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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1674, Tue Nov 7 13:29:23 2006 UTC
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1    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): updated -> release 0.9975-6
4    
5    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
8            now returns symmetric.
9    
10            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
11    
12            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
13            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
14    
15            * R/Auxiliaries.R (.type.kind): added
16    
17    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
20            running src/CSparse_install.sh
21    
22            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
23    
24    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
27            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
28    
29            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
30    
31            * tests/Class+Meth.R (tstMatrixClass): now assure
32            the (important in method programming) property :
33    
34                    ###>>  Every "Matrix" is either
35                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
36    
37                    (where "*" stands for "Matrix")
38    
39            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
40    
41            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
42            * tests/validObj.R: checks for "comparison"
43    
44            * R/sparseMatrix.R ([): improved indexing for sparse;
45                    trying to keep <symmetric>[ n, n] symmmetric
46    
47            * tests/indexing.R: indexing for logical sparse now ok
48    
49    
50    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * src/Tsparse.c: use xTsparse_validate() , and hence remove
53    
54            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
55    
56    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
59    
60            * tests/simple.R: validObject() checking the above.
61    
62            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
63            replacing both dgCMatrix_validate and lgCM*.
64    
65            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
66            fix dimnames setting in other places.
67            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
68    
69    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
72    
73            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
74            symmetry test, via
75            * R/Auxiliaries.R (.as.dgC.0.factors):
76    
77    2006-11-01  Douglas Bates  <bates@r-project.org>
78    
79            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
80            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
81            <CsparseMatrix>) added
82    
83    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * tests/matprod.R: add a variation of Harri's example
86    
87            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
88            recursive infinitely.
89    
90            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
91    
92            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
93    
94    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
97            matrix if possible; test m+m == 2*m; now test dgRMatrix.
98            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
99            satisfy the above test.
100    
101    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
104    
105            * R/dgCMatrix.R: solve(a, b="missing") based on
106            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
107            RHS = NULL.
108    
109            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
110            add more (needed) [t]crossprod() methods.
111    
112            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
113    
114            * R/Auxiliaries.R (as_CspClass): cleanup
115            (drop0): internal utility for "Csparse_drop(*, 0)"
116            (.bail.out.2): encourage active feedback
117    
118    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/dMatrix.R(Compare): new(), then slots [no validity check]
121    
122            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
123            non-valid or 'sorted' case).
124    
125            * R/dsparseMatrix.R: add "chol" method.
126            * R/ddenseMatrix.R: ditto
127    
128            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
129            * NAMESPACE (Ops)
130            * R/diagMatrix.R (diag2T): simple utility used "higher level"
131            coercion; deprecating direct lower level coercions.
132    
133            * R/*.R (seq): use seq_len() and seq_along() where possible.
134    
135    
136    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * DESCRIPTION (Version): 0.9975-5 ready for release
139    
140    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
143    
144    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/AllClass.R (corMatrix): add 'validity' check;
147                    comment out unused "LDL" class definition
148            * NAMESPACE: mention, but do not export "LDL" class
149            * R/corMatrix.R: new (simple), needed for R-devel with
150            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
151              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
152    
153    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
156            use Rprintf and R's error handling.
157    
158    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
161            * tests/matprod.R: add tests for the bug fixed.
162    
163    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
166            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
167    
168    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
171    
172    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.9975-3
175    
176            * R/diagMatrix.R (bdiag): new function constructing block diagonal
177            (sparse) matrices.
178            * man/bdiag.Rd: docu + examples
179    
180            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
181    
182            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
183            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
184    
185            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
186            that result is sparse or diagonal (and not dense).
187    
188            * man/Subassign-methods.Rd: fix examples
189    
190            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
191            should always return a sparse (and not sometimes a diagonal) matrix.
192    
193    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
196    
197    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
198    
199            * DESCRIPTION (Version): 0.9975-2
200    
201            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
202    
203    2006-10-02  Douglas Bates  <bates@R-project.org>
204    
205            * tests/dg_Matrix.R: Simplify test taking into account new code.
206    
207    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
210    
211            * R/lsTMatrix.R: new files w/ missing methods
212            * R/nsTMatrix.R:  "  'for completeness'
213    
214            * tests/Class+Meth.R: a bit less 'not.ok.classes'
215    
216            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
217    
218    
219    2006-09-28  Douglas Bates  <bates@R-project.org>
220    
221            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
222            included.
223    
224            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
225            Export C-callable functions used in Zt_create in lme4.
226    
227    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * DESCRIPTION (Version): 0.9975-1
230    
231            * tests/simple.R: less checks fail; using NA, found that our
232                    kronecker() is not base-compatible with NA's.
233    
234            * R/dMatrix.R: "Compare" method now implemented for all cases
235    
236            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
237    
238            * man/dtpMatrix-class.Rd: mention length of 'x' slot
239    
240            * src/dtpMatrix.c (dtpMatrix_validate): fix check
241            * src/dspMatrix.c (dspMatrix_validate): ditto
242    
243            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
244              including coercion to [nl]tTMatrix.
245    
246            * R/diagMatrix.R (show): print a header line as for other classes.
247    
248    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * src/Makefile.win (SUBDIRS): fix typo
251    
252    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
255    
256    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
257    
258            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
259            symmetric and y missing in R code using %*% (cholmod_aat doesn't
260            accept a symmetric matrix).
261            * tests/group-methods.R: Uncomment test of crossprod applied to
262            lsCMatrix objects.
263    
264    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/AllClass.R (symmetricMatrix): add validity method (available
267            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
268    
269            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
270    
271            * tests/indexing.Rout.save:
272            * tests/indexing.R: additions, mainly for 'lsparse'
273    
274            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
275            case.
276    
277            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
278    
279    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
282                    as 'N' (1-letter - Ok?)
283    
284            * tests/group-methods.R: add test for logical + NAs
285    
286            * R/dMatrix.R ("Compare"): fix to work with NA's
287    
288            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
289    
290            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
291                    which is implemented.
292    
293    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * src/chm_common.c: coerce logical <-> double instead of
296            typecasting;  needed for "l" matrix handling in cholmod.
297    
298            * tests/other-pkgs.R (graph): small extension in "graph" checks.
299    
300            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
301            (Tsp2grNEL): other fixes needed
302    
303    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
306                    Matrices, since "lMatrix", also "lsparseM" can have NA
307            * R/ndenseMatrix.R, etc: new source files
308            * man/nsparseMatrix-classes.Rd, etc: new help files
309            * tests/: adaptions
310            * src/chm_common.c (chm_dense_to_SEXP): and others:
311                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
312            * src/Csparse.c, etc: ditto
313    
314    2006-09-11  Douglas Bates  <bates@R-project.org>
315    
316            * src/Mutils.[ch],init.c inst/include/*.h: Move the
317            alloc_d**Matrix functions to the lme4 package.
318    
319    2006-09-09  Douglas Bates  <bates@R-project.org>
320    
321            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
322            fixed
323    
324    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/lMatrix.R: new
327    
328            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
329    
330            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
331            * man/tcrossprod.Rd: ditto
332    
333    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
334    
335            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
336            for exported functions
337            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
338            Remove partitioning algorithms for sparse matrix reordering.  The
339            copyright on the Metis code was problematic and the methods were
340            rarely used.
341            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
342            operations are now done entirely in CHOLMOD code.
343    
344    2006-09-06  Douglas Bates  <bates@R-project.org>
345    
346            * src/Mutils.h: Remove functions that are no longer used.
347    
348    2006-09-04  Douglas Bates  <bates@R-project.org>
349    
350            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
351            * src/DEPS.mkf: update
352    
353    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * created branches/Matrix-for-R-2.3.x;  on trunk: do
356            * DESCRIPTION (Version): 0.9975-0
357            (Depends): R (>= 2.4.0)
358    
359    2006-09-01  Douglas Bates  <bates@R-project.org>
360    
361            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
362    
363    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
366            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
367    
368            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
369    
370    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
373            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
374            * R/dsparseMatrix.R: ditto
375            * R/Csparse.R: ditto
376    
377    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dMatrix.R (Compare): improve availability of "<", etc
380            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
381    
382    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
385            of a 0-index which was used as 1-index (..hmm)
386    
387            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
388    
389            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
390            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
391            (.is.diagonal): ditto
392    
393            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
394    
395            * R/Matrix.R (Matrix): also work for NA data
396    
397    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
400            in all cases.
401    
402    2006-08-27  Douglas Bates  <bates@R-project.org>
403    
404            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
405            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
406    
407    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
410            subclasses of "ddenseMatrix"
411            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
412            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
413            instead of half dozen specialized ones.
414    
415    2006-08-25  Douglas Bates  <bates@R-project.org>
416    
417            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
418            <tillard@cirad.fr> - ordering standard errors to match effects.
419    
420    2006-08-24  Douglas Bates  <bates@R-project.org>
421    
422            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
423            on R_ldl.
424            * R/lCholCMatrix.R,
425            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
426            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
427            * many files in ./R and ./src: Use more general version of
428            dup_mMatrix_as_dgeMatrix to simplify method definitions.
429            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
430            dtpMatrix, dspMatrix and dppMatrix conversions.
431    
432    
433    2006-08-23  Douglas Bates  <bates@R-project.org>
434    
435            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
436            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
437            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
438            dgeMatrix_crossprod (may need to do this in other places).
439            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
440            generic and method for dsCMatrix.  Use CHOLMOD for chol().
441    
442    2006-08-22  Douglas Bates  <bates@R-project.org>
443    
444            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
445            types of classed Matrices, matrices or numeric or logical vectors.
446            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
447            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
448            to Mutils.h (as an inline) and change name to Matrix_check_class;
449            fixes in as_cholmod_factor and chm_factor_to_SEXP.
450            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
451            dsCMatrix_matrix_solve.  Comment out vestigial functions.
452            * src/Csparse.c: use diag_P and uplo_P macros.
453    
454    2006-08-21  Douglas Bates  <bates@R-project.org>
455    
456            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
457            valgrind.
458            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
459            inverses.
460            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
461            -Wall warnings.
462            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
463            Use dup_mMatrix_as_dgeMatrix.
464    
465    2006-08-20  Douglas Bates  <bates@R-project.org>
466    
467            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
468            * tests/sparseQR.R: Added
469            * man/sparseQR-class.Rd: Document methods for qr.* generics
470            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
471    
472    2006-08-19  Douglas Bates  <bates@R-project.org>
473    
474            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
475            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
476            and qr.fitted.
477            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
478            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
479    
480    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
483            the base version has no "..." argument.
484    
485            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
486    
487            * R/Matrix.R: define and
488            * NAMESPACE: export as.numeric() and as.logical() methods.
489                    Let's hope these do not badly slow down something...
490            Finally export the zapsmall() method.
491    
492    2006-08-17  Douglas Bates  <bates@R-project.org>
493    
494            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
495            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
496            * src/dtCMatrix.c :Remove code that is no longer used
497            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
498    
499    2006-08-14  Douglas Bates  <bates@R-project.org>
500    
501            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
502            Csparse_to_logical and Csparse_symmetric_to_general.
503            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
504            coercion methods between CsparseMatrix and TsparseMatrix.
505    
506    2006-08-14  Douglas Bates  <bates@R-project.org>
507    
508            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
509            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
510            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
511            possible.
512    
513    2006-08-12  Douglas Bates  <bates@R-project.org>
514    
515            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
516              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
517              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
518              generalize conversions between TsparseMatrix, CsparseMatrix,
519              denseMatrix and matrix.  Preserve triangularity property and
520              propagate Dimnames in the easy cases.
521    
522    2006-08-10  Douglas Bates  <bates@R-project.org>
523    
524            * src/lmer.c: adjust checks in glmer_init for S4SXP
525            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
526            before S4SXP but for the wrong reasons.
527    
528    2006-08-08  Douglas Bates  <bates@R-project.org>
529    
530            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
531            Later modified to return the upper triangle only.
532            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
533    
534    2006-08-07  Douglas Bates  <bates@R-project.org>
535    
536            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
537            R-level conversion to a sparse symmetric class.
538            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
539            Remove conversion to sparse symmetric classes (now done in C code).
540    
541    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
544            * man/band.Rd:  adapt the \dontshow{} unit test.
545    
546    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * DESCRIPTION (Version): 0.995-14  for CRAN
549    
550            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
551    
552            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
553            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
554    
555            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
556            * R/Tsparse.R (tril, triu, band): methods
557            * R/dgRMatrix.R (tril, ...):    ditto
558            * man/band.Rd:                  ditto
559    
560    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/Matrix.R (head, tail): directly use utils:::head.matrix
563                    to be up-to-date automatically.
564    
565    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
568    
569            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
570            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
571            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
572            such that the S4 objects are always created by the current version
573            of R and 'Matrix' class definitions.
574    
575    2006-08-01  Douglas Bates  <bates@R-project.org>
576    
577            * R/lmer.R (LMEoptimize method), tests/lmer.R,
578            inst/external/test3comp.rda: Added warnings for convergence on
579            boundary and test cases.
580    
581            * src/lmer.c (mer_postVar): Modified to return the variances that
582            are marginal to the fixed effects, not conditional on them (which
583            is what the bVar slot contents represent).
584    
585    2006-07-31  Douglas Bates  <bates@R-project.org>
586    
587            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
588            function which calls the C function mer_hat_trace2.
589    
590            * man/ranef.Rd: Include description of "postVar" argument and
591            producing a caterpillar plot.
592    
593    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * NAMESPACE:    change  "correlation" to "corMatrix"
596            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
597            * R/dpoMatrix.R: ditto
598            * R/lmer.R:      ditto
599    
600    2006-07-28  Douglas Bates  <bates@R-project.org>
601    
602            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
603            RZXinv slot's contents into a separate internal function that can
604            be used in mer_hat_trace.
605    
606    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
609            via new smart
610            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
611            utility functions.
612    
613    
614    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Csparse.R (tril, triu, band): do return *triangular* classed
617            matrices when appropriate; band() even symmetric ones.
618            (replCmat): extend to potentially all "CsparseMatrix"
619            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
620            allow subassignment for special sparse matrices.
621    
622            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
623    
624            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
625            argument; in glmer_*(): print only if(verbose).
626    
627            speed-optimize a few places by moving REAL(.) out of loops.
628    
629            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
630    
631    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
634                    since that wrongly triggers also for M[ logi , ]
635    
636            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
637            a symmetric matrix that results in a non-symmetric one.
638            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
639    
640            * R/dMatrix.R: make round(M) work as round(M, 0)
641    
642            * R/dgTMatrix.R (image): coordinate system and axis now use
643            1-based indices, not 0-based ones.
644    
645            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
646            * tests/indexing.R: test it.
647    
648            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
649            * man/isSymmetric-methods.Rd: and document it.
650    
651            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
652            * man/SparseM-conv.Rd: docu them
653    
654            * tests/other-pkgs.R: renamed from tests/graph.R and add example
655                    for 'SparseM' conversions
656    
657    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
658    
659            * R/Matrix.R (head): added head() and tail() methods.
660    
661    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * DESCRIPTION (Version): 0.995-12 released to CRAN
664    
665    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * tests/simple.R: add check for correct dsT -> dgT coercion;
668                    add check for correct printing of symmetric sparse matrices.
669    
670            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
671            for sparse symmetric matrices.
672    
673            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
674            diagonal twice.
675    
676    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
677    
678            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
679            being applied to the x slot (detected by Brian Ripley).
680    
681    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
684    
685            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
686    
687    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * src/lgCMatrix.c (lgCMatrix_diag): new function
690            * R/lgCMatrix.R (diag): for new method
691    
692            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
693                 ==> construction of illegal "*gTMatrix" via new() should
694                 now be much less easy:
695            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
696    
697            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
698                    directly.
699            * man/Matrix.Rd: documents it.
700    
701    2006-07-06  Douglas Bates  <bates@R-project.org>
702    
703            * src/pedigree.c (pedigree_inbreeding): Correction in
704            initialization.  This function is not currently being used and is
705            not fully tested.
706    
707            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
708            Introduced the glmer class.  Added code for mcmcmsamp on glmer
709            objects.  Modified validity check on pedigree objects to account
710            for nonparallel patterns of missingness of parents.
711    
712            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
713            class.
714    
715    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/pMatrix.R: coercion pMatrix -> Tsparse
718    
719    2006-06-12  Douglas Bates  <bates@R-project.org>
720    
721            * DESCRIPTION (Version): 0.995-11 released to CRAN
722    
723            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
724            the output from mcmcsamp.
725    
726    2006-06-10  Douglas Bates  <bates@R-project.org>
727    
728            * R/lmer.R (simulestimate): added C code for calculating the trace
729            of the hat matrix.
730    
731    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
734            classes.
735            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
736    
737    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/dgTMatrix.R (colSums): etc. All four of
740            colSums(), rowSums(), colMeans(), rowMeans() now should work for
741            all "Matrices".
742    
743    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * R/lmer.R (panel.ci): Add a reference line at zero and a
746            background grid to the qqmath plot of ranef.lmer.
747    
748    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
749    
750            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
751            grouping factors to be specified in the formula as (1|foo/bar).
752    
753    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * R/lmer.R (findbars and others): Change check of is.numeric to
756            !is.language to resolve the bug reported by Jacob Wegelin.
757    
758            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
759            code to evaluate inbreeding coefficients without calculating T,
760            based on code in Sargolzaei and Iwaisaki's paper.
761    
762    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
763    
764            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
765            generic and mer methods for isNested and denomDF. This denomDF was
766            an attempt to emulate that in lme but I don't think that makes
767            sense.  Use the trace of the hat matrix instead.
768    
769  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
772          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.
773          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
774    
775    
776  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 893 
893          * 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)
894          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
895          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
896          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
897    
898  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
# Line 329  Line 1097 
1097  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1100          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1101          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1102    
1103  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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