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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1724, Sat Jan 13 21:06:51 2007 UTC
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1    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
4            as method for   M[ ij ] <- v
5            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
6    
7            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
8            FALSE answer
9    
10            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
11            * tests/indexing.R: test it, and some of the above
12    
13    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/Auxiliaries.R (is_duplicatedT): new utility
16    
17    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * src/init.c (R_init_Matrix): export cholmod_scale
20    
21    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
24            base::as.matrix to (x, ...)
25    
26    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
29            file; start using "Logic", hence
30    
31            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
32            * NAMESPACE: import and export "Logic"
33    
34    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
37            only needed previously to R version 2.5.0.
38    
39    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
42    
43            * R/Tsparse.R (replTmat): fix subassignment of triangular
44            * R/Csparse.R (replCmat): ditto
45            * tests/indexing.R: more tests, incl the above fix
46    
47    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Auxiliaries.R (drop0): extend for non CSparse
50            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
51    
52            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
53                    use uplo correctly (!); other places: use uplo_P() macro
54    
55            * R/Csparse.R (replCmat): call diagU2N() when needed
56            * R/Tsparse.R (replTmat): ditto
57    
58            * src/dtCMatrix.c (tCMatrix_validate): new
59            * src/dtTMatrix.c (tTMatrix_validate): new, used in
60            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
61    
62            * R/diagMatrix.R (replDiag): to use in [<-
63    
64    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
67                    also more general diagU2N().
68    
69    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
72            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
73    
74    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * tests/bind.R: a few more cases
77            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
78    
79            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
80            * R/ddenseMatrix.R (cbind2/rbind2)
81            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
82            * tests/indexing.R
83            * tests/indexing.Rout.save: updated
84    
85    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
88            * tests/indexing.R
89    
90    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
93            align with proper position of "0", i.e., right for integers.
94            argument 'align' by default is "fancy".
95    
96    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
99            * R/Csparse.R: and fix "Compare" for more cases.
100            * tests/Class+Meth.R: test some of these (m == m, m != m)
101    
102    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/lsparseMatrix.R: all() and any() methods
105            * R/ldenseMatrix.R:      ditto
106            * NAMESPACE, R/Matrix.R: ditto
107    
108            * man/all-methods.Rd: document them minimally
109    
110            * tests/simple.R: add a few examples for these
111    
112    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Tsparse.R ([): fix long standing typo in symmetric case
115            * man/dsCMatrix-class.Rd: add example exhibiting the above case
116    
117    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
120            to LL before converting to a sparse matrix. (The LDL form can be
121            converted to a sparse matrix but it is implicitly a unit
122            triangular matrix and a diagonal matrix overwritten on the diagonal.)
123    
124    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
125    
126            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
127    
128    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
129    
130            * DESCRIPTION (Version): updated -> release 0.9975-7
131            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
132    
133    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
136    
137    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
138    
139            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
140            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
141            is exactly singular.
142    
143    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * DESCRIPTION (Date): updated -> release 0.9975-6
146    
147    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
150            now returns symmetric.
151    
152            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
153    
154            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
155            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
156    
157            * R/Auxiliaries.R (.type.kind): added
158    
159    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
162            running src/CSparse_install.sh
163    
164            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
165    
166    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
169            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
170    
171            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
172    
173            * tests/Class+Meth.R (tstMatrixClass): now assure
174            the (important in method programming) property :
175    
176                    ###>>  Every "Matrix" is either
177                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
178    
179                    (where "*" stands for "Matrix")
180    
181            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
182    
183            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
184            * tests/validObj.R: checks for "comparison"
185    
186            * R/sparseMatrix.R ([): improved indexing for sparse;
187                    trying to keep <symmetric>[ n, n] symmmetric
188    
189            * tests/indexing.R: indexing for logical sparse now ok
190    
191    
192    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * src/Tsparse.c: use xTsparse_validate() , and hence remove
195    
196            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
197    
198    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
201    
202            * tests/simple.R: validObject() checking the above.
203    
204            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
205            replacing both dgCMatrix_validate and lgCM*.
206    
207            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
208            fix dimnames setting in other places.
209            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
210    
211    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
214    
215            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
216            symmetry test, via
217            * R/Auxiliaries.R (.as.dgC.0.factors):
218    
219    2006-11-01  Douglas Bates  <bates@r-project.org>
220    
221            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
222            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
223            <CsparseMatrix>) added
224    
225    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * tests/matprod.R: add a variation of Harri's example
228    
229            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
230            recursive infinitely.
231    
232            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
233    
234            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
235    
236    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
239            matrix if possible; test m+m == 2*m; now test dgRMatrix.
240            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
241            satisfy the above test.
242    
243    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
246    
247            * R/dgCMatrix.R: solve(a, b="missing") based on
248            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
249            RHS = NULL.
250    
251            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
252            add more (needed) [t]crossprod() methods.
253    
254            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
255    
256            * R/Auxiliaries.R (as_CspClass): cleanup
257            (drop0): internal utility for "Csparse_drop(*, 0)"
258            (.bail.out.2): encourage active feedback
259    
260    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dMatrix.R(Compare): new(), then slots [no validity check]
263    
264            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
265            non-valid or 'sorted' case).
266    
267            * R/dsparseMatrix.R: add "chol" method.
268            * R/ddenseMatrix.R: ditto
269    
270            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
271            * NAMESPACE (Ops)
272            * R/diagMatrix.R (diag2T): simple utility used "higher level"
273            coercion; deprecating direct lower level coercions.
274    
275            * R/*.R (seq): use seq_len() and seq_along() where possible.
276    
277    
278    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Version): 0.9975-5 ready for release
281    
282    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
285    
286    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/AllClass.R (corMatrix): add 'validity' check;
289                    comment out unused "LDL" class definition
290            * NAMESPACE: mention, but do not export "LDL" class
291            * R/corMatrix.R: new (simple), needed for R-devel with
292            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
293              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
294    
295    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
298            use Rprintf and R's error handling.
299    
300    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
303            * tests/matprod.R: add tests for the bug fixed.
304    
305    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
308            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
309    
310    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
313    
314    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * DESCRIPTION (Version): 0.9975-3
317    
318            * R/diagMatrix.R (bdiag): new function constructing block diagonal
319            (sparse) matrices.
320            * man/bdiag.Rd: docu + examples
321    
322            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
323    
324            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
325            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
326    
327            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
328            that result is sparse or diagonal (and not dense).
329    
330            * man/Subassign-methods.Rd: fix examples
331    
332            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
333            should always return a sparse (and not sometimes a diagonal) matrix.
334    
335    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
338    
339    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * DESCRIPTION (Version): 0.9975-2
342    
343            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
344    
345    2006-10-02  Douglas Bates  <bates@R-project.org>
346    
347            * tests/dg_Matrix.R: Simplify test taking into account new code.
348    
349    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
352    
353            * R/lsTMatrix.R: new files w/ missing methods
354            * R/nsTMatrix.R:  "  'for completeness'
355    
356            * tests/Class+Meth.R: a bit less 'not.ok.classes'
357    
358            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
359    
360    
361    2006-09-28  Douglas Bates  <bates@R-project.org>
362    
363            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
364            included.
365    
366            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
367            Export C-callable functions used in Zt_create in lme4.
368    
369    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version): 0.9975-1
372    
373            * tests/simple.R: less checks fail; using NA, found that our
374                    kronecker() is not base-compatible with NA's.
375    
376            * R/dMatrix.R: "Compare" method now implemented for all cases
377    
378            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
379    
380            * man/dtpMatrix-class.Rd: mention length of 'x' slot
381    
382            * src/dtpMatrix.c (dtpMatrix_validate): fix check
383            * src/dspMatrix.c (dspMatrix_validate): ditto
384    
385            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
386              including coercion to [nl]tTMatrix.
387    
388            * R/diagMatrix.R (show): print a header line as for other classes.
389    
390    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * src/Makefile.win (SUBDIRS): fix typo
393    
394    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
397    
398    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
401            symmetric and y missing in R code using %*% (cholmod_aat doesn't
402            accept a symmetric matrix).
403            * tests/group-methods.R: Uncomment test of crossprod applied to
404            lsCMatrix objects.
405    
406    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/AllClass.R (symmetricMatrix): add validity method (available
409            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
410    
411            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
412    
413            * tests/indexing.Rout.save:
414            * tests/indexing.R: additions, mainly for 'lsparse'
415    
416            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
417            case.
418    
419            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
420    
421    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
424                    as 'N' (1-letter - Ok?)
425    
426            * tests/group-methods.R: add test for logical + NAs
427    
428            * R/dMatrix.R ("Compare"): fix to work with NA's
429    
430            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
431    
432            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
433                    which is implemented.
434    
435    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * src/chm_common.c: coerce logical <-> double instead of
438            typecasting;  needed for "l" matrix handling in cholmod.
439    
440            * tests/other-pkgs.R (graph): small extension in "graph" checks.
441    
442            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
443            (Tsp2grNEL): other fixes needed
444    
445    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
448                    Matrices, since "lMatrix", also "lsparseM" can have NA
449            * R/ndenseMatrix.R, etc: new source files
450            * man/nsparseMatrix-classes.Rd, etc: new help files
451            * tests/: adaptions
452            * src/chm_common.c (chm_dense_to_SEXP): and others:
453                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
454            * src/Csparse.c, etc: ditto
455    
456    2006-09-11  Douglas Bates  <bates@R-project.org>
457    
458            * src/Mutils.[ch],init.c inst/include/*.h: Move the
459            alloc_d**Matrix functions to the lme4 package.
460    
461    2006-09-09  Douglas Bates  <bates@R-project.org>
462    
463            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
464            fixed
465    
466    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/lMatrix.R: new
469    
470            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
471    
472            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
473            * man/tcrossprod.Rd: ditto
474    
475    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
476    
477            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
478            for exported functions
479            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
480            Remove partitioning algorithms for sparse matrix reordering.  The
481            copyright on the Metis code was problematic and the methods were
482            rarely used.
483            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
484            operations are now done entirely in CHOLMOD code.
485    
486    2006-09-06  Douglas Bates  <bates@R-project.org>
487    
488            * src/Mutils.h: Remove functions that are no longer used.
489    
490    2006-09-04  Douglas Bates  <bates@R-project.org>
491    
492            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
493            * src/DEPS.mkf: update
494    
495    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * created branches/Matrix-for-R-2.3.x;  on trunk: do
498            * DESCRIPTION (Version): 0.9975-0
499            (Depends): R (>= 2.4.0)
500    
501    2006-09-01  Douglas Bates  <bates@R-project.org>
502    
503            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
504    
505    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
508            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
509    
510            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
511    
512    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
515            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
516            * R/dsparseMatrix.R: ditto
517            * R/Csparse.R: ditto
518    
519    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dMatrix.R (Compare): improve availability of "<", etc
522            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
523    
524    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
527            of a 0-index which was used as 1-index (..hmm)
528    
529            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
530    
531            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
532            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
533            (.is.diagonal): ditto
534    
535            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
536    
537            * R/Matrix.R (Matrix): also work for NA data
538    
539    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
542            in all cases.
543    
544    2006-08-27  Douglas Bates  <bates@R-project.org>
545    
546            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
547            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
548    
549    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
552            subclasses of "ddenseMatrix"
553            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
554            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
555            instead of half dozen specialized ones.
556    
557    2006-08-25  Douglas Bates  <bates@R-project.org>
558    
559            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
560            <tillard@cirad.fr> - ordering standard errors to match effects.
561    
562    2006-08-24  Douglas Bates  <bates@R-project.org>
563    
564            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
565            on R_ldl.
566            * R/lCholCMatrix.R,
567            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
568            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
569            * many files in ./R and ./src: Use more general version of
570            dup_mMatrix_as_dgeMatrix to simplify method definitions.
571            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
572            dtpMatrix, dspMatrix and dppMatrix conversions.
573    
574    
575    2006-08-23  Douglas Bates  <bates@R-project.org>
576    
577            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
578            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
579            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
580            dgeMatrix_crossprod (may need to do this in other places).
581            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
582            generic and method for dsCMatrix.  Use CHOLMOD for chol().
583    
584    2006-08-22  Douglas Bates  <bates@R-project.org>
585    
586            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
587            types of classed Matrices, matrices or numeric or logical vectors.
588            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
589            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
590            to Mutils.h (as an inline) and change name to Matrix_check_class;
591            fixes in as_cholmod_factor and chm_factor_to_SEXP.
592            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
593            dsCMatrix_matrix_solve.  Comment out vestigial functions.
594            * src/Csparse.c: use diag_P and uplo_P macros.
595    
596    2006-08-21  Douglas Bates  <bates@R-project.org>
597    
598            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
599            valgrind.
600            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
601            inverses.
602            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
603            -Wall warnings.
604            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
605            Use dup_mMatrix_as_dgeMatrix.
606    
607    2006-08-20  Douglas Bates  <bates@R-project.org>
608    
609            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
610            * tests/sparseQR.R: Added
611            * man/sparseQR-class.Rd: Document methods for qr.* generics
612            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
613    
614    2006-08-19  Douglas Bates  <bates@R-project.org>
615    
616            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
617            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
618            and qr.fitted.
619            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
620            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
621    
622    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
625            the base version has no "..." argument.
626    
627            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
628    
629            * R/Matrix.R: define and
630            * NAMESPACE: export as.numeric() and as.logical() methods.
631                    Let's hope these do not badly slow down something...
632            Finally export the zapsmall() method.
633    
634    2006-08-17  Douglas Bates  <bates@R-project.org>
635    
636            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
637            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
638            * src/dtCMatrix.c :Remove code that is no longer used
639            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
640    
641    2006-08-14  Douglas Bates  <bates@R-project.org>
642    
643            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
644            Csparse_to_logical and Csparse_symmetric_to_general.
645            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
646            coercion methods between CsparseMatrix and TsparseMatrix.
647    
648    2006-08-14  Douglas Bates  <bates@R-project.org>
649    
650            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
651            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
652            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
653            possible.
654    
655    2006-08-12  Douglas Bates  <bates@R-project.org>
656    
657            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
658              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
659              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
660              generalize conversions between TsparseMatrix, CsparseMatrix,
661              denseMatrix and matrix.  Preserve triangularity property and
662              propagate Dimnames in the easy cases.
663    
664    2006-08-10  Douglas Bates  <bates@R-project.org>
665    
666            * src/lmer.c: adjust checks in glmer_init for S4SXP
667            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
668            before S4SXP but for the wrong reasons.
669    
670    2006-08-08  Douglas Bates  <bates@R-project.org>
671    
672            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
673            Later modified to return the upper triangle only.
674            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
675    
676    2006-08-07  Douglas Bates  <bates@R-project.org>
677    
678            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
679            R-level conversion to a sparse symmetric class.
680            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
681            Remove conversion to sparse symmetric classes (now done in C code).
682    
683    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
686            * man/band.Rd:  adapt the \dontshow{} unit test.
687    
688    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * DESCRIPTION (Version): 0.995-14  for CRAN
691    
692            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
693    
694            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
695            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
696    
697            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
698            * R/Tsparse.R (tril, triu, band): methods
699            * R/dgRMatrix.R (tril, ...):    ditto
700            * man/band.Rd:                  ditto
701    
702    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Matrix.R (head, tail): directly use utils:::head.matrix
705                    to be up-to-date automatically.
706    
707    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
710    
711            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
712            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
713            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
714            such that the S4 objects are always created by the current version
715            of R and 'Matrix' class definitions.
716    
717    2006-08-01  Douglas Bates  <bates@R-project.org>
718    
719            * R/lmer.R (LMEoptimize method), tests/lmer.R,
720            inst/external/test3comp.rda: Added warnings for convergence on
721            boundary and test cases.
722    
723            * src/lmer.c (mer_postVar): Modified to return the variances that
724            are marginal to the fixed effects, not conditional on them (which
725            is what the bVar slot contents represent).
726    
727    2006-07-31  Douglas Bates  <bates@R-project.org>
728    
729            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
730            function which calls the C function mer_hat_trace2.
731    
732            * man/ranef.Rd: Include description of "postVar" argument and
733            producing a caterpillar plot.
734    
735    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * NAMESPACE:    change  "correlation" to "corMatrix"
738            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
739            * R/dpoMatrix.R: ditto
740            * R/lmer.R:      ditto
741    
742    2006-07-28  Douglas Bates  <bates@R-project.org>
743    
744            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
745            RZXinv slot's contents into a separate internal function that can
746            be used in mer_hat_trace.
747    
748    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
751            via new smart
752            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
753            utility functions.
754    
755    
756    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/Csparse.R (tril, triu, band): do return *triangular* classed
759            matrices when appropriate; band() even symmetric ones.
760            (replCmat): extend to potentially all "CsparseMatrix"
761            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
762            allow subassignment for special sparse matrices.
763    
764            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
765    
766            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
767            argument; in glmer_*(): print only if(verbose).
768    
769            speed-optimize a few places by moving REAL(.) out of loops.
770    
771            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
772    
773    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
776                    since that wrongly triggers also for M[ logi , ]
777    
778            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
779            a symmetric matrix that results in a non-symmetric one.
780            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
781    
782            * R/dMatrix.R: make round(M) work as round(M, 0)
783    
784            * R/dgTMatrix.R (image): coordinate system and axis now use
785            1-based indices, not 0-based ones.
786    
787            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
788            * tests/indexing.R: test it.
789    
790            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
791            * man/isSymmetric-methods.Rd: and document it.
792    
793            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
794            * man/SparseM-conv.Rd: docu them
795    
796            * tests/other-pkgs.R: renamed from tests/graph.R and add example
797                    for 'SparseM' conversions
798    
799    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
800    
801            * R/Matrix.R (head): added head() and tail() methods.
802    
803    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * DESCRIPTION (Version): 0.995-12 released to CRAN
806    
807    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * tests/simple.R: add check for correct dsT -> dgT coercion;
810                    add check for correct printing of symmetric sparse matrices.
811    
812            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
813            for sparse symmetric matrices.
814    
815            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
816            diagonal twice.
817    
818    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
819    
820            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
821            being applied to the x slot (detected by Brian Ripley).
822    
823    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
826    
827            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
828    
829    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * src/lgCMatrix.c (lgCMatrix_diag): new function
832            * R/lgCMatrix.R (diag): for new method
833    
834            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
835                 ==> construction of illegal "*gTMatrix" via new() should
836                 now be much less easy:
837            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
838    
839            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
840                    directly.
841            * man/Matrix.Rd: documents it.
842    
843    2006-07-06  Douglas Bates  <bates@R-project.org>
844    
845            * src/pedigree.c (pedigree_inbreeding): Correction in
846            initialization.  This function is not currently being used and is
847            not fully tested.
848    
849            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
850            Introduced the glmer class.  Added code for mcmcmsamp on glmer
851            objects.  Modified validity check on pedigree objects to account
852            for nonparallel patterns of missingness of parents.
853    
854            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
855            class.
856    
857    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/pMatrix.R: coercion pMatrix -> Tsparse
860    
861    2006-06-12  Douglas Bates  <bates@R-project.org>
862    
863            * DESCRIPTION (Version): 0.995-11 released to CRAN
864    
865            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
866            the output from mcmcsamp.
867    
868  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
869    
870          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
871            of the hat matrix.
872    
873  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
876          classes.          classes.
877            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
878    
879  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
# Line 43  Line 912 
912    
913          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
914          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.
915          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
916    
917    
918  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 1035 
1035          * 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)
1036          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1037          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1038          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1039    
1040  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
# Line 370  Line 1239 
1239  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1240    
1241          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1242          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1243          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1244    
1245  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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