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Annotation of /pkg/ChangeLog

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

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