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

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