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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1705, Sat Dec 16 12:37:25 2006 UTC
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1    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
4            align with proper position of "0", i.e., right for integers.
5            argument 'align' by default is "fancy".
6    
7    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
10            * R/Csparse.R: and fix "Compare" for more cases.
11            * tests/Class+Meth.R: test some of these (m == m, m != m)
12    
13    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/lsparseMatrix.R: all() and any() methods
16            * R/ldenseMatrix.R:      ditto
17            * NAMESPACE, R/Matrix.R: ditto
18    
19            * man/all-methods.Rd: document them minimally
20    
21            * tests/simple.R: add a few examples for these
22    
23    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([): fix long standing typo in symmetric case
26            * man/dsCMatrix-class.Rd: add example exhibiting the above case
27    
28    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
29    
30            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
31            to LL before converting to a sparse matrix. (The LDL form can be
32            converted to a sparse matrix but it is implicitly a unit
33            triangular matrix and a diagonal matrix overwritten on the diagonal.)
34    
35    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
38    
39    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * DESCRIPTION (Version): updated -> release 0.9975-7
42            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
43    
44    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
47    
48    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
49    
50            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
51            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
52            is exactly singular.
53    
54    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Date): updated -> release 0.9975-6
57    
58    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
61            now returns symmetric.
62    
63            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
64    
65            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
66            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
67    
68            * R/Auxiliaries.R (.type.kind): added
69    
70    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
73            running src/CSparse_install.sh
74    
75            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
76    
77    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
80            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
81    
82            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
83    
84            * tests/Class+Meth.R (tstMatrixClass): now assure
85            the (important in method programming) property :
86    
87                    ###>>  Every "Matrix" is either
88                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
89    
90                    (where "*" stands for "Matrix")
91    
92            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
93    
94            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
95            * tests/validObj.R: checks for "comparison"
96    
97            * R/sparseMatrix.R ([): improved indexing for sparse;
98                    trying to keep <symmetric>[ n, n] symmmetric
99    
100            * tests/indexing.R: indexing for logical sparse now ok
101    
102    
103    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/Tsparse.c: use xTsparse_validate() , and hence remove
106    
107            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
108    
109    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
112    
113            * tests/simple.R: validObject() checking the above.
114    
115            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
116            replacing both dgCMatrix_validate and lgCM*.
117    
118            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
119            fix dimnames setting in other places.
120            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
121    
122    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
125    
126            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
127            symmetry test, via
128            * R/Auxiliaries.R (.as.dgC.0.factors):
129    
130    2006-11-01  Douglas Bates  <bates@r-project.org>
131    
132            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
133            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
134            <CsparseMatrix>) added
135    
136    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/matprod.R: add a variation of Harri's example
139    
140            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
141            recursive infinitely.
142    
143            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
144    
145            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
146    
147    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
150            matrix if possible; test m+m == 2*m; now test dgRMatrix.
151            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
152            satisfy the above test.
153    
154    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
157    
158            * R/dgCMatrix.R: solve(a, b="missing") based on
159            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
160            RHS = NULL.
161    
162            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
163            add more (needed) [t]crossprod() methods.
164    
165            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
166    
167            * R/Auxiliaries.R (as_CspClass): cleanup
168            (drop0): internal utility for "Csparse_drop(*, 0)"
169            (.bail.out.2): encourage active feedback
170    
171    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R(Compare): new(), then slots [no validity check]
174    
175            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
176            non-valid or 'sorted' case).
177    
178            * R/dsparseMatrix.R: add "chol" method.
179            * R/ddenseMatrix.R: ditto
180    
181            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
182            * NAMESPACE (Ops)
183            * R/diagMatrix.R (diag2T): simple utility used "higher level"
184            coercion; deprecating direct lower level coercions.
185    
186            * R/*.R (seq): use seq_len() and seq_along() where possible.
187    
188    
189    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * DESCRIPTION (Version): 0.9975-5 ready for release
192    
193    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
196    
197    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllClass.R (corMatrix): add 'validity' check;
200                    comment out unused "LDL" class definition
201            * NAMESPACE: mention, but do not export "LDL" class
202            * R/corMatrix.R: new (simple), needed for R-devel with
203            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
204              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
205    
206    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
209            use Rprintf and R's error handling.
210    
211    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
214            * tests/matprod.R: add tests for the bug fixed.
215    
216    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
219            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
220    
221    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
224    
225    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.9975-3
228    
229            * R/diagMatrix.R (bdiag): new function constructing block diagonal
230            (sparse) matrices.
231            * man/bdiag.Rd: docu + examples
232    
233            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
234    
235            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
236            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
237    
238            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
239            that result is sparse or diagonal (and not dense).
240    
241            * man/Subassign-methods.Rd: fix examples
242    
243            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
244            should always return a sparse (and not sometimes a diagonal) matrix.
245    
246    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
249    
250    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * DESCRIPTION (Version): 0.9975-2
253    
254            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
255    
256    2006-10-02  Douglas Bates  <bates@R-project.org>
257    
258            * tests/dg_Matrix.R: Simplify test taking into account new code.
259    
260    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
263    
264            * R/lsTMatrix.R: new files w/ missing methods
265            * R/nsTMatrix.R:  "  'for completeness'
266    
267            * tests/Class+Meth.R: a bit less 'not.ok.classes'
268    
269            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
270    
271    
272    2006-09-28  Douglas Bates  <bates@R-project.org>
273    
274            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
275            included.
276    
277            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
278            Export C-callable functions used in Zt_create in lme4.
279    
280    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version): 0.9975-1
283    
284            * tests/simple.R: less checks fail; using NA, found that our
285                    kronecker() is not base-compatible with NA's.
286    
287            * R/dMatrix.R: "Compare" method now implemented for all cases
288    
289            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
290    
291            * man/dtpMatrix-class.Rd: mention length of 'x' slot
292    
293            * src/dtpMatrix.c (dtpMatrix_validate): fix check
294            * src/dspMatrix.c (dspMatrix_validate): ditto
295    
296            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
297              including coercion to [nl]tTMatrix.
298    
299            * R/diagMatrix.R (show): print a header line as for other classes.
300    
301    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Makefile.win (SUBDIRS): fix typo
304    
305    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
308    
309    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
312            symmetric and y missing in R code using %*% (cholmod_aat doesn't
313            accept a symmetric matrix).
314            * tests/group-methods.R: Uncomment test of crossprod applied to
315            lsCMatrix objects.
316    
317    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R (symmetricMatrix): add validity method (available
320            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
321    
322            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
323    
324            * tests/indexing.Rout.save:
325            * tests/indexing.R: additions, mainly for 'lsparse'
326    
327            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
328            case.
329    
330            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
331    
332    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
335                    as 'N' (1-letter - Ok?)
336    
337            * tests/group-methods.R: add test for logical + NAs
338    
339            * R/dMatrix.R ("Compare"): fix to work with NA's
340    
341            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
342    
343            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
344                    which is implemented.
345    
346    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * src/chm_common.c: coerce logical <-> double instead of
349            typecasting;  needed for "l" matrix handling in cholmod.
350    
351            * tests/other-pkgs.R (graph): small extension in "graph" checks.
352    
353            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
354            (Tsp2grNEL): other fixes needed
355    
356    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
359                    Matrices, since "lMatrix", also "lsparseM" can have NA
360            * R/ndenseMatrix.R, etc: new source files
361            * man/nsparseMatrix-classes.Rd, etc: new help files
362            * tests/: adaptions
363            * src/chm_common.c (chm_dense_to_SEXP): and others:
364                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
365            * src/Csparse.c, etc: ditto
366    
367    2006-09-11  Douglas Bates  <bates@R-project.org>
368    
369            * src/Mutils.[ch],init.c inst/include/*.h: Move the
370            alloc_d**Matrix functions to the lme4 package.
371    
372    2006-09-09  Douglas Bates  <bates@R-project.org>
373    
374            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
375            fixed
376    
377    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/lMatrix.R: new
380    
381            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
382    
383            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
384            * man/tcrossprod.Rd: ditto
385    
386    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
389            for exported functions
390            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
391            Remove partitioning algorithms for sparse matrix reordering.  The
392            copyright on the Metis code was problematic and the methods were
393            rarely used.
394            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
395            operations are now done entirely in CHOLMOD code.
396    
397    2006-09-06  Douglas Bates  <bates@R-project.org>
398    
399            * src/Mutils.h: Remove functions that are no longer used.
400    
401    2006-09-04  Douglas Bates  <bates@R-project.org>
402    
403            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
404            * src/DEPS.mkf: update
405    
406    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * created branches/Matrix-for-R-2.3.x;  on trunk: do
409            * DESCRIPTION (Version): 0.9975-0
410            (Depends): R (>= 2.4.0)
411    
412    2006-09-01  Douglas Bates  <bates@R-project.org>
413    
414            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
415    
416    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
419            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
420    
421            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
422    
423    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
426            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
427            * R/dsparseMatrix.R: ditto
428            * R/Csparse.R: ditto
429    
430    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/dMatrix.R (Compare): improve availability of "<", etc
433            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
434    
435    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
438            of a 0-index which was used as 1-index (..hmm)
439    
440            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
441    
442            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
443            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
444            (.is.diagonal): ditto
445    
446            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
447    
448            * R/Matrix.R (Matrix): also work for NA data
449    
450    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
453            in all cases.
454    
455    2006-08-27  Douglas Bates  <bates@R-project.org>
456    
457            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
458            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
459    
460    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
463            subclasses of "ddenseMatrix"
464            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
465            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
466            instead of half dozen specialized ones.
467    
468    2006-08-25  Douglas Bates  <bates@R-project.org>
469    
470            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
471            <tillard@cirad.fr> - ordering standard errors to match effects.
472    
473    2006-08-24  Douglas Bates  <bates@R-project.org>
474    
475            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
476            on R_ldl.
477            * R/lCholCMatrix.R,
478            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
479            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
480            * many files in ./R and ./src: Use more general version of
481            dup_mMatrix_as_dgeMatrix to simplify method definitions.
482            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
483            dtpMatrix, dspMatrix and dppMatrix conversions.
484    
485    
486    2006-08-23  Douglas Bates  <bates@R-project.org>
487    
488            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
489            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
490            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
491            dgeMatrix_crossprod (may need to do this in other places).
492            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
493            generic and method for dsCMatrix.  Use CHOLMOD for chol().
494    
495    2006-08-22  Douglas Bates  <bates@R-project.org>
496    
497            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
498            types of classed Matrices, matrices or numeric or logical vectors.
499            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
500            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
501            to Mutils.h (as an inline) and change name to Matrix_check_class;
502            fixes in as_cholmod_factor and chm_factor_to_SEXP.
503            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
504            dsCMatrix_matrix_solve.  Comment out vestigial functions.
505            * src/Csparse.c: use diag_P and uplo_P macros.
506    
507    2006-08-21  Douglas Bates  <bates@R-project.org>
508    
509            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
510            valgrind.
511            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
512            inverses.
513            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
514            -Wall warnings.
515            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
516            Use dup_mMatrix_as_dgeMatrix.
517    
518    2006-08-20  Douglas Bates  <bates@R-project.org>
519    
520            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
521            * tests/sparseQR.R: Added
522            * man/sparseQR-class.Rd: Document methods for qr.* generics
523            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
524    
525    2006-08-19  Douglas Bates  <bates@R-project.org>
526    
527            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
528            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
529            and qr.fitted.
530            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
531            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
532    
533    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
536            the base version has no "..." argument.
537    
538            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
539    
540            * R/Matrix.R: define and
541            * NAMESPACE: export as.numeric() and as.logical() methods.
542                    Let's hope these do not badly slow down something...
543            Finally export the zapsmall() method.
544    
545    2006-08-17  Douglas Bates  <bates@R-project.org>
546    
547            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
548            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
549            * src/dtCMatrix.c :Remove code that is no longer used
550            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
551    
552    2006-08-14  Douglas Bates  <bates@R-project.org>
553    
554            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
555            Csparse_to_logical and Csparse_symmetric_to_general.
556            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
557            coercion methods between CsparseMatrix and TsparseMatrix.
558    
559    2006-08-14  Douglas Bates  <bates@R-project.org>
560    
561            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
562            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
563            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
564            possible.
565    
566    2006-08-12  Douglas Bates  <bates@R-project.org>
567    
568            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
569              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
570              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
571              generalize conversions between TsparseMatrix, CsparseMatrix,
572              denseMatrix and matrix.  Preserve triangularity property and
573              propagate Dimnames in the easy cases.
574    
575    2006-08-10  Douglas Bates  <bates@R-project.org>
576    
577            * src/lmer.c: adjust checks in glmer_init for S4SXP
578            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
579            before S4SXP but for the wrong reasons.
580    
581    2006-08-08  Douglas Bates  <bates@R-project.org>
582    
583            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
584            Later modified to return the upper triangle only.
585            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
586    
587    2006-08-07  Douglas Bates  <bates@R-project.org>
588    
589            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
590            R-level conversion to a sparse symmetric class.
591            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
592            Remove conversion to sparse symmetric classes (now done in C code).
593    
594    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
597            * man/band.Rd:  adapt the \dontshow{} unit test.
598    
599    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Version): 0.995-14  for CRAN
602    
603            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
604    
605            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
606            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
607    
608            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
609            * R/Tsparse.R (tril, triu, band): methods
610            * R/dgRMatrix.R (tril, ...):    ditto
611            * man/band.Rd:                  ditto
612    
613    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Matrix.R (head, tail): directly use utils:::head.matrix
616                    to be up-to-date automatically.
617    
618    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
621    
622            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
623            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
624            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
625            such that the S4 objects are always created by the current version
626            of R and 'Matrix' class definitions.
627    
628    2006-08-01  Douglas Bates  <bates@R-project.org>
629    
630            * R/lmer.R (LMEoptimize method), tests/lmer.R,
631            inst/external/test3comp.rda: Added warnings for convergence on
632            boundary and test cases.
633    
634            * src/lmer.c (mer_postVar): Modified to return the variances that
635            are marginal to the fixed effects, not conditional on them (which
636            is what the bVar slot contents represent).
637    
638    2006-07-31  Douglas Bates  <bates@R-project.org>
639    
640            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
641            function which calls the C function mer_hat_trace2.
642    
643            * man/ranef.Rd: Include description of "postVar" argument and
644            producing a caterpillar plot.
645    
646    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * NAMESPACE:    change  "correlation" to "corMatrix"
649            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
650            * R/dpoMatrix.R: ditto
651            * R/lmer.R:      ditto
652    
653    2006-07-28  Douglas Bates  <bates@R-project.org>
654    
655            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
656            RZXinv slot's contents into a separate internal function that can
657            be used in mer_hat_trace.
658    
659    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
662            via new smart
663            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
664            utility functions.
665    
666    
667    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/Csparse.R (tril, triu, band): do return *triangular* classed
670            matrices when appropriate; band() even symmetric ones.
671            (replCmat): extend to potentially all "CsparseMatrix"
672            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
673            allow subassignment for special sparse matrices.
674    
675            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
676    
677            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
678            argument; in glmer_*(): print only if(verbose).
679    
680            speed-optimize a few places by moving REAL(.) out of loops.
681    
682            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
683    
684    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
687                    since that wrongly triggers also for M[ logi , ]
688    
689            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
690            a symmetric matrix that results in a non-symmetric one.
691            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
692    
693            * R/dMatrix.R: make round(M) work as round(M, 0)
694    
695            * R/dgTMatrix.R (image): coordinate system and axis now use
696            1-based indices, not 0-based ones.
697    
698            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
699            * tests/indexing.R: test it.
700    
701            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
702            * man/isSymmetric-methods.Rd: and document it.
703    
704            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
705            * man/SparseM-conv.Rd: docu them
706    
707            * tests/other-pkgs.R: renamed from tests/graph.R and add example
708                    for 'SparseM' conversions
709    
710    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
711    
712            * R/Matrix.R (head): added head() and tail() methods.
713    
714    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * DESCRIPTION (Version): 0.995-12 released to CRAN
717    
718    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * tests/simple.R: add check for correct dsT -> dgT coercion;
721                    add check for correct printing of symmetric sparse matrices.
722    
723            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
724            for sparse symmetric matrices.
725    
726            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
727            diagonal twice.
728    
729    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
730    
731            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
732            being applied to the x slot (detected by Brian Ripley).
733    
734    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
737    
738            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
739    
740    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * src/lgCMatrix.c (lgCMatrix_diag): new function
743            * R/lgCMatrix.R (diag): for new method
744    
745            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
746                 ==> construction of illegal "*gTMatrix" via new() should
747                 now be much less easy:
748            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
749    
750            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
751                    directly.
752            * man/Matrix.Rd: documents it.
753    
754    2006-07-06  Douglas Bates  <bates@R-project.org>
755    
756            * src/pedigree.c (pedigree_inbreeding): Correction in
757            initialization.  This function is not currently being used and is
758            not fully tested.
759    
760            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
761            Introduced the glmer class.  Added code for mcmcmsamp on glmer
762            objects.  Modified validity check on pedigree objects to account
763            for nonparallel patterns of missingness of parents.
764    
765            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
766            class.
767    
768    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/pMatrix.R: coercion pMatrix -> Tsparse
771    
772    2006-06-12  Douglas Bates  <bates@R-project.org>
773    
774            * DESCRIPTION (Version): 0.995-11 released to CRAN
775    
776            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
777            the output from mcmcsamp.
778    
779    2006-06-10  Douglas Bates  <bates@R-project.org>
780    
781            * R/lmer.R (simulestimate): added C code for calculating the trace
782            of the hat matrix.
783    
784    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
787            classes.
788            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
789    
790    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/dgTMatrix.R (colSums): etc. All four of
793            colSums(), rowSums(), colMeans(), rowMeans() now should work for
794            all "Matrices".
795    
796    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
797    
798            * R/lmer.R (panel.ci): Add a reference line at zero and a
799            background grid to the qqmath plot of ranef.lmer.
800    
801    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
802    
803            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
804            grouping factors to be specified in the formula as (1|foo/bar).
805    
806    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * R/lmer.R (findbars and others): Change check of is.numeric to
809            !is.language to resolve the bug reported by Jacob Wegelin.
810    
811            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
812            code to evaluate inbreeding coefficients without calculating T,
813            based on code in Sargolzaei and Iwaisaki's paper.
814    
815    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
816    
817            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
818            generic and mer methods for isNested and denomDF. This denomDF was
819            an attempt to emulate that in lme but I don't think that makes
820            sense.  Use the trace of the hat matrix instead.
821    
822  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
825          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.
826          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
827    
828    
829  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 946 
946          * 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)
947          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
948          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
949          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
950    
951  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
# Line 329  Line 1150 
1150  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1153          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1154          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1155    
1156  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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