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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1696, Mon Dec 11 21:41:37 2006 UTC
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1    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): fix long standing typo in symmetric case
4            * man/dsCMatrix-class.Rd: add example exhibiting the above case
5    
6    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
9            to LL before converting to a sparse matrix. (The LDL form can be
10            converted to a sparse matrix but it is implicitly a unit
11            triangular matrix and a diagonal matrix overwritten on the diagonal.)
12    
13    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
16    
17    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * DESCRIPTION (Version): updated -> release 0.9975-7
20            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
21    
22    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
25    
26    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
29            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
30            is exactly singular.
31    
32    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Date): updated -> release 0.9975-6
35    
36    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
39            now returns symmetric.
40    
41            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
42    
43            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
44            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
45    
46            * R/Auxiliaries.R (.type.kind): added
47    
48    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
51            running src/CSparse_install.sh
52    
53            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
54    
55    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
58            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
59    
60            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
61    
62            * tests/Class+Meth.R (tstMatrixClass): now assure
63            the (important in method programming) property :
64    
65                    ###>>  Every "Matrix" is either
66                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
67    
68                    (where "*" stands for "Matrix")
69    
70            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
71    
72            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
73            * tests/validObj.R: checks for "comparison"
74    
75            * R/sparseMatrix.R ([): improved indexing for sparse;
76                    trying to keep <symmetric>[ n, n] symmmetric
77    
78            * tests/indexing.R: indexing for logical sparse now ok
79    
80    
81    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * src/Tsparse.c: use xTsparse_validate() , and hence remove
84    
85            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
86    
87    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
90    
91            * tests/simple.R: validObject() checking the above.
92    
93            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
94            replacing both dgCMatrix_validate and lgCM*.
95    
96            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
97            fix dimnames setting in other places.
98            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
99    
100    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
103    
104            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
105            symmetry test, via
106            * R/Auxiliaries.R (.as.dgC.0.factors):
107    
108    2006-11-01  Douglas Bates  <bates@r-project.org>
109    
110            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
111            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
112            <CsparseMatrix>) added
113    
114    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * tests/matprod.R: add a variation of Harri's example
117    
118            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
119            recursive infinitely.
120    
121            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
122    
123            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
124    
125    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
128            matrix if possible; test m+m == 2*m; now test dgRMatrix.
129            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
130            satisfy the above test.
131    
132    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
135    
136            * R/dgCMatrix.R: solve(a, b="missing") based on
137            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
138            RHS = NULL.
139    
140            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
141            add more (needed) [t]crossprod() methods.
142    
143            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
144    
145            * R/Auxiliaries.R (as_CspClass): cleanup
146            (drop0): internal utility for "Csparse_drop(*, 0)"
147            (.bail.out.2): encourage active feedback
148    
149    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dMatrix.R(Compare): new(), then slots [no validity check]
152    
153            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
154            non-valid or 'sorted' case).
155    
156            * R/dsparseMatrix.R: add "chol" method.
157            * R/ddenseMatrix.R: ditto
158    
159            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
160            * NAMESPACE (Ops)
161            * R/diagMatrix.R (diag2T): simple utility used "higher level"
162            coercion; deprecating direct lower level coercions.
163    
164            * R/*.R (seq): use seq_len() and seq_along() where possible.
165    
166    
167    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * DESCRIPTION (Version): 0.9975-5 ready for release
170    
171    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
174    
175    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/AllClass.R (corMatrix): add 'validity' check;
178                    comment out unused "LDL" class definition
179            * NAMESPACE: mention, but do not export "LDL" class
180            * R/corMatrix.R: new (simple), needed for R-devel with
181            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
182              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
183    
184    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
187            use Rprintf and R's error handling.
188    
189    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
192            * tests/matprod.R: add tests for the bug fixed.
193    
194    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
195    
196            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
197            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
198    
199    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
202    
203    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.9975-3
206    
207            * R/diagMatrix.R (bdiag): new function constructing block diagonal
208            (sparse) matrices.
209            * man/bdiag.Rd: docu + examples
210    
211            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
212    
213            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
214            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
215    
216            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
217            that result is sparse or diagonal (and not dense).
218    
219            * man/Subassign-methods.Rd: fix examples
220    
221            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
222            should always return a sparse (and not sometimes a diagonal) matrix.
223    
224    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
227    
228    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
229    
230            * DESCRIPTION (Version): 0.9975-2
231    
232            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
233    
234    2006-10-02  Douglas Bates  <bates@R-project.org>
235    
236            * tests/dg_Matrix.R: Simplify test taking into account new code.
237    
238    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
241    
242            * R/lsTMatrix.R: new files w/ missing methods
243            * R/nsTMatrix.R:  "  'for completeness'
244    
245            * tests/Class+Meth.R: a bit less 'not.ok.classes'
246    
247            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
248    
249    
250    2006-09-28  Douglas Bates  <bates@R-project.org>
251    
252            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
253            included.
254    
255            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
256            Export C-callable functions used in Zt_create in lme4.
257    
258    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * DESCRIPTION (Version): 0.9975-1
261    
262            * tests/simple.R: less checks fail; using NA, found that our
263                    kronecker() is not base-compatible with NA's.
264    
265            * R/dMatrix.R: "Compare" method now implemented for all cases
266    
267            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
268    
269            * man/dtpMatrix-class.Rd: mention length of 'x' slot
270    
271            * src/dtpMatrix.c (dtpMatrix_validate): fix check
272            * src/dspMatrix.c (dspMatrix_validate): ditto
273    
274            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
275              including coercion to [nl]tTMatrix.
276    
277            * R/diagMatrix.R (show): print a header line as for other classes.
278    
279    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/Makefile.win (SUBDIRS): fix typo
282    
283    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
286    
287    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
290            symmetric and y missing in R code using %*% (cholmod_aat doesn't
291            accept a symmetric matrix).
292            * tests/group-methods.R: Uncomment test of crossprod applied to
293            lsCMatrix objects.
294    
295    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/AllClass.R (symmetricMatrix): add validity method (available
298            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
299    
300            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
301    
302            * tests/indexing.Rout.save:
303            * tests/indexing.R: additions, mainly for 'lsparse'
304    
305            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
306            case.
307    
308            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
309    
310    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
313                    as 'N' (1-letter - Ok?)
314    
315            * tests/group-methods.R: add test for logical + NAs
316    
317            * R/dMatrix.R ("Compare"): fix to work with NA's
318    
319            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
320    
321            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
322                    which is implemented.
323    
324    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/chm_common.c: coerce logical <-> double instead of
327            typecasting;  needed for "l" matrix handling in cholmod.
328    
329            * tests/other-pkgs.R (graph): small extension in "graph" checks.
330    
331            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
332            (Tsp2grNEL): other fixes needed
333    
334    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
337                    Matrices, since "lMatrix", also "lsparseM" can have NA
338            * R/ndenseMatrix.R, etc: new source files
339            * man/nsparseMatrix-classes.Rd, etc: new help files
340            * tests/: adaptions
341            * src/chm_common.c (chm_dense_to_SEXP): and others:
342                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
343            * src/Csparse.c, etc: ditto
344    
345    2006-09-11  Douglas Bates  <bates@R-project.org>
346    
347            * src/Mutils.[ch],init.c inst/include/*.h: Move the
348            alloc_d**Matrix functions to the lme4 package.
349    
350    2006-09-09  Douglas Bates  <bates@R-project.org>
351    
352            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
353            fixed
354    
355    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/lMatrix.R: new
358    
359            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
360    
361            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
362            * man/tcrossprod.Rd: ditto
363    
364    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
367            for exported functions
368            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
369            Remove partitioning algorithms for sparse matrix reordering.  The
370            copyright on the Metis code was problematic and the methods were
371            rarely used.
372            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
373            operations are now done entirely in CHOLMOD code.
374    
375    2006-09-06  Douglas Bates  <bates@R-project.org>
376    
377            * src/Mutils.h: Remove functions that are no longer used.
378    
379    2006-09-04  Douglas Bates  <bates@R-project.org>
380    
381            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
382            * src/DEPS.mkf: update
383    
384    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * created branches/Matrix-for-R-2.3.x;  on trunk: do
387            * DESCRIPTION (Version): 0.9975-0
388            (Depends): R (>= 2.4.0)
389    
390    2006-09-01  Douglas Bates  <bates@R-project.org>
391    
392            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
393    
394    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
397            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
398    
399            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
400    
401    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
404            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
405            * R/dsparseMatrix.R: ditto
406            * R/Csparse.R: ditto
407    
408    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/dMatrix.R (Compare): improve availability of "<", etc
411            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
412    
413    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
416            of a 0-index which was used as 1-index (..hmm)
417    
418            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
419    
420            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
421            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
422            (.is.diagonal): ditto
423    
424            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
425    
426            * R/Matrix.R (Matrix): also work for NA data
427    
428    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
431            in all cases.
432    
433    2006-08-27  Douglas Bates  <bates@R-project.org>
434    
435            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
436            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
437    
438    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
441            subclasses of "ddenseMatrix"
442            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
443            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
444            instead of half dozen specialized ones.
445    
446    2006-08-25  Douglas Bates  <bates@R-project.org>
447    
448            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
449            <tillard@cirad.fr> - ordering standard errors to match effects.
450    
451    2006-08-24  Douglas Bates  <bates@R-project.org>
452    
453            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
454            on R_ldl.
455            * R/lCholCMatrix.R,
456            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
457            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
458            * many files in ./R and ./src: Use more general version of
459            dup_mMatrix_as_dgeMatrix to simplify method definitions.
460            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
461            dtpMatrix, dspMatrix and dppMatrix conversions.
462    
463    
464    2006-08-23  Douglas Bates  <bates@R-project.org>
465    
466            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
467            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
468            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
469            dgeMatrix_crossprod (may need to do this in other places).
470            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
471            generic and method for dsCMatrix.  Use CHOLMOD for chol().
472    
473    2006-08-22  Douglas Bates  <bates@R-project.org>
474    
475            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
476            types of classed Matrices, matrices or numeric or logical vectors.
477            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
478            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
479            to Mutils.h (as an inline) and change name to Matrix_check_class;
480            fixes in as_cholmod_factor and chm_factor_to_SEXP.
481            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
482            dsCMatrix_matrix_solve.  Comment out vestigial functions.
483            * src/Csparse.c: use diag_P and uplo_P macros.
484    
485    2006-08-21  Douglas Bates  <bates@R-project.org>
486    
487            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
488            valgrind.
489            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
490            inverses.
491            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
492            -Wall warnings.
493            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
494            Use dup_mMatrix_as_dgeMatrix.
495    
496    2006-08-20  Douglas Bates  <bates@R-project.org>
497    
498            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
499            * tests/sparseQR.R: Added
500            * man/sparseQR-class.Rd: Document methods for qr.* generics
501            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
502    
503    2006-08-19  Douglas Bates  <bates@R-project.org>
504    
505            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
506            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
507            and qr.fitted.
508            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
509            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
510    
511    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
514            the base version has no "..." argument.
515    
516            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
517    
518            * R/Matrix.R: define and
519            * NAMESPACE: export as.numeric() and as.logical() methods.
520                    Let's hope these do not badly slow down something...
521            Finally export the zapsmall() method.
522    
523    2006-08-17  Douglas Bates  <bates@R-project.org>
524    
525            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
526            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
527            * src/dtCMatrix.c :Remove code that is no longer used
528            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
529    
530    2006-08-14  Douglas Bates  <bates@R-project.org>
531    
532            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
533            Csparse_to_logical and Csparse_symmetric_to_general.
534            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
535            coercion methods between CsparseMatrix and TsparseMatrix.
536    
537    2006-08-14  Douglas Bates  <bates@R-project.org>
538    
539            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
540            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
541            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
542            possible.
543    
544    2006-08-12  Douglas Bates  <bates@R-project.org>
545    
546            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
547              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
548              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
549              generalize conversions between TsparseMatrix, CsparseMatrix,
550              denseMatrix and matrix.  Preserve triangularity property and
551              propagate Dimnames in the easy cases.
552    
553    2006-08-10  Douglas Bates  <bates@R-project.org>
554    
555            * src/lmer.c: adjust checks in glmer_init for S4SXP
556            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
557            before S4SXP but for the wrong reasons.
558    
559    2006-08-08  Douglas Bates  <bates@R-project.org>
560    
561            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
562            Later modified to return the upper triangle only.
563            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
564    
565    2006-08-07  Douglas Bates  <bates@R-project.org>
566    
567            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
568            R-level conversion to a sparse symmetric class.
569            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
570            Remove conversion to sparse symmetric classes (now done in C code).
571    
572    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
575            * man/band.Rd:  adapt the \dontshow{} unit test.
576    
577    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * DESCRIPTION (Version): 0.995-14  for CRAN
580    
581            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
582    
583            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
584            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
585    
586            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
587            * R/Tsparse.R (tril, triu, band): methods
588            * R/dgRMatrix.R (tril, ...):    ditto
589            * man/band.Rd:                  ditto
590    
591    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/Matrix.R (head, tail): directly use utils:::head.matrix
594                    to be up-to-date automatically.
595    
596    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
599    
600            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
601            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
602            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
603            such that the S4 objects are always created by the current version
604            of R and 'Matrix' class definitions.
605    
606    2006-08-01  Douglas Bates  <bates@R-project.org>
607    
608            * R/lmer.R (LMEoptimize method), tests/lmer.R,
609            inst/external/test3comp.rda: Added warnings for convergence on
610            boundary and test cases.
611    
612            * src/lmer.c (mer_postVar): Modified to return the variances that
613            are marginal to the fixed effects, not conditional on them (which
614            is what the bVar slot contents represent).
615    
616    2006-07-31  Douglas Bates  <bates@R-project.org>
617    
618            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
619            function which calls the C function mer_hat_trace2.
620    
621            * man/ranef.Rd: Include description of "postVar" argument and
622            producing a caterpillar plot.
623    
624    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * NAMESPACE:    change  "correlation" to "corMatrix"
627            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
628            * R/dpoMatrix.R: ditto
629            * R/lmer.R:      ditto
630    
631    2006-07-28  Douglas Bates  <bates@R-project.org>
632    
633            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
634            RZXinv slot's contents into a separate internal function that can
635            be used in mer_hat_trace.
636    
637    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
640            via new smart
641            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
642            utility functions.
643    
644    
645    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Csparse.R (tril, triu, band): do return *triangular* classed
648            matrices when appropriate; band() even symmetric ones.
649            (replCmat): extend to potentially all "CsparseMatrix"
650            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
651            allow subassignment for special sparse matrices.
652    
653            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
654    
655            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
656            argument; in glmer_*(): print only if(verbose).
657    
658            speed-optimize a few places by moving REAL(.) out of loops.
659    
660            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
661    
662    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
665                    since that wrongly triggers also for M[ logi , ]
666    
667            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
668            a symmetric matrix that results in a non-symmetric one.
669            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
670    
671            * R/dMatrix.R: make round(M) work as round(M, 0)
672    
673            * R/dgTMatrix.R (image): coordinate system and axis now use
674            1-based indices, not 0-based ones.
675    
676            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
677            * tests/indexing.R: test it.
678    
679            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
680            * man/isSymmetric-methods.Rd: and document it.
681    
682            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
683            * man/SparseM-conv.Rd: docu them
684    
685            * tests/other-pkgs.R: renamed from tests/graph.R and add example
686                    for 'SparseM' conversions
687    
688    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
689    
690            * R/Matrix.R (head): added head() and tail() methods.
691    
692    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * DESCRIPTION (Version): 0.995-12 released to CRAN
695    
696    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * tests/simple.R: add check for correct dsT -> dgT coercion;
699                    add check for correct printing of symmetric sparse matrices.
700    
701            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
702            for sparse symmetric matrices.
703    
704            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
705            diagonal twice.
706    
707    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
708    
709            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
710            being applied to the x slot (detected by Brian Ripley).
711    
712    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
715    
716            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
717    
718    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * src/lgCMatrix.c (lgCMatrix_diag): new function
721            * R/lgCMatrix.R (diag): for new method
722    
723            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
724                 ==> construction of illegal "*gTMatrix" via new() should
725                 now be much less easy:
726            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
727    
728            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
729                    directly.
730            * man/Matrix.Rd: documents it.
731    
732    2006-07-06  Douglas Bates  <bates@R-project.org>
733    
734            * src/pedigree.c (pedigree_inbreeding): Correction in
735            initialization.  This function is not currently being used and is
736            not fully tested.
737    
738            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
739            Introduced the glmer class.  Added code for mcmcmsamp on glmer
740            objects.  Modified validity check on pedigree objects to account
741            for nonparallel patterns of missingness of parents.
742    
743            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
744            class.
745    
746    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/pMatrix.R: coercion pMatrix -> Tsparse
749    
750    2006-06-12  Douglas Bates  <bates@R-project.org>
751    
752            * DESCRIPTION (Version): 0.995-11 released to CRAN
753    
754            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
755            the output from mcmcsamp.
756    
757  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
758    
759          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
760            of the hat matrix.
761    
762  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
765          classes.          classes.
766            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
767    
768  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
# Line 43  Line 801 
801    
802          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
803          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.
804          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
805    
806    
807  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 924 
924          * 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)
925          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
926          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
927          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
928    
929  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
# Line 370  Line 1128 
1128  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1129    
1130          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1131          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1132          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1133    
1134  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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