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

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