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

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