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Annotation of /pkg/ChangeLog

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

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