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Annotation of /pkg/ChangeLog

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Revision 801 - (view) (download)

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

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