# SCM Repository

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

# Diff of /pkg/ChangeLog

revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1657, Wed Nov 1 16:29:53 2006 UTC
# Line 1  Line 1
1  2004-11-16  Douglas Bates  <bates@bates1-home>  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>
626
627            * src/pedigree.c (pedigree_inbreeding): Correction in
628            initialization.  This function is not currently being used and is
629            not fully tested.
630
631            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
632            Introduced the glmer class.  Added code for mcmcmsamp on glmer
633            objects.  Modified validity check on pedigree objects to account
634            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>
644
645            * DESCRIPTION (Version): 0.995-11 released to CRAN
646
647            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
648            the output from mcmcsamp.
649
650    2006-06-10  Douglas Bates  <bates@R-project.org>
651
652            * R/lmer.R (simulestimate): added C code for calculating the trace
653            of the hat matrix.
654
655    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
656
657            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
658            classes.
659            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
660
661    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
662
663            * R/dgTMatrix.R (colSums): etc. All four of
664            colSums(), rowSums(), colMeans(), rowMeans() now should work for
665            all "Matrices".
666
667    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
668
669            * R/lmer.R (panel.ci): Add a reference line at zero and a
670            background grid to the qqmath plot of ranef.lmer.
671
672    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
673
674            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
675            grouping factors to be specified in the formula as (1|foo/bar).
676
677    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
678
679            * R/lmer.R (findbars and others): Change check of is.numeric to
680            !is.language to resolve the bug reported by Jacob Wegelin.
681
682            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
683            code to evaluate inbreeding coefficients without calculating T,
684            based on code in Sargolzaei and Iwaisaki's paper.
685
686    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
687
688            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
689            generic and mer methods for isNested and denomDF. This denomDF was
690            an attempt to emulate that in lme but I don't think that makes
691            sense.  Use the trace of the hat matrix instead.
692
693    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
694
695            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
696            the C code depending on a slot structure that's no longer valid.
697            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
698
699
700    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
701
702            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
703            of lowerTriMatrix generic and methods to tril (also upper to triu)
704            and added a general band extractor.
705
706    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
707
708            * R/pedigree.R (pedigree): Replace sire and dam values outside the
709            allowable range with NAs. Added a corresponding check in the
710            validity check for the pedigree class.
711
712            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
713            crossprod methods now inherits from symmetricMatrix.
714
715    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
716
717            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
718            generics lowerTriMatrix and upperTriMatrix along with methods for
719            the Csparse virtual class.  Also added a C function Csparse_band
720            that implements these methods by calling cholmod_band.
721
722    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
723
724            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
725            erased when it was NULL.  This led to invalid subselections!
726
727    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
728
729            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
730            in method for "t" so as not to lose the unit diagonal property.
731
732    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
733
734            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
735            and methods.  This is now an option to the ranef method for the
736            mer class.
737
738            * src/cs_utils.c: Ensure that the nz component is -1 for a
739            compressed column-oriented matrix.  Minor formatting cleanup.
740
741            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
742            objects.
743
744    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
745
746            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
747            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
748
749    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
750
751            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
752            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
753
754            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
755            for the dtCMatrix class.
756
757    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
758
759            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
760            and methods for it.
761
762    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
763
764            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
765            arguments, such that M %*% 1:6 now works
766            * Tests/matprod.R: test the above
767
768    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
769
770            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
771            the ranef.lmer class.
772
773            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
774            methods to extract the posterior variances from the bVar slot.
775
776    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
777
778            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
779            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
780
781            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
782            * tests/simple: (extended)
783
784            * R/sparseMatrix.R (isTriangular): now using much improved
785            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
786
787    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
788
789            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
790            (problem report from Franklin Parlamis).  This should be done
791            generally.
792
793    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
794
795            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
796            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
797            update the plot methods.
798
799    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
800
801            * R/lmer.R (resid and ranef methods):  Added methods for the
802            "residuals" and "resid" generic but only for linear mixed model
803            fits.  Changed the ranef method to return a list of data frames so
804            that the plot methods now work.
805
806    2006-03-16  Douglas Bates  <bates@bates2>
807
808            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
809            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
810
811            * DESCRIPTION (Date): New release
812
813    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
814
815            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
816
817            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
818            * man/KNex.Rd: and other help files
819            * tests/*.R: several ones needed adaption
820            * inst/doc/Comparisons.Rnw: ditto
821
822    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
823
824            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
825
826            * tests/indexing.R: tests for new [<- methods for sparse matrices.
827
828    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
829
830            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
831
832            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
833
834    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
835
836            * R/dMatrix.R: enable things like  M [ M < 10 ]
837            * R/dgeMatrix.R: implement it
838
839    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
840
841            * R/AllClass.R: define "summary.mer" and "*.lmer"
842            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
843            * R/lmer.R (show): now works with summary()
844
845    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
846
847            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
848            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
849                    support the above
850
851    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
852
853            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
854            Use glmFit\$prior.weights for weights in a glmm.
855            Allow an option usePQL = FALSE to skip the PQL steps for the
856            Laplace method (and, in time, the AGQ method).
857
858            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
859            into a separate function internal_mer_Xfactor to be able to call
860            it from internal_bhat.
861
862    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
863
864            * tests/Class+Meth.R (tstMatrixClass): function for much better
865            testing; now again of all actual classes.
866
867            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
868                    use macros and define make_d_matrix_* and make_i_matrix_*
869                    where _i_ is for the ldense routines:
870
871            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
872            * src/ldense.c (lsyMatrix_as_lgeMatrix):
873
874            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
875
876
877    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
878
879            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
880                    many different kinds of matrices.
881            * R/*.R: quite a few new methods were needed for R CMD check with
882                    new Matrix().  Very good for users playing around.
883
884
885    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
886
887            * src/dgeMatrix.c (dMatrix_validate): new
888            * src/Mutils.c (dense_nonpacked_validate): new
889
890            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
891
892
893    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
894
895            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
896
897    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
898
899            * DESCRIPTION (Version): 0.99-6 released to CRAN
900
901            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
902            segfault in cases with multiple non-nested grouping factors.
903
904    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
905
906            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
907                    (Depends): also on 'utils'
908
909            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
910            * R/diagMatrix.R (Diagonal): constructor and methods for
911            diagonal matrices
912
913            * R/ltTMatrix.R: new "minimal methods"
914
915    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
916
917            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
918            all methods (and help files).
919
920    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
921
922            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
923                    for case (dimn.  op  no_dimn.)
924
925    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
926
927            * DESCRIPTION (Version): 0.99-2  released to CRAN
928
929    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
930
931            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
932            by Julian Faraway.
933
934    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
935
936            * R/Auxiliaries.R (try_as): new utility
937            * R/sparseMatrix.R: use try_as() in coercion to original class
938
939    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
940
941            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
942
943    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
944
946
947            * R/Matrix.R (as.array), (as.vector): new
948
949    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
950
951            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
952                    default.
953            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
954                    "pMatrix" now contains "sparseMatrix"
955
956    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
957
958            * tests/Class+Meth.R: new tests; t(t(m)) == m
959
960            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
961
962            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
963            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
964
965            * R/dspMatrix.R: typo in "t" method
966
967    2005-09-18  Douglas Bates  <bates@wisc.edu>
968
969            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
970            * R/Tsparse.R: instead of R/gTMatrix.R
971            * R/Csparse.R: new
972            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
973            * src/Tsparse.c: new; many trivial methods calling cholmod_()
974            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
975                            via cholmod
976
977    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
978
979            * R/Auxiliaries.R (non0ind): new function using new C code
980            * src/dgCMatrix.c (compressed_non_0_ij): new utility
981
982    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
983
984            * src/chm_common.h: header file required by all C sources that
985            call CHOLMOD functions.  It defines a cholmod_common structure
986            called 'c' whose address is passed as the last argument to
987            (virtually) every CHOLMOD function.
988
989            * src/Pattern.c: Simple example of the use of CHOLMOD.
990
991            * src/init.c: initialize and finalize the cholmod_common structure.
992
993            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
994            LDL and CCOLAMD from the U. of Florida sparse matrix library.
995
996    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
997
998            * inst/test-tools.R: new file collecting the utility functions used
999                    in ./tests/*.R
1000
1001            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1002            * R/Matrix.R (cbind2): methods for NULL and missing
1003
1004    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1005
1006            * R/AllClass.R: new "index" class for "[" and "[<-":
1007                    First cut at "symmetricMatrix" and "triangularMatrix"
1008            * R/gTMatrix.R (.ind.prep): new function;
1009                    Logical and character indexing now work too.
1010            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1011            * tests/indexing.R: new, including *.Rout.save
1012            * tests/dgTMatrix.R: new
1013
1014    2005-08-29  Douglas Bates  <bates@wisc.edu>
1015
1016            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1017            indicator pos not being updated.  Also enforced upper triangular
1018            for symmetric case.  Need to coerce edges component of elements of
1019            edge list - grr! (Why don't they define their classes cleanly?)
1020
1021    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1022
1023            * R/Matrix.R:  added first "[<-" methods; not yet functional
1024            * R/denseMatrix.R: ditto
1025            * man/Subassign-methods.Rd: new help file for these
1026
1027    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1028
1029            * DESCRIPTION (Version): 0.98-6
1030
1031            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1032            matrices.
1033
1034    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1035
1036            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1037                    as( <logical>, "matrix")
1038
1039            * R/pMatrix.R: coercion to "lgTMatrix"
1040
1041            * R/gTMatrix.R: new virtual class to define "[" methods for.
1042            * man/gTMatrix-class.Rd:
1043            * General slight re-organization of where "[" methods are defined.
1044              more to come.
1045
1046    2005-08-18  Douglas Bates  <bates@wisc.edu>
1047
1048            * DESCRIPTION (Version): 0.98-5  released to CRAN
1049
1050            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1051            * .....
1052
1053    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1054
1055            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1056            or glmer objects.
1057
1058    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1059
1060            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1061
1062    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1063
1064            * R/HBMM.R: finish re-writing R-only code.
1065
1066    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1067
1068            * man/externalFormats.Rd: move documentation for writeHB and
1069            writeMM here.
1070
1071            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1072            (suggested by Paul Roecker).
1073
1074            * tests/validObj.R (assertError): Comment out test that is failing
1075            after recent changes in r-devel.
1076
1077
1078    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1079
1080            * R/AllClass.R: intermediate virtual class "denseMatrix"
1081            * man/denseMatrix-class.Rd
1082            * NAMESPACE: export it, and also export
1083            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1084
1085    2005-08-10  Douglas Bates  <bates@wisc.edu>
1086
1087            * DESCRIPTION (Version): 0.98-3 to CRAN
1088
1089            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1090            matrix_solve code (which was really, really wrong).
1091
1092    2005-08-07  Douglas Bates  <bates@wisc.edu>
1093
1094            * DESCRIPTION (Version): 0.98-2
1095
1097
1098            * R/lmer.R (abbrvNms): new
1099            * R/lmer.R (mcmcsamp): allow transformed parameters
1101            for the Harwell-Boeing and the MatrixMarket formats.
1102
1103    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1104
1106            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1107
1108            * TODO: note the dtpMatrix (docu) bug
1109
1110            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1111            in order to ensure that new as.matrix() is used by old functions,
1112            e.g., svd(), qr(), eigen(), dist(),..;
1113                  apply(), also matplot() or pairs().
1114
1115
1116    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1117
1118            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1120
1121    2005-07-27  Douglas Bates  <bates@wisc.edu>
1122
1123            * man/sleepstudy.Rd: Added the sleep data set.
1124            * DESCRIPTION (Version): 0.98-1  released to CRAN
1125
1126    2005-07-12  Douglas Bates  <bates@wisc.edu>
1127            * man/sleepstudy.Rd: Added the sleep data set.
1128
1129            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1130            .Call calls that were producing spurious output.
1131
1132    2005-07-05  Douglas Bates  <bates@wisc.edu>
1133
1134            * R/lmer.R (lmer): stored updated variance component estimates in
1135            mer object for the generalized model.  (Bug reported by Renaud
1136            Lancelot).
1137
1138    2005-07-03  Douglas Bates  <bates@wisc.edu>
1139
1140            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1141            unidimensional case.
1142
1143    2005-06-08  Douglas Bates  <bates@wisc.edu>
1144
1145            * DESCRIPTION (Version): 0.96-1
1146
1147            * moved  lmer-class' R and C code moved from lme4 to here
1148
1149    2005-06-04  Douglas Bates  <bates@wisc.edu>
1150
1151            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1152            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1153
1154    2005-06-02  Douglas Bates  <bates@wisc.edu>
1155
1156            * src/Makefile.win: Forgot to update this when Makefile changed.
1157
1158    2005-05-11  Douglas Bates  <bates@wisc.edu>
1159
1160            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1161            bug reported by Kurt Hornik and Michael Hahsler.
1162
1163    2005-05-10  Douglas Bates  <bates@wisc.edu>
1164
1165            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1166            logical sparse matrices.  These will also be used in the symbolic
1167            analysis for lmer objects.
1168
1169            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1170            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1171
1172    2005-05-06  Douglas Bates  <bates@wisc.edu>
1173
1174            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1175            colMeans, colSums, rowMeans and rowSums.
1176
1177    2005-04-18  Douglas Bates  <bates@wisc.edu>
1178
1179            * src/lgCMatrix.[ch]: code for _validate method and stub for
1180            multiplication operation.
1181
1182            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1183            to dgetrs.
1184
1185            * src/init.c: Fix cut-and-paste error in definition of
1186            dgeMatrix_matrix_solve
1187
1188            * src/{many files}: Tighten code by using ALLOC_SLOT.
1189
1190    2005-04-15  Douglas Bates  <bates@wisc.edu>
1191
1192            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1193
1194            * DESCRIPTION: Eliminate import of stats.
1195
1196
1197    2005-04-06  Douglas Bates  <bates@wisc.edu>
1198
1199            * R/AllClass.R : add logical sparse matrix classes
1200
1201    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1202
1203            * R/dgTMatrix.R: add "[" method for triplet matrices
1204            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1205
1206    2005-03-31  Douglas Bates  <bates@wisc.edu>
1207
1208            * DESCRIPTION (Version): release 0.95-5 to CRAN
1209
1210            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1211            * R/sparseMatrix.R: %*%, crossprod()
1212            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1213            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1214            * src/lmer.c (lmer_fitted): fix thinko
1215
1216    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1217
1218            * R/AllClass.R: add two virtual sparse classes ``on top''
1219
1220    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
1221
1222            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1223                    correspondingly fix examples and tests/ since new()
1224                    doesn't work for virtual classes.
1225
1226    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1227
1228            * R/Matrix.R (as.matrix): method and one for unname()
1229            * tests/dpoMatrix.R: tests should now be less platform dependent;
1230              also run for R 2.1.0; using as.matrix()
1231
1232    2005-03-15  Douglas Bates  <bates@wisc.edu>
1233
1234            * R/pMatrix.R: "pMatrix" class added
1235            * ....
1236
1237    2005-03-14  Douglas Bates  <bates@wisc.edu>
1238
1239            * R/dtpMatrix.R: Add unpack method and an example.
1240
1241            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1242            of general symmetric matrices and associated S4 methods.
1243
1244    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1245            +
1246    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1247
1248            * R/dgeMatrix.R (setAs): and many other files: more coercion,
1249              crossprod() and "%*%" methods added; tests, too.
1250            * tests/matprod.R: new, for testing these
1251
1252    2005-03-03  Douglas Bates  <bates@wisc.edu>
1253
1255
1256    2005-03-02  Douglas Bates  <bates@wisc.edu>
1257
1258            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1259
1260    2005-02-28  Douglas Bates  <bates@wisc.edu>
1261
1262            * src/*.c,po/,inst/po: Internationalization and localization of
1263            the package.
1264
1265            * src/ldl.[ch]: Removed these as their contents are referenced in the
1266            R_ldl.c file.
1267
1268            * src/flame.[ch]: Removed these source files.
1269
1270            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1271
1272            * src/LU.[ch],src/init.c: absorb in factorizations
1273
1274            * src/Mutils.h: prepare for internationalization
1275
1276            * src/cblas.h: move the enum definitions to Mutils.h and remove
1277            this file
1278
1279    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1280
1281            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1282
1283            * R/dtrMatrix.R: fix t() method
1284
1285            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1286            * NAMESPACE: export them (and import generics from "methods")
1287            * tests/group-methods.R : and test them.
1288
1289            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1290            border case
1291
1292    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1293
1294            * DESCRIPTION (Version): 0.95-2  released to CRAN
1295
1296            * src/dgBCMatrix.c:
1297            * src/lmer.c: many changes
1298            * ...
1299
1300    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1301
1302            * R/Matrix.R: add more sophisticated show() method.
1303
1304    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1305
1306            * */* : almost complete reorganization of classes.
1307
1308    2005-01-26  Douglas Bates  <bates@wisc.edu>
1309
1310            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1311            for the geMatrix class.
1312
1313    2005-01-24  Douglas Bates  <bates@wisc.edu>
1314
1315            * src/Makefile (clean): Remove *.a and *.so
1316
1317            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1318
1319    2005-01-23  Douglas Bates  <bates@wisc.edu>
1320
1321            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1322            had an effect in cases with more than 2 grouping factors.
1323
1324    2005-01-03  Douglas Bates  <bates@wisc.edu>
1325
1326            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1327
1328    2004-12-23  Douglas Bates  <bates@wisc.edu>
1329
1330            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1331            and R_useDynamicSymbols (suggested by B.D.Ripley).
1332
1333    2004-12-14  Douglas Bates  <bates@wisc.edu>
1334
1335            * R/sscMatrix.R: Add determinant methods
1336
1337            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1338            for tripletMatrix to matrix.
1339
1340    2004-12-13  Douglas Bates  <bates@wisc.edu>
1341
1342            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1343            no longer used.
1344
1345            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1346            with dynamic allocation of scratch arrays.
1347
1348            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1349            for multivariate random effects with multiple grouping factors.
1350            Fixes part but not all of #15.
1351
1352    2004-12-03  Douglas Bates  <bates@wisc.edu>
1353
1354            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1355            scalar grouping factors corrected.
1356
1357    2004-11-29  Douglas Bates  <bates@wisc.edu>
1358
1359            * src/bCrosstab.c: remove diag_update which is no longer used
1360
1361    2004-11-16  Douglas Bates  <bates@wisc.edu>
1362
1363          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1364          .h file can be included.          .h file can be included.
1365
1366  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1367
1368          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1369          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1370
1371          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1372
1373  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1374
1375          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1376
1377  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1378
1379          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1380
1381  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1382
1383          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1384
1385  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1386
1387          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1388
1389  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1390
1391          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1392          routines.          routines.
1393
1394  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1395
1396          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1397
1398  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1399
1400          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1401

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