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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1673, Mon Nov 6 20:54:26 2006 UTC
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1    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
4            now returns symmetric.
5    
6            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
7    
8            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
9            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
10    
11            * R/Auxiliaries.R (.type.kind): added
12    
13    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
16            running src/CSparse_install.sh
17    
18            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
19    
20    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
23            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
24    
25            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
26    
27            * tests/Class+Meth.R (tstMatrixClass): now assure
28            the (important in method programming) property :
29    
30                    ###>>  Every "Matrix" is either
31                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
32    
33                    (where "*" stands for "Matrix")
34    
35            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
36    
37            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
38            * tests/validObj.R: checks for "comparison"
39    
40            * R/sparseMatrix.R ([): improved indexing for sparse;
41                    trying to keep <symmetric>[ n, n] symmmetric
42    
43            * tests/indexing.R: indexing for logical sparse now ok
44    
45    
46    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * src/Tsparse.c: use xTsparse_validate() , and hence remove
49    
50            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
51    
52    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
55    
56            * tests/simple.R: validObject() checking the above.
57    
58            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
59            replacing both dgCMatrix_validate and lgCM*.
60    
61            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
62            fix dimnames setting in other places.
63            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
64    
65    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
68    
69            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
70            symmetry test, via
71            * R/Auxiliaries.R (.as.dgC.0.factors):
72    
73    2006-11-01  Douglas Bates  <bates@r-project.org>
74    
75            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
76            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
77            <CsparseMatrix>) added
78    
79    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * tests/matprod.R: add a variation of Harri's example
82    
83            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
84            recursive infinitely.
85    
86            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
87    
88            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
89    
90    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
93            matrix if possible; test m+m == 2*m; now test dgRMatrix.
94            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
95            satisfy the above test.
96    
97    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
100    
101            * R/dgCMatrix.R: solve(a, b="missing") based on
102            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
103            RHS = NULL.
104    
105            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
106            add more (needed) [t]crossprod() methods.
107    
108            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
109    
110            * R/Auxiliaries.R (as_CspClass): cleanup
111            (drop0): internal utility for "Csparse_drop(*, 0)"
112            (.bail.out.2): encourage active feedback
113    
114    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dMatrix.R(Compare): new(), then slots [no validity check]
117    
118            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
119            non-valid or 'sorted' case).
120    
121            * R/dsparseMatrix.R: add "chol" method.
122            * R/ddenseMatrix.R: ditto
123    
124            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
125            * NAMESPACE (Ops)
126            * R/diagMatrix.R (diag2T): simple utility used "higher level"
127            coercion; deprecating direct lower level coercions.
128    
129            * R/*.R (seq): use seq_len() and seq_along() where possible.
130    
131    
132    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.9975-5 ready for release
135    
136    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
139    
140    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllClass.R (corMatrix): add 'validity' check;
143                    comment out unused "LDL" class definition
144            * NAMESPACE: mention, but do not export "LDL" class
145            * R/corMatrix.R: new (simple), needed for R-devel with
146            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
147              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
148    
149    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
150    
151            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
152            use Rprintf and R's error handling.
153    
154    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
157            * tests/matprod.R: add tests for the bug fixed.
158    
159    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
162            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
163    
164    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
167    
168    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Version): 0.9975-3
171    
172            * R/diagMatrix.R (bdiag): new function constructing block diagonal
173            (sparse) matrices.
174            * man/bdiag.Rd: docu + examples
175    
176            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
177    
178            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
179            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
180    
181            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
182            that result is sparse or diagonal (and not dense).
183    
184            * man/Subassign-methods.Rd: fix examples
185    
186            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
187            should always return a sparse (and not sometimes a diagonal) matrix.
188    
189    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
192    
193    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * DESCRIPTION (Version): 0.9975-2
196    
197            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
198    
199    2006-10-02  Douglas Bates  <bates@R-project.org>
200    
201            * tests/dg_Matrix.R: Simplify test taking into account new code.
202    
203    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
206    
207            * R/lsTMatrix.R: new files w/ missing methods
208            * R/nsTMatrix.R:  "  'for completeness'
209    
210            * tests/Class+Meth.R: a bit less 'not.ok.classes'
211    
212            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
213    
214    
215    2006-09-28  Douglas Bates  <bates@R-project.org>
216    
217            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
218            included.
219    
220            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
221            Export C-callable functions used in Zt_create in lme4.
222    
223    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * DESCRIPTION (Version): 0.9975-1
226    
227            * tests/simple.R: less checks fail; using NA, found that our
228                    kronecker() is not base-compatible with NA's.
229    
230            * R/dMatrix.R: "Compare" method now implemented for all cases
231    
232            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
233    
234            * man/dtpMatrix-class.Rd: mention length of 'x' slot
235    
236            * src/dtpMatrix.c (dtpMatrix_validate): fix check
237            * src/dspMatrix.c (dspMatrix_validate): ditto
238    
239            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
240              including coercion to [nl]tTMatrix.
241    
242            * R/diagMatrix.R (show): print a header line as for other classes.
243    
244    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Makefile.win (SUBDIRS): fix typo
247    
248    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
251    
252    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
255            symmetric and y missing in R code using %*% (cholmod_aat doesn't
256            accept a symmetric matrix).
257            * tests/group-methods.R: Uncomment test of crossprod applied to
258            lsCMatrix objects.
259    
260    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/AllClass.R (symmetricMatrix): add validity method (available
263            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
264    
265            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
266    
267            * tests/indexing.Rout.save:
268            * tests/indexing.R: additions, mainly for 'lsparse'
269    
270            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
271            case.
272    
273            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
274    
275    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
278                    as 'N' (1-letter - Ok?)
279    
280            * tests/group-methods.R: add test for logical + NAs
281    
282            * R/dMatrix.R ("Compare"): fix to work with NA's
283    
284            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
285    
286            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
287                    which is implemented.
288    
289    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/chm_common.c: coerce logical <-> double instead of
292            typecasting;  needed for "l" matrix handling in cholmod.
293    
294            * tests/other-pkgs.R (graph): small extension in "graph" checks.
295    
296            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
297            (Tsp2grNEL): other fixes needed
298    
299    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
302                    Matrices, since "lMatrix", also "lsparseM" can have NA
303            * R/ndenseMatrix.R, etc: new source files
304            * man/nsparseMatrix-classes.Rd, etc: new help files
305            * tests/: adaptions
306            * src/chm_common.c (chm_dense_to_SEXP): and others:
307                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
308            * src/Csparse.c, etc: ditto
309    
310    2006-09-11  Douglas Bates  <bates@R-project.org>
311    
312            * src/Mutils.[ch],init.c inst/include/*.h: Move the
313            alloc_d**Matrix functions to the lme4 package.
314    
315    2006-09-09  Douglas Bates  <bates@R-project.org>
316    
317            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
318            fixed
319    
320    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/lMatrix.R: new
323    
324            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
325    
326            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
327            * man/tcrossprod.Rd: ditto
328    
329    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
332            for exported functions
333            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
334            Remove partitioning algorithms for sparse matrix reordering.  The
335            copyright on the Metis code was problematic and the methods were
336            rarely used.
337            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
338            operations are now done entirely in CHOLMOD code.
339    
340    2006-09-06  Douglas Bates  <bates@R-project.org>
341    
342            * src/Mutils.h: Remove functions that are no longer used.
343    
344    2006-09-04  Douglas Bates  <bates@R-project.org>
345    
346            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
347            * src/DEPS.mkf: update
348    
349    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * created branches/Matrix-for-R-2.3.x;  on trunk: do
352            * DESCRIPTION (Version): 0.9975-0
353            (Depends): R (>= 2.4.0)
354    
355    2006-09-01  Douglas Bates  <bates@R-project.org>
356    
357            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
358    
359    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
362            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
363    
364            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
365    
366    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
369            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
370            * R/dsparseMatrix.R: ditto
371            * R/Csparse.R: ditto
372    
373    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dMatrix.R (Compare): improve availability of "<", etc
376            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
377    
378    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
381            of a 0-index which was used as 1-index (..hmm)
382    
383            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
384    
385            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
386            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
387            (.is.diagonal): ditto
388    
389            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
390    
391            * R/Matrix.R (Matrix): also work for NA data
392    
393    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
396            in all cases.
397    
398    2006-08-27  Douglas Bates  <bates@R-project.org>
399    
400            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
401            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
402    
403    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
406            subclasses of "ddenseMatrix"
407            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
408            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
409            instead of half dozen specialized ones.
410    
411    2006-08-25  Douglas Bates  <bates@R-project.org>
412    
413            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
414            <tillard@cirad.fr> - ordering standard errors to match effects.
415    
416    2006-08-24  Douglas Bates  <bates@R-project.org>
417    
418            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
419            on R_ldl.
420            * R/lCholCMatrix.R,
421            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
422            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
423            * many files in ./R and ./src: Use more general version of
424            dup_mMatrix_as_dgeMatrix to simplify method definitions.
425            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
426            dtpMatrix, dspMatrix and dppMatrix conversions.
427    
428    
429    2006-08-23  Douglas Bates  <bates@R-project.org>
430    
431            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
432            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
433            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
434            dgeMatrix_crossprod (may need to do this in other places).
435            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
436            generic and method for dsCMatrix.  Use CHOLMOD for chol().
437    
438    2006-08-22  Douglas Bates  <bates@R-project.org>
439    
440            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
441            types of classed Matrices, matrices or numeric or logical vectors.
442            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
443            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
444            to Mutils.h (as an inline) and change name to Matrix_check_class;
445            fixes in as_cholmod_factor and chm_factor_to_SEXP.
446            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
447            dsCMatrix_matrix_solve.  Comment out vestigial functions.
448            * src/Csparse.c: use diag_P and uplo_P macros.
449    
450    2006-08-21  Douglas Bates  <bates@R-project.org>
451    
452            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
453            valgrind.
454            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
455            inverses.
456            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
457            -Wall warnings.
458            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
459            Use dup_mMatrix_as_dgeMatrix.
460    
461    2006-08-20  Douglas Bates  <bates@R-project.org>
462    
463            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
464            * tests/sparseQR.R: Added
465            * man/sparseQR-class.Rd: Document methods for qr.* generics
466            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
467    
468    2006-08-19  Douglas Bates  <bates@R-project.org>
469    
470            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
471            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
472            and qr.fitted.
473            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
474            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
475    
476    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
479            the base version has no "..." argument.
480    
481            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
482    
483            * R/Matrix.R: define and
484            * NAMESPACE: export as.numeric() and as.logical() methods.
485                    Let's hope these do not badly slow down something...
486            Finally export the zapsmall() method.
487    
488    2006-08-17  Douglas Bates  <bates@R-project.org>
489    
490            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
491            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
492            * src/dtCMatrix.c :Remove code that is no longer used
493            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
494    
495    2006-08-14  Douglas Bates  <bates@R-project.org>
496    
497            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
498            Csparse_to_logical and Csparse_symmetric_to_general.
499            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
500            coercion methods between CsparseMatrix and TsparseMatrix.
501    
502    2006-08-14  Douglas Bates  <bates@R-project.org>
503    
504            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
505            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
506            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
507            possible.
508    
509    2006-08-12  Douglas Bates  <bates@R-project.org>
510    
511            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
512              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
513              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
514              generalize conversions between TsparseMatrix, CsparseMatrix,
515              denseMatrix and matrix.  Preserve triangularity property and
516              propagate Dimnames in the easy cases.
517    
518    2006-08-10  Douglas Bates  <bates@R-project.org>
519    
520            * src/lmer.c: adjust checks in glmer_init for S4SXP
521            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
522            before S4SXP but for the wrong reasons.
523    
524    2006-08-08  Douglas Bates  <bates@R-project.org>
525    
526            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
527            Later modified to return the upper triangle only.
528            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
529    
530    2006-08-07  Douglas Bates  <bates@R-project.org>
531    
532            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
533            R-level conversion to a sparse symmetric class.
534            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
535            Remove conversion to sparse symmetric classes (now done in C code).
536    
537    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
540            * man/band.Rd:  adapt the \dontshow{} unit test.
541    
542    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.995-14  for CRAN
545    
546            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
547    
548            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
549            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
550    
551            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
552            * R/Tsparse.R (tril, triu, band): methods
553            * R/dgRMatrix.R (tril, ...):    ditto
554            * man/band.Rd:                  ditto
555    
556    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Matrix.R (head, tail): directly use utils:::head.matrix
559                    to be up-to-date automatically.
560    
561    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
564    
565            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
566            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
567            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
568            such that the S4 objects are always created by the current version
569            of R and 'Matrix' class definitions.
570    
571    2006-08-01  Douglas Bates  <bates@R-project.org>
572    
573            * R/lmer.R (LMEoptimize method), tests/lmer.R,
574            inst/external/test3comp.rda: Added warnings for convergence on
575            boundary and test cases.
576    
577            * src/lmer.c (mer_postVar): Modified to return the variances that
578            are marginal to the fixed effects, not conditional on them (which
579            is what the bVar slot contents represent).
580    
581    2006-07-31  Douglas Bates  <bates@R-project.org>
582    
583            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
584            function which calls the C function mer_hat_trace2.
585    
586            * man/ranef.Rd: Include description of "postVar" argument and
587            producing a caterpillar plot.
588    
589    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * NAMESPACE:    change  "correlation" to "corMatrix"
592            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
593            * R/dpoMatrix.R: ditto
594            * R/lmer.R:      ditto
595    
596    2006-07-28  Douglas Bates  <bates@R-project.org>
597    
598            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
599            RZXinv slot's contents into a separate internal function that can
600            be used in mer_hat_trace.
601    
602    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
605            via new smart
606            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
607            utility functions.
608    
609    
610    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Csparse.R (tril, triu, band): do return *triangular* classed
613            matrices when appropriate; band() even symmetric ones.
614            (replCmat): extend to potentially all "CsparseMatrix"
615            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
616            allow subassignment for special sparse matrices.
617    
618            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
619    
620            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
621            argument; in glmer_*(): print only if(verbose).
622    
623            speed-optimize a few places by moving REAL(.) out of loops.
624    
625            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
626    
627    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
630                    since that wrongly triggers also for M[ logi , ]
631    
632            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
633            a symmetric matrix that results in a non-symmetric one.
634            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
635    
636            * R/dMatrix.R: make round(M) work as round(M, 0)
637    
638            * R/dgTMatrix.R (image): coordinate system and axis now use
639            1-based indices, not 0-based ones.
640    
641            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
642            * tests/indexing.R: test it.
643    
644            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
645            * man/isSymmetric-methods.Rd: and document it.
646    
647            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
648            * man/SparseM-conv.Rd: docu them
649    
650            * tests/other-pkgs.R: renamed from tests/graph.R and add example
651                    for 'SparseM' conversions
652    
653    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
654    
655            * R/Matrix.R (head): added head() and tail() methods.
656    
657    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * DESCRIPTION (Version): 0.995-12 released to CRAN
660    
661    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * tests/simple.R: add check for correct dsT -> dgT coercion;
664                    add check for correct printing of symmetric sparse matrices.
665    
666            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
667            for sparse symmetric matrices.
668    
669            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
670            diagonal twice.
671    
672    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
673    
674            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
675            being applied to the x slot (detected by Brian Ripley).
676    
677    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
680    
681            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
682    
683    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/lgCMatrix.c (lgCMatrix_diag): new function
686            * R/lgCMatrix.R (diag): for new method
687    
688            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
689                 ==> construction of illegal "*gTMatrix" via new() should
690                 now be much less easy:
691            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
692    
693            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
694                    directly.
695            * man/Matrix.Rd: documents it.
696    
697    2006-07-06  Douglas Bates  <bates@R-project.org>
698    
699            * src/pedigree.c (pedigree_inbreeding): Correction in
700            initialization.  This function is not currently being used and is
701            not fully tested.
702    
703            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
704            Introduced the glmer class.  Added code for mcmcmsamp on glmer
705            objects.  Modified validity check on pedigree objects to account
706            for nonparallel patterns of missingness of parents.
707    
708            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
709            class.
710    
711    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/pMatrix.R: coercion pMatrix -> Tsparse
714    
715    2006-06-12  Douglas Bates  <bates@R-project.org>
716    
717            * DESCRIPTION (Version): 0.995-11 released to CRAN
718    
719            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
720            the output from mcmcsamp.
721    
722    2006-06-10  Douglas Bates  <bates@R-project.org>
723    
724            * R/lmer.R (simulestimate): added C code for calculating the trace
725            of the hat matrix.
726    
727    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
730            classes.
731            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
732    
733    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/dgTMatrix.R (colSums): etc. All four of
736            colSums(), rowSums(), colMeans(), rowMeans() now should work for
737            all "Matrices".
738    
739  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
740    
741          * 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 766 
766    
767          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
768          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.
769          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
770    
771    
772  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 889 
889          * 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)
890          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
891          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
892          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
893    
894  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
# Line 355  Line 1093 
1093  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1096          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1097          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1098    
1099  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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