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Annotation of /pkg/ChangeLog

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

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