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

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