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[matrix] Diff of /pkg/ChangeLog
 [matrix] / pkg / ChangeLog

Diff of /pkg/ChangeLog

revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1657, Wed Nov 1 16:29:53 2006 UTC
# Line 1  Line 1
1    2006-11-01  Douglas Bates  <bates@r-project.org>
2
3            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
4            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
6
7    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
8
9            * tests/matprod.R: add a variation of Harri's example
10
11            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
12            recursive infinitely.
13
14            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
15
16            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
17
18    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
19
20            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
21            matrix if possible; test m+m == 2*m; now test dgRMatrix.
22            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
23            satisfy the above test.
24
25    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
26
27            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
28
29            * R/dgCMatrix.R: solve(a, b="missing") based on
30            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
31            RHS = NULL.
32
33            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
34            add more (needed) [t]crossprod() methods.
35
37
38            * R/Auxiliaries.R (as_CspClass): cleanup
39            (drop0): internal utility for "Csparse_drop(*, 0)"
40            (.bail.out.2): encourage active feedback
41
42    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
43
44            * R/dMatrix.R(Compare): new(), then slots [no validity check]
45
46            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
47            non-valid or 'sorted' case).
48
49            * R/dsparseMatrix.R: add "chol" method.
50            * R/ddenseMatrix.R: ditto
51
52            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
53            * NAMESPACE (Ops)
54            * R/diagMatrix.R (diag2T): simple utility used "higher level"
55            coercion; deprecating direct lower level coercions.
56
57            * R/*.R (seq): use seq_len() and seq_along() where possible.
58
59
60    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
61
62            * DESCRIPTION (Version): 0.9975-5 ready for release
63
64    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
65
66            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
67
68    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
69
70            * R/AllClass.R (corMatrix): add 'validity' check;
71                    comment out unused "LDL" class definition
72            * NAMESPACE: mention, but do not export "LDL" class
73            * R/corMatrix.R: new (simple), needed for R-devel with
74            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
75              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
76
77    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
78
79            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
80            use Rprintf and R's error handling.
81
82    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
83
84            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
85            * tests/matprod.R: add tests for the bug fixed.
86
87    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
88
89            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
90            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
91
92    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
93
94            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
95
96    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97
98            * DESCRIPTION (Version): 0.9975-3
99
100            * R/diagMatrix.R (bdiag): new function constructing block diagonal
101            (sparse) matrices.
102            * man/bdiag.Rd: docu + examples
103
104            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
105
106            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
107            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
108
109            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
110            that result is sparse or diagonal (and not dense).
111
112            * man/Subassign-methods.Rd: fix examples
113
114            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
115            should always return a sparse (and not sometimes a diagonal) matrix.
116
117    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118
119            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
120
121    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
122
123            * DESCRIPTION (Version): 0.9975-2
124
125            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
126
127    2006-10-02  Douglas Bates  <bates@R-project.org>
128
129            * tests/dg_Matrix.R: Simplify test taking into account new code.
130
131    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
132
133            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
134
135            * R/lsTMatrix.R: new files w/ missing methods
136            * R/nsTMatrix.R:  "  'for completeness'
137
138            * tests/Class+Meth.R: a bit less 'not.ok.classes'
139
140            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
141
142
143    2006-09-28  Douglas Bates  <bates@R-project.org>
144
145            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
146            included.
147
148            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
149            Export C-callable functions used in Zt_create in lme4.
150
151    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
152
153            * DESCRIPTION (Version): 0.9975-1
154
155            * tests/simple.R: less checks fail; using NA, found that our
156                    kronecker() is not base-compatible with NA's.
157
158            * R/dMatrix.R: "Compare" method now implemented for all cases
159
160            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
161
162            * man/dtpMatrix-class.Rd: mention length of 'x' slot
163
164            * src/dtpMatrix.c (dtpMatrix_validate): fix check
165            * src/dspMatrix.c (dspMatrix_validate): ditto
166
167            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
168              including coercion to [nl]tTMatrix.
169
170            * R/diagMatrix.R (show): print a header line as for other classes.
171
172    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
173
174            * src/Makefile.win (SUBDIRS): fix typo
175
176    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
177
178            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
179
180    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
181
182            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
183            symmetric and y missing in R code using %*% (cholmod_aat doesn't
184            accept a symmetric matrix).
185            * tests/group-methods.R: Uncomment test of crossprod applied to
186            lsCMatrix objects.
187
188    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
189
190            * R/AllClass.R (symmetricMatrix): add validity method (available
191            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
192
193            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
194
195            * tests/indexing.Rout.save:
196            * tests/indexing.R: additions, mainly for 'lsparse'
197
198            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
199            case.
200
201            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
202
203    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
204
205            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
206                    as 'N' (1-letter - Ok?)
207
208            * tests/group-methods.R: add test for logical + NAs
209
210            * R/dMatrix.R ("Compare"): fix to work with NA's
211
212            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
213
214            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
215                    which is implemented.
216
217    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218
219            * src/chm_common.c: coerce logical <-> double instead of
220            typecasting;  needed for "l" matrix handling in cholmod.
221
222            * tests/other-pkgs.R (graph): small extension in "graph" checks.
223
224            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
225            (Tsp2grNEL): other fixes needed
226
227    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
228
229            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
230                    Matrices, since "lMatrix", also "lsparseM" can have NA
231            * R/ndenseMatrix.R, etc: new source files
232            * man/nsparseMatrix-classes.Rd, etc: new help files
234            * src/chm_common.c (chm_dense_to_SEXP): and others:
235                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
236            * src/Csparse.c, etc: ditto
237
238    2006-09-11  Douglas Bates  <bates@R-project.org>
239
240            * src/Mutils.[ch],init.c inst/include/*.h: Move the
241            alloc_d**Matrix functions to the lme4 package.
242
243    2006-09-09  Douglas Bates  <bates@R-project.org>
244
245            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
246            fixed
247
248    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
249
250            * R/lMatrix.R: new
251
252            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
253
254            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
255            * man/tcrossprod.Rd: ditto
256
257    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
258
259            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
260            for exported functions
261            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
262            Remove partitioning algorithms for sparse matrix reordering.  The
263            copyright on the Metis code was problematic and the methods were
264            rarely used.
265            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
266            operations are now done entirely in CHOLMOD code.
267
268    2006-09-06  Douglas Bates  <bates@R-project.org>
269
270            * src/Mutils.h: Remove functions that are no longer used.
271
272    2006-09-04  Douglas Bates  <bates@R-project.org>
273
274            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
275            * src/DEPS.mkf: update
276
277    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
278
279            * created branches/Matrix-for-R-2.3.x;  on trunk: do
280            * DESCRIPTION (Version): 0.9975-0
281            (Depends): R (>= 2.4.0)
282
283    2006-09-01  Douglas Bates  <bates@R-project.org>
284
285            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
286
287    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
288
289            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
290            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
291
292            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
293
294    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
295
296            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
297            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
298            * R/dsparseMatrix.R: ditto
299            * R/Csparse.R: ditto
300
301    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
302
303            * R/dMatrix.R (Compare): improve availability of "<", etc
304            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
305
306    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
307
308            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
309            of a 0-index which was used as 1-index (..hmm)
310
311            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
312
313            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
314            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
315            (.is.diagonal): ditto
316
317            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
318
319            * R/Matrix.R (Matrix): also work for NA data
320
321    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
322
323            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
324            in all cases.
325
326    2006-08-27  Douglas Bates  <bates@R-project.org>
327
328            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
329            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
330
331    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
332
333            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
334            subclasses of "ddenseMatrix"
335            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
336            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
337            instead of half dozen specialized ones.
338
339    2006-08-25  Douglas Bates  <bates@R-project.org>
340
341            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
342            <tillard@cirad.fr> - ordering standard errors to match effects.
343
344    2006-08-24  Douglas Bates  <bates@R-project.org>
345
346            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
347            on R_ldl.
348            * R/lCholCMatrix.R,
349            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
350            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
351            * many files in ./R and ./src: Use more general version of
352            dup_mMatrix_as_dgeMatrix to simplify method definitions.
353            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
354            dtpMatrix, dspMatrix and dppMatrix conversions.
355
356
357    2006-08-23  Douglas Bates  <bates@R-project.org>
358
359            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
360            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
361            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
362            dgeMatrix_crossprod (may need to do this in other places).
363            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
364            generic and method for dsCMatrix.  Use CHOLMOD for chol().
365
366    2006-08-22  Douglas Bates  <bates@R-project.org>
367
368            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
369            types of classed Matrices, matrices or numeric or logical vectors.
370            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
371            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
372            to Mutils.h (as an inline) and change name to Matrix_check_class;
373            fixes in as_cholmod_factor and chm_factor_to_SEXP.
374            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
375            dsCMatrix_matrix_solve.  Comment out vestigial functions.
376            * src/Csparse.c: use diag_P and uplo_P macros.
377
378    2006-08-21  Douglas Bates  <bates@R-project.org>
379
380            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
381            valgrind.
382            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
383            inverses.
384            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
385            -Wall warnings.
386            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
387            Use dup_mMatrix_as_dgeMatrix.
388
389    2006-08-20  Douglas Bates  <bates@R-project.org>
390
391            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
393            * man/sparseQR-class.Rd: Document methods for qr.* generics
394            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
395
396    2006-08-19  Douglas Bates  <bates@R-project.org>
397
398            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
399            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
400            and qr.fitted.
401            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
402            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
403
404    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
405
406            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
407            the base version has no "..." argument.
408
409            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
410
411            * R/Matrix.R: define and
412            * NAMESPACE: export as.numeric() and as.logical() methods.
413                    Let's hope these do not badly slow down something...
414            Finally export the zapsmall() method.
415
416    2006-08-17  Douglas Bates  <bates@R-project.org>
417
418            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
419            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
420            * src/dtCMatrix.c :Remove code that is no longer used
421            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
422
423    2006-08-14  Douglas Bates  <bates@R-project.org>
424
425            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
426            Csparse_to_logical and Csparse_symmetric_to_general.
427            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
428            coercion methods between CsparseMatrix and TsparseMatrix.
429
430    2006-08-14  Douglas Bates  <bates@R-project.org>
431
432            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
433            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
434            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
435            possible.
436
437    2006-08-12  Douglas Bates  <bates@R-project.org>
438
439            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
440              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
441              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
442              generalize conversions between TsparseMatrix, CsparseMatrix,
443              denseMatrix and matrix.  Preserve triangularity property and
444              propagate Dimnames in the easy cases.
445
446    2006-08-10  Douglas Bates  <bates@R-project.org>
447
448            * src/lmer.c: adjust checks in glmer_init for S4SXP
449            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
450            before S4SXP but for the wrong reasons.
451
452    2006-08-08  Douglas Bates  <bates@R-project.org>
453
454            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
455            Later modified to return the upper triangle only.
456            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
457
458    2006-08-07  Douglas Bates  <bates@R-project.org>
459
460            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
461            R-level conversion to a sparse symmetric class.
462            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
463            Remove conversion to sparse symmetric classes (now done in C code).
464
465    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
466
467            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
468            * man/band.Rd:  adapt the \dontshow{} unit test.
469
470    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
471
472            * DESCRIPTION (Version): 0.995-14  for CRAN
473
474            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
475
476            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
477            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
478
479            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
480            * R/Tsparse.R (tril, triu, band): methods
481            * R/dgRMatrix.R (tril, ...):    ditto
482            * man/band.Rd:                  ditto
483
484    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
485
487                    to be up-to-date automatically.
488
489    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
490
491            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
492
493            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
494            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
495            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
496            such that the S4 objects are always created by the current version
497            of R and 'Matrix' class definitions.
498
499    2006-08-01  Douglas Bates  <bates@R-project.org>
500
501            * R/lmer.R (LMEoptimize method), tests/lmer.R,
502            inst/external/test3comp.rda: Added warnings for convergence on
503            boundary and test cases.
504
505            * src/lmer.c (mer_postVar): Modified to return the variances that
506            are marginal to the fixed effects, not conditional on them (which
507            is what the bVar slot contents represent).
508
509    2006-07-31  Douglas Bates  <bates@R-project.org>
510
511            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
512            function which calls the C function mer_hat_trace2.
513
514            * man/ranef.Rd: Include description of "postVar" argument and
515            producing a caterpillar plot.
516
517    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
518
519            * NAMESPACE:    change  "correlation" to "corMatrix"
520            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
521            * R/dpoMatrix.R: ditto
522            * R/lmer.R:      ditto
523
524    2006-07-28  Douglas Bates  <bates@R-project.org>
525
526            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
527            RZXinv slot's contents into a separate internal function that can
528            be used in mer_hat_trace.
529
530    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
531
532            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
533            via new smart
534            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
535            utility functions.
536
537
538    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
539
540            * R/Csparse.R (tril, triu, band): do return *triangular* classed
541            matrices when appropriate; band() even symmetric ones.
542            (replCmat): extend to potentially all "CsparseMatrix"
543            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
544            allow subassignment for special sparse matrices.
545
546            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
547
548            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
549            argument; in glmer_*(): print only if(verbose).
550
551            speed-optimize a few places by moving REAL(.) out of loops.
552
553            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
554
555    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
556
557            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
558                    since that wrongly triggers also for M[ logi , ]
559
560            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
561            a symmetric matrix that results in a non-symmetric one.
562            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
563
564            * R/dMatrix.R: make round(M) work as round(M, 0)
565
566            * R/dgTMatrix.R (image): coordinate system and axis now use
567            1-based indices, not 0-based ones.
568
569            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
570            * tests/indexing.R: test it.
571
572            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
573            * man/isSymmetric-methods.Rd: and document it.
574
575            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
576            * man/SparseM-conv.Rd: docu them
577
578            * tests/other-pkgs.R: renamed from tests/graph.R and add example
579                    for 'SparseM' conversions
580
581    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
582
584
585    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
586
587            * DESCRIPTION (Version): 0.995-12 released to CRAN
588
589    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
590
591            * tests/simple.R: add check for correct dsT -> dgT coercion;
592                    add check for correct printing of symmetric sparse matrices.
593
594            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
595            for sparse symmetric matrices.
596
597            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
598            diagonal twice.
599
600    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
601
602            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
603            being applied to the x slot (detected by Brian Ripley).
604
605    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
606
607            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
608
609            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
610
611    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
612
613            * src/lgCMatrix.c (lgCMatrix_diag): new function
614            * R/lgCMatrix.R (diag): for new method
615
616            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
617                 ==> construction of illegal "*gTMatrix" via new() should
618                 now be much less easy:
619            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
620
621            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
622                    directly.
623            * man/Matrix.Rd: documents it.
624
625  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
626
627          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 633
633          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
634          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
635
636            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
637            class.
638
639    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
640
641            * R/pMatrix.R: coercion pMatrix -> Tsparse
642
643  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
644
645            * DESCRIPTION (Version): 0.995-11 released to CRAN
646
647          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
648          the output from mcmcsamp.          the output from mcmcsamp.
649
# Line 23  Line 656
656
657          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
658          classes.          classes.
659            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
660
661  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
662
# Line 60  Line 694
694
695          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
696          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.
697          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
698
699
700  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 817
817          * 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)
818          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
819          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
820          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
821
822  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
823
# Line 387  Line 1021
1021  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1022
1023          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1024          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1025          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1026
1027  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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