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1 : bates 714 2005-05-06 Douglas Bates <bates@bates1-home>
2 :    
3 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
4 :     colMeans, colSums, rowMeans and rowSums.
5 :    
6 : bates 692 2005-04-18 Douglas Bates <bates@bates1-home>
7 :    
8 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
9 :     multiplication operation.
10 :    
11 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
12 :     to dgetrs.
13 :    
14 :     * src/init.c: Fix cut-and-paste error in definition of
15 :     dgeMatrix_matrix_solve
16 :    
17 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
18 :    
19 :     2005-04-15 Douglas Bates <bates@bates1-home>
20 :    
21 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
22 :    
23 :     * DESCRIPTION: Eliminate import of stats.
24 :    
25 :    
26 :     2005-04-06 Douglas Bates <bates@bates1-home>
27 :    
28 :     * R/AllClass.R : add logical sparse matrix classes
29 :    
30 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
31 :    
32 :     * R/dgTMatrix.R: add "[" method for triplet matrices
33 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
34 :    
35 :     2005-03-31 Douglas Bates <bates@bates1-home>
36 :    
37 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
38 :    
39 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
40 :     * R/sparseMatrix.R: %*%, crossprod()
41 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
42 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
43 :     * src/lmer.c (lmer_fitted): fix thinko
44 :    
45 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
46 :    
47 :     * R/AllClass.R: add two virtual sparse classes ``on top''
48 :    
49 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
50 :    
51 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
52 :     correspondingly fix examples and tests/ since new()
53 :     doesn't work for virtual classes.
54 :    
55 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
56 :    
57 :     * R/Matrix.R (as.matrix): method and one for unname()
58 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
59 :     also run for R 2.1.0; using as.matrix()
60 :    
61 :     2005-03-15 Douglas Bates <bates@bates1-home>
62 :    
63 :     * R/pMatrix.R: "pMatrix" class added
64 :     * ....
65 :    
66 : bates 645 2005-03-14 Douglas Bates <bates@bates1-home>
67 :    
68 :     * R/dtpMatrix.R: Add unpack method and an example.
69 :    
70 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
71 :     of general symmetric matrices and associated S4 methods.
72 :    
73 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
74 :     +
75 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
76 :    
77 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
78 :     crossprod() and "%*%" methods added; tests, too.
79 :     * tests/matprod.R: new, for testing these
80 :    
81 : bates 599 2005-03-03 Douglas Bates <bates@bates1-home>
82 :    
83 :     * src/lmer.c (lmer_fitted): Added.
84 :    
85 : bates 596 2005-03-02 Douglas Bates <bates@bates1-home>
86 :    
87 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
88 :    
89 : bates 582 2005-02-28 Douglas Bates <bates@bates1-home>
90 :    
91 :     * src/*.c,po/,inst/po: Internationalization and localization of
92 :     the package.
93 :    
94 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
95 :     R_ldl.c file.
96 :    
97 :     * src/flame.[ch]: Removed these source files.
98 : maechler 658
99 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
100 :    
101 :     * src/LU.[ch],src/init.c: absorb in factorizations
102 :    
103 :     * src/Mutils.h: prepare for internationalization
104 :    
105 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
106 :     this file
107 :    
108 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
111 :    
112 :     * R/dtrMatrix.R: fix t() method
113 :    
114 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
115 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
116 : maechler 578 * tests/group-methods.R : and test them.
117 :    
118 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
119 :     border case
120 :    
121 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
122 :    
123 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
124 : maechler 578
125 :     * src/dgBCMatrix.c:
126 :     * src/lmer.c: many changes
127 :     * ...
128 :    
129 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * R/Matrix.R: add more sophisticated show() method.
132 :    
133 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
134 :    
135 :     * */* : almost complete reorganization of classes.
136 :    
137 : bates 460 2005-01-26 Douglas Bates <bates@bates7>
138 :    
139 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
140 :     for the geMatrix class.
141 :    
142 :     2005-01-24 Douglas Bates <bates@bates7>
143 :    
144 :     * src/Makefile (clean): Remove *.a and *.so
145 :    
146 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
147 :    
148 :     2005-01-23 Douglas Bates <bates@bates7>
149 :    
150 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
151 : bates 460 had an effect in cases with more than 2 grouping factors.
152 :    
153 : bates 415 2005-01-03 Douglas Bates <bates@bates1-home>
154 :    
155 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
156 :    
157 : bates 410 2004-12-23 Douglas Bates <bates@bates1-home>
158 :    
159 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
160 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
161 :    
162 : bates 392 2004-12-14 Douglas Bates <bates@bates1-home>
163 :    
164 :     * R/sscMatrix.R: Add determinant methods
165 :    
166 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
167 :     for tripletMatrix to matrix.
168 :    
169 : bates 388 2004-12-13 Douglas Bates <bates@bates1-home>
170 :    
171 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
172 :     no longer used.
173 :    
174 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
175 :     with dynamic allocation of scratch arrays.
176 :    
177 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
178 :     for multivariate random effects with multiple grouping factors.
179 :     Fixes part but not all of #15.
180 :    
181 : bates 375 2004-12-03 Douglas Bates <bates@bates1-home>
182 :    
183 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
184 :     scalar grouping factors corrected.
185 :    
186 :     2004-11-29 Douglas Bates <bates@bates1-home>
187 :    
188 :     * src/bCrosstab.c: remove diag_update which is no longer used
189 :    
190 : bates 350 2004-11-16 Douglas Bates <bates@bates1-home>
191 :    
192 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
193 :     .h file can be included.
194 :    
195 : bates 342 2004-11-12 Douglas Bates <bates@bates1-home>
196 :    
197 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
198 : bates 342 Complete allocation of slots in NEW_OBJECT.
199 :    
200 :     * src/Mutils.h: Moved list of symbols to an include file
201 :    
202 :     2004-11-11 Douglas Bates <bates@bates1-home>
203 :    
204 :     * src/geMutils.c (Matrix_init): remove unused function
205 :    
206 :     2004-11-10 Douglas Bates <bates@bates1-home>
207 :    
208 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
209 :    
210 : bates 327 2004-11-05 Douglas Bates <bates@bates1-home>
211 :    
212 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
213 :    
214 : bates 303 2004-10-27 Douglas Bates <bates@bates1-home>
215 :    
216 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
217 :    
218 : bates 296 2004-10-04 Douglas Bates <bates@bates1-home>
219 :    
220 :     * src/init.c: Created R_init_Matrix and added registration of C
221 :     routines.
222 :    
223 : bates 283 2004-10-02 Douglas Bates <bates@bates1-home>
224 :    
225 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
226 :    
227 : bates 229 2004-06-15 Douglas Bates <bates@bates7>
228 :    
229 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
230 :    
231 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
232 :    
233 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
234 :    
235 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
236 :    
237 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
238 :     ssclme_update_mm
239 :    
240 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
241 :    
242 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
243 :     in the order of unconstrained and constrained parameters.
244 :     (ssclme_gradient): Added the gradients (not yet correct for
245 :     multidimensional, unconstrained case).
246 :    
247 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
248 :    
249 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
250 :    
251 :     * src/Makefile.win: Remove unneeded ranlib call
252 :    
253 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
254 :    
255 :     * DESCRIPTION (Version): New release
256 :    
257 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
258 :    
259 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
260 :    
261 :     * src/triplet_to_col.c: Create triplet_to_col as a native
262 : maechler 658 function, not the version from umfpack. There were problems with
263 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
264 :     only one umfpack routine being used so I moved it here.
265 :    
266 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
267 :    
268 :     * src/ssclme.c (ssclme_variances): New function.
269 :    
270 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
271 :    
272 :     * src/ssclme.c (ssclme_fitted): Added function.
273 :    
274 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
275 :    
276 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
277 :     store the dimnames in the XtX and bVar slots
278 :     (ssclme_update_mm): Change the dimensions of the bVar slot
279 :     components and the returned value from ssclme_ranef.
280 :    
281 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
282 :    
283 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
284 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
285 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
286 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
287 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
288 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
289 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
290 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
291 :     Moved the pdMat classes from the lme4 package.
292 :    
293 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
294 :    
295 :     * man/ssclme-class.Rd: Update definition and documentation of the
296 :     ssclme class to include the DIsqrt slot.
297 :    
298 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
299 :     (much faster using dsyrk, a level 3 BLAS routine).
300 :    
301 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
302 :    
303 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
304 :    
305 :     * tests/ssclme.R: Modify the test to account for the permutation
306 :     of the levels of the grouping factors.
307 :    
308 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
309 :    
310 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
311 :     directly into the ssclme class definition.
312 :    
313 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
314 :    
315 :     * DESCRIPTION (Date): New release
316 :    
317 :     * man/ssclme-class.Rd: new file.
318 :    
319 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
320 :     works and it's fast!
321 :    
322 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
323 :    
324 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
325 :    
326 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
327 :    
328 :     * DESCRIPTION (Date): New release
329 :    
330 :     * NAMESPACE: Don't export ssclme.
331 :    
332 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
333 :     school data.
334 :    
335 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
336 :    
337 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
338 :     keep track of the fixed-effects and the response. Counts also
339 :     gets an extra element, which is always one.
340 :    
341 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
342 :    
343 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
344 :    
345 :     * src/cscMatrix.c (csc_transpose): new function
346 :    
347 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
348 :     (csc_components_transpose): new function
349 :    
350 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
351 :    
352 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
353 :     triplets
354 :    
355 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
356 :    
357 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
358 :    
359 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
360 :     and all other .h files in src.
361 :    
362 :     * src/Makefile.win: This and other Makefile.win files contributed
363 :     by Brian Ripley.
364 :    
365 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
366 :    
367 :     * R/syMatrix.R: Added methods for "%*%".
368 :    
369 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
370 :     poMatrix object.
371 :    
372 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
373 :    
374 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
375 :    
376 :     2004-01-25 Douglas Bates <bates@bates2_home>
377 :    
378 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
379 :    
380 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
381 :     of nrow.
382 :    
383 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
384 :    
385 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
386 :     subdirectories.
387 :    
388 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
389 :    
390 :     * src/taucs.h: Accidently referred to global header files
391 :     instead of local files.
392 :    
393 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
394 :    
395 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
396 :     and methods and replaced all classes with S4 classes.
397 :    
398 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
399 :    
400 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
401 :    
402 :     * src/R_LapackPP.cc: Change method of calculating determinants
403 :    
404 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
405 :    
406 :     * DESCRIPTION (Version): removed empty data directory as requested
407 :     by CRAN maintainers. Changed version number and date.
408 :    
409 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
410 :    
411 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
412 :     under Windows.
413 :    
414 :     * Added configure.win and src/Makevars.win as requested by Brian
415 :     Ripley.
416 :    
417 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
418 :    
419 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
420 :     Hornik.
421 :    
422 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
423 :    
424 :     * configure.ac: Replaced configure.in with configure.ac
425 :     contributed by Kurt Hornik.
426 :    
427 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
428 :     version for R-1.5.0
429 :    
430 : maechler 512
431 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
432 :    
433 :     * man/eigen.Rd: Removed the .Alias in the example

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