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Annotation of /pkg/ChangeLog

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1 : maechler 834 2005-08-07 Douglas Bates <bates@localhost.localdomain>
2 :    
3 :     * DESCRIPTION (Version): 0.98-2
4 :    
5 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
6 :    
7 :     * R/lmer.R (abbrvNms): new
8 :     * R/lmer.R (mcmcsamp): allow transformed parameters
9 :    
10 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
11 :    
12 :     * man/dtrMatrix-class.Rd: add examples
13 :     * man/dtpMatrix-class.Rd: dito; plus note about PROBLEM
14 :    
15 :     * TODO: note the dtpMatrix (docu) bug
16 :    
17 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
18 :     in order to ensure that new as.matrix() is used by old functions,
19 :     e.g., svd(), qr(), eigen(), dist(),..;
20 :     apply(), also matplot() or pairs().
21 :    
22 :    
23 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
24 :    
25 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
26 :     add comments about 'control' / lmerControl() arguments
27 :    
28 : bates 820 2005-07-27 Douglas Bates <bates@localhost.localdomain>
29 :    
30 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
31 : bates 820
32 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
33 :    
34 : bates 809 2005-07-12 Douglas Bates <bates@localhost.localdomain>
35 :    
36 :     * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
37 :     .Call calls that were producing spurious output.
38 :    
39 : bates 801 2005-07-05 Douglas Bates <bates@bates1-home>
40 :    
41 :     * R/lmer.R (lmer): stored updated variance component estimates in
42 :     mer object for the generalized model. (Bug reported by Renaud
43 :     Lancelot).
44 :    
45 : bates 794 2005-07-03 Douglas Bates <bates@bates1-home>
46 :    
47 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
48 :     unidimensional case.
49 :    
50 : maechler 791 2005-06-08 Douglas Bates <bates@bates1-home>
51 :    
52 :     * DESCRIPTION (Version): 0.96-1
53 :    
54 :     * moved lmer-class' R and C code moved from lme4 to here
55 :    
56 : bates 763 2005-06-04 Douglas Bates <bates@bates1-home>
57 :    
58 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
59 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
60 :    
61 :     2005-06-02 Douglas Bates <bates@bates1-home>
62 :    
63 :     * src/Makefile.win: Forgot to update this when Makefile changed.
64 :    
65 : bates 726 2005-05-11 Douglas Bates <bates@bates1-home>
66 :    
67 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
68 :     bug reported by Kurt Hornik and Michael Hahsler.
69 :    
70 : bates 725 2005-05-10 Douglas Bates <bates@bates1-home>
71 :    
72 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
73 :     logical sparse matrices. These will also be used in the symbolic
74 :     analysis for lmer objects.
75 :    
76 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
77 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
78 : maechler 791
79 : bates 714 2005-05-06 Douglas Bates <bates@bates1-home>
80 :    
81 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
82 :     colMeans, colSums, rowMeans and rowSums.
83 :    
84 : bates 692 2005-04-18 Douglas Bates <bates@bates1-home>
85 :    
86 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
87 :     multiplication operation.
88 :    
89 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
90 :     to dgetrs.
91 :    
92 :     * src/init.c: Fix cut-and-paste error in definition of
93 :     dgeMatrix_matrix_solve
94 :    
95 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
96 :    
97 :     2005-04-15 Douglas Bates <bates@bates1-home>
98 :    
99 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
100 :    
101 :     * DESCRIPTION: Eliminate import of stats.
102 :    
103 : maechler 791
104 : bates 692 2005-04-06 Douglas Bates <bates@bates1-home>
105 :    
106 :     * R/AllClass.R : add logical sparse matrix classes
107 :    
108 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 :     * R/dgTMatrix.R: add "[" method for triplet matrices
111 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
112 :    
113 :     2005-03-31 Douglas Bates <bates@bates1-home>
114 :    
115 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
116 :    
117 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
118 :     * R/sparseMatrix.R: %*%, crossprod()
119 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
120 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
121 :     * src/lmer.c (lmer_fitted): fix thinko
122 :    
123 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
124 :    
125 :     * R/AllClass.R: add two virtual sparse classes ``on top''
126 :    
127 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
128 :    
129 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
130 :     correspondingly fix examples and tests/ since new()
131 :     doesn't work for virtual classes.
132 :    
133 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
134 :    
135 :     * R/Matrix.R (as.matrix): method and one for unname()
136 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
137 :     also run for R 2.1.0; using as.matrix()
138 :    
139 :     2005-03-15 Douglas Bates <bates@bates1-home>
140 :    
141 :     * R/pMatrix.R: "pMatrix" class added
142 :     * ....
143 :    
144 : bates 645 2005-03-14 Douglas Bates <bates@bates1-home>
145 :    
146 :     * R/dtpMatrix.R: Add unpack method and an example.
147 :    
148 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
149 :     of general symmetric matrices and associated S4 methods.
150 :    
151 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
152 :     +
153 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
154 :    
155 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
156 :     crossprod() and "%*%" methods added; tests, too.
157 :     * tests/matprod.R: new, for testing these
158 :    
159 : bates 599 2005-03-03 Douglas Bates <bates@bates1-home>
160 :    
161 :     * src/lmer.c (lmer_fitted): Added.
162 :    
163 : bates 596 2005-03-02 Douglas Bates <bates@bates1-home>
164 :    
165 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
166 :    
167 : bates 582 2005-02-28 Douglas Bates <bates@bates1-home>
168 :    
169 :     * src/*.c,po/,inst/po: Internationalization and localization of
170 :     the package.
171 :    
172 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
173 :     R_ldl.c file.
174 :    
175 :     * src/flame.[ch]: Removed these source files.
176 : maechler 658
177 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
178 :    
179 :     * src/LU.[ch],src/init.c: absorb in factorizations
180 :    
181 :     * src/Mutils.h: prepare for internationalization
182 :    
183 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
184 :     this file
185 :    
186 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
187 :    
188 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
189 :    
190 :     * R/dtrMatrix.R: fix t() method
191 :    
192 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
193 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
194 : maechler 578 * tests/group-methods.R : and test them.
195 :    
196 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
197 :     border case
198 :    
199 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
200 :    
201 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
202 : maechler 578
203 :     * src/dgBCMatrix.c:
204 :     * src/lmer.c: many changes
205 :     * ...
206 :    
207 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
208 :    
209 :     * R/Matrix.R: add more sophisticated show() method.
210 :    
211 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
212 :    
213 :     * */* : almost complete reorganization of classes.
214 :    
215 : bates 460 2005-01-26 Douglas Bates <bates@bates7>
216 :    
217 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
218 :     for the geMatrix class.
219 :    
220 :     2005-01-24 Douglas Bates <bates@bates7>
221 :    
222 :     * src/Makefile (clean): Remove *.a and *.so
223 :    
224 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
225 :    
226 :     2005-01-23 Douglas Bates <bates@bates7>
227 :    
228 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
229 : bates 460 had an effect in cases with more than 2 grouping factors.
230 :    
231 : bates 415 2005-01-03 Douglas Bates <bates@bates1-home>
232 :    
233 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
234 :    
235 : bates 410 2004-12-23 Douglas Bates <bates@bates1-home>
236 :    
237 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
238 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
239 :    
240 : bates 392 2004-12-14 Douglas Bates <bates@bates1-home>
241 :    
242 :     * R/sscMatrix.R: Add determinant methods
243 :    
244 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
245 :     for tripletMatrix to matrix.
246 :    
247 : bates 388 2004-12-13 Douglas Bates <bates@bates1-home>
248 :    
249 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
250 :     no longer used.
251 :    
252 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
253 :     with dynamic allocation of scratch arrays.
254 :    
255 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
256 :     for multivariate random effects with multiple grouping factors.
257 :     Fixes part but not all of #15.
258 :    
259 : bates 375 2004-12-03 Douglas Bates <bates@bates1-home>
260 :    
261 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
262 :     scalar grouping factors corrected.
263 :    
264 :     2004-11-29 Douglas Bates <bates@bates1-home>
265 :    
266 :     * src/bCrosstab.c: remove diag_update which is no longer used
267 :    
268 : bates 350 2004-11-16 Douglas Bates <bates@bates1-home>
269 :    
270 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
271 :     .h file can be included.
272 :    
273 : bates 342 2004-11-12 Douglas Bates <bates@bates1-home>
274 :    
275 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
276 : bates 342 Complete allocation of slots in NEW_OBJECT.
277 :    
278 :     * src/Mutils.h: Moved list of symbols to an include file
279 :    
280 :     2004-11-11 Douglas Bates <bates@bates1-home>
281 :    
282 :     * src/geMutils.c (Matrix_init): remove unused function
283 :    
284 :     2004-11-10 Douglas Bates <bates@bates1-home>
285 :    
286 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
287 :    
288 : bates 327 2004-11-05 Douglas Bates <bates@bates1-home>
289 :    
290 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
291 :    
292 : bates 303 2004-10-27 Douglas Bates <bates@bates1-home>
293 :    
294 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
295 :    
296 : bates 296 2004-10-04 Douglas Bates <bates@bates1-home>
297 :    
298 :     * src/init.c: Created R_init_Matrix and added registration of C
299 :     routines.
300 :    
301 : bates 283 2004-10-02 Douglas Bates <bates@bates1-home>
302 :    
303 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
304 :    
305 : bates 229 2004-06-15 Douglas Bates <bates@bates7>
306 :    
307 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
308 :    
309 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
310 :    
311 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
312 :    
313 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
314 :    
315 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
316 :     ssclme_update_mm
317 :    
318 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
319 :    
320 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
321 :     in the order of unconstrained and constrained parameters.
322 :     (ssclme_gradient): Added the gradients (not yet correct for
323 :     multidimensional, unconstrained case).
324 :    
325 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
326 :    
327 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
328 :    
329 :     * src/Makefile.win: Remove unneeded ranlib call
330 :    
331 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
332 :    
333 :     * DESCRIPTION (Version): New release
334 :    
335 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
336 :    
337 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
338 :    
339 :     * src/triplet_to_col.c: Create triplet_to_col as a native
340 : maechler 658 function, not the version from umfpack. There were problems with
341 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
342 :     only one umfpack routine being used so I moved it here.
343 :    
344 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
345 :    
346 :     * src/ssclme.c (ssclme_variances): New function.
347 :    
348 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
349 :    
350 :     * src/ssclme.c (ssclme_fitted): Added function.
351 :    
352 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
353 :    
354 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
355 :     store the dimnames in the XtX and bVar slots
356 :     (ssclme_update_mm): Change the dimensions of the bVar slot
357 :     components and the returned value from ssclme_ranef.
358 :    
359 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
360 :    
361 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
362 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
363 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
364 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
365 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
366 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
367 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
368 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
369 :     Moved the pdMat classes from the lme4 package.
370 :    
371 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
372 :    
373 :     * man/ssclme-class.Rd: Update definition and documentation of the
374 :     ssclme class to include the DIsqrt slot.
375 :    
376 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
377 :     (much faster using dsyrk, a level 3 BLAS routine).
378 :    
379 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
380 :    
381 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
382 :    
383 :     * tests/ssclme.R: Modify the test to account for the permutation
384 :     of the levels of the grouping factors.
385 :    
386 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
387 :    
388 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
389 :     directly into the ssclme class definition.
390 :    
391 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
392 :    
393 :     * DESCRIPTION (Date): New release
394 :    
395 :     * man/ssclme-class.Rd: new file.
396 :    
397 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
398 :     works and it's fast!
399 :    
400 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
401 :    
402 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
403 :    
404 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
405 :    
406 :     * DESCRIPTION (Date): New release
407 :    
408 :     * NAMESPACE: Don't export ssclme.
409 :    
410 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
411 :     school data.
412 :    
413 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
414 :    
415 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
416 :     keep track of the fixed-effects and the response. Counts also
417 :     gets an extra element, which is always one.
418 :    
419 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
420 :    
421 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
422 :    
423 :     * src/cscMatrix.c (csc_transpose): new function
424 :    
425 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
426 :     (csc_components_transpose): new function
427 :    
428 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
429 :    
430 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
431 :     triplets
432 :    
433 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
434 :    
435 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
436 :    
437 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
438 :     and all other .h files in src.
439 :    
440 :     * src/Makefile.win: This and other Makefile.win files contributed
441 :     by Brian Ripley.
442 :    
443 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
444 :    
445 :     * R/syMatrix.R: Added methods for "%*%".
446 :    
447 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
448 :     poMatrix object.
449 :    
450 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
451 :    
452 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
453 :    
454 :     2004-01-25 Douglas Bates <bates@bates2_home>
455 :    
456 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
457 :    
458 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
459 :     of nrow.
460 :    
461 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
462 :    
463 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
464 :     subdirectories.
465 :    
466 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
467 :    
468 :     * src/taucs.h: Accidently referred to global header files
469 :     instead of local files.
470 :    
471 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
472 :    
473 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
474 :     and methods and replaced all classes with S4 classes.
475 :    
476 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
477 :    
478 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
479 :    
480 :     * src/R_LapackPP.cc: Change method of calculating determinants
481 :    
482 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
483 :    
484 :     * DESCRIPTION (Version): removed empty data directory as requested
485 :     by CRAN maintainers. Changed version number and date.
486 :    
487 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
488 :    
489 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
490 :     under Windows.
491 :    
492 :     * Added configure.win and src/Makevars.win as requested by Brian
493 :     Ripley.
494 :    
495 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
496 :    
497 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
498 :     Hornik.
499 :    
500 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
501 :    
502 :     * configure.ac: Replaced configure.in with configure.ac
503 :     contributed by Kurt Hornik.
504 :    
505 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
506 :     version for R-1.5.0
507 :    
508 : maechler 512
509 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
510 :    
511 :     * man/eigen.Rd: Removed the .Alias in the example

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