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revision 848, Thu Aug 11 07:41:59 2005 UTC revision 1688, Sat Dec 9 00:29:45 2006 UTC
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1    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): updated -> release 0.9975-7
4            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
5    
6    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
9    
10    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
13            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
14            is exactly singular.
15    
16    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * DESCRIPTION (Date): updated -> release 0.9975-6
19    
20    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
23            now returns symmetric.
24    
25            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
26    
27            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
28            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
29    
30            * R/Auxiliaries.R (.type.kind): added
31    
32    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
35            running src/CSparse_install.sh
36    
37            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
38    
39    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
42            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
43    
44            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
45    
46            * tests/Class+Meth.R (tstMatrixClass): now assure
47            the (important in method programming) property :
48    
49                    ###>>  Every "Matrix" is either
50                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
51    
52                    (where "*" stands for "Matrix")
53    
54            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
55    
56            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
57            * tests/validObj.R: checks for "comparison"
58    
59            * R/sparseMatrix.R ([): improved indexing for sparse;
60                    trying to keep <symmetric>[ n, n] symmmetric
61    
62            * tests/indexing.R: indexing for logical sparse now ok
63    
64    
65    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * src/Tsparse.c: use xTsparse_validate() , and hence remove
68    
69            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
70    
71    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
74    
75            * tests/simple.R: validObject() checking the above.
76    
77            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
78            replacing both dgCMatrix_validate and lgCM*.
79    
80            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
81            fix dimnames setting in other places.
82            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
83    
84    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
87    
88            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
89            symmetry test, via
90            * R/Auxiliaries.R (.as.dgC.0.factors):
91    
92    2006-11-01  Douglas Bates  <bates@r-project.org>
93    
94            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
95            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
96            <CsparseMatrix>) added
97    
98    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * tests/matprod.R: add a variation of Harri's example
101    
102            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
103            recursive infinitely.
104    
105            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
106    
107            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
108    
109    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
112            matrix if possible; test m+m == 2*m; now test dgRMatrix.
113            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
114            satisfy the above test.
115    
116    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
119    
120            * R/dgCMatrix.R: solve(a, b="missing") based on
121            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
122            RHS = NULL.
123    
124            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
125            add more (needed) [t]crossprod() methods.
126    
127            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
128    
129            * R/Auxiliaries.R (as_CspClass): cleanup
130            (drop0): internal utility for "Csparse_drop(*, 0)"
131            (.bail.out.2): encourage active feedback
132    
133    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/dMatrix.R(Compare): new(), then slots [no validity check]
136    
137            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
138            non-valid or 'sorted' case).
139    
140            * R/dsparseMatrix.R: add "chol" method.
141            * R/ddenseMatrix.R: ditto
142    
143            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
144            * NAMESPACE (Ops)
145            * R/diagMatrix.R (diag2T): simple utility used "higher level"
146            coercion; deprecating direct lower level coercions.
147    
148            * R/*.R (seq): use seq_len() and seq_along() where possible.
149    
150    
151    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.9975-5 ready for release
154    
155    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
158    
159    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/AllClass.R (corMatrix): add 'validity' check;
162                    comment out unused "LDL" class definition
163            * NAMESPACE: mention, but do not export "LDL" class
164            * R/corMatrix.R: new (simple), needed for R-devel with
165            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
166              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
167    
168    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
171            use Rprintf and R's error handling.
172    
173    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
176            * tests/matprod.R: add tests for the bug fixed.
177    
178    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
181            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
182    
183    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
186    
187    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * DESCRIPTION (Version): 0.9975-3
190    
191            * R/diagMatrix.R (bdiag): new function constructing block diagonal
192            (sparse) matrices.
193            * man/bdiag.Rd: docu + examples
194    
195            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
196    
197            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
198            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
199    
200            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
201            that result is sparse or diagonal (and not dense).
202    
203            * man/Subassign-methods.Rd: fix examples
204    
205            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
206            should always return a sparse (and not sometimes a diagonal) matrix.
207    
208    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
211    
212    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * DESCRIPTION (Version): 0.9975-2
215    
216            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
217    
218    2006-10-02  Douglas Bates  <bates@R-project.org>
219    
220            * tests/dg_Matrix.R: Simplify test taking into account new code.
221    
222    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
225    
226            * R/lsTMatrix.R: new files w/ missing methods
227            * R/nsTMatrix.R:  "  'for completeness'
228    
229            * tests/Class+Meth.R: a bit less 'not.ok.classes'
230    
231            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
232    
233    
234    2006-09-28  Douglas Bates  <bates@R-project.org>
235    
236            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
237            included.
238    
239            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
240            Export C-callable functions used in Zt_create in lme4.
241    
242    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * DESCRIPTION (Version): 0.9975-1
245    
246            * tests/simple.R: less checks fail; using NA, found that our
247                    kronecker() is not base-compatible with NA's.
248    
249            * R/dMatrix.R: "Compare" method now implemented for all cases
250    
251            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
252    
253            * man/dtpMatrix-class.Rd: mention length of 'x' slot
254    
255            * src/dtpMatrix.c (dtpMatrix_validate): fix check
256            * src/dspMatrix.c (dspMatrix_validate): ditto
257    
258            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
259              including coercion to [nl]tTMatrix.
260    
261            * R/diagMatrix.R (show): print a header line as for other classes.
262    
263    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * src/Makefile.win (SUBDIRS): fix typo
266    
267    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
270    
271    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
274            symmetric and y missing in R code using %*% (cholmod_aat doesn't
275            accept a symmetric matrix).
276            * tests/group-methods.R: Uncomment test of crossprod applied to
277            lsCMatrix objects.
278    
279    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/AllClass.R (symmetricMatrix): add validity method (available
282            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
283    
284            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
285    
286            * tests/indexing.Rout.save:
287            * tests/indexing.R: additions, mainly for 'lsparse'
288    
289            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
290            case.
291    
292            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
293    
294    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
297                    as 'N' (1-letter - Ok?)
298    
299            * tests/group-methods.R: add test for logical + NAs
300    
301            * R/dMatrix.R ("Compare"): fix to work with NA's
302    
303            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
304    
305            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
306                    which is implemented.
307    
308    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * src/chm_common.c: coerce logical <-> double instead of
311            typecasting;  needed for "l" matrix handling in cholmod.
312    
313            * tests/other-pkgs.R (graph): small extension in "graph" checks.
314    
315            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
316            (Tsp2grNEL): other fixes needed
317    
318    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
321                    Matrices, since "lMatrix", also "lsparseM" can have NA
322            * R/ndenseMatrix.R, etc: new source files
323            * man/nsparseMatrix-classes.Rd, etc: new help files
324            * tests/: adaptions
325            * src/chm_common.c (chm_dense_to_SEXP): and others:
326                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
327            * src/Csparse.c, etc: ditto
328    
329    2006-09-11  Douglas Bates  <bates@R-project.org>
330    
331            * src/Mutils.[ch],init.c inst/include/*.h: Move the
332            alloc_d**Matrix functions to the lme4 package.
333    
334    2006-09-09  Douglas Bates  <bates@R-project.org>
335    
336            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
337            fixed
338    
339    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/lMatrix.R: new
342    
343            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
344    
345            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
346            * man/tcrossprod.Rd: ditto
347    
348    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
351            for exported functions
352            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
353            Remove partitioning algorithms for sparse matrix reordering.  The
354            copyright on the Metis code was problematic and the methods were
355            rarely used.
356            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
357            operations are now done entirely in CHOLMOD code.
358    
359    2006-09-06  Douglas Bates  <bates@R-project.org>
360    
361            * src/Mutils.h: Remove functions that are no longer used.
362    
363    2006-09-04  Douglas Bates  <bates@R-project.org>
364    
365            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
366            * src/DEPS.mkf: update
367    
368    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * created branches/Matrix-for-R-2.3.x;  on trunk: do
371            * DESCRIPTION (Version): 0.9975-0
372            (Depends): R (>= 2.4.0)
373    
374    2006-09-01  Douglas Bates  <bates@R-project.org>
375    
376            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
377    
378    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
381            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
382    
383            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
384    
385    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
388            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
389            * R/dsparseMatrix.R: ditto
390            * R/Csparse.R: ditto
391    
392    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dMatrix.R (Compare): improve availability of "<", etc
395            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
396    
397    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
400            of a 0-index which was used as 1-index (..hmm)
401    
402            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
403    
404            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
405            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
406            (.is.diagonal): ditto
407    
408            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
409    
410            * R/Matrix.R (Matrix): also work for NA data
411    
412    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
415            in all cases.
416    
417    2006-08-27  Douglas Bates  <bates@R-project.org>
418    
419            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
420            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
421    
422    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
425            subclasses of "ddenseMatrix"
426            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
427            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
428            instead of half dozen specialized ones.
429    
430    2006-08-25  Douglas Bates  <bates@R-project.org>
431    
432            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
433            <tillard@cirad.fr> - ordering standard errors to match effects.
434    
435    2006-08-24  Douglas Bates  <bates@R-project.org>
436    
437            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
438            on R_ldl.
439            * R/lCholCMatrix.R,
440            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
441            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
442            * many files in ./R and ./src: Use more general version of
443            dup_mMatrix_as_dgeMatrix to simplify method definitions.
444            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
445            dtpMatrix, dspMatrix and dppMatrix conversions.
446    
447    
448    2006-08-23  Douglas Bates  <bates@R-project.org>
449    
450            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
451            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
452            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
453            dgeMatrix_crossprod (may need to do this in other places).
454            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
455            generic and method for dsCMatrix.  Use CHOLMOD for chol().
456    
457    2006-08-22  Douglas Bates  <bates@R-project.org>
458    
459            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
460            types of classed Matrices, matrices or numeric or logical vectors.
461            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
462            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
463            to Mutils.h (as an inline) and change name to Matrix_check_class;
464            fixes in as_cholmod_factor and chm_factor_to_SEXP.
465            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
466            dsCMatrix_matrix_solve.  Comment out vestigial functions.
467            * src/Csparse.c: use diag_P and uplo_P macros.
468    
469    2006-08-21  Douglas Bates  <bates@R-project.org>
470    
471            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
472            valgrind.
473            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
474            inverses.
475            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
476            -Wall warnings.
477            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
478            Use dup_mMatrix_as_dgeMatrix.
479    
480    2006-08-20  Douglas Bates  <bates@R-project.org>
481    
482            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
483            * tests/sparseQR.R: Added
484            * man/sparseQR-class.Rd: Document methods for qr.* generics
485            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
486    
487    2006-08-19  Douglas Bates  <bates@R-project.org>
488    
489            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
490            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
491            and qr.fitted.
492            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
493            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
494    
495    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
498            the base version has no "..." argument.
499    
500            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
501    
502            * R/Matrix.R: define and
503            * NAMESPACE: export as.numeric() and as.logical() methods.
504                    Let's hope these do not badly slow down something...
505            Finally export the zapsmall() method.
506    
507    2006-08-17  Douglas Bates  <bates@R-project.org>
508    
509            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
510            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
511            * src/dtCMatrix.c :Remove code that is no longer used
512            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
513    
514    2006-08-14  Douglas Bates  <bates@R-project.org>
515    
516            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
517            Csparse_to_logical and Csparse_symmetric_to_general.
518            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
519            coercion methods between CsparseMatrix and TsparseMatrix.
520    
521    2006-08-14  Douglas Bates  <bates@R-project.org>
522    
523            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
524            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
525            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
526            possible.
527    
528    2006-08-12  Douglas Bates  <bates@R-project.org>
529    
530            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
531              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
532              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
533              generalize conversions between TsparseMatrix, CsparseMatrix,
534              denseMatrix and matrix.  Preserve triangularity property and
535              propagate Dimnames in the easy cases.
536    
537    2006-08-10  Douglas Bates  <bates@R-project.org>
538    
539            * src/lmer.c: adjust checks in glmer_init for S4SXP
540            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
541            before S4SXP but for the wrong reasons.
542    
543    2006-08-08  Douglas Bates  <bates@R-project.org>
544    
545            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
546            Later modified to return the upper triangle only.
547            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
548    
549    2006-08-07  Douglas Bates  <bates@R-project.org>
550    
551            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
552            R-level conversion to a sparse symmetric class.
553            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
554            Remove conversion to sparse symmetric classes (now done in C code).
555    
556    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
559            * man/band.Rd:  adapt the \dontshow{} unit test.
560    
561    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.995-14  for CRAN
564    
565            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
566    
567            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
568            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
569    
570            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
571            * R/Tsparse.R (tril, triu, band): methods
572            * R/dgRMatrix.R (tril, ...):    ditto
573            * man/band.Rd:                  ditto
574    
575    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Matrix.R (head, tail): directly use utils:::head.matrix
578                    to be up-to-date automatically.
579    
580    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
583    
584            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
585            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
586            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
587            such that the S4 objects are always created by the current version
588            of R and 'Matrix' class definitions.
589    
590    2006-08-01  Douglas Bates  <bates@R-project.org>
591    
592            * R/lmer.R (LMEoptimize method), tests/lmer.R,
593            inst/external/test3comp.rda: Added warnings for convergence on
594            boundary and test cases.
595    
596            * src/lmer.c (mer_postVar): Modified to return the variances that
597            are marginal to the fixed effects, not conditional on them (which
598            is what the bVar slot contents represent).
599    
600    2006-07-31  Douglas Bates  <bates@R-project.org>
601    
602            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
603            function which calls the C function mer_hat_trace2.
604    
605            * man/ranef.Rd: Include description of "postVar" argument and
606            producing a caterpillar plot.
607    
608    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * NAMESPACE:    change  "correlation" to "corMatrix"
611            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
612            * R/dpoMatrix.R: ditto
613            * R/lmer.R:      ditto
614    
615    2006-07-28  Douglas Bates  <bates@R-project.org>
616    
617            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
618            RZXinv slot's contents into a separate internal function that can
619            be used in mer_hat_trace.
620    
621    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
624            via new smart
625            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
626            utility functions.
627    
628    
629    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Csparse.R (tril, triu, band): do return *triangular* classed
632            matrices when appropriate; band() even symmetric ones.
633            (replCmat): extend to potentially all "CsparseMatrix"
634            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
635            allow subassignment for special sparse matrices.
636    
637            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
638    
639            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
640            argument; in glmer_*(): print only if(verbose).
641    
642            speed-optimize a few places by moving REAL(.) out of loops.
643    
644            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
645    
646    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
649                    since that wrongly triggers also for M[ logi , ]
650    
651            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
652            a symmetric matrix that results in a non-symmetric one.
653            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
654    
655            * R/dMatrix.R: make round(M) work as round(M, 0)
656    
657            * R/dgTMatrix.R (image): coordinate system and axis now use
658            1-based indices, not 0-based ones.
659    
660            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
661            * tests/indexing.R: test it.
662    
663            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
664            * man/isSymmetric-methods.Rd: and document it.
665    
666            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
667            * man/SparseM-conv.Rd: docu them
668    
669            * tests/other-pkgs.R: renamed from tests/graph.R and add example
670                    for 'SparseM' conversions
671    
672    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
673    
674            * R/Matrix.R (head): added head() and tail() methods.
675    
676    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * DESCRIPTION (Version): 0.995-12 released to CRAN
679    
680    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * tests/simple.R: add check for correct dsT -> dgT coercion;
683                    add check for correct printing of symmetric sparse matrices.
684    
685            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
686            for sparse symmetric matrices.
687    
688            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
689            diagonal twice.
690    
691    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
692    
693            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
694            being applied to the x slot (detected by Brian Ripley).
695    
696    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
699    
700            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
701    
702    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * src/lgCMatrix.c (lgCMatrix_diag): new function
705            * R/lgCMatrix.R (diag): for new method
706    
707            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
708                 ==> construction of illegal "*gTMatrix" via new() should
709                 now be much less easy:
710            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
711    
712            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
713                    directly.
714            * man/Matrix.Rd: documents it.
715    
716    2006-07-06  Douglas Bates  <bates@R-project.org>
717    
718            * src/pedigree.c (pedigree_inbreeding): Correction in
719            initialization.  This function is not currently being used and is
720            not fully tested.
721    
722            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
723            Introduced the glmer class.  Added code for mcmcmsamp on glmer
724            objects.  Modified validity check on pedigree objects to account
725            for nonparallel patterns of missingness of parents.
726    
727            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
728            class.
729    
730    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/pMatrix.R: coercion pMatrix -> Tsparse
733    
734    2006-06-12  Douglas Bates  <bates@R-project.org>
735    
736            * DESCRIPTION (Version): 0.995-11 released to CRAN
737    
738            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
739            the output from mcmcsamp.
740    
741    2006-06-10  Douglas Bates  <bates@R-project.org>
742    
743            * R/lmer.R (simulestimate): added C code for calculating the trace
744            of the hat matrix.
745    
746    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
749            classes.
750            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
751    
752    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/dgTMatrix.R (colSums): etc. All four of
755            colSums(), rowSums(), colMeans(), rowMeans() now should work for
756            all "Matrices".
757    
758    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
759    
760            * R/lmer.R (panel.ci): Add a reference line at zero and a
761            background grid to the qqmath plot of ranef.lmer.
762    
763    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
764    
765            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
766            grouping factors to be specified in the formula as (1|foo/bar).
767    
768    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * R/lmer.R (findbars and others): Change check of is.numeric to
771            !is.language to resolve the bug reported by Jacob Wegelin.
772    
773            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
774            code to evaluate inbreeding coefficients without calculating T,
775            based on code in Sargolzaei and Iwaisaki's paper.
776    
777    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
778    
779            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
780            generic and mer methods for isNested and denomDF. This denomDF was
781            an attempt to emulate that in lme but I don't think that makes
782            sense.  Use the trace of the hat matrix instead.
783    
784    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
787            the C code depending on a slot structure that's no longer valid.
788            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
789    
790    
791    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
792    
793            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
794            of lowerTriMatrix generic and methods to tril (also upper to triu)
795            and added a general band extractor.
796    
797    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
798    
799            * R/pedigree.R (pedigree): Replace sire and dam values outside the
800            allowable range with NAs. Added a corresponding check in the
801            validity check for the pedigree class.
802    
803            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
804            crossprod methods now inherits from symmetricMatrix.
805    
806    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
809            generics lowerTriMatrix and upperTriMatrix along with methods for
810            the Csparse virtual class.  Also added a C function Csparse_band
811            that implements these methods by calling cholmod_band.
812    
813    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
816            erased when it was NULL.  This led to invalid subselections!
817    
818    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
819    
820            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
821            in method for "t" so as not to lose the unit diagonal property.
822    
823    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
824    
825            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
826            and methods.  This is now an option to the ranef method for the
827            mer class.
828    
829            * src/cs_utils.c: Ensure that the nz component is -1 for a
830            compressed column-oriented matrix.  Minor formatting cleanup.
831    
832            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
833            objects.
834    
835    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
838            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
839    
840    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
841    
842            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
843            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
844    
845            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
846            for the dtCMatrix class.
847    
848    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
849    
850            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
851            and methods for it.
852    
853    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
856            arguments, such that M %*% 1:6 now works
857            * Tests/matprod.R: test the above
858    
859    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
860    
861            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
862            the ranef.lmer class.
863    
864            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
865            methods to extract the posterior variances from the bVar slot.
866    
867    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
870            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
871    
872            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
873            * tests/simple: (extended)
874    
875            * R/sparseMatrix.R (isTriangular): now using much improved
876            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
877    
878    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
879    
880            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
881            (problem report from Franklin Parlamis).  This should be done
882            generally.
883    
884    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
885    
886            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
887            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
888            update the plot methods.
889    
890    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
891    
892            * R/lmer.R (resid and ranef methods):  Added methods for the
893            "residuals" and "resid" generic but only for linear mixed model
894            fits.  Changed the ranef method to return a list of data frames so
895            that the plot methods now work.
896    
897    2006-03-16  Douglas Bates  <bates@bates2>
898    
899            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
900            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
901    
902            * DESCRIPTION (Date): New release
903    
904    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
907    
908            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
909            * man/KNex.Rd: and other help files
910            * tests/*.R: several ones needed adaption
911            * inst/doc/Comparisons.Rnw: ditto
912    
913    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
916    
917            * tests/indexing.R: tests for new [<- methods for sparse matrices.
918    
919    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
922    
923            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
924    
925    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/dMatrix.R: enable things like  M [ M < 10 ]
928            * R/dgeMatrix.R: implement it
929    
930    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/AllClass.R: define "summary.mer" and "*.lmer"
933            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
934            * R/lmer.R (show): now works with summary()
935    
936    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
939            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
940                    support the above
941    
942    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
943    
944            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
945            Use glmFit$prior.weights for weights in a glmm.
946            Allow an option usePQL = FALSE to skip the PQL steps for the
947            Laplace method (and, in time, the AGQ method).
948    
949            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
950            into a separate function internal_mer_Xfactor to be able to call
951            it from internal_bhat.
952    
953    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * tests/Class+Meth.R (tstMatrixClass): function for much better
956            testing; now again of all actual classes.
957    
958            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
959                    use macros and define make_d_matrix_* and make_i_matrix_*
960                    where _i_ is for the ldense routines:
961    
962            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
963            * src/ldense.c (lsyMatrix_as_lgeMatrix):
964    
965            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
966    
967    
968    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
971                    many different kinds of matrices.
972            * R/*.R: quite a few new methods were needed for R CMD check with
973                    new Matrix().  Very good for users playing around.
974    
975    
976    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * src/dgeMatrix.c (dMatrix_validate): new
979            * src/Mutils.c (dense_nonpacked_validate): new
980    
981            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
982    
983    
984    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
985    
986            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
987    
988    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
989    
990            * DESCRIPTION (Version): 0.99-6 released to CRAN
991    
992            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
993            segfault in cases with multiple non-nested grouping factors.
994    
995    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
998                    (Depends): also on 'utils'
999    
1000            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1001            * R/diagMatrix.R (Diagonal): constructor and methods for
1002            diagonal matrices
1003    
1004            * R/ltTMatrix.R: new "minimal methods"
1005    
1006    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1009            all methods (and help files).
1010    
1011    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1014                    for case (dimn.  op  no_dimn.)
1015    
1016    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1017    
1018            * DESCRIPTION (Version): 0.99-2  released to CRAN
1019    
1020    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1021    
1022            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1023            by Julian Faraway.
1024    
1025    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Auxiliaries.R (try_as): new utility
1028            * R/sparseMatrix.R: use try_as() in coercion to original class
1029    
1030    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1033    
1034    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/Auxiliaries.R (dimNamesCheck): added
1037    
1038            * R/Matrix.R (as.array), (as.vector): new
1039    
1040    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1043                    default.
1044            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1045                    "pMatrix" now contains "sparseMatrix"
1046    
1047    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * tests/Class+Meth.R: new tests; t(t(m)) == m
1050    
1051            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1052    
1053            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1054            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1055    
1056            * R/dspMatrix.R: typo in "t" method
1057    
1058    2005-09-18  Douglas Bates  <bates@wisc.edu>
1059    
1060            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1061            * R/Tsparse.R: instead of R/gTMatrix.R
1062            * R/Csparse.R: new
1063            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1064            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1065            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1066                            via cholmod
1067    
1068    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * R/Auxiliaries.R (non0ind): new function using new C code
1071            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1072    
1073    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1074    
1075            * src/chm_common.h: header file required by all C sources that
1076            call CHOLMOD functions.  It defines a cholmod_common structure
1077            called 'c' whose address is passed as the last argument to
1078            (virtually) every CHOLMOD function.
1079    
1080            * src/Pattern.c: Simple example of the use of CHOLMOD.
1081    
1082            * src/init.c: initialize and finalize the cholmod_common structure.
1083    
1084            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1085            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1086    
1087    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1088    
1089            * inst/test-tools.R: new file collecting the utility functions used
1090                    in ./tests/*.R
1091    
1092            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1093            * R/Matrix.R (cbind2): methods for NULL and missing
1094    
1095    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/AllClass.R: new "index" class for "[" and "[<-":
1098                    First cut at "symmetricMatrix" and "triangularMatrix"
1099            * R/gTMatrix.R (.ind.prep): new function;
1100                    Logical and character indexing now work too.
1101            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1102            * tests/indexing.R: new, including *.Rout.save
1103            * tests/dgTMatrix.R: new
1104    
1105    2005-08-29  Douglas Bates  <bates@wisc.edu>
1106    
1107            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1108            indicator pos not being updated.  Also enforced upper triangular
1109            for symmetric case.  Need to coerce edges component of elements of
1110            edge list - grr! (Why don't they define their classes cleanly?)
1111    
1112    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * R/Matrix.R:  added first "[<-" methods; not yet functional
1115            * R/denseMatrix.R: ditto
1116            * man/Subassign-methods.Rd: new help file for these
1117    
1118    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1119    
1120            * DESCRIPTION (Version): 0.98-6
1121    
1122            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1123            matrices.
1124    
1125    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1128                    as( <logical>, "matrix")
1129    
1130            * R/pMatrix.R: coercion to "lgTMatrix"
1131    
1132            * R/gTMatrix.R: new virtual class to define "[" methods for.
1133            * man/gTMatrix-class.Rd:
1134            * General slight re-organization of where "[" methods are defined.
1135              more to come.
1136    
1137    2005-08-18  Douglas Bates  <bates@wisc.edu>
1138    
1139            * DESCRIPTION (Version): 0.98-5  released to CRAN
1140    
1141            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1142            * .....
1143    
1144    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1145    
1146            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1147            or glmer objects.
1148    
1149    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1152    
1153    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1154    
1155            * R/HBMM.R: finish re-writing R-only code.
1156    
1157    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1158    
1159            * man/externalFormats.Rd: move documentation for writeHB and
1160            writeMM here.
1161    
1162            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1163            (suggested by Paul Roecker).
1164    
1165            * tests/validObj.R (assertError): Comment out test that is failing
1166            after recent changes in r-devel.
1167    
1168    
1169  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171          * R/AllClass.R: intermediate virtual class "denseMatrix"          * R/AllClass.R: intermediate virtual class "denseMatrix"

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