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Annotation of /pkg/ChangeLog

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

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