a
932            compressed column-oriented matrix.  Minor formatting cleanup.
933    
934            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
935            objects.
936    
937    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
940            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
941    
942    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
943    
944            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
945            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
946    
947            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
948            for the dtCMatrix class.
949    
950    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
951    
952            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
953            and methods for it.
954    
955    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
958            arguments, such that M %*% 1:6 now works
959            * Tests/matprod.R: test the above
960    
961    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
962    
963            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
964            the ranef.lmer class.
965    
966            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
967            methods to extract the posterior variances from the bVar slot.
968    
969    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
972            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
973    
974            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
975            * tests/simple: (extended)
976    
977            * R/sparseMatrix.R (isTriangular): now using much improved
978            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
979    
980    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
981    
982            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
983            (problem report from Franklin Parlamis).  This should be done
984            generally.
985    
986    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
987    
988            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
989            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
990            update the plot methods.
991    
992    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
993    
994            * R/lmer.R (resid and ranef methods):  Added methods for the
995            "residuals" and "resid" generic but only for linear mixed model
996            fits.  Changed the ranef method to return a list of data frames so
997            that the plot methods now work.
998    
999    2006-03-16  Douglas Bates  <bates@bates2>
1000    
1001            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1002            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1003    
1004            * DESCRIPTION (Date): New release
1005    
1006    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1009    
1010            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1011            * man/KNex.Rd: and other help files
1012            * tests/*.R: several ones needed adaption
1013            * inst/doc/Comparisons.Rnw: ditto
1014    
1015    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1018    
1019            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1020    
1021    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1024    
1025            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1026    
1027    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * R/dMatrix.R: enable things like  M [ M < 10 ]
1030            * R/dgeMatrix.R: implement it
1031    
1032    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/AllClass.R: define "summary.mer" and "*.lmer"
1035            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1036            * R/lmer.R (show): now works with summary()
1037    
1038    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1041            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1042                    support the above
1043    
1044    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1045    
1046            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1047            Use glmFit$prior.weights for weights in a glmm.
1048            Allow an option usePQL = FALSE to skip the PQL steps for the
1049            Laplace method (and, in time, the AGQ method).
1050    
1051            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1052            into a separate function internal_mer_Xfactor to be able to call
1053            it from internal_bhat.
1054    
1055    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * tests/Class+Meth.R (tstMatrixClass): function for much better
1058            testing; now again of all actual classes.
1059    
1060            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1061                    use macros and define make_d_matrix_* and make_i_matrix_*
1062                    where _i_ is for the ldense routines:
1063    
1064            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1065            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1066    
1067            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1068    
1069    
1070    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1073                    many different kinds of matrices.
1074            * R/*.R: quite a few new methods were needed for R CMD check with
1075                    new Matrix().  Very good for users playing around.
1076    
1077    
1078    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * src/dgeMatrix.c (dMatrix_validate): new
1081            * src/Mutils.c (dense_nonpacked_validate): new
1082    
1083            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1084    
1085    
1086    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1087    
1088            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1089    
1090    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1091    
1092            * DESCRIPTION (Version): 0.99-6 released to CRAN
1093    
1094            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1095            segfault in cases with multiple non-nested grouping factors.
1096    
1097    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1100                    (Depends): also on 'utils'
1101    
1102            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1103            * R/diagMatrix.R (Diagonal): constructor and methods for
1104            diagonal matrices
1105    
1106            * R/ltTMatrix.R: new "minimal methods"
1107    
1108    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1111            all methods (and help files).
1112    
1113    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1116                    for case (dimn.  op  no_dimn.)
1117    
1118    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1119    
1120            * DESCRIPTION (Version): 0.99-2  released to CRAN
1121    
1122    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1123    
1124            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1125            by Julian Faraway.
1126    
1127    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/Auxiliaries.R (try_as): new utility
1130            * R/sparseMatrix.R: use try_as() in coercion to original class
1131    
1132    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1135    
1136    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * R/Auxiliaries.R (dimNamesCheck): added
1139    
1140            * R/Matrix.R (as.array), (as.vector): new
1141    
1142    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1145                    default.
1146            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1147                    "pMatrix" now contains "sparseMatrix"
1148    
1149    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * tests/Class+Meth.R: new tests; t(t(m)) == m
1152    
1153            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1154    
1155            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1156            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1157    
1158            * R/dspMatrix.R: typo in "t" method
1159    
1160    2005-09-18  Douglas Bates  <bates@wisc.edu>
1161    
1162            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1163            * R/Tsparse.R: instead of R/gTMatrix.R
1164            * R/Csparse.R: new
1165            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1166            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1167            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1168                            via cholmod
1169    
1170    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/Auxiliaries.R (non0ind): new function using new C code
1173            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1174    
1175    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1176    
1177            * src/chm_common.h: header file required by all C sources that
1178            call CHOLMOD functions.  It defines a cholmod_common structure
1179            called 'c' whose address is passed as the last argument to
1180            (virtually) every CHOLMOD function.
1181    
1182            * src/Pattern.c: Simple example of the use of CHOLMOD.
1183    
1184            * src/init.c: initialize and finalize the cholmod_common structure.
1185    
1186            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1187            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1188    
1189    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1190    
1191            * inst/test-tools.R: new file collecting the utility functions used
1192                    in ./tests/*.R
1193    
1194            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1195            * R/Matrix.R (cbind2): methods for NULL and missing
1196    
1197    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/AllClass.R: new "index" class for "[" and "[<-":
1200                    First cut at "symmetricMatrix" and "triangularMatrix"
1201            * R/gTMatrix.R (.ind.prep): new function;
1202                    Logical and character indexing now work too.
1203            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1204            * tests/indexing.R: new, including *.Rout.save
1205            * tests/dgTMatrix.R: new
1206    
1207    2005-08-29  Douglas Bates  <bates@wisc.edu>
1208    
1209            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1210            indicator pos not being updated.  Also enforced upper triangular
1211            for symmetric case.  Need to coerce edges component of elements of
1212            edge list - grr! (Why don't they define their classes cleanly?)
1213    
1214    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1215    
1216            * R/Matrix.R:  added first "[<-" methods; not yet functional
1217            * R/denseMatrix.R: ditto
1218            * man/Subassign-methods.Rd: new help file for these
1219    
1220    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1221    
1222            * DESCRIPTION (Version): 0.98-6
1223    
1224            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1225            matrices.
1226    
1227    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1230                    as( <logical>, "matrix")
1231    
1232            * R/pMatrix.R: coercion to "lgTMatrix"
1233    
1234            * R/gTMatrix.R: new virtual class to define "[" methods for.
1235            * man/gTMatrix-class.Rd:
1236            * General slight re-organization of where "[" methods are defined.
1237              more to come.
1238    
1239    2005-08-18  Douglas Bates  <bates@wisc.edu>
1240    
1241            * DESCRIPTION (Version): 0.98-5  released to CRAN
1242    
1243            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1244            * .....
1245    
1246    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1247    
1248            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1249            or glmer objects.
1250    
1251    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1254    
1255    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1256    
1257            * R/HBMM.R: finish re-writing R-only code.
1258    
1259    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1260    
1261            * man/externalFormats.Rd: move documentation for writeHB and
1262            writeMM here.
1263    
1264            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1265            (suggested by Paul Roecker).
1266    
1267            * tests/validObj.R (assertError): Comment out test that is failing
1268            after recent changes in r-devel.
1269    
1270    
1271    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * R/AllClass.R: intermediate virtual class "denseMatrix"
1274            * man/denseMatrix-class.Rd
1275            * NAMESPACE: export it, and also export
1276            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1277    
1278    2005-08-10  Douglas Bates  <bates@wisc.edu>
1279    
1280            * DESCRIPTION (Version): 0.98-3 to CRAN
1281    
1282            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1283            matrix_solve code (which was really, really wrong).
1284    
1285    2005-08-07  Douglas Bates  <bates@wisc.edu>
1286    
1287            * DESCRIPTION (Version): 0.98-2
1288    
1289            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1290    
1291            * R/lmer.R (abbrvNms): new
1292            * R/lmer.R (mcmcsamp): allow transformed parameters
1293            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1294            for the Harwell-Boeing and the MatrixMarket formats.
1295    
1296    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1297    
1298            * man/dtrMatrix-class.Rd: add examples
1299            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1300    
1301            * TODO: note the dtpMatrix (docu) bug
1302    
1303            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1304            in order to ensure that new as.matrix() is used by old functions,
1305            e.g., svd(), qr(), eigen(), dist(),..;
1306                  apply(), also matplot() or pairs().
1307    
1308    
1309    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1310    
1311            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1312              add comments about 'control' / lmerControl() arguments
1313    
1314    2005-07-27  Douglas Bates  <bates@wisc.edu>
1315    
1316            * man/sleepstudy.Rd: Added the sleep data set.
1317            * DESCRIPTION (Version): 0.98-1  released to CRAN
1318    
1319    2005-07-12  Douglas Bates  <bates@wisc.edu>
1320            * man/sleepstudy.Rd: Added the sleep data set.
1321    
1322            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1323            .Call calls that were producing spurious output.
1324    
1325    2005-07-05  Douglas Bates  <bates@wisc.edu>
1326    
1327            * R/lmer.R (lmer): stored updated variance component estimates in
1328            mer object for the generalized model.  (Bug reported by Renaud
1329            Lancelot).
1330    
1331    2005-07-03  Douglas Bates  <bates@wisc.edu>
1332    
1333            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1334            unidimensional case.
1335    
1336    2005-06-08  Douglas Bates  <bates@wisc.edu>
1337    
1338            * DESCRIPTION (Version): 0.96-1
1339    
1340            * moved  lmer-class' R and C code moved from lme4 to here
1341    
1342    2005-06-04  Douglas Bates  <bates@wisc.edu>
1343    
1344            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1345            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1346    
1347    2005-06-02  Douglas Bates  <bates@wisc.edu>
1348    
1349            * src/Makefile.win: Forgot to update this when Makefile changed.
1350    
1351    2005-05-11  Douglas Bates  <bates@wisc.edu>
1352    
1353          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1354          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1355    
1356  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1357    
1358          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1359          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1362 
1362          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1363          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1364    
1365  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1366    
1367          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1368          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1369    
1370  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1371    
1372          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1373          multiplication operation.          multiplication operation.
# Line 30  Line 1380 
1380    
1381          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1382    
1383  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1384    
1385          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1386    
1387          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1388    
1389    
1390  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1391    
1392          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1393    
# Line 46  Line 1396 
1396          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1397          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1398    
1399  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1400    
1401          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1402    
# Line 72  Line 1422 
1422          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1423            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1424    
1425  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1426    
1427          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1428          * ....          * ....
1429    
1430  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1431    
1432          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1433    
# Line 92  Line 1442 
1442            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1443          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1444    
1445  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1446    
1447          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1448    
1449  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1450    
1451          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1452    
1453  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1454    
1455          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1456          the package.          the package.
# Line 148  Line 1498 
1498    
1499          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1500    
1501  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1502    
1503          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1504          for the geMatrix class.          for the geMatrix class.
1505    
1506  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1507    
1508          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1509    
1510          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1511    
1512  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1513    
1514          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1515          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1516    
1517  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1518    
1519          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1520    
1521  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1522    
1523          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1524          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1525    
1526  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1527    
1528          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1529    
1530          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1531          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1532    
1533  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1534    
1535          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1536          no longer used.          no longer used.
# Line 192  Line 1542 
1542          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1543          Fixes part but not all of #15.          Fixes part but not all of #15.
1544    
1545  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1546    
1547          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1548          scalar grouping factors corrected.          scalar grouping factors corrected.
1549    
1550  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1551    
1552          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1553    
1554  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1555    
1556          * 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
1557          .h file can be included.          .h file can be included.
1558    
1559  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1560    
1561          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1562          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1563    
1564          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1565    
1566  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1567    
1568          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1569    
1570  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1571    
1572          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1573    
1574  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1575    
1576          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1577    
1578  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1579    
1580          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1581    
1582  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1583    
1584          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1585          routines.          routines.
1586    
1587  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1588    
1589          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1590    
1591  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1592    
1593          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1594    

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