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Annotation of /pkg/ChangeLog

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Revision 809 - (view) (download)

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

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