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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1716, Sat Jan 6 02:01:24 2007 UTC
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1    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/init.c (R_init_Matrix): export cholmod_scale
4    
5    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
8            file; start using "Logic", hence
9    
10            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
11            * NAMESPACE: import and export "Logic"
12    
13    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
16            only needed previously to R version 2.5.0.
17    
18    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
21    
22            * R/Tsparse.R (replTmat): fix subassignment of triangular
23            * R/Csparse.R (replCmat): ditto
24            * tests/indexing.R: more tests, incl the above fix
25    
26    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (drop0): extend for non CSparse
29            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
30    
31            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
32                    use uplo correctly (!); other places: use uplo_P() macro
33    
34            * R/Csparse.R (replCmat): call diagU2N() when needed
35            * R/Tsparse.R (replTmat): ditto
36    
37            * src/dtCMatrix.c (tCMatrix_validate): new
38            * src/dtTMatrix.c (tTMatrix_validate): new, used in
39            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
40    
41            * R/diagMatrix.R (replDiag): to use in [<-
42    
43    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
46                    also more general diagU2N().
47    
48    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
51            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
52    
53    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * tests/bind.R: a few more cases
56            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
57    
58            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
59            * R/ddenseMatrix.R (cbind2/rbind2)
60            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
61            * tests/indexing.R
62            * tests/indexing.Rout.save: updated
63    
64    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
67            * tests/indexing.R
68    
69    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
72            align with proper position of "0", i.e., right for integers.
73            argument 'align' by default is "fancy".
74    
75    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
78            * R/Csparse.R: and fix "Compare" for more cases.
79            * tests/Class+Meth.R: test some of these (m == m, m != m)
80    
81    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/lsparseMatrix.R: all() and any() methods
84            * R/ldenseMatrix.R:      ditto
85            * NAMESPACE, R/Matrix.R: ditto
86    
87            * man/all-methods.Rd: document them minimally
88    
89            * tests/simple.R: add a few examples for these
90    
91    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ([): fix long standing typo in symmetric case
94            * man/dsCMatrix-class.Rd: add example exhibiting the above case
95    
96    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
99            to LL before converting to a sparse matrix. (The LDL form can be
100            converted to a sparse matrix but it is implicitly a unit
101            triangular matrix and a diagonal matrix overwritten on the diagonal.)
102    
103    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
104    
105            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
106    
107    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * DESCRIPTION (Version): updated -> release 0.9975-7
110            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
111    
112    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
115    
116    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
119            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
120            is exactly singular.
121    
122    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * DESCRIPTION (Date): updated -> release 0.9975-6
125    
126    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
129            now returns symmetric.
130    
131            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
132    
133            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
134            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
135    
136            * R/Auxiliaries.R (.type.kind): added
137    
138    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
141            running src/CSparse_install.sh
142    
143            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
144    
145    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
148            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
149    
150            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
151    
152            * tests/Class+Meth.R (tstMatrixClass): now assure
153            the (important in method programming) property :
154    
155                    ###>>  Every "Matrix" is either
156                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
157    
158                    (where "*" stands for "Matrix")
159    
160            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
161    
162            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
163            * tests/validObj.R: checks for "comparison"
164    
165            * R/sparseMatrix.R ([): improved indexing for sparse;
166                    trying to keep <symmetric>[ n, n] symmmetric
167    
168            * tests/indexing.R: indexing for logical sparse now ok
169    
170    
171    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * src/Tsparse.c: use xTsparse_validate() , and hence remove
174    
175            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
176    
177    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
180    
181            * tests/simple.R: validObject() checking the above.
182    
183            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
184            replacing both dgCMatrix_validate and lgCM*.
185    
186            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
187            fix dimnames setting in other places.
188            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
189    
190    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
193    
194            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
195            symmetry test, via
196            * R/Auxiliaries.R (.as.dgC.0.factors):
197    
198    2006-11-01  Douglas Bates  <bates@r-project.org>
199    
200            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
201            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
202            <CsparseMatrix>) added
203    
204    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * tests/matprod.R: add a variation of Harri's example
207    
208            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
209            recursive infinitely.
210    
211            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
212    
213            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
214    
215    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
218            matrix if possible; test m+m == 2*m; now test dgRMatrix.
219            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
220            satisfy the above test.
221    
222    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
225    
226            * R/dgCMatrix.R: solve(a, b="missing") based on
227            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
228            RHS = NULL.
229    
230            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
231            add more (needed) [t]crossprod() methods.
232    
233            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
234    
235            * R/Auxiliaries.R (as_CspClass): cleanup
236            (drop0): internal utility for "Csparse_drop(*, 0)"
237            (.bail.out.2): encourage active feedback
238    
239    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dMatrix.R(Compare): new(), then slots [no validity check]
242    
243            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
244            non-valid or 'sorted' case).
245    
246            * R/dsparseMatrix.R: add "chol" method.
247            * R/ddenseMatrix.R: ditto
248    
249            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
250            * NAMESPACE (Ops)
251            * R/diagMatrix.R (diag2T): simple utility used "higher level"
252            coercion; deprecating direct lower level coercions.
253    
254            * R/*.R (seq): use seq_len() and seq_along() where possible.
255    
256    
257    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.9975-5 ready for release
260    
261    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
264    
265    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/AllClass.R (corMatrix): add 'validity' check;
268                    comment out unused "LDL" class definition
269            * NAMESPACE: mention, but do not export "LDL" class
270            * R/corMatrix.R: new (simple), needed for R-devel with
271            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
272              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
273    
274    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
275    
276            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
277            use Rprintf and R's error handling.
278    
279    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
282            * tests/matprod.R: add tests for the bug fixed.
283    
284    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
287            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
288    
289    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
292    
293    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * DESCRIPTION (Version): 0.9975-3
296    
297            * R/diagMatrix.R (bdiag): new function constructing block diagonal
298            (sparse) matrices.
299            * man/bdiag.Rd: docu + examples
300    
301            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
302    
303            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
304            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
305    
306            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
307            that result is sparse or diagonal (and not dense).
308    
309            * man/Subassign-methods.Rd: fix examples
310    
311            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
312            should always return a sparse (and not sometimes a diagonal) matrix.
313    
314    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
317    
318    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): 0.9975-2
321    
322            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
323    
324    2006-10-02  Douglas Bates  <bates@R-project.org>
325    
326            * tests/dg_Matrix.R: Simplify test taking into account new code.
327    
328    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
331    
332            * R/lsTMatrix.R: new files w/ missing methods
333            * R/nsTMatrix.R:  "  'for completeness'
334    
335            * tests/Class+Meth.R: a bit less 'not.ok.classes'
336    
337            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
338    
339    
340    2006-09-28  Douglas Bates  <bates@R-project.org>
341    
342            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
343            included.
344    
345            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
346            Export C-callable functions used in Zt_create in lme4.
347    
348    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * DESCRIPTION (Version): 0.9975-1
351    
352            * tests/simple.R: less checks fail; using NA, found that our
353                    kronecker() is not base-compatible with NA's.
354    
355            * R/dMatrix.R: "Compare" method now implemented for all cases
356    
357            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
358    
359            * man/dtpMatrix-class.Rd: mention length of 'x' slot
360    
361            * src/dtpMatrix.c (dtpMatrix_validate): fix check
362            * src/dspMatrix.c (dspMatrix_validate): ditto
363    
364            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
365              including coercion to [nl]tTMatrix.
366    
367            * R/diagMatrix.R (show): print a header line as for other classes.
368    
369    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * src/Makefile.win (SUBDIRS): fix typo
372    
373    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
376    
377    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
380            symmetric and y missing in R code using %*% (cholmod_aat doesn't
381            accept a symmetric matrix).
382            * tests/group-methods.R: Uncomment test of crossprod applied to
383            lsCMatrix objects.
384    
385    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/AllClass.R (symmetricMatrix): add validity method (available
388            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
389    
390            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
391    
392            * tests/indexing.Rout.save:
393            * tests/indexing.R: additions, mainly for 'lsparse'
394    
395            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
396            case.
397    
398            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
399    
400    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
403                    as 'N' (1-letter - Ok?)
404    
405            * tests/group-methods.R: add test for logical + NAs
406    
407            * R/dMatrix.R ("Compare"): fix to work with NA's
408    
409            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
410    
411            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
412                    which is implemented.
413    
414    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/chm_common.c: coerce logical <-> double instead of
417            typecasting;  needed for "l" matrix handling in cholmod.
418    
419            * tests/other-pkgs.R (graph): small extension in "graph" checks.
420    
421            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
422            (Tsp2grNEL): other fixes needed
423    
424    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
427                    Matrices, since "lMatrix", also "lsparseM" can have NA
428            * R/ndenseMatrix.R, etc: new source files
429            * man/nsparseMatrix-classes.Rd, etc: new help files
430            * tests/: adaptions
431            * src/chm_common.c (chm_dense_to_SEXP): and others:
432                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
433            * src/Csparse.c, etc: ditto
434    
435    2006-09-11  Douglas Bates  <bates@R-project.org>
436    
437            * src/Mutils.[ch],init.c inst/include/*.h: Move the
438            alloc_d**Matrix functions to the lme4 package.
439    
440    2006-09-09  Douglas Bates  <bates@R-project.org>
441    
442            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
443            fixed
444    
445    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/lMatrix.R: new
448    
449            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
450    
451            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
452            * man/tcrossprod.Rd: ditto
453    
454    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
455    
456            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
457            for exported functions
458            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
459            Remove partitioning algorithms for sparse matrix reordering.  The
460            copyright on the Metis code was problematic and the methods were
461            rarely used.
462            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
463            operations are now done entirely in CHOLMOD code.
464    
465    2006-09-06  Douglas Bates  <bates@R-project.org>
466    
467            * src/Mutils.h: Remove functions that are no longer used.
468    
469    2006-09-04  Douglas Bates  <bates@R-project.org>
470    
471            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
472            * src/DEPS.mkf: update
473    
474    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * created branches/Matrix-for-R-2.3.x;  on trunk: do
477            * DESCRIPTION (Version): 0.9975-0
478            (Depends): R (>= 2.4.0)
479    
480    2006-09-01  Douglas Bates  <bates@R-project.org>
481    
482            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
483    
484    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
487            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
488    
489            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
490    
491    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
494            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
495            * R/dsparseMatrix.R: ditto
496            * R/Csparse.R: ditto
497    
498    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/dMatrix.R (Compare): improve availability of "<", etc
501            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
502    
503    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
506            of a 0-index which was used as 1-index (..hmm)
507    
508            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
509    
510            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
511            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
512            (.is.diagonal): ditto
513    
514            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
515    
516            * R/Matrix.R (Matrix): also work for NA data
517    
518    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
521            in all cases.
522    
523    2006-08-27  Douglas Bates  <bates@R-project.org>
524    
525            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
526            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
527    
528    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
531            subclasses of "ddenseMatrix"
532            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
533            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
534            instead of half dozen specialized ones.
535    
536    2006-08-25  Douglas Bates  <bates@R-project.org>
537    
538            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
539            <tillard@cirad.fr> - ordering standard errors to match effects.
540    
541    2006-08-24  Douglas Bates  <bates@R-project.org>
542    
543            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
544            on R_ldl.
545            * R/lCholCMatrix.R,
546            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
547            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
548            * many files in ./R and ./src: Use more general version of
549            dup_mMatrix_as_dgeMatrix to simplify method definitions.
550            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
551            dtpMatrix, dspMatrix and dppMatrix conversions.
552    
553    
554    2006-08-23  Douglas Bates  <bates@R-project.org>
555    
556            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
557            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
558            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
559            dgeMatrix_crossprod (may need to do this in other places).
560            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
561            generic and method for dsCMatrix.  Use CHOLMOD for chol().
562    
563    2006-08-22  Douglas Bates  <bates@R-project.org>
564    
565            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
566            types of classed Matrices, matrices or numeric or logical vectors.
567            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
568            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
569            to Mutils.h (as an inline) and change name to Matrix_check_class;
570            fixes in as_cholmod_factor and chm_factor_to_SEXP.
571            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
572            dsCMatrix_matrix_solve.  Comment out vestigial functions.
573            * src/Csparse.c: use diag_P and uplo_P macros.
574    
575    2006-08-21  Douglas Bates  <bates@R-project.org>
576    
577            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
578            valgrind.
579            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
580            inverses.
581            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
582            -Wall warnings.
583            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
584            Use dup_mMatrix_as_dgeMatrix.
585    
586    2006-08-20  Douglas Bates  <bates@R-project.org>
587    
588            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
589            * tests/sparseQR.R: Added
590            * man/sparseQR-class.Rd: Document methods for qr.* generics
591            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
592    
593    2006-08-19  Douglas Bates  <bates@R-project.org>
594    
595            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
596            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
597            and qr.fitted.
598            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
599            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
600    
601    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
604            the base version has no "..." argument.
605    
606            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
607    
608            * R/Matrix.R: define and
609            * NAMESPACE: export as.numeric() and as.logical() methods.
610                    Let's hope these do not badly slow down something...
611            Finally export the zapsmall() method.
612    
613    2006-08-17  Douglas Bates  <bates@R-project.org>
614    
615            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
616            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
617            * src/dtCMatrix.c :Remove code that is no longer used
618            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
619    
620    2006-08-14  Douglas Bates  <bates@R-project.org>
621    
622            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
623            Csparse_to_logical and Csparse_symmetric_to_general.
624            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
625            coercion methods between CsparseMatrix and TsparseMatrix.
626    
627    2006-08-14  Douglas Bates  <bates@R-project.org>
628    
629            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
630            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
631            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
632            possible.
633    
634    2006-08-12  Douglas Bates  <bates@R-project.org>
635    
636            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
637              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
638              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
639              generalize conversions between TsparseMatrix, CsparseMatrix,
640              denseMatrix and matrix.  Preserve triangularity property and
641              propagate Dimnames in the easy cases.
642    
643    2006-08-10  Douglas Bates  <bates@R-project.org>
644    
645            * src/lmer.c: adjust checks in glmer_init for S4SXP
646            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
647            before S4SXP but for the wrong reasons.
648    
649    2006-08-08  Douglas Bates  <bates@R-project.org>
650    
651            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
652            Later modified to return the upper triangle only.
653            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
654    
655    2006-08-07  Douglas Bates  <bates@R-project.org>
656    
657            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
658            R-level conversion to a sparse symmetric class.
659            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
660            Remove conversion to sparse symmetric classes (now done in C code).
661    
662    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
665            * man/band.Rd:  adapt the \dontshow{} unit test.
666    
667    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * DESCRIPTION (Version): 0.995-14  for CRAN
670    
671            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
672    
673            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
674            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
675    
676            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
677            * R/Tsparse.R (tril, triu, band): methods
678            * R/dgRMatrix.R (tril, ...):    ditto
679            * man/band.Rd:                  ditto
680    
681    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Matrix.R (head, tail): directly use utils:::head.matrix
684                    to be up-to-date automatically.
685    
686    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
689    
690            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
691            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
692            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
693            such that the S4 objects are always created by the current version
694            of R and 'Matrix' class definitions.
695    
696    2006-08-01  Douglas Bates  <bates@R-project.org>
697    
698            * R/lmer.R (LMEoptimize method), tests/lmer.R,
699            inst/external/test3comp.rda: Added warnings for convergence on
700            boundary and test cases.
701    
702            * src/lmer.c (mer_postVar): Modified to return the variances that
703            are marginal to the fixed effects, not conditional on them (which
704            is what the bVar slot contents represent).
705    
706    2006-07-31  Douglas Bates  <bates@R-project.org>
707    
708            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
709            function which calls the C function mer_hat_trace2.
710    
711            * man/ranef.Rd: Include description of "postVar" argument and
712            producing a caterpillar plot.
713    
714    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * NAMESPACE:    change  "correlation" to "corMatrix"
717            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
718            * R/dpoMatrix.R: ditto
719            * R/lmer.R:      ditto
720    
721    2006-07-28  Douglas Bates  <bates@R-project.org>
722    
723            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
724            RZXinv slot's contents into a separate internal function that can
725            be used in mer_hat_trace.
726    
727    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
730            via new smart
731            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
732            utility functions.
733    
734    
735    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Csparse.R (tril, triu, band): do return *triangular* classed
738            matrices when appropriate; band() even symmetric ones.
739            (replCmat): extend to potentially all "CsparseMatrix"
740            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
741            allow subassignment for special sparse matrices.
742    
743            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
744    
745            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
746            argument; in glmer_*(): print only if(verbose).
747    
748            speed-optimize a few places by moving REAL(.) out of loops.
749    
750            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
751    
752    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
755                    since that wrongly triggers also for M[ logi , ]
756    
757            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
758            a symmetric matrix that results in a non-symmetric one.
759            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
760    
761            * R/dMatrix.R: make round(M) work as round(M, 0)
762    
763            * R/dgTMatrix.R (image): coordinate system and axis now use
764            1-based indices, not 0-based ones.
765    
766            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
767            * tests/indexing.R: test it.
768    
769            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
770            * man/isSymmetric-methods.Rd: and document it.
771    
772            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
773            * man/SparseM-conv.Rd: docu them
774    
775            * tests/other-pkgs.R: renamed from tests/graph.R and add example
776                    for 'SparseM' conversions
777    
778    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
779    
780            * R/Matrix.R (head): added head() and tail() methods.
781    
782    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * DESCRIPTION (Version): 0.995-12 released to CRAN
785    
786    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * tests/simple.R: add check for correct dsT -> dgT coercion;
789                    add check for correct printing of symmetric sparse matrices.
790    
791            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
792            for sparse symmetric matrices.
793    
794            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
795            diagonal twice.
796    
797    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
798    
799            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
800            being applied to the x slot (detected by Brian Ripley).
801    
802    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
805    
806            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
807    
808    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * src/lgCMatrix.c (lgCMatrix_diag): new function
811            * R/lgCMatrix.R (diag): for new method
812    
813            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
814                 ==> construction of illegal "*gTMatrix" via new() should
815                 now be much less easy:
816            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
817    
818            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
819                    directly.
820            * man/Matrix.Rd: documents it.
821    
822    2006-07-06  Douglas Bates  <bates@R-project.org>
823    
824            * src/pedigree.c (pedigree_inbreeding): Correction in
825            initialization.  This function is not currently being used and is
826            not fully tested.
827    
828            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
829            Introduced the glmer class.  Added code for mcmcmsamp on glmer
830            objects.  Modified validity check on pedigree objects to account
831            for nonparallel patterns of missingness of parents.
832    
833            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
834            class.
835    
836    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/pMatrix.R: coercion pMatrix -> Tsparse
839    
840    2006-06-12  Douglas Bates  <bates@R-project.org>
841    
842            * DESCRIPTION (Version): 0.995-11 released to CRAN
843    
844            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
845            the output from mcmcsamp.
846    
847  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
848    
849          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
850            of the hat matrix.
851    
852  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
855          classes.          classes.
856            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
857    
858  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
# Line 43  Line 891 
891    
892          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
893          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
894          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
895    
896    
897  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 1014 
1014          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1015          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1016          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1017          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1018    
1019  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
# Line 370  Line 1218 
1218  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1221          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1222          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1223    
1224  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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