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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1708, Fri Dec 22 19:53:37 2006 UTC
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1    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
4                    also more general diagU2N().
5    
6    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
9            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
10    
11    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * tests/bind.R: a few more cases
14            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
15    
16            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
17            * R/ddenseMatrix.R (cbind2/rbind2)
18            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
19            * tests/indexing.R
20            * tests/indexing.Rout.save: updated
21    
22    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
25            * tests/indexing.R
26    
27    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
30            align with proper position of "0", i.e., right for integers.
31            argument 'align' by default is "fancy".
32    
33    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
36            * R/Csparse.R: and fix "Compare" for more cases.
37            * tests/Class+Meth.R: test some of these (m == m, m != m)
38    
39    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/lsparseMatrix.R: all() and any() methods
42            * R/ldenseMatrix.R:      ditto
43            * NAMESPACE, R/Matrix.R: ditto
44    
45            * man/all-methods.Rd: document them minimally
46    
47            * tests/simple.R: add a few examples for these
48    
49    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/Tsparse.R ([): fix long standing typo in symmetric case
52            * man/dsCMatrix-class.Rd: add example exhibiting the above case
53    
54    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
57            to LL before converting to a sparse matrix. (The LDL form can be
58            converted to a sparse matrix but it is implicitly a unit
59            triangular matrix and a diagonal matrix overwritten on the diagonal.)
60    
61    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
64    
65    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * DESCRIPTION (Version): updated -> release 0.9975-7
68            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
69    
70    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
73    
74    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
75    
76            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
77            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
78            is exactly singular.
79    
80    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * DESCRIPTION (Date): updated -> release 0.9975-6
83    
84    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
87            now returns symmetric.
88    
89            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
90    
91            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
92            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
93    
94            * R/Auxiliaries.R (.type.kind): added
95    
96    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
99            running src/CSparse_install.sh
100    
101            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
102    
103    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
106            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
107    
108            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
109    
110            * tests/Class+Meth.R (tstMatrixClass): now assure
111            the (important in method programming) property :
112    
113                    ###>>  Every "Matrix" is either
114                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
115    
116                    (where "*" stands for "Matrix")
117    
118            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
119    
120            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
121            * tests/validObj.R: checks for "comparison"
122    
123            * R/sparseMatrix.R ([): improved indexing for sparse;
124                    trying to keep <symmetric>[ n, n] symmmetric
125    
126            * tests/indexing.R: indexing for logical sparse now ok
127    
128    
129    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/Tsparse.c: use xTsparse_validate() , and hence remove
132    
133            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
134    
135    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
138    
139            * tests/simple.R: validObject() checking the above.
140    
141            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
142            replacing both dgCMatrix_validate and lgCM*.
143    
144            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
145            fix dimnames setting in other places.
146            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
147    
148    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
151    
152            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
153            symmetry test, via
154            * R/Auxiliaries.R (.as.dgC.0.factors):
155    
156    2006-11-01  Douglas Bates  <bates@r-project.org>
157    
158            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
159            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
160            <CsparseMatrix>) added
161    
162    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * tests/matprod.R: add a variation of Harri's example
165    
166            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
167            recursive infinitely.
168    
169            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
170    
171            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
172    
173    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
176            matrix if possible; test m+m == 2*m; now test dgRMatrix.
177            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
178            satisfy the above test.
179    
180    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
183    
184            * R/dgCMatrix.R: solve(a, b="missing") based on
185            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
186            RHS = NULL.
187    
188            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
189            add more (needed) [t]crossprod() methods.
190    
191            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
192    
193            * R/Auxiliaries.R (as_CspClass): cleanup
194            (drop0): internal utility for "Csparse_drop(*, 0)"
195            (.bail.out.2): encourage active feedback
196    
197    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/dMatrix.R(Compare): new(), then slots [no validity check]
200    
201            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
202            non-valid or 'sorted' case).
203    
204            * R/dsparseMatrix.R: add "chol" method.
205            * R/ddenseMatrix.R: ditto
206    
207            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
208            * NAMESPACE (Ops)
209            * R/diagMatrix.R (diag2T): simple utility used "higher level"
210            coercion; deprecating direct lower level coercions.
211    
212            * R/*.R (seq): use seq_len() and seq_along() where possible.
213    
214    
215    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * DESCRIPTION (Version): 0.9975-5 ready for release
218    
219    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
222    
223    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/AllClass.R (corMatrix): add 'validity' check;
226                    comment out unused "LDL" class definition
227            * NAMESPACE: mention, but do not export "LDL" class
228            * R/corMatrix.R: new (simple), needed for R-devel with
229            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
230              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
231    
232    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
235            use Rprintf and R's error handling.
236    
237    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
240            * tests/matprod.R: add tests for the bug fixed.
241    
242    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
245            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
246    
247    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
248    
249            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
250    
251    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * DESCRIPTION (Version): 0.9975-3
254    
255            * R/diagMatrix.R (bdiag): new function constructing block diagonal
256            (sparse) matrices.
257            * man/bdiag.Rd: docu + examples
258    
259            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
260    
261            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
262            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
263    
264            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
265            that result is sparse or diagonal (and not dense).
266    
267            * man/Subassign-methods.Rd: fix examples
268    
269            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
270            should always return a sparse (and not sometimes a diagonal) matrix.
271    
272    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
275    
276    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
277    
278            * DESCRIPTION (Version): 0.9975-2
279    
280            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
281    
282    2006-10-02  Douglas Bates  <bates@R-project.org>
283    
284            * tests/dg_Matrix.R: Simplify test taking into account new code.
285    
286    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
289    
290            * R/lsTMatrix.R: new files w/ missing methods
291            * R/nsTMatrix.R:  "  'for completeness'
292    
293            * tests/Class+Meth.R: a bit less 'not.ok.classes'
294    
295            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
296    
297    
298    2006-09-28  Douglas Bates  <bates@R-project.org>
299    
300            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
301            included.
302    
303            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
304            Export C-callable functions used in Zt_create in lme4.
305    
306    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * DESCRIPTION (Version): 0.9975-1
309    
310            * tests/simple.R: less checks fail; using NA, found that our
311                    kronecker() is not base-compatible with NA's.
312    
313            * R/dMatrix.R: "Compare" method now implemented for all cases
314    
315            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
316    
317            * man/dtpMatrix-class.Rd: mention length of 'x' slot
318    
319            * src/dtpMatrix.c (dtpMatrix_validate): fix check
320            * src/dspMatrix.c (dspMatrix_validate): ditto
321    
322            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
323              including coercion to [nl]tTMatrix.
324    
325            * R/diagMatrix.R (show): print a header line as for other classes.
326    
327    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/Makefile.win (SUBDIRS): fix typo
330    
331    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
334    
335    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
338            symmetric and y missing in R code using %*% (cholmod_aat doesn't
339            accept a symmetric matrix).
340            * tests/group-methods.R: Uncomment test of crossprod applied to
341            lsCMatrix objects.
342    
343    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/AllClass.R (symmetricMatrix): add validity method (available
346            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
347    
348            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
349    
350            * tests/indexing.Rout.save:
351            * tests/indexing.R: additions, mainly for 'lsparse'
352    
353            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
354            case.
355    
356            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
357    
358    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
361                    as 'N' (1-letter - Ok?)
362    
363            * tests/group-methods.R: add test for logical + NAs
364    
365            * R/dMatrix.R ("Compare"): fix to work with NA's
366    
367            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
368    
369            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
370                    which is implemented.
371    
372    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/chm_common.c: coerce logical <-> double instead of
375            typecasting;  needed for "l" matrix handling in cholmod.
376    
377            * tests/other-pkgs.R (graph): small extension in "graph" checks.
378    
379            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
380            (Tsp2grNEL): other fixes needed
381    
382    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
385                    Matrices, since "lMatrix", also "lsparseM" can have NA
386            * R/ndenseMatrix.R, etc: new source files
387            * man/nsparseMatrix-classes.Rd, etc: new help files
388            * tests/: adaptions
389            * src/chm_common.c (chm_dense_to_SEXP): and others:
390                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
391            * src/Csparse.c, etc: ditto
392    
393    2006-09-11  Douglas Bates  <bates@R-project.org>
394    
395            * src/Mutils.[ch],init.c inst/include/*.h: Move the
396            alloc_d**Matrix functions to the lme4 package.
397    
398    2006-09-09  Douglas Bates  <bates@R-project.org>
399    
400            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
401            fixed
402    
403    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/lMatrix.R: new
406    
407            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
408    
409            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
410            * man/tcrossprod.Rd: ditto
411    
412    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
415            for exported functions
416            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
417            Remove partitioning algorithms for sparse matrix reordering.  The
418            copyright on the Metis code was problematic and the methods were
419            rarely used.
420            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
421            operations are now done entirely in CHOLMOD code.
422    
423    2006-09-06  Douglas Bates  <bates@R-project.org>
424    
425            * src/Mutils.h: Remove functions that are no longer used.
426    
427    2006-09-04  Douglas Bates  <bates@R-project.org>
428    
429            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
430            * src/DEPS.mkf: update
431    
432    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * created branches/Matrix-for-R-2.3.x;  on trunk: do
435            * DESCRIPTION (Version): 0.9975-0
436            (Depends): R (>= 2.4.0)
437    
438    2006-09-01  Douglas Bates  <bates@R-project.org>
439    
440            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
441    
442    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
445            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
446    
447            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
448    
449    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
452            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
453            * R/dsparseMatrix.R: ditto
454            * R/Csparse.R: ditto
455    
456    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/dMatrix.R (Compare): improve availability of "<", etc
459            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
460    
461    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
464            of a 0-index which was used as 1-index (..hmm)
465    
466            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
467    
468            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
469            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
470            (.is.diagonal): ditto
471    
472            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
473    
474            * R/Matrix.R (Matrix): also work for NA data
475    
476    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
479            in all cases.
480    
481    2006-08-27  Douglas Bates  <bates@R-project.org>
482    
483            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
484            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
485    
486    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
489            subclasses of "ddenseMatrix"
490            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
491            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
492            instead of half dozen specialized ones.
493    
494    2006-08-25  Douglas Bates  <bates@R-project.org>
495    
496            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
497            <tillard@cirad.fr> - ordering standard errors to match effects.
498    
499    2006-08-24  Douglas Bates  <bates@R-project.org>
500    
501            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
502            on R_ldl.
503            * R/lCholCMatrix.R,
504            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
505            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
506            * many files in ./R and ./src: Use more general version of
507            dup_mMatrix_as_dgeMatrix to simplify method definitions.
508            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
509            dtpMatrix, dspMatrix and dppMatrix conversions.
510    
511    
512    2006-08-23  Douglas Bates  <bates@R-project.org>
513    
514            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
515            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
516            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
517            dgeMatrix_crossprod (may need to do this in other places).
518            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
519            generic and method for dsCMatrix.  Use CHOLMOD for chol().
520    
521    2006-08-22  Douglas Bates  <bates@R-project.org>
522    
523            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
524            types of classed Matrices, matrices or numeric or logical vectors.
525            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
526            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
527            to Mutils.h (as an inline) and change name to Matrix_check_class;
528            fixes in as_cholmod_factor and chm_factor_to_SEXP.
529            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
530            dsCMatrix_matrix_solve.  Comment out vestigial functions.
531            * src/Csparse.c: use diag_P and uplo_P macros.
532    
533    2006-08-21  Douglas Bates  <bates@R-project.org>
534    
535            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
536            valgrind.
537            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
538            inverses.
539            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
540            -Wall warnings.
541            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
542            Use dup_mMatrix_as_dgeMatrix.
543    
544    2006-08-20  Douglas Bates  <bates@R-project.org>
545    
546            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
547            * tests/sparseQR.R: Added
548            * man/sparseQR-class.Rd: Document methods for qr.* generics
549            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
550    
551    2006-08-19  Douglas Bates  <bates@R-project.org>
552    
553            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
554            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
555            and qr.fitted.
556            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
557            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
558    
559    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
562            the base version has no "..." argument.
563    
564            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
565    
566            * R/Matrix.R: define and
567            * NAMESPACE: export as.numeric() and as.logical() methods.
568                    Let's hope these do not badly slow down something...
569            Finally export the zapsmall() method.
570    
571    2006-08-17  Douglas Bates  <bates@R-project.org>
572    
573            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
574            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
575            * src/dtCMatrix.c :Remove code that is no longer used
576            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
577    
578    2006-08-14  Douglas Bates  <bates@R-project.org>
579    
580            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
581            Csparse_to_logical and Csparse_symmetric_to_general.
582            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
583            coercion methods between CsparseMatrix and TsparseMatrix.
584    
585    2006-08-14  Douglas Bates  <bates@R-project.org>
586    
587            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
588            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
589            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
590            possible.
591    
592    2006-08-12  Douglas Bates  <bates@R-project.org>
593    
594            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
595              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
596              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
597              generalize conversions between TsparseMatrix, CsparseMatrix,
598              denseMatrix and matrix.  Preserve triangularity property and
599              propagate Dimnames in the easy cases.
600    
601    2006-08-10  Douglas Bates  <bates@R-project.org>
602    
603            * src/lmer.c: adjust checks in glmer_init for S4SXP
604            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
605            before S4SXP but for the wrong reasons.
606    
607    2006-08-08  Douglas Bates  <bates@R-project.org>
608    
609            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
610            Later modified to return the upper triangle only.
611            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
612    
613    2006-08-07  Douglas Bates  <bates@R-project.org>
614    
615            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
616            R-level conversion to a sparse symmetric class.
617            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
618            Remove conversion to sparse symmetric classes (now done in C code).
619    
620    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
623            * man/band.Rd:  adapt the \dontshow{} unit test.
624    
625    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * DESCRIPTION (Version): 0.995-14  for CRAN
628    
629            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
630    
631            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
632            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
633    
634            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
635            * R/Tsparse.R (tril, triu, band): methods
636            * R/dgRMatrix.R (tril, ...):    ditto
637            * man/band.Rd:                  ditto
638    
639    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/Matrix.R (head, tail): directly use utils:::head.matrix
642                    to be up-to-date automatically.
643    
644    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
647    
648            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
649            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
650            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
651            such that the S4 objects are always created by the current version
652            of R and 'Matrix' class definitions.
653    
654    2006-08-01  Douglas Bates  <bates@R-project.org>
655    
656            * R/lmer.R (LMEoptimize method), tests/lmer.R,
657            inst/external/test3comp.rda: Added warnings for convergence on
658            boundary and test cases.
659    
660            * src/lmer.c (mer_postVar): Modified to return the variances that
661            are marginal to the fixed effects, not conditional on them (which
662            is what the bVar slot contents represent).
663    
664    2006-07-31  Douglas Bates  <bates@R-project.org>
665    
666            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
667            function which calls the C function mer_hat_trace2.
668    
669            * man/ranef.Rd: Include description of "postVar" argument and
670            producing a caterpillar plot.
671    
672    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * NAMESPACE:    change  "correlation" to "corMatrix"
675            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
676            * R/dpoMatrix.R: ditto
677            * R/lmer.R:      ditto
678    
679    2006-07-28  Douglas Bates  <bates@R-project.org>
680    
681            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
682            RZXinv slot's contents into a separate internal function that can
683            be used in mer_hat_trace.
684    
685    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
688            via new smart
689            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
690            utility functions.
691    
692    
693    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/Csparse.R (tril, triu, band): do return *triangular* classed
696            matrices when appropriate; band() even symmetric ones.
697            (replCmat): extend to potentially all "CsparseMatrix"
698            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
699            allow subassignment for special sparse matrices.
700    
701            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
702    
703            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
704            argument; in glmer_*(): print only if(verbose).
705    
706            speed-optimize a few places by moving REAL(.) out of loops.
707    
708            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
709    
710    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
713                    since that wrongly triggers also for M[ logi , ]
714    
715            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
716            a symmetric matrix that results in a non-symmetric one.
717            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
718    
719            * R/dMatrix.R: make round(M) work as round(M, 0)
720    
721            * R/dgTMatrix.R (image): coordinate system and axis now use
722            1-based indices, not 0-based ones.
723    
724            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
725            * tests/indexing.R: test it.
726    
727            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
728            * man/isSymmetric-methods.Rd: and document it.
729    
730            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
731            * man/SparseM-conv.Rd: docu them
732    
733            * tests/other-pkgs.R: renamed from tests/graph.R and add example
734                    for 'SparseM' conversions
735    
736    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
737    
738            * R/Matrix.R (head): added head() and tail() methods.
739    
740    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * DESCRIPTION (Version): 0.995-12 released to CRAN
743    
744    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * tests/simple.R: add check for correct dsT -> dgT coercion;
747                    add check for correct printing of symmetric sparse matrices.
748    
749            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
750            for sparse symmetric matrices.
751    
752            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
753            diagonal twice.
754    
755    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
756    
757            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
758            being applied to the x slot (detected by Brian Ripley).
759    
760    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
763    
764            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
765    
766    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * src/lgCMatrix.c (lgCMatrix_diag): new function
769            * R/lgCMatrix.R (diag): for new method
770    
771            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
772                 ==> construction of illegal "*gTMatrix" via new() should
773                 now be much less easy:
774            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
775    
776            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
777                    directly.
778            * man/Matrix.Rd: documents it.
779    
780    2006-07-06  Douglas Bates  <bates@R-project.org>
781    
782            * src/pedigree.c (pedigree_inbreeding): Correction in
783            initialization.  This function is not currently being used and is
784            not fully tested.
785    
786            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
787            Introduced the glmer class.  Added code for mcmcmsamp on glmer
788            objects.  Modified validity check on pedigree objects to account
789            for nonparallel patterns of missingness of parents.
790    
791            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
792            class.
793    
794    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/pMatrix.R: coercion pMatrix -> Tsparse
797    
798    2006-06-12  Douglas Bates  <bates@R-project.org>
799    
800            * DESCRIPTION (Version): 0.995-11 released to CRAN
801    
802            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
803            the output from mcmcsamp.
804    
805    2006-06-10  Douglas Bates  <bates@R-project.org>
806    
807            * R/lmer.R (simulestimate): added C code for calculating the trace
808            of the hat matrix.
809    
810    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
813            classes.
814            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
815    
816    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/dgTMatrix.R (colSums): etc. All four of
819            colSums(), rowSums(), colMeans(), rowMeans() now should work for
820            all "Matrices".
821    
822  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
823    
824          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 849 
849    
850          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
851          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.
852          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
853    
854    
855  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 972 
972          * 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)
973          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
974          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
975          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
976    
977  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
# Line 355  Line 1176 
1176  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1179          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1180          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1181    
1182  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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