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revision 687, Fri Apr 1 07:36:09 2005 UTC revision 1803, Tue Mar 27 16:43:22 2007 UTC
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1    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: new file collecting kronecker() methods in one
4                    place.  Goal: become much faster!
5    
6    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
9            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
10            can be much faster.
11    
12            * tests/matprod.R: add regression tests for these (upper & lower).
13    
14    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Matrix.R (diff): method for our Matrices.
17    
18            * R/sparseMatrix.R (isDiagonal): check dim()!
19    
20    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (dim<-): new method for "reshape()" built on a
23            proposal from Tamas Papp.
24    
25    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
28    
29            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
30            rather define and export  cBind() and rBind() only.
31            --> useRs *must* change code that used to have cbind()/rbind() !!
32    
33            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
34            * R/bind.Rout.save: ditto
35    
36    2007-02-16  Douglas Bates  <bates@r-project.org>
37    
38            * DESCRIPTION (Date, Version): 0.9975-11 with new date
39            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
40            const modifier on declaration of the array 'valid'
41    
42    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
45    
46    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
49    
50            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
51            * tests/simple.R: test the above and some of these coercions:
52    
53            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
54                    be careful to avoid infinite recursion, using new coercions in
55            * R/ngCMatrix.R and nsC... and ntC...
56            * R/lsparseMatrix.R: ditto
57    
58            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
59    
60            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
61            * R/Rsparse.R: reactivate .Call()s
62    
63            * tests/Class+Meth.R: a bit more on actual classes
64    
65    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
68    
69    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.9975-10 to upload
72    
73            * tests/Class+Meth.R (tstMatrixClass): require coercions to
74            specific classes less unconditionally.
75    
76            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
77    
78            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
79    
80            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
81            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
82            R_to_CMatrix segfaults on one platform.
83            Eliminate most coercion method to *specific* classes, and replace
84            with virtual classes coercions.
85    
86    
87    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * src/init.c: export the CHM...._validate() placeholders, since
90            they *are* called.
91    
92            * tests/Class+Meth.R (classCanCoerce): and starting to test
93            all as(<from>, <to>)
94    
95    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
98            * tests/indexing.R: tested now
99            * tests/indexing.Rout.save: updated
100    
101            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
102            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
103            appropriate.
104    
105            * NAMESPACE: export a trivial
106            * R/Matrix.R: drop() Matrix-method
107    
108            * R/AllClass.R: moved all prototypes to virtual super classes.
109    
110            * R/Rsparse.R: many more coercions to have less exceptions in
111            * tests/Class+Meth.R:
112    
113            * R/Ops.R (Compare): tweak for case with NA
114            * tests/simpl.R: hence another 'FIXME' eliminated
115    
116    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
119            objects.
120    
121            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
122              and more of "!", "&", "|", all, any; coercions
123    
124            * R/Rsparse.R: many coercions (which enable quite a few other
125            methods), thanks to enhancements in
126            * src/dgCMatrix.c (R_to_CMatrix): new, and
127            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
128            symmetric & triangular and ..RMatrix objects.
129    
130            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
131            renamed file from src/dsTMatrix.c;
132            now dealing with symmetric and triangular Tsparse coercions, both
133            to dense and general.
134    
135    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
138    
139            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
140            where sensible when the <numeric> is of length > 1.
141    
142    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R ([<-): for M[] <- value: fix length
145    
146    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
149            * R/ndenseMatrix.R: new coercions n* -> l*
150    
151    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
154    
155            * R/Ops.R ("Logic"): and other "Ops", many updates
156    
157    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * src/Mutils.h (SET_DimNames): new utility
160    
161            * R/Auxiliaries.R (nnzero): improved and now exported via
162    
163            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
164    
165    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (!): fix typo.
168    
169    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (as_Csparse): and quite a few others:
172                    allow to pass class definition --> speedup
173            * R/sparseMatrix.R: apply the above
174    
175            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
176    
177            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
178            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
179            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
180    
181            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
182    
183            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
184            and use it for "sparse*" as well, since it's faster than the
185            as_Csparse(.) way.
186    
187    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
190    
191    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
194            as method for   M[ ij ] <- v
195            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
196    
197            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
198            FALSE answer
199    
200            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
201            * tests/indexing.R: test it, and some of the above
202    
203    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (is_duplicatedT): new utility
206    
207    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * src/init.c (R_init_Matrix): export cholmod_scale
210    
211    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
214            base::as.matrix to (x, ...)
215    
216    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
219            file; start using "Logic", hence
220    
221            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
222            * NAMESPACE: import and export "Logic"
223    
224    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
227            only needed previously to R version 2.5.0.
228    
229    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
232    
233            * R/Tsparse.R (replTmat): fix subassignment of triangular
234            * R/Csparse.R (replCmat): ditto
235            * tests/indexing.R: more tests, incl the above fix
236    
237    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Auxiliaries.R (drop0): extend for non CSparse
240            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
241    
242            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
243                    use uplo correctly (!); other places: use uplo_P() macro
244    
245            * R/Csparse.R (replCmat): call diagU2N() when needed
246            * R/Tsparse.R (replTmat): ditto
247    
248            * src/dtCMatrix.c (tCMatrix_validate): new
249            * src/dtTMatrix.c (tTMatrix_validate): new, used in
250            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
251    
252            * R/diagMatrix.R (replDiag): to use in [<-
253    
254    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
257                    also more general diagU2N().
258    
259    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
262            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
263    
264    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/bind.R: a few more cases
267            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
268    
269            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
270            * R/ddenseMatrix.R (cbind2/rbind2)
271            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
272            * tests/indexing.R
273            * tests/indexing.Rout.save: updated
274    
275    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
278            * tests/indexing.R
279    
280    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
283            align with proper position of "0", i.e., right for integers.
284            argument 'align' by default is "fancy".
285    
286    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
289            * R/Csparse.R: and fix "Compare" for more cases.
290            * tests/Class+Meth.R: test some of these (m == m, m != m)
291    
292    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/lsparseMatrix.R: all() and any() methods
295            * R/ldenseMatrix.R:      ditto
296            * NAMESPACE, R/Matrix.R: ditto
297    
298            * man/all-methods.Rd: document them minimally
299    
300            * tests/simple.R: add a few examples for these
301    
302    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Tsparse.R ([): fix long standing typo in symmetric case
305            * man/dsCMatrix-class.Rd: add example exhibiting the above case
306    
307    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
310            to LL before converting to a sparse matrix. (The LDL form can be
311            converted to a sparse matrix but it is implicitly a unit
312            triangular matrix and a diagonal matrix overwritten on the diagonal.)
313    
314    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
317    
318    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): updated -> release 0.9975-7
321            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
322    
323    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
326    
327    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
330            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
331            is exactly singular.
332    
333    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): updated -> release 0.9975-6
336    
337    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
340            now returns symmetric.
341    
342            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
343    
344            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
345            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
346    
347            * R/Auxiliaries.R (.type.kind): added
348    
349    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
352            running src/CSparse_install.sh
353    
354            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
355    
356    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
359            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
360    
361            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
362    
363            * tests/Class+Meth.R (tstMatrixClass): now assure
364            the (important in method programming) property :
365    
366                    ###>>  Every "Matrix" is either
367                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
368    
369                    (where "*" stands for "Matrix")
370    
371            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
372    
373            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
374            * tests/validObj.R: checks for "comparison"
375    
376            * R/sparseMatrix.R ([): improved indexing for sparse;
377                    trying to keep <symmetric>[ n, n] symmmetric
378    
379            * tests/indexing.R: indexing for logical sparse now ok
380    
381    
382    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/Tsparse.c: use xTsparse_validate() , and hence remove
385    
386            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
387    
388    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
391    
392            * tests/simple.R: validObject() checking the above.
393    
394            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
395            replacing both dgCMatrix_validate and lgCM*.
396    
397            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
398            fix dimnames setting in other places.
399            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
400    
401    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
404    
405            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
406            symmetry test, via
407            * R/Auxiliaries.R (.as.dgC.0.factors):
408    
409    2006-11-01  Douglas Bates  <bates@r-project.org>
410    
411            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
412            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
413            <CsparseMatrix>) added
414    
415    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * tests/matprod.R: add a variation of Harri's example
418    
419            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
420            recursive infinitely.
421    
422            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
423    
424            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
425    
426    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
429            matrix if possible; test m+m == 2*m; now test dgRMatrix.
430            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
431            satisfy the above test.
432    
433    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
436    
437            * R/dgCMatrix.R: solve(a, b="missing") based on
438            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
439            RHS = NULL.
440    
441            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
442            add more (needed) [t]crossprod() methods.
443    
444            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
445    
446            * R/Auxiliaries.R (as_CspClass): cleanup
447            (drop0): internal utility for "Csparse_drop(*, 0)"
448            (.bail.out.2): encourage active feedback
449    
450    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/dMatrix.R(Compare): new(), then slots [no validity check]
453    
454            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
455            non-valid or 'sorted' case).
456    
457            * R/dsparseMatrix.R: add "chol" method.
458            * R/ddenseMatrix.R: ditto
459    
460            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
461            * NAMESPACE (Ops)
462            * R/diagMatrix.R (diag2T): simple utility used "higher level"
463            coercion; deprecating direct lower level coercions.
464    
465            * R/*.R (seq): use seq_len() and seq_along() where possible.
466    
467    
468    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * DESCRIPTION (Version): 0.9975-5 ready for release
471    
472    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
475    
476    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllClass.R (corMatrix): add 'validity' check;
479                    comment out unused "LDL" class definition
480            * NAMESPACE: mention, but do not export "LDL" class
481            * R/corMatrix.R: new (simple), needed for R-devel with
482            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
483              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
484    
485    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
486    
487            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
488            use Rprintf and R's error handling.
489    
490    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
493            * tests/matprod.R: add tests for the bug fixed.
494    
495    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
496    
497            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
498            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
499    
500    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
501    
502            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
503    
504    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.9975-3
507    
508            * R/diagMatrix.R (bdiag): new function constructing block diagonal
509            (sparse) matrices.
510            * man/bdiag.Rd: docu + examples
511    
512            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
513    
514            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
515            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
516    
517            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
518            that result is sparse or diagonal (and not dense).
519    
520            * man/Subassign-methods.Rd: fix examples
521    
522            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
523            should always return a sparse (and not sometimes a diagonal) matrix.
524    
525    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
528    
529    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * DESCRIPTION (Version): 0.9975-2
532    
533            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
534    
535    2006-10-02  Douglas Bates  <bates@R-project.org>
536    
537            * tests/dg_Matrix.R: Simplify test taking into account new code.
538    
539    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
542    
543            * R/lsTMatrix.R: new files w/ missing methods
544            * R/nsTMatrix.R:  "  'for completeness'
545    
546            * tests/Class+Meth.R: a bit less 'not.ok.classes'
547    
548            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
549    
550    
551    2006-09-28  Douglas Bates  <bates@R-project.org>
552    
553            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
554            included.
555    
556            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
557            Export C-callable functions used in Zt_create in lme4.
558    
559    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * DESCRIPTION (Version): 0.9975-1
562    
563            * tests/simple.R: less checks fail; using NA, found that our
564                    kronecker() is not base-compatible with NA's.
565    
566            * R/dMatrix.R: "Compare" method now implemented for all cases
567    
568            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
569    
570            * man/dtpMatrix-class.Rd: mention length of 'x' slot
571    
572            * src/dtpMatrix.c (dtpMatrix_validate): fix check
573            * src/dspMatrix.c (dspMatrix_validate): ditto
574    
575            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
576              including coercion to [nl]tTMatrix.
577    
578            * R/diagMatrix.R (show): print a header line as for other classes.
579    
580    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/Makefile.win (SUBDIRS): fix typo
583    
584    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
587    
588    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
591            symmetric and y missing in R code using %*% (cholmod_aat doesn't
592            accept a symmetric matrix).
593            * tests/group-methods.R: Uncomment test of crossprod applied to
594            lsCMatrix objects.
595    
596    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/AllClass.R (symmetricMatrix): add validity method (available
599            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
600    
601            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
602    
603            * tests/indexing.Rout.save:
604            * tests/indexing.R: additions, mainly for 'lsparse'
605    
606            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
607            case.
608    
609            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
610    
611    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
614                    as 'N' (1-letter - Ok?)
615    
616            * tests/group-methods.R: add test for logical + NAs
617    
618            * R/dMatrix.R ("Compare"): fix to work with NA's
619    
620            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
621    
622            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
623                    which is implemented.
624    
625    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * src/chm_common.c: coerce logical <-> double instead of
628            typecasting;  needed for "l" matrix handling in cholmod.
629    
630            * tests/other-pkgs.R (graph): small extension in "graph" checks.
631    
632            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
633            (Tsp2grNEL): other fixes needed
634    
635    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
638                    Matrices, since "lMatrix", also "lsparseM" can have NA
639            * R/ndenseMatrix.R, etc: new source files
640            * man/nsparseMatrix-classes.Rd, etc: new help files
641            * tests/: adaptions
642            * src/chm_common.c (chm_dense_to_SEXP): and others:
643                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
644            * src/Csparse.c, etc: ditto
645    
646    2006-09-11  Douglas Bates  <bates@R-project.org>
647    
648            * src/Mutils.[ch],init.c inst/include/*.h: Move the
649            alloc_d**Matrix functions to the lme4 package.
650    
651    2006-09-09  Douglas Bates  <bates@R-project.org>
652    
653            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
654            fixed
655    
656    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/lMatrix.R: new
659    
660            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
661    
662            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
663            * man/tcrossprod.Rd: ditto
664    
665    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
666    
667            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
668            for exported functions
669            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
670            Remove partitioning algorithms for sparse matrix reordering.  The
671            copyright on the Metis code was problematic and the methods were
672            rarely used.
673            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
674            operations are now done entirely in CHOLMOD code.
675    
676    2006-09-06  Douglas Bates  <bates@R-project.org>
677    
678            * src/Mutils.h: Remove functions that are no longer used.
679    
680    2006-09-04  Douglas Bates  <bates@R-project.org>
681    
682            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
683            * src/DEPS.mkf: update
684    
685    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * created branches/Matrix-for-R-2.3.x;  on trunk: do
688            * DESCRIPTION (Version): 0.9975-0
689            (Depends): R (>= 2.4.0)
690    
691    2006-09-01  Douglas Bates  <bates@R-project.org>
692    
693            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
694    
695    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
698            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
699    
700            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
701    
702    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
705            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
706            * R/dsparseMatrix.R: ditto
707            * R/Csparse.R: ditto
708    
709    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/dMatrix.R (Compare): improve availability of "<", etc
712            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
713    
714    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
717            of a 0-index which was used as 1-index (..hmm)
718    
719            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
720    
721            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
722            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
723            (.is.diagonal): ditto
724    
725            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
726    
727            * R/Matrix.R (Matrix): also work for NA data
728    
729    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
732            in all cases.
733    
734    2006-08-27  Douglas Bates  <bates@R-project.org>
735    
736            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
737            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
738    
739    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
742            subclasses of "ddenseMatrix"
743            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
744            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
745            instead of half dozen specialized ones.
746    
747    2006-08-25  Douglas Bates  <bates@R-project.org>
748    
749            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
750            <tillard@cirad.fr> - ordering standard errors to match effects.
751    
752    2006-08-24  Douglas Bates  <bates@R-project.org>
753    
754            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
755            on R_ldl.
756            * R/lCholCMatrix.R,
757            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
758            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
759            * many files in ./R and ./src: Use more general version of
760            dup_mMatrix_as_dgeMatrix to simplify method definitions.
761            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
762            dtpMatrix, dspMatrix and dppMatrix conversions.
763    
764    
765    2006-08-23  Douglas Bates  <bates@R-project.org>
766    
767            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
768            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
769            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
770            dgeMatrix_crossprod (may need to do this in other places).
771            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
772            generic and method for dsCMatrix.  Use CHOLMOD for chol().
773    
774    2006-08-22  Douglas Bates  <bates@R-project.org>
775    
776            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
777            types of classed Matrices, matrices or numeric or logical vectors.
778            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
779            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
780            to Mutils.h (as an inline) and change name to Matrix_check_class;
781            fixes in as_cholmod_factor and chm_factor_to_SEXP.
782            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
783            dsCMatrix_matrix_solve.  Comment out vestigial functions.
784            * src/Csparse.c: use diag_P and uplo_P macros.
785    
786    2006-08-21  Douglas Bates  <bates@R-project.org>
787    
788            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
789            valgrind.
790            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
791            inverses.
792            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
793            -Wall warnings.
794            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
795            Use dup_mMatrix_as_dgeMatrix.
796    
797    2006-08-20  Douglas Bates  <bates@R-project.org>
798    
799            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
800            * tests/sparseQR.R: Added
801            * man/sparseQR-class.Rd: Document methods for qr.* generics
802            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
803    
804    2006-08-19  Douglas Bates  <bates@R-project.org>
805    
806            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
807            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
808            and qr.fitted.
809            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
810            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
811    
812    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
815            the base version has no "..." argument.
816    
817            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
818    
819            * R/Matrix.R: define and
820            * NAMESPACE: export as.numeric() and as.logical() methods.
821                    Let's hope these do not badly slow down something...
822            Finally export the zapsmall() method.
823    
824    2006-08-17  Douglas Bates  <bates@R-project.org>
825    
826            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
827            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
828            * src/dtCMatrix.c :Remove code that is no longer used
829            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
830    
831    2006-08-14  Douglas Bates  <bates@R-project.org>
832    
833            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
834            Csparse_to_logical and Csparse_symmetric_to_general.
835            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
836            coercion methods between CsparseMatrix and TsparseMatrix.
837    
838    2006-08-14  Douglas Bates  <bates@R-project.org>
839    
840            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
841            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
842            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
843            possible.
844    
845    2006-08-12  Douglas Bates  <bates@R-project.org>
846    
847            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
848              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
849              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
850              generalize conversions between TsparseMatrix, CsparseMatrix,
851              denseMatrix and matrix.  Preserve triangularity property and
852              propagate Dimnames in the easy cases.
853    
854    2006-08-10  Douglas Bates  <bates@R-project.org>
855    
856            * src/lmer.c: adjust checks in glmer_init for S4SXP
857            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
858            before S4SXP but for the wrong reasons.
859    
860    2006-08-08  Douglas Bates  <bates@R-project.org>
861    
862            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
863            Later modified to return the upper triangle only.
864            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
865    
866    2006-08-07  Douglas Bates  <bates@R-project.org>
867    
868            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
869            R-level conversion to a sparse symmetric class.
870            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
871            Remove conversion to sparse symmetric classes (now done in C code).
872    
873    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
876            * man/band.Rd:  adapt the \dontshow{} unit test.
877    
878    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * DESCRIPTION (Version): 0.995-14  for CRAN
881    
882            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
883    
884            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
885            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
886    
887            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
888            * R/Tsparse.R (tril, triu, band): methods
889            * R/dgRMatrix.R (tril, ...):    ditto
890            * man/band.Rd:                  ditto
891    
892    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * R/Matrix.R (head, tail): directly use utils:::head.matrix
895                    to be up-to-date automatically.
896    
897    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
900    
901            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
902            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
903            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
904            such that the S4 objects are always created by the current version
905            of R and 'Matrix' class definitions.
906    
907    2006-08-01  Douglas Bates  <bates@R-project.org>
908    
909            * R/lmer.R (LMEoptimize method), tests/lmer.R,
910            inst/external/test3comp.rda: Added warnings for convergence on
911            boundary and test cases.
912    
913            * src/lmer.c (mer_postVar): Modified to return the variances that
914            are marginal to the fixed effects, not conditional on them (which
915            is what the bVar slot contents represent).
916    
917    2006-07-31  Douglas Bates  <bates@R-project.org>
918    
919            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
920            function which calls the C function mer_hat_trace2.
921    
922            * man/ranef.Rd: Include description of "postVar" argument and
923            producing a caterpillar plot.
924    
925    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * NAMESPACE:    change  "correlation" to "corMatrix"
928            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
929            * R/dpoMatrix.R: ditto
930            * R/lmer.R:      ditto
931    
932    2006-07-28  Douglas Bates  <bates@R-project.org>
933    
934            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
935            RZXinv slot's contents into a separate internal function that can
936            be used in mer_hat_trace.
937    
938    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
941            via new smart
942            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
943            utility functions.
944    
945    
946    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/Csparse.R (tril, triu, band): do return *triangular* classed
949            matrices when appropriate; band() even symmetric ones.
950            (replCmat): extend to potentially all "CsparseMatrix"
951            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
952            allow subassignment for special sparse matrices.
953    
954            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
955    
956            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
957            argument; in glmer_*(): print only if(verbose).
958    
959            speed-optimize a few places by moving REAL(.) out of loops.
960    
961            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
962    
963    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
966                    since that wrongly triggers also for M[ logi , ]
967    
968            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
969            a symmetric matrix that results in a non-symmetric one.
970            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
971    
972            * R/dMatrix.R: make round(M) work as round(M, 0)
973    
974            * R/dgTMatrix.R (image): coordinate system and axis now use
975            1-based indices, not 0-based ones.
976    
977            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
978            * tests/indexing.R: test it.
979    
980            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
981            * man/isSymmetric-methods.Rd: and document it.
982    
983            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
984            * man/SparseM-conv.Rd: docu them
985    
986            * tests/other-pkgs.R: renamed from tests/graph.R and add example
987                    for 'SparseM' conversions
988    
989    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
990    
991            * R/Matrix.R (head): added head() and tail() methods.
992    
993    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * DESCRIPTION (Version): 0.995-12 released to CRAN
996    
997    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * tests/simple.R: add check for correct dsT -> dgT coercion;
1000                    add check for correct printing of symmetric sparse matrices.
1001    
1002            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1003            for sparse symmetric matrices.
1004    
1005            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1006            diagonal twice.
1007    
1008    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1009    
1010            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1011            being applied to the x slot (detected by Brian Ripley).
1012    
1013    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1016    
1017            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1018    
1019    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * src/lgCMatrix.c (lgCMatrix_diag): new function
1022            * R/lgCMatrix.R (diag): for new method
1023    
1024            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1025                 ==> construction of illegal "*gTMatrix" via new() should
1026                 now be much less easy:
1027            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1028    
1029            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1030                    directly.
1031            * man/Matrix.Rd: documents it.
1032    
1033    2006-07-06  Douglas Bates  <bates@R-project.org>
1034    
1035            * src/pedigree.c (pedigree_inbreeding): Correction in
1036            initialization.  This function is not currently being used and is
1037            not fully tested.
1038    
1039            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1040            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1041            objects.  Modified validity check on pedigree objects to account
1042            for nonparallel patterns of missingness of parents.
1043    
1044            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1045            class.
1046    
1047    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/pMatrix.R: coercion pMatrix -> Tsparse
1050    
1051    2006-06-12  Douglas Bates  <bates@R-project.org>
1052    
1053            * DESCRIPTION (Version): 0.995-11 released to CRAN
1054    
1055            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1056            the output from mcmcsamp.
1057    
1058    2006-06-10  Douglas Bates  <bates@R-project.org>
1059    
1060            * R/lmer.R (simulestimate): added C code for calculating the trace
1061            of the hat matrix.
1062    
1063    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1066            classes.
1067            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1068    
1069    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/dgTMatrix.R (colSums): etc. All four of
1072            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1073            all "Matrices".
1074    
1075    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1076    
1077            * R/lmer.R (panel.ci): Add a reference line at zero and a
1078            background grid to the qqmath plot of ranef.lmer.
1079    
1080    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1081    
1082            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1083            grouping factors to be specified in the formula as (1|foo/bar).
1084    
1085    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1086    
1087            * R/lmer.R (findbars and others): Change check of is.numeric to
1088            !is.language to resolve the bug reported by Jacob Wegelin.
1089    
1090            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1091            code to evaluate inbreeding coefficients without calculating T,
1092            based on code in Sargolzaei and Iwaisaki's paper.
1093    
1094    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1095    
1096            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1097            generic and mer methods for isNested and denomDF. This denomDF was
1098            an attempt to emulate that in lme but I don't think that makes
1099            sense.  Use the trace of the hat matrix instead.
1100    
1101    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1104            the C code depending on a slot structure that's no longer valid.
1105            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1106    
1107    
1108    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1109    
1110            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1111            of lowerTriMatrix generic and methods to tril (also upper to triu)
1112            and added a general band extractor.
1113    
1114    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1115    
1116            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1117            allowable range with NAs. Added a corresponding check in the
1118            validity check for the pedigree class.
1119    
1120            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1121            crossprod methods now inherits from symmetricMatrix.
1122    
1123    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1124    
1125            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1126            generics lowerTriMatrix and upperTriMatrix along with methods for
1127            the Csparse virtual class.  Also added a C function Csparse_band
1128            that implements these methods by calling cholmod_band.
1129    
1130    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1131    
1132            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1133            erased when it was NULL.  This led to invalid subselections!
1134    
1135    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1136    
1137            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1138            in method for "t" so as not to lose the unit diagonal property.
1139    
1140    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1141    
1142            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1143            and methods.  This is now an option to the ranef method for the
1144            mer class.
1145    
1146            * src/cs_utils.c: Ensure that the nz component is -1 for a
1147            compressed column-oriented matrix.  Minor formatting cleanup.
1148    
1149            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1150            objects.
1151    
1152    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1153    
1154            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1155            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1156    
1157    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1158    
1159            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1160            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1161    
1162            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1163            for the dtCMatrix class.
1164    
1165    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1166    
1167            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1168            and methods for it.
1169    
1170    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1173            arguments, such that M %*% 1:6 now works
1174            * Tests/matprod.R: test the above
1175    
1176    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1177    
1178            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1179            the ranef.lmer class.
1180    
1181            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1182            methods to extract the posterior variances from the bVar slot.
1183    
1184    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1187            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1188    
1189            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1190            * tests/simple: (extended)
1191    
1192            * R/sparseMatrix.R (isTriangular): now using much improved
1193            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1194    
1195    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1196    
1197            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1198            (problem report from Franklin Parlamis).  This should be done
1199            generally.
1200    
1201    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1202    
1203            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1204            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1205            update the plot methods.
1206    
1207    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1208    
1209            * R/lmer.R (resid and ranef methods):  Added methods for the
1210            "residuals" and "resid" generic but only for linear mixed model
1211            fits.  Changed the ranef method to return a list of data frames so
1212            that the plot methods now work.
1213    
1214    2006-03-16  Douglas Bates  <bates@bates2>
1215    
1216            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1217            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1218    
1219            * DESCRIPTION (Date): New release
1220    
1221    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1224    
1225            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1226            * man/KNex.Rd: and other help files
1227            * tests/*.R: several ones needed adaption
1228            * inst/doc/Comparisons.Rnw: ditto
1229    
1230    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
1232            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1233    
1234            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1235    
1236    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1239    
1240            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1241    
1242    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/dMatrix.R: enable things like  M [ M < 10 ]
1245            * R/dgeMatrix.R: implement it
1246    
1247    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1248    
1249            * R/AllClass.R: define "summary.mer" and "*.lmer"
1250            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1251            * R/lmer.R (show): now works with summary()
1252    
1253    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1256            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1257                    support the above
1258    
1259    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1260    
1261            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1262            Use glmFit$prior.weights for weights in a glmm.
1263            Allow an option usePQL = FALSE to skip the PQL steps for the
1264            Laplace method (and, in time, the AGQ method).
1265    
1266            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1267            into a separate function internal_mer_Xfactor to be able to call
1268            it from internal_bhat.
1269    
1270    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * tests/Class+Meth.R (tstMatrixClass): function for much better
1273            testing; now again of all actual classes.
1274    
1275            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1276                    use macros and define make_d_matrix_* and make_i_matrix_*
1277                    where _i_ is for the ldense routines:
1278    
1279            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1280            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1281    
1282            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1283    
1284    
1285    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1288                    many different kinds of matrices.
1289            * R/*.R: quite a few new methods were needed for R CMD check with
1290                    new Matrix().  Very good for users playing around.
1291    
1292    
1293    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1294    
1295            * src/dgeMatrix.c (dMatrix_validate): new
1296            * src/Mutils.c (dense_nonpacked_validate): new
1297    
1298            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1299    
1300    
1301    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1302    
1303            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1304    
1305    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1306    
1307            * DESCRIPTION (Version): 0.99-6 released to CRAN
1308    
1309            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1310            segfault in cases with multiple non-nested grouping factors.
1311    
1312    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1315                    (Depends): also on 'utils'
1316    
1317            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1318            * R/diagMatrix.R (Diagonal): constructor and methods for
1319            diagonal matrices
1320    
1321            * R/ltTMatrix.R: new "minimal methods"
1322    
1323    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1324    
1325            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1326            all methods (and help files).
1327    
1328    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1331                    for case (dimn.  op  no_dimn.)
1332    
1333    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1334    
1335            * DESCRIPTION (Version): 0.99-2  released to CRAN
1336    
1337    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1338    
1339            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1340            by Julian Faraway.
1341    
1342    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1343    
1344            * R/Auxiliaries.R (try_as): new utility
1345            * R/sparseMatrix.R: use try_as() in coercion to original class
1346    
1347    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1350    
1351    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1352    
1353            * R/Auxiliaries.R (dimNamesCheck): added
1354    
1355            * R/Matrix.R (as.array), (as.vector): new
1356    
1357    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1360                    default.
1361            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1362                    "pMatrix" now contains "sparseMatrix"
1363    
1364    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1365    
1366            * tests/Class+Meth.R: new tests; t(t(m)) == m
1367    
1368            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1369    
1370            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1371            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1372    
1373            * R/dspMatrix.R: typo in "t" method
1374    
1375    2005-09-18  Douglas Bates  <bates@wisc.edu>
1376    
1377            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1378            * R/Tsparse.R: instead of R/gTMatrix.R
1379            * R/Csparse.R: new
1380            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1381            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1382            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1383                            via cholmod
1384    
1385    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1386    
1387            * R/Auxiliaries.R (non0ind): new function using new C code
1388            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1389    
1390    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1391    
1392            * src/chm_common.h: header file required by all C sources that
1393            call CHOLMOD functions.  It defines a cholmod_common structure
1394            called 'c' whose address is passed as the last argument to
1395            (virtually) every CHOLMOD function.
1396    
1397            * src/Pattern.c: Simple example of the use of CHOLMOD.
1398    
1399            * src/init.c: initialize and finalize the cholmod_common structure.
1400    
1401            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1402            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1403    
1404    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1405    
1406            * inst/test-tools.R: new file collecting the utility functions used
1407                    in ./tests/*.R
1408    
1409            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1410            * R/Matrix.R (cbind2): methods for NULL and missing
1411    
1412    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1413    
1414            * R/AllClass.R: new "index" class for "[" and "[<-":
1415                    First cut at "symmetricMatrix" and "triangularMatrix"
1416            * R/gTMatrix.R (.ind.prep): new function;
1417                    Logical and character indexing now work too.
1418            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1419            * tests/indexing.R: new, including *.Rout.save
1420            * tests/dgTMatrix.R: new
1421    
1422    2005-08-29  Douglas Bates  <bates@wisc.edu>
1423    
1424            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1425            indicator pos not being updated.  Also enforced upper triangular
1426            for symmetric case.  Need to coerce edges component of elements of
1427            edge list - grr! (Why don't they define their classes cleanly?)
1428    
1429    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1430    
1431            * R/Matrix.R:  added first "[<-" methods; not yet functional
1432            * R/denseMatrix.R: ditto
1433            * man/Subassign-methods.Rd: new help file for these
1434    
1435    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * DESCRIPTION (Version): 0.98-6
1438    
1439            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1440            matrices.
1441    
1442    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1443    
1444            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1445                    as( <logical>, "matrix")
1446    
1447            * R/pMatrix.R: coercion to "lgTMatrix"
1448    
1449            * R/gTMatrix.R: new virtual class to define "[" methods for.
1450            * man/gTMatrix-class.Rd:
1451            * General slight re-organization of where "[" methods are defined.
1452              more to come.
1453    
1454    2005-08-18  Douglas Bates  <bates@wisc.edu>
1455    
1456            * DESCRIPTION (Version): 0.98-5  released to CRAN
1457    
1458            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1459            * .....
1460    
1461    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1462    
1463            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1464            or glmer objects.
1465    
1466    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1467    
1468            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1469    
1470    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1471    
1472            * R/HBMM.R: finish re-writing R-only code.
1473    
1474    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1475    
1476            * man/externalFormats.Rd: move documentation for writeHB and
1477            writeMM here.
1478    
1479            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1480            (suggested by Paul Roecker).
1481    
1482            * tests/validObj.R (assertError): Comment out test that is failing
1483            after recent changes in r-devel.
1484    
1485    
1486    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1487    
1488            * R/AllClass.R: intermediate virtual class "denseMatrix"
1489            * man/denseMatrix-class.Rd
1490            * NAMESPACE: export it, and also export
1491            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1492    
1493    2005-08-10  Douglas Bates  <bates@wisc.edu>
1494    
1495            * DESCRIPTION (Version): 0.98-3 to CRAN
1496    
1497            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1498            matrix_solve code (which was really, really wrong).
1499    
1500    2005-08-07  Douglas Bates  <bates@wisc.edu>
1501    
1502            * DESCRIPTION (Version): 0.98-2
1503    
1504            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1505    
1506            * R/lmer.R (abbrvNms): new
1507            * R/lmer.R (mcmcsamp): allow transformed parameters
1508            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1509            for the Harwell-Boeing and the MatrixMarket formats.
1510    
1511    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1512    
1513            * man/dtrMatrix-class.Rd: add examples
1514            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1515    
1516            * TODO: note the dtpMatrix (docu) bug
1517    
1518            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1519            in order to ensure that new as.matrix() is used by old functions,
1520            e.g., svd(), qr(), eigen(), dist(),..;
1521                  apply(), also matplot() or pairs().
1522    
1523    
1524    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1527              add comments about 'control' / lmerControl() arguments
1528    
1529    2005-07-27  Douglas Bates  <bates@wisc.edu>
1530    
1531            * man/sleepstudy.Rd: Added the sleep data set.
1532            * DESCRIPTION (Version): 0.98-1  released to CRAN
1533    
1534    2005-07-12  Douglas Bates  <bates@wisc.edu>
1535            * man/sleepstudy.Rd: Added the sleep data set.
1536    
1537            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1538            .Call calls that were producing spurious output.
1539    
1540    2005-07-05  Douglas Bates  <bates@wisc.edu>
1541    
1542            * R/lmer.R (lmer): stored updated variance component estimates in
1543            mer object for the generalized model.  (Bug reported by Renaud
1544            Lancelot).
1545    
1546    2005-07-03  Douglas Bates  <bates@wisc.edu>
1547    
1548            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1549            unidimensional case.
1550    
1551    2005-06-08  Douglas Bates  <bates@wisc.edu>
1552    
1553            * DESCRIPTION (Version): 0.96-1
1554    
1555            * moved  lmer-class' R and C code moved from lme4 to here
1556    
1557    2005-06-04  Douglas Bates  <bates@wisc.edu>
1558    
1559            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1560            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1561    
1562    2005-06-02  Douglas Bates  <bates@wisc.edu>
1563    
1564            * src/Makefile.win: Forgot to update this when Makefile changed.
1565    
1566    2005-05-11  Douglas Bates  <bates@wisc.edu>
1567    
1568            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1569            bug reported by Kurt Hornik and Michael Hahsler.
1570    
1571    2005-05-10  Douglas Bates  <bates@wisc.edu>
1572    
1573            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1574            logical sparse matrices.  These will also be used in the symbolic
1575            analysis for lmer objects.
1576    
1577            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1578            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1579    
1580    2005-05-06  Douglas Bates  <bates@wisc.edu>
1581    
1582            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1583            colMeans, colSums, rowMeans and rowSums.
1584    
1585    2005-04-18  Douglas Bates  <bates@wisc.edu>
1586    
1587            * src/lgCMatrix.[ch]: code for _validate method and stub for
1588            multiplication operation.
1589    
1590            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1591            to dgetrs.
1592    
1593            * src/init.c: Fix cut-and-paste error in definition of
1594            dgeMatrix_matrix_solve
1595    
1596            * src/{many files}: Tighten code by using ALLOC_SLOT.
1597    
1598    2005-04-15  Douglas Bates  <bates@wisc.edu>
1599    
1600            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1601    
1602            * DESCRIPTION: Eliminate import of stats.
1603    
1604    
1605    2005-04-06  Douglas Bates  <bates@wisc.edu>
1606    
1607            * R/AllClass.R : add logical sparse matrix classes
1608    
1609  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1610    
1611          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1612          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1613    
1614  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1615    
1616          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1617    
# Line 29  Line 1637 
1637          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1638            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1639    
1640  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1641    
1642          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1643          * ....          * ....
1644    
1645  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1646    
1647          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1648    
# Line 49  Line 1657 
1657            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1658          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1659    
1660  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1661    
1662          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1663    
1664  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1665    
1666          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1667    
1668  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1669    
1670          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1671          the package.          the package.
# Line 105  Line 1713 
1713    
1714          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1715    
1716  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1717    
1718          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1719          for the geMatrix class.          for the geMatrix class.
1720    
1721  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1722    
1723          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1724    
1725          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1726    
1727  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1728    
1729          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1730          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1731    
1732  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1733    
1734          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1735    
1736  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1737    
1738          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1739          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1740    
1741  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1742    
1743          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1744    
1745          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1746          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1747    
1748  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1749    
1750          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1751          no longer used.          no longer used.
# Line 149  Line 1757 
1757          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1758          Fixes part but not all of #15.          Fixes part but not all of #15.
1759    
1760  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1761    
1762          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1763          scalar grouping factors corrected.          scalar grouping factors corrected.
1764    
1765  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1766    
1767          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1768    
1769  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1770    
1771          * 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
1772          .h file can be included.          .h file can be included.
1773    
1774  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1775    
1776          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1777          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1778    
1779          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1780    
1781  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1782    
1783          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1784    
1785  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1786    
1787          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1788    
1789  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1790    
1791          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1792    
1793  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1794    
1795          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1796    
1797  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1798    
1799          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1800          routines.          routines.
1801    
1802  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1803    
1804          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1805    
1806  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1807    
1808          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1809    

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