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Annotation of /pkg/ChangeLog

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

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