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Annotation of /pkg/ChangeLog

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

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