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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1665, Fri Nov 3 23:18:07 2006 UTC
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1    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
4            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
5    
6            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
7    
8            * tests/Class+Meth.R (tstMatrixClass): now assure
9            the (important in method programming) property :
10    
11                    ###>>  Every "Matrix" is either
12                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
13    
14                    (where "*" stands for "Matrix")
15    
16            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
17    
18            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
19            * tests/validObj.R: checks for "comparison"
20    
21            * R/sparseMatrix.R ([): improved indexing for sparse;
22                    trying to keep <symmetric>[ n, n] symmmetric
23    
24            * tests/indexing.R: indexing for logical sparse now ok
25    
26    
27    
28    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/Tsparse.c: use xTsparse_validate() , and hence remove
31    
32            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
33    
34    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
37    
38            * tests/simple.R: validObject() checking the above.
39    
40            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
41            replacing both dgCMatrix_validate and lgCM*.
42    
43            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
44            fix dimnames setting in other places.
45            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
46    
47    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
50    
51            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
52            symmetry test, via
53            * R/Auxiliaries.R (.as.dgC.0.factors):
54    
55    2006-11-01  Douglas Bates  <bates@r-project.org>
56    
57            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
58            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
59            <CsparseMatrix>) added
60    
61    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * tests/matprod.R: add a variation of Harri's example
64    
65            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
66            recursive infinitely.
67    
68            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
69    
70            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
71    
72    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
75            matrix if possible; test m+m == 2*m; now test dgRMatrix.
76            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
77            satisfy the above test.
78    
79    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
82    
83            * R/dgCMatrix.R: solve(a, b="missing") based on
84            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
85            RHS = NULL.
86    
87            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
88            add more (needed) [t]crossprod() methods.
89    
90            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
91    
92            * R/Auxiliaries.R (as_CspClass): cleanup
93            (drop0): internal utility for "Csparse_drop(*, 0)"
94            (.bail.out.2): encourage active feedback
95    
96    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dMatrix.R(Compare): new(), then slots [no validity check]
99    
100            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
101            non-valid or 'sorted' case).
102    
103            * R/dsparseMatrix.R: add "chol" method.
104            * R/ddenseMatrix.R: ditto
105    
106            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
107            * NAMESPACE (Ops)
108            * R/diagMatrix.R (diag2T): simple utility used "higher level"
109            coercion; deprecating direct lower level coercions.
110    
111            * R/*.R (seq): use seq_len() and seq_along() where possible.
112    
113    
114    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.9975-5 ready for release
117    
118    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
121    
122    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllClass.R (corMatrix): add 'validity' check;
125                    comment out unused "LDL" class definition
126            * NAMESPACE: mention, but do not export "LDL" class
127            * R/corMatrix.R: new (simple), needed for R-devel with
128            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
129              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
130    
131    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
132    
133            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
134            use Rprintf and R's error handling.
135    
136    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
139            * tests/matprod.R: add tests for the bug fixed.
140    
141    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
144            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
145    
146    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
147    
148            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
149    
150    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.9975-3
153    
154            * R/diagMatrix.R (bdiag): new function constructing block diagonal
155            (sparse) matrices.
156            * man/bdiag.Rd: docu + examples
157    
158            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
159    
160            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
161            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
162    
163            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
164            that result is sparse or diagonal (and not dense).
165    
166            * man/Subassign-methods.Rd: fix examples
167    
168            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
169            should always return a sparse (and not sometimes a diagonal) matrix.
170    
171    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
174    
175    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
176    
177            * DESCRIPTION (Version): 0.9975-2
178    
179            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
180    
181    2006-10-02  Douglas Bates  <bates@R-project.org>
182    
183            * tests/dg_Matrix.R: Simplify test taking into account new code.
184    
185    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
188    
189            * R/lsTMatrix.R: new files w/ missing methods
190            * R/nsTMatrix.R:  "  'for completeness'
191    
192            * tests/Class+Meth.R: a bit less 'not.ok.classes'
193    
194            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
195    
196    
197    2006-09-28  Douglas Bates  <bates@R-project.org>
198    
199            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
200            included.
201    
202            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
203            Export C-callable functions used in Zt_create in lme4.
204    
205    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * DESCRIPTION (Version): 0.9975-1
208    
209            * tests/simple.R: less checks fail; using NA, found that our
210                    kronecker() is not base-compatible with NA's.
211    
212            * R/dMatrix.R: "Compare" method now implemented for all cases
213    
214            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
215    
216            * man/dtpMatrix-class.Rd: mention length of 'x' slot
217    
218            * src/dtpMatrix.c (dtpMatrix_validate): fix check
219            * src/dspMatrix.c (dspMatrix_validate): ditto
220    
221            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
222              including coercion to [nl]tTMatrix.
223    
224            * R/diagMatrix.R (show): print a header line as for other classes.
225    
226    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * src/Makefile.win (SUBDIRS): fix typo
229    
230    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
233    
234    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
235    
236            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
237            symmetric and y missing in R code using %*% (cholmod_aat doesn't
238            accept a symmetric matrix).
239            * tests/group-methods.R: Uncomment test of crossprod applied to
240            lsCMatrix objects.
241    
242    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/AllClass.R (symmetricMatrix): add validity method (available
245            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
246    
247            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
248    
249            * tests/indexing.Rout.save:
250            * tests/indexing.R: additions, mainly for 'lsparse'
251    
252            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
253            case.
254    
255            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
256    
257    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
260                    as 'N' (1-letter - Ok?)
261    
262            * tests/group-methods.R: add test for logical + NAs
263    
264            * R/dMatrix.R ("Compare"): fix to work with NA's
265    
266            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
267    
268            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
269                    which is implemented.
270    
271    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * src/chm_common.c: coerce logical <-> double instead of
274            typecasting;  needed for "l" matrix handling in cholmod.
275    
276            * tests/other-pkgs.R (graph): small extension in "graph" checks.
277    
278            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
279            (Tsp2grNEL): other fixes needed
280    
281    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
284                    Matrices, since "lMatrix", also "lsparseM" can have NA
285            * R/ndenseMatrix.R, etc: new source files
286            * man/nsparseMatrix-classes.Rd, etc: new help files
287            * tests/: adaptions
288            * src/chm_common.c (chm_dense_to_SEXP): and others:
289                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
290            * src/Csparse.c, etc: ditto
291    
292    2006-09-11  Douglas Bates  <bates@R-project.org>
293    
294            * src/Mutils.[ch],init.c inst/include/*.h: Move the
295            alloc_d**Matrix functions to the lme4 package.
296    
297    2006-09-09  Douglas Bates  <bates@R-project.org>
298    
299            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
300            fixed
301    
302    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/lMatrix.R: new
305    
306            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
307    
308            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
309            * man/tcrossprod.Rd: ditto
310    
311    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
314            for exported functions
315            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
316            Remove partitioning algorithms for sparse matrix reordering.  The
317            copyright on the Metis code was problematic and the methods were
318            rarely used.
319            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
320            operations are now done entirely in CHOLMOD code.
321    
322    2006-09-06  Douglas Bates  <bates@R-project.org>
323    
324            * src/Mutils.h: Remove functions that are no longer used.
325    
326    2006-09-04  Douglas Bates  <bates@R-project.org>
327    
328            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
329            * src/DEPS.mkf: update
330    
331    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * created branches/Matrix-for-R-2.3.x;  on trunk: do
334            * DESCRIPTION (Version): 0.9975-0
335            (Depends): R (>= 2.4.0)
336    
337    2006-09-01  Douglas Bates  <bates@R-project.org>
338    
339            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
340    
341    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
344            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
345    
346            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
347    
348    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
351            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
352            * R/dsparseMatrix.R: ditto
353            * R/Csparse.R: ditto
354    
355    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/dMatrix.R (Compare): improve availability of "<", etc
358            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
359    
360    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
363            of a 0-index which was used as 1-index (..hmm)
364    
365            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
366    
367            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
368            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
369            (.is.diagonal): ditto
370    
371            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
372    
373            * R/Matrix.R (Matrix): also work for NA data
374    
375    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
378            in all cases.
379    
380    2006-08-27  Douglas Bates  <bates@R-project.org>
381    
382            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
383            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
384    
385    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
388            subclasses of "ddenseMatrix"
389            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
390            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
391            instead of half dozen specialized ones.
392    
393    2006-08-25  Douglas Bates  <bates@R-project.org>
394    
395            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
396            <tillard@cirad.fr> - ordering standard errors to match effects.
397    
398    2006-08-24  Douglas Bates  <bates@R-project.org>
399    
400            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
401            on R_ldl.
402            * R/lCholCMatrix.R,
403            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
404            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
405            * many files in ./R and ./src: Use more general version of
406            dup_mMatrix_as_dgeMatrix to simplify method definitions.
407            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
408            dtpMatrix, dspMatrix and dppMatrix conversions.
409    
410    
411    2006-08-23  Douglas Bates  <bates@R-project.org>
412    
413            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
414            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
415            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
416            dgeMatrix_crossprod (may need to do this in other places).
417            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
418            generic and method for dsCMatrix.  Use CHOLMOD for chol().
419    
420    2006-08-22  Douglas Bates  <bates@R-project.org>
421    
422            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
423            types of classed Matrices, matrices or numeric or logical vectors.
424            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
425            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
426            to Mutils.h (as an inline) and change name to Matrix_check_class;
427            fixes in as_cholmod_factor and chm_factor_to_SEXP.
428            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
429            dsCMatrix_matrix_solve.  Comment out vestigial functions.
430            * src/Csparse.c: use diag_P and uplo_P macros.
431    
432    2006-08-21  Douglas Bates  <bates@R-project.org>
433    
434            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
435            valgrind.
436            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
437            inverses.
438            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
439            -Wall warnings.
440            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
441            Use dup_mMatrix_as_dgeMatrix.
442    
443    2006-08-20  Douglas Bates  <bates@R-project.org>
444    
445            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
446            * tests/sparseQR.R: Added
447            * man/sparseQR-class.Rd: Document methods for qr.* generics
448            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
449    
450    2006-08-19  Douglas Bates  <bates@R-project.org>
451    
452            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
453            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
454            and qr.fitted.
455            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
456            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
457    
458    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
461            the base version has no "..." argument.
462    
463            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
464    
465            * R/Matrix.R: define and
466            * NAMESPACE: export as.numeric() and as.logical() methods.
467                    Let's hope these do not badly slow down something...
468            Finally export the zapsmall() method.
469    
470    2006-08-17  Douglas Bates  <bates@R-project.org>
471    
472            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
473            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
474            * src/dtCMatrix.c :Remove code that is no longer used
475            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
476    
477    2006-08-14  Douglas Bates  <bates@R-project.org>
478    
479            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
480            Csparse_to_logical and Csparse_symmetric_to_general.
481            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
482            coercion methods between CsparseMatrix and TsparseMatrix.
483    
484    2006-08-14  Douglas Bates  <bates@R-project.org>
485    
486            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
487            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
488            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
489            possible.
490    
491    2006-08-12  Douglas Bates  <bates@R-project.org>
492    
493            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
494              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
495              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
496              generalize conversions between TsparseMatrix, CsparseMatrix,
497              denseMatrix and matrix.  Preserve triangularity property and
498              propagate Dimnames in the easy cases.
499    
500    2006-08-10  Douglas Bates  <bates@R-project.org>
501    
502            * src/lmer.c: adjust checks in glmer_init for S4SXP
503            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
504            before S4SXP but for the wrong reasons.
505    
506    2006-08-08  Douglas Bates  <bates@R-project.org>
507    
508            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
509            Later modified to return the upper triangle only.
510            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
511    
512    2006-08-07  Douglas Bates  <bates@R-project.org>
513    
514            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
515            R-level conversion to a sparse symmetric class.
516            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
517            Remove conversion to sparse symmetric classes (now done in C code).
518    
519    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
522            * man/band.Rd:  adapt the \dontshow{} unit test.
523    
524    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Version): 0.995-14  for CRAN
527    
528            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
529    
530            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
531            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
532    
533            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
534            * R/Tsparse.R (tril, triu, band): methods
535            * R/dgRMatrix.R (tril, ...):    ditto
536            * man/band.Rd:                  ditto
537    
538    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Matrix.R (head, tail): directly use utils:::head.matrix
541                    to be up-to-date automatically.
542    
543    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
546    
547            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
548            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
549            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
550            such that the S4 objects are always created by the current version
551            of R and 'Matrix' class definitions.
552    
553    2006-08-01  Douglas Bates  <bates@R-project.org>
554    
555            * R/lmer.R (LMEoptimize method), tests/lmer.R,
556            inst/external/test3comp.rda: Added warnings for convergence on
557            boundary and test cases.
558    
559            * src/lmer.c (mer_postVar): Modified to return the variances that
560            are marginal to the fixed effects, not conditional on them (which
561            is what the bVar slot contents represent).
562    
563    2006-07-31  Douglas Bates  <bates@R-project.org>
564    
565            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
566            function which calls the C function mer_hat_trace2.
567    
568            * man/ranef.Rd: Include description of "postVar" argument and
569            producing a caterpillar plot.
570    
571    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * NAMESPACE:    change  "correlation" to "corMatrix"
574            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
575            * R/dpoMatrix.R: ditto
576            * R/lmer.R:      ditto
577    
578    2006-07-28  Douglas Bates  <bates@R-project.org>
579    
580            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
581            RZXinv slot's contents into a separate internal function that can
582            be used in mer_hat_trace.
583    
584    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
587            via new smart
588            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
589            utility functions.
590    
591    
592    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Csparse.R (tril, triu, band): do return *triangular* classed
595            matrices when appropriate; band() even symmetric ones.
596            (replCmat): extend to potentially all "CsparseMatrix"
597            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
598            allow subassignment for special sparse matrices.
599    
600            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
601    
602            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
603            argument; in glmer_*(): print only if(verbose).
604    
605            speed-optimize a few places by moving REAL(.) out of loops.
606    
607            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
608    
609    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
612                    since that wrongly triggers also for M[ logi , ]
613    
614            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
615            a symmetric matrix that results in a non-symmetric one.
616            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
617    
618            * R/dMatrix.R: make round(M) work as round(M, 0)
619    
620            * R/dgTMatrix.R (image): coordinate system and axis now use
621            1-based indices, not 0-based ones.
622    
623            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
624            * tests/indexing.R: test it.
625    
626            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
627            * man/isSymmetric-methods.Rd: and document it.
628    
629            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
630            * man/SparseM-conv.Rd: docu them
631    
632            * tests/other-pkgs.R: renamed from tests/graph.R and add example
633                    for 'SparseM' conversions
634    
635    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
636    
637            * R/Matrix.R (head): added head() and tail() methods.
638    
639    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * DESCRIPTION (Version): 0.995-12 released to CRAN
642    
643    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * tests/simple.R: add check for correct dsT -> dgT coercion;
646                    add check for correct printing of symmetric sparse matrices.
647    
648            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
649            for sparse symmetric matrices.
650    
651            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
652            diagonal twice.
653    
654    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
655    
656            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
657            being applied to the x slot (detected by Brian Ripley).
658    
659    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
662    
663            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
664    
665    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * src/lgCMatrix.c (lgCMatrix_diag): new function
668            * R/lgCMatrix.R (diag): for new method
669    
670            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
671                 ==> construction of illegal "*gTMatrix" via new() should
672                 now be much less easy:
673            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
674    
675            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
676                    directly.
677            * man/Matrix.Rd: documents it.
678    
679    2006-07-06  Douglas Bates  <bates@R-project.org>
680    
681            * src/pedigree.c (pedigree_inbreeding): Correction in
682            initialization.  This function is not currently being used and is
683            not fully tested.
684    
685            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
686            Introduced the glmer class.  Added code for mcmcmsamp on glmer
687            objects.  Modified validity check on pedigree objects to account
688            for nonparallel patterns of missingness of parents.
689    
690            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
691            class.
692    
693    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/pMatrix.R: coercion pMatrix -> Tsparse
696    
697    2006-06-12  Douglas Bates  <bates@R-project.org>
698    
699            * DESCRIPTION (Version): 0.995-11 released to CRAN
700    
701            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
702            the output from mcmcsamp.
703    
704  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
705    
706          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
707            of the hat matrix.
708    
709  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
712          classes.          classes.
713            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
714    
715  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
# Line 43  Line 748 
748    
749          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
750          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.
751          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
752    
753    
754  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 871 
871          * 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)
872          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
873          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
874          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
875    
876  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
# Line 370  Line 1075 
1075  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1078          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1079          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1080    
1081  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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