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Annotation of /pkg/ChangeLog

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Revision 460 - (view) (download)

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

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