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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1738, Tue Jan 23 17:17:15 2007 UTC
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1    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
4    
5            * R/Ops.R ("Logic"): and other "Ops", many updates
6    
7    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/Mutils.h (SET_DimNames): new utility
10    
11            * R/Auxiliaries.R (nnzero): improved and now exported via
12    
13            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
14    
15    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/diagMatrix.R (!): fix typo.
18    
19    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Auxiliaries.R (as_Csparse): and quite a few others:
22                    allow to pass class definition --> speedup
23            * R/sparseMatrix.R: apply the above
24    
25            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
26    
27            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
28            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
29            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
30    
31            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
32    
33            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
34            and use it for "sparse*" as well, since it's faster than the
35            as_Csparse(.) way.
36    
37    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
40    
41    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
44            as method for   M[ ij ] <- v
45            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
46    
47            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
48            FALSE answer
49    
50            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
51            * tests/indexing.R: test it, and some of the above
52    
53    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (is_duplicatedT): new utility
56    
57    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
58    
59            * src/init.c (R_init_Matrix): export cholmod_scale
60    
61    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
64            base::as.matrix to (x, ...)
65    
66    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
69            file; start using "Logic", hence
70    
71            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
72            * NAMESPACE: import and export "Logic"
73    
74    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
77            only needed previously to R version 2.5.0.
78    
79    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
82    
83            * R/Tsparse.R (replTmat): fix subassignment of triangular
84            * R/Csparse.R (replCmat): ditto
85            * tests/indexing.R: more tests, incl the above fix
86    
87    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Auxiliaries.R (drop0): extend for non CSparse
90            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
91    
92            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
93                    use uplo correctly (!); other places: use uplo_P() macro
94    
95            * R/Csparse.R (replCmat): call diagU2N() when needed
96            * R/Tsparse.R (replTmat): ditto
97    
98            * src/dtCMatrix.c (tCMatrix_validate): new
99            * src/dtTMatrix.c (tTMatrix_validate): new, used in
100            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
101    
102            * R/diagMatrix.R (replDiag): to use in [<-
103    
104    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
107                    also more general diagU2N().
108    
109    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
112            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
113    
114    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * tests/bind.R: a few more cases
117            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
118    
119            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
120            * R/ddenseMatrix.R (cbind2/rbind2)
121            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
122            * tests/indexing.R
123            * tests/indexing.Rout.save: updated
124    
125    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
128            * tests/indexing.R
129    
130    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
133            align with proper position of "0", i.e., right for integers.
134            argument 'align' by default is "fancy".
135    
136    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
139            * R/Csparse.R: and fix "Compare" for more cases.
140            * tests/Class+Meth.R: test some of these (m == m, m != m)
141    
142    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/lsparseMatrix.R: all() and any() methods
145            * R/ldenseMatrix.R:      ditto
146            * NAMESPACE, R/Matrix.R: ditto
147    
148            * man/all-methods.Rd: document them minimally
149    
150            * tests/simple.R: add a few examples for these
151    
152    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Tsparse.R ([): fix long standing typo in symmetric case
155            * man/dsCMatrix-class.Rd: add example exhibiting the above case
156    
157    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
160            to LL before converting to a sparse matrix. (The LDL form can be
161            converted to a sparse matrix but it is implicitly a unit
162            triangular matrix and a diagonal matrix overwritten on the diagonal.)
163    
164    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
167    
168    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * DESCRIPTION (Version): updated -> release 0.9975-7
171            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
172    
173    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
176    
177    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
178    
179            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
180            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
181            is exactly singular.
182    
183    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Date): updated -> release 0.9975-6
186    
187    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
190            now returns symmetric.
191    
192            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
193    
194            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
195            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
196    
197            * R/Auxiliaries.R (.type.kind): added
198    
199    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
202            running src/CSparse_install.sh
203    
204            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
205    
206    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
209            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
210    
211            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
212    
213            * tests/Class+Meth.R (tstMatrixClass): now assure
214            the (important in method programming) property :
215    
216                    ###>>  Every "Matrix" is either
217                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
218    
219                    (where "*" stands for "Matrix")
220    
221            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
222    
223            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
224            * tests/validObj.R: checks for "comparison"
225    
226            * R/sparseMatrix.R ([): improved indexing for sparse;
227                    trying to keep <symmetric>[ n, n] symmmetric
228    
229            * tests/indexing.R: indexing for logical sparse now ok
230    
231    
232    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * src/Tsparse.c: use xTsparse_validate() , and hence remove
235    
236            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
237    
238    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
241    
242            * tests/simple.R: validObject() checking the above.
243    
244            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
245            replacing both dgCMatrix_validate and lgCM*.
246    
247            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
248            fix dimnames setting in other places.
249            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
250    
251    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
254    
255            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
256            symmetry test, via
257            * R/Auxiliaries.R (.as.dgC.0.factors):
258    
259    2006-11-01  Douglas Bates  <bates@r-project.org>
260    
261            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
262            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
263            <CsparseMatrix>) added
264    
265    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * tests/matprod.R: add a variation of Harri's example
268    
269            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
270            recursive infinitely.
271    
272            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
273    
274            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
275    
276    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
279            matrix if possible; test m+m == 2*m; now test dgRMatrix.
280            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
281            satisfy the above test.
282    
283    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
286    
287            * R/dgCMatrix.R: solve(a, b="missing") based on
288            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
289            RHS = NULL.
290    
291            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
292            add more (needed) [t]crossprod() methods.
293    
294            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
295    
296            * R/Auxiliaries.R (as_CspClass): cleanup
297            (drop0): internal utility for "Csparse_drop(*, 0)"
298            (.bail.out.2): encourage active feedback
299    
300    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dMatrix.R(Compare): new(), then slots [no validity check]
303    
304            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
305            non-valid or 'sorted' case).
306    
307            * R/dsparseMatrix.R: add "chol" method.
308            * R/ddenseMatrix.R: ditto
309    
310            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
311            * NAMESPACE (Ops)
312            * R/diagMatrix.R (diag2T): simple utility used "higher level"
313            coercion; deprecating direct lower level coercions.
314    
315            * R/*.R (seq): use seq_len() and seq_along() where possible.
316    
317    
318    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * DESCRIPTION (Version): 0.9975-5 ready for release
321    
322    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
323    
324            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
325    
326    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/AllClass.R (corMatrix): add 'validity' check;
329                    comment out unused "LDL" class definition
330            * NAMESPACE: mention, but do not export "LDL" class
331            * R/corMatrix.R: new (simple), needed for R-devel with
332            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
333              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
334    
335    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
338            use Rprintf and R's error handling.
339    
340    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
343            * tests/matprod.R: add tests for the bug fixed.
344    
345    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
346    
347            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
348            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
349    
350    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
353    
354    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.9975-3
357    
358            * R/diagMatrix.R (bdiag): new function constructing block diagonal
359            (sparse) matrices.
360            * man/bdiag.Rd: docu + examples
361    
362            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
363    
364            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
365            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
366    
367            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
368            that result is sparse or diagonal (and not dense).
369    
370            * man/Subassign-methods.Rd: fix examples
371    
372            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
373            should always return a sparse (and not sometimes a diagonal) matrix.
374    
375    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
378    
379    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
380    
381            * DESCRIPTION (Version): 0.9975-2
382    
383            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
384    
385    2006-10-02  Douglas Bates  <bates@R-project.org>
386    
387            * tests/dg_Matrix.R: Simplify test taking into account new code.
388    
389    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
392    
393            * R/lsTMatrix.R: new files w/ missing methods
394            * R/nsTMatrix.R:  "  'for completeness'
395    
396            * tests/Class+Meth.R: a bit less 'not.ok.classes'
397    
398            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
399    
400    
401    2006-09-28  Douglas Bates  <bates@R-project.org>
402    
403            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
404            included.
405    
406            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
407            Export C-callable functions used in Zt_create in lme4.
408    
409    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * DESCRIPTION (Version): 0.9975-1
412    
413            * tests/simple.R: less checks fail; using NA, found that our
414                    kronecker() is not base-compatible with NA's.
415    
416            * R/dMatrix.R: "Compare" method now implemented for all cases
417    
418            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
419    
420            * man/dtpMatrix-class.Rd: mention length of 'x' slot
421    
422            * src/dtpMatrix.c (dtpMatrix_validate): fix check
423            * src/dspMatrix.c (dspMatrix_validate): ditto
424    
425            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
426              including coercion to [nl]tTMatrix.
427    
428            * R/diagMatrix.R (show): print a header line as for other classes.
429    
430    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * src/Makefile.win (SUBDIRS): fix typo
433    
434    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
437    
438    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
441            symmetric and y missing in R code using %*% (cholmod_aat doesn't
442            accept a symmetric matrix).
443            * tests/group-methods.R: Uncomment test of crossprod applied to
444            lsCMatrix objects.
445    
446    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/AllClass.R (symmetricMatrix): add validity method (available
449            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
450    
451            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
452    
453            * tests/indexing.Rout.save:
454            * tests/indexing.R: additions, mainly for 'lsparse'
455    
456            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
457            case.
458    
459            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
460    
461    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
464                    as 'N' (1-letter - Ok?)
465    
466            * tests/group-methods.R: add test for logical + NAs
467    
468            * R/dMatrix.R ("Compare"): fix to work with NA's
469    
470            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
471    
472            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
473                    which is implemented.
474    
475    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/chm_common.c: coerce logical <-> double instead of
478            typecasting;  needed for "l" matrix handling in cholmod.
479    
480            * tests/other-pkgs.R (graph): small extension in "graph" checks.
481    
482            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
483            (Tsp2grNEL): other fixes needed
484    
485    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
488                    Matrices, since "lMatrix", also "lsparseM" can have NA
489            * R/ndenseMatrix.R, etc: new source files
490            * man/nsparseMatrix-classes.Rd, etc: new help files
491            * tests/: adaptions
492            * src/chm_common.c (chm_dense_to_SEXP): and others:
493                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
494            * src/Csparse.c, etc: ditto
495    
496    2006-09-11  Douglas Bates  <bates@R-project.org>
497    
498            * src/Mutils.[ch],init.c inst/include/*.h: Move the
499            alloc_d**Matrix functions to the lme4 package.
500    
501    2006-09-09  Douglas Bates  <bates@R-project.org>
502    
503            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
504            fixed
505    
506    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/lMatrix.R: new
509    
510            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
511    
512            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
513            * man/tcrossprod.Rd: ditto
514    
515    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
516    
517            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
518            for exported functions
519            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
520            Remove partitioning algorithms for sparse matrix reordering.  The
521            copyright on the Metis code was problematic and the methods were
522            rarely used.
523            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
524            operations are now done entirely in CHOLMOD code.
525    
526    2006-09-06  Douglas Bates  <bates@R-project.org>
527    
528            * src/Mutils.h: Remove functions that are no longer used.
529    
530    2006-09-04  Douglas Bates  <bates@R-project.org>
531    
532            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
533            * src/DEPS.mkf: update
534    
535    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * created branches/Matrix-for-R-2.3.x;  on trunk: do
538            * DESCRIPTION (Version): 0.9975-0
539            (Depends): R (>= 2.4.0)
540    
541    2006-09-01  Douglas Bates  <bates@R-project.org>
542    
543            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
544    
545    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
548            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
549    
550            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
551    
552    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
555            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
556            * R/dsparseMatrix.R: ditto
557            * R/Csparse.R: ditto
558    
559    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/dMatrix.R (Compare): improve availability of "<", etc
562            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
563    
564    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
567            of a 0-index which was used as 1-index (..hmm)
568    
569            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
570    
571            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
572            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
573            (.is.diagonal): ditto
574    
575            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
576    
577            * R/Matrix.R (Matrix): also work for NA data
578    
579    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
582            in all cases.
583    
584    2006-08-27  Douglas Bates  <bates@R-project.org>
585    
586            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
587            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
588    
589    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
592            subclasses of "ddenseMatrix"
593            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
594            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
595            instead of half dozen specialized ones.
596    
597    2006-08-25  Douglas Bates  <bates@R-project.org>
598    
599            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
600            <tillard@cirad.fr> - ordering standard errors to match effects.
601    
602    2006-08-24  Douglas Bates  <bates@R-project.org>
603    
604            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
605            on R_ldl.
606            * R/lCholCMatrix.R,
607            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
608            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
609            * many files in ./R and ./src: Use more general version of
610            dup_mMatrix_as_dgeMatrix to simplify method definitions.
611            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
612            dtpMatrix, dspMatrix and dppMatrix conversions.
613    
614    
615    2006-08-23  Douglas Bates  <bates@R-project.org>
616    
617            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
618            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
619            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
620            dgeMatrix_crossprod (may need to do this in other places).
621            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
622            generic and method for dsCMatrix.  Use CHOLMOD for chol().
623    
624    2006-08-22  Douglas Bates  <bates@R-project.org>
625    
626            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
627            types of classed Matrices, matrices or numeric or logical vectors.
628            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
629            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
630            to Mutils.h (as an inline) and change name to Matrix_check_class;
631            fixes in as_cholmod_factor and chm_factor_to_SEXP.
632            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
633            dsCMatrix_matrix_solve.  Comment out vestigial functions.
634            * src/Csparse.c: use diag_P and uplo_P macros.
635    
636    2006-08-21  Douglas Bates  <bates@R-project.org>
637    
638            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
639            valgrind.
640            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
641            inverses.
642            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
643            -Wall warnings.
644            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
645            Use dup_mMatrix_as_dgeMatrix.
646    
647    2006-08-20  Douglas Bates  <bates@R-project.org>
648    
649            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
650            * tests/sparseQR.R: Added
651            * man/sparseQR-class.Rd: Document methods for qr.* generics
652            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
653    
654    2006-08-19  Douglas Bates  <bates@R-project.org>
655    
656            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
657            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
658            and qr.fitted.
659            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
660            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
661    
662    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
665            the base version has no "..." argument.
666    
667            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
668    
669            * R/Matrix.R: define and
670            * NAMESPACE: export as.numeric() and as.logical() methods.
671                    Let's hope these do not badly slow down something...
672            Finally export the zapsmall() method.
673    
674    2006-08-17  Douglas Bates  <bates@R-project.org>
675    
676            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
677            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
678            * src/dtCMatrix.c :Remove code that is no longer used
679            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
680    
681    2006-08-14  Douglas Bates  <bates@R-project.org>
682    
683            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
684            Csparse_to_logical and Csparse_symmetric_to_general.
685            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
686            coercion methods between CsparseMatrix and TsparseMatrix.
687    
688    2006-08-14  Douglas Bates  <bates@R-project.org>
689    
690            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
691            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
692            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
693            possible.
694    
695    2006-08-12  Douglas Bates  <bates@R-project.org>
696    
697            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
698              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
699              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
700              generalize conversions between TsparseMatrix, CsparseMatrix,
701              denseMatrix and matrix.  Preserve triangularity property and
702              propagate Dimnames in the easy cases.
703    
704    2006-08-10  Douglas Bates  <bates@R-project.org>
705    
706            * src/lmer.c: adjust checks in glmer_init for S4SXP
707            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
708            before S4SXP but for the wrong reasons.
709    
710    2006-08-08  Douglas Bates  <bates@R-project.org>
711    
712            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
713            Later modified to return the upper triangle only.
714            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
715    
716    2006-08-07  Douglas Bates  <bates@R-project.org>
717    
718            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
719            R-level conversion to a sparse symmetric class.
720            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
721            Remove conversion to sparse symmetric classes (now done in C code).
722    
723    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
726            * man/band.Rd:  adapt the \dontshow{} unit test.
727    
728    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * DESCRIPTION (Version): 0.995-14  for CRAN
731    
732            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
733    
734            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
735            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
736    
737            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
738            * R/Tsparse.R (tril, triu, band): methods
739            * R/dgRMatrix.R (tril, ...):    ditto
740            * man/band.Rd:                  ditto
741    
742    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Matrix.R (head, tail): directly use utils:::head.matrix
745                    to be up-to-date automatically.
746    
747    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
750    
751            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
752            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
753            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
754            such that the S4 objects are always created by the current version
755            of R and 'Matrix' class definitions.
756    
757    2006-08-01  Douglas Bates  <bates@R-project.org>
758    
759            * R/lmer.R (LMEoptimize method), tests/lmer.R,
760            inst/external/test3comp.rda: Added warnings for convergence on
761            boundary and test cases.
762    
763            * src/lmer.c (mer_postVar): Modified to return the variances that
764            are marginal to the fixed effects, not conditional on them (which
765            is what the bVar slot contents represent).
766    
767    2006-07-31  Douglas Bates  <bates@R-project.org>
768    
769            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
770            function which calls the C function mer_hat_trace2.
771    
772            * man/ranef.Rd: Include description of "postVar" argument and
773            producing a caterpillar plot.
774    
775    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * NAMESPACE:    change  "correlation" to "corMatrix"
778            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
779            * R/dpoMatrix.R: ditto
780            * R/lmer.R:      ditto
781    
782    2006-07-28  Douglas Bates  <bates@R-project.org>
783    
784            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
785            RZXinv slot's contents into a separate internal function that can
786            be used in mer_hat_trace.
787    
788    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
791            via new smart
792            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
793            utility functions.
794    
795    
796    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/Csparse.R (tril, triu, band): do return *triangular* classed
799            matrices when appropriate; band() even symmetric ones.
800            (replCmat): extend to potentially all "CsparseMatrix"
801            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
802            allow subassignment for special sparse matrices.
803    
804            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
805    
806            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
807            argument; in glmer_*(): print only if(verbose).
808    
809            speed-optimize a few places by moving REAL(.) out of loops.
810    
811            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
812    
813    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
816                    since that wrongly triggers also for M[ logi , ]
817    
818            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
819            a symmetric matrix that results in a non-symmetric one.
820            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
821    
822            * R/dMatrix.R: make round(M) work as round(M, 0)
823    
824            * R/dgTMatrix.R (image): coordinate system and axis now use
825            1-based indices, not 0-based ones.
826    
827            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
828            * tests/indexing.R: test it.
829    
830            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
831            * man/isSymmetric-methods.Rd: and document it.
832    
833            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
834            * man/SparseM-conv.Rd: docu them
835    
836            * tests/other-pkgs.R: renamed from tests/graph.R and add example
837                    for 'SparseM' conversions
838    
839    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
840    
841            * R/Matrix.R (head): added head() and tail() methods.
842    
843    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * DESCRIPTION (Version): 0.995-12 released to CRAN
846    
847    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * tests/simple.R: add check for correct dsT -> dgT coercion;
850                    add check for correct printing of symmetric sparse matrices.
851    
852            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
853            for sparse symmetric matrices.
854    
855            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
856            diagonal twice.
857    
858    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
859    
860            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
861            being applied to the x slot (detected by Brian Ripley).
862    
863    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
866    
867            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
868    
869    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * src/lgCMatrix.c (lgCMatrix_diag): new function
872            * R/lgCMatrix.R (diag): for new method
873    
874            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
875                 ==> construction of illegal "*gTMatrix" via new() should
876                 now be much less easy:
877            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
878    
879            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
880                    directly.
881            * man/Matrix.Rd: documents it.
882    
883    2006-07-06  Douglas Bates  <bates@R-project.org>
884    
885            * src/pedigree.c (pedigree_inbreeding): Correction in
886            initialization.  This function is not currently being used and is
887            not fully tested.
888    
889            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
890            Introduced the glmer class.  Added code for mcmcmsamp on glmer
891            objects.  Modified validity check on pedigree objects to account
892            for nonparallel patterns of missingness of parents.
893    
894            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
895            class.
896    
897    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * R/pMatrix.R: coercion pMatrix -> Tsparse
900    
901    2006-06-12  Douglas Bates  <bates@R-project.org>
902    
903            * DESCRIPTION (Version): 0.995-11 released to CRAN
904    
905            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
906            the output from mcmcsamp.
907    
908    2006-06-10  Douglas Bates  <bates@R-project.org>
909    
910            * R/lmer.R (simulestimate): added C code for calculating the trace
911            of the hat matrix.
912    
913    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
916            classes.
917            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
918    
919    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/dgTMatrix.R (colSums): etc. All four of
922            colSums(), rowSums(), colMeans(), rowMeans() now should work for
923            all "Matrices".
924    
925    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
926    
927            * R/lmer.R (panel.ci): Add a reference line at zero and a
928            background grid to the qqmath plot of ranef.lmer.
929    
930    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
931    
932            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
933            grouping factors to be specified in the formula as (1|foo/bar).
934    
935    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
936    
937            * R/lmer.R (findbars and others): Change check of is.numeric to
938            !is.language to resolve the bug reported by Jacob Wegelin.
939    
940            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
941            code to evaluate inbreeding coefficients without calculating T,
942            based on code in Sargolzaei and Iwaisaki's paper.
943    
944    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
945    
946            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
947            generic and mer methods for isNested and denomDF. This denomDF was
948            an attempt to emulate that in lme but I don't think that makes
949            sense.  Use the trace of the hat matrix instead.
950    
951    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
954            the C code depending on a slot structure that's no longer valid.
955            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
956    
957    
958    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
959    
960            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
961            of lowerTriMatrix generic and methods to tril (also upper to triu)
962            and added a general band extractor.
963    
964    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
965    
966            * R/pedigree.R (pedigree): Replace sire and dam values outside the
967            allowable range with NAs. Added a corresponding check in the
968            validity check for the pedigree class.
969    
970            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
971            crossprod methods now inherits from symmetricMatrix.
972    
973    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
974    
975            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
976            generics lowerTriMatrix and upperTriMatrix along with methods for
977            the Csparse virtual class.  Also added a C function Csparse_band
978            that implements these methods by calling cholmod_band.
979    
980    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
983            erased when it was NULL.  This led to invalid subselections!
984    
985    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
986    
987            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
988            in method for "t" so as not to lose the unit diagonal property.
989    
990    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
991    
992            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
993            and methods.  This is now an option to the ranef method for the
994            mer class.
995    
996            * src/cs_utils.c: Ensure that the nz component is -1 for a
997            compressed column-oriented matrix.  Minor formatting cleanup.
998    
999            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1000            objects.
1001    
1002    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1005            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1006    
1007    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1008    
1009            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1010            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1011    
1012            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1013            for the dtCMatrix class.
1014    
1015    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1016    
1017            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1018            and methods for it.
1019    
1020    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1023            arguments, such that M %*% 1:6 now works
1024            * Tests/matprod.R: test the above
1025    
1026    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1027    
1028            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1029            the ranef.lmer class.
1030    
1031            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1032            methods to extract the posterior variances from the bVar slot.
1033    
1034    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1037            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1038    
1039            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1040            * tests/simple: (extended)
1041    
1042            * R/sparseMatrix.R (isTriangular): now using much improved
1043            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1044    
1045    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1046    
1047            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1048            (problem report from Franklin Parlamis).  This should be done
1049            generally.
1050    
1051    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1052    
1053            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1054            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1055            update the plot methods.
1056    
1057    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1058    
1059            * R/lmer.R (resid and ranef methods):  Added methods for the
1060            "residuals" and "resid" generic but only for linear mixed model
1061            fits.  Changed the ranef method to return a list of data frames so
1062            that the plot methods now work.
1063    
1064    2006-03-16  Douglas Bates  <bates@bates2>
1065    
1066            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1067            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1068    
1069            * DESCRIPTION (Date): New release
1070    
1071    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1074    
1075            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1076            * man/KNex.Rd: and other help files
1077            * tests/*.R: several ones needed adaption
1078            * inst/doc/Comparisons.Rnw: ditto
1079    
1080    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1083    
1084            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1085    
1086    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1087    
1088            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1089    
1090            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1091    
1092    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1093    
1094            * R/dMatrix.R: enable things like  M [ M < 10 ]
1095            * R/dgeMatrix.R: implement it
1096    
1097    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * R/AllClass.R: define "summary.mer" and "*.lmer"
1100            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1101            * R/lmer.R (show): now works with summary()
1102    
1103    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1106            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1107                    support the above
1108    
1109    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1110    
1111            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1112            Use glmFit$prior.weights for weights in a glmm.
1113            Allow an option usePQL = FALSE to skip the PQL steps for the
1114            Laplace method (and, in time, the AGQ method).
1115    
1116            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1117            into a separate function internal_mer_Xfactor to be able to call
1118            it from internal_bhat.
1119    
1120    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * tests/Class+Meth.R (tstMatrixClass): function for much better
1123            testing; now again of all actual classes.
1124    
1125            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1126                    use macros and define make_d_matrix_* and make_i_matrix_*
1127                    where _i_ is for the ldense routines:
1128    
1129            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1130            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1131    
1132            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1133    
1134    
1135    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1138                    many different kinds of matrices.
1139            * R/*.R: quite a few new methods were needed for R CMD check with
1140                    new Matrix().  Very good for users playing around.
1141    
1142    
1143    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * src/dgeMatrix.c (dMatrix_validate): new
1146            * src/Mutils.c (dense_nonpacked_validate): new
1147    
1148            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1149    
1150    
1151    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1152    
1153            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1154    
1155    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1156    
1157            * DESCRIPTION (Version): 0.99-6 released to CRAN
1158    
1159            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1160            segfault in cases with multiple non-nested grouping factors.
1161    
1162    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1165                    (Depends): also on 'utils'
1166    
1167            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1168            * R/diagMatrix.R (Diagonal): constructor and methods for
1169            diagonal matrices
1170    
1171            * R/ltTMatrix.R: new "minimal methods"
1172    
1173    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1174    
1175            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1176            all methods (and help files).
1177    
1178    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1181                    for case (dimn.  op  no_dimn.)
1182    
1183    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1184    
1185            * DESCRIPTION (Version): 0.99-2  released to CRAN
1186    
1187    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1188    
1189            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1190            by Julian Faraway.
1191    
1192    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/Auxiliaries.R (try_as): new utility
1195            * R/sparseMatrix.R: use try_as() in coercion to original class
1196    
1197    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1200    
1201    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/Auxiliaries.R (dimNamesCheck): added
1204    
1205            * R/Matrix.R (as.array), (as.vector): new
1206    
1207    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1210                    default.
1211            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1212                    "pMatrix" now contains "sparseMatrix"
1213    
1214    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1215    
1216            * tests/Class+Meth.R: new tests; t(t(m)) == m
1217    
1218            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1219    
1220            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1221            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1222    
1223            * R/dspMatrix.R: typo in "t" method
1224    
1225    2005-09-18  Douglas Bates  <bates@wisc.edu>
1226    
1227            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1228            * R/Tsparse.R: instead of R/gTMatrix.R
1229            * R/Csparse.R: new
1230            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1231            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1232            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1233                            via cholmod
1234    
1235    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1236    
1237            * R/Auxiliaries.R (non0ind): new function using new C code
1238            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1239    
1240    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1241    
1242            * src/chm_common.h: header file required by all C sources that
1243            call CHOLMOD functions.  It defines a cholmod_common structure
1244            called 'c' whose address is passed as the last argument to
1245            (virtually) every CHOLMOD function.
1246    
1247            * src/Pattern.c: Simple example of the use of CHOLMOD.
1248    
1249            * src/init.c: initialize and finalize the cholmod_common structure.
1250    
1251            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1252            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1253    
1254    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1255    
1256            * inst/test-tools.R: new file collecting the utility functions used
1257                    in ./tests/*.R
1258    
1259            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1260            * R/Matrix.R (cbind2): methods for NULL and missing
1261    
1262    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1263    
1264            * R/AllClass.R: new "index" class for "[" and "[<-":
1265                    First cut at "symmetricMatrix" and "triangularMatrix"
1266            * R/gTMatrix.R (.ind.prep): new function;
1267                    Logical and character indexing now work too.
1268            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1269            * tests/indexing.R: new, including *.Rout.save
1270            * tests/dgTMatrix.R: new
1271    
1272  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
1273    
1274          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
# Line 8  Line 1279 
1279  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1282          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1283          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1284    
1285  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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