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Annotation of /pkg/ChangeLog

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Revision 596 - (view) (download)

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

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