SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1259 - (view) (download)

1 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
2 :    
3 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
4 :     in method for "t" so as not to lose the unit diagonal property.
5 :    
6 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
7 :    
8 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
9 :     and methods. This is now an option to the ranef method for the
10 :     mer class.
11 :    
12 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
13 :     compressed column-oriented matrix. Minor formatting cleanup.
14 :    
15 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
16 :     objects.
17 :    
18 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
19 :    
20 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
21 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
22 :    
23 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
24 :    
25 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
26 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
27 :    
28 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
29 :     for the dtCMatrix class.
30 : maechler 1253
31 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
32 :    
33 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
34 :     and methods for it.
35 :    
36 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
37 :    
38 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
39 :     arguments, such that M %*% 1:6 now works
40 :     * Tests/matprod.R: test the above
41 :    
42 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
43 : bates 1243
44 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
45 :     the ranef.lmer class.
46 :    
47 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
48 :     methods to extract the posterior variances from the bVar slot.
49 :    
50 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
51 :    
52 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
53 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
54 :    
55 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
56 :     * tests/simple: (extended)
57 :    
58 :     * R/sparseMatrix.R (isTriangular): now using much improved
59 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
60 :    
61 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
62 :    
63 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
64 :     (problem report from Franklin Parlamis). This should be done
65 : maechler 1238 generally.
66 : bates 1236
67 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
68 :    
69 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
70 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
71 :     update the plot methods.
72 :    
73 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
74 :    
75 :     * R/lmer.R (resid and ranef methods): Added methods for the
76 :     "residuals" and "resid" generic but only for linear mixed model
77 :     fits. Changed the ranef method to return a list of data frames so
78 :     that the plot methods now work.
79 :    
80 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
81 :    
82 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
83 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
84 :    
85 :     * DESCRIPTION (Date): New release
86 :    
87 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
88 :    
89 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
90 :    
91 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
92 :     * man/KNex.Rd: and other help files
93 :     * tests/*.R: several ones needed adaption
94 :     * inst/doc/Comparisons.Rnw: dito
95 :    
96 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
97 :    
98 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
99 :    
100 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
101 :    
102 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
103 :    
104 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
105 :    
106 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
107 :    
108 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 :     * R/dMatrix.R: enable things like M [ M < 10 ]
111 :     * R/dgeMatrix.R: implement it
112 :    
113 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
114 :    
115 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
116 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
117 :     * R/lmer.R (show): now works with summary()
118 :    
119 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
120 :    
121 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
122 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
123 :     support the above
124 :    
125 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
126 :    
127 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
128 :     Use glmFit$prior.weights for weights in a glmm.
129 :     Allow an option usePQL = FALSE to skip the PQL steps for the
130 :     Laplace method (and, in time, the AGQ method).
131 :    
132 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
133 :     into a separate function internal_mer_Xfactor to be able to call
134 :     it from internal_bhat.
135 :    
136 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
137 :    
138 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
139 :     testing; now again of all actual classes.
140 :    
141 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
142 :     use macros and define make_d_matrix_* and make_i_matrix_*
143 :     where _i_ is for the ldense routines:
144 :    
145 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
146 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
147 :    
148 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
149 :    
150 :    
151 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
154 :     many different kinds of matrices.
155 :     * R/*.R: quite a few new methods were needed for R CMD check with
156 :     new Matrix(). Very good for users playing around.
157 :    
158 :    
159 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
160 :    
161 :     * src/dgeMatrix.c (dMatrix_validate): new
162 :     * src/Mutils.c (dense_nonpacked_validate): new
163 :    
164 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
165 :    
166 :    
167 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
168 :    
169 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
170 :    
171 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
172 : bates 1119
173 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
174 :    
175 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
176 :     segfault in cases with multiple non-nested grouping factors.
177 :    
178 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
179 :    
180 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
181 :     (Depends): also on 'utils'
182 :    
183 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
184 :     * R/diagMatrix.R (Diagonal): constructor and methods for
185 :     diagonal matrices
186 :    
187 :     * R/ltTMatrix.R: new "minimal methods"
188 :    
189 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
190 :    
191 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
192 :     all methods (and help files).
193 :    
194 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
195 :    
196 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
197 :     for case (dimn. op no_dimn.)
198 :    
199 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
200 :    
201 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
202 : maechler 1084
203 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
204 :    
205 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
206 :     by Julian Faraway.
207 :    
208 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
209 :    
210 :     * R/Auxiliaries.R (try_as): new utility
211 :     * R/sparseMatrix.R: use try_as() in coercion to original class
212 :    
213 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
214 :    
215 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
216 :    
217 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
218 :    
219 :     * R/Auxiliaries.R (dimNamesCheck): added
220 :    
221 :     * R/Matrix.R (as.array), (as.vector): new
222 :    
223 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
224 :    
225 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
226 : maechler 956 default.
227 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
228 :     "pMatrix" now contains "sparseMatrix"
229 : maechler 954
230 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
231 :    
232 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
233 :    
234 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
235 :    
236 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
237 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
238 :    
239 :     * R/dspMatrix.R: typo in "t" method
240 :    
241 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
242 :    
243 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
244 :     * R/Tsparse.R: instead of R/gTMatrix.R
245 :     * R/Csparse.R: new
246 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
247 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
248 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
249 :     via cholmod
250 :    
251 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
252 :    
253 :     * R/Auxiliaries.R (non0ind): new function using new C code
254 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
255 :    
256 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
257 :    
258 :     * src/chm_common.h: header file required by all C sources that
259 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
260 : bates 917 called 'c' whose address is passed as the last argument to
261 :     (virtually) every CHOLMOD function.
262 :    
263 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
264 :    
265 :     * src/init.c: initialize and finalize the cholmod_common structure.
266 :    
267 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
268 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
269 :    
270 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
271 :    
272 :     * inst/test-tools.R: new file collecting the utility functions used
273 :     in ./tests/*.R
274 :    
275 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
276 :     * R/Matrix.R (cbind2): methods for NULL and missing
277 :    
278 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * R/AllClass.R: new "index" class for "[" and "[<-":
281 :     First cut at "symmetricMatrix" and "triangularMatrix"
282 :     * R/gTMatrix.R (.ind.prep): new function;
283 : maechler 1174 Logical and character indexing now work too.
284 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
285 :     * tests/indexing.R: new, including *.Rout.save
286 :     * tests/dgTMatrix.R: new
287 :    
288 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
289 :    
290 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
291 :     indicator pos not being updated. Also enforced upper triangular
292 :     for symmetric case. Need to coerce edges component of elements of
293 :     edge list - grr! (Why don't they define their classes cleanly?)
294 :    
295 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
296 :    
297 :     * R/Matrix.R: added first "[<-" methods; not yet functional
298 :     * R/denseMatrix.R: dito
299 :     * man/Subassign-methods.Rd: new help file for these
300 :    
301 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
302 :    
303 :     * DESCRIPTION (Version): 0.98-6
304 :    
305 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
306 :     matrices.
307 :    
308 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
309 :    
310 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
311 :     as( <logical>, "matrix")
312 :    
313 :     * R/pMatrix.R: coercion to "lgTMatrix"
314 :    
315 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
316 :     * man/gTMatrix-class.Rd:
317 :     * General slight re-organization of where "[" methods are defined.
318 :     more to come.
319 :    
320 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
321 : maechler 868
322 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
323 : maechler 871
324 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
325 :     * .....
326 :    
327 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
328 :    
329 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
330 :     or glmer objects.
331 :    
332 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
333 :    
334 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
335 :    
336 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
337 :    
338 :     * R/HBMM.R: finish re-writing R-only code.
339 :    
340 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
341 :    
342 :     * man/externalFormats.Rd: move documentation for writeHB and
343 :     writeMM here.
344 :    
345 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
346 :     (suggested by Paul Roecker).
347 :    
348 :     * tests/validObj.R (assertError): Comment out test that is failing
349 :     after recent changes in r-devel.
350 :    
351 : maechler 860
352 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
353 :    
354 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
355 :     * man/denseMatrix-class.Rd
356 :     * NAMESPACE: export it, and also export
357 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
358 :    
359 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
360 :    
361 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
362 :    
363 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
364 :     matrix_solve code (which was really, really wrong).
365 :    
366 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
367 : maechler 834
368 :     * DESCRIPTION (Version): 0.98-2
369 :    
370 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
371 :    
372 :     * R/lmer.R (abbrvNms): new
373 :     * R/lmer.R (mcmcsamp): allow transformed parameters
374 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
375 :     for the Harwell-Boeing and the MatrixMarket formats.
376 : maechler 834
377 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
378 :    
379 :     * man/dtrMatrix-class.Rd: add examples
380 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
381 : maechler 834
382 :     * TODO: note the dtpMatrix (docu) bug
383 :    
384 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
385 :     in order to ensure that new as.matrix() is used by old functions,
386 :     e.g., svd(), qr(), eigen(), dist(),..;
387 :     apply(), also matplot() or pairs().
388 :    
389 :    
390 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
391 :    
392 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
393 :     add comments about 'control' / lmerControl() arguments
394 :    
395 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
396 : bates 820
397 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
398 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
399 : bates 820
400 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
401 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
402 :    
403 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
404 :     .Call calls that were producing spurious output.
405 :    
406 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
407 : bates 801
408 :     * R/lmer.R (lmer): stored updated variance component estimates in
409 :     mer object for the generalized model. (Bug reported by Renaud
410 :     Lancelot).
411 :    
412 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
413 : bates 794
414 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
415 :     unidimensional case.
416 :    
417 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
418 : maechler 791
419 :     * DESCRIPTION (Version): 0.96-1
420 :    
421 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
422 : maechler 791
423 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
424 : bates 763
425 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
426 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
427 :    
428 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
429 : bates 763
430 :     * src/Makefile.win: Forgot to update this when Makefile changed.
431 :    
432 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
433 : bates 726
434 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
435 :     bug reported by Kurt Hornik and Michael Hahsler.
436 :    
437 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
438 : bates 725
439 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
440 :     logical sparse matrices. These will also be used in the symbolic
441 :     analysis for lmer objects.
442 :    
443 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
444 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
445 : maechler 791
446 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
447 : bates 714
448 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
449 :     colMeans, colSums, rowMeans and rowSums.
450 :    
451 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
452 : bates 692
453 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
454 :     multiplication operation.
455 :    
456 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
457 :     to dgetrs.
458 :    
459 :     * src/init.c: Fix cut-and-paste error in definition of
460 :     dgeMatrix_matrix_solve
461 :    
462 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
463 :    
464 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
465 : bates 692
466 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
467 :    
468 :     * DESCRIPTION: Eliminate import of stats.
469 :    
470 : maechler 791
471 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
472 : bates 692
473 :     * R/AllClass.R : add logical sparse matrix classes
474 :    
475 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
476 :    
477 :     * R/dgTMatrix.R: add "[" method for triplet matrices
478 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
479 :    
480 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
481 : maechler 687
482 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
483 :    
484 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
485 :     * R/sparseMatrix.R: %*%, crossprod()
486 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
487 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
488 :     * src/lmer.c (lmer_fitted): fix thinko
489 :    
490 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * R/AllClass.R: add two virtual sparse classes ``on top''
493 :    
494 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
495 :    
496 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
497 :     correspondingly fix examples and tests/ since new()
498 :     doesn't work for virtual classes.
499 :    
500 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
501 :    
502 :     * R/Matrix.R (as.matrix): method and one for unname()
503 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
504 :     also run for R 2.1.0; using as.matrix()
505 :    
506 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
507 : maechler 658
508 :     * R/pMatrix.R: "pMatrix" class added
509 :     * ....
510 :    
511 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
512 : bates 645
513 :     * R/dtpMatrix.R: Add unpack method and an example.
514 :    
515 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
516 :     of general symmetric matrices and associated S4 methods.
517 :    
518 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
519 :     +
520 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
521 :    
522 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
523 :     crossprod() and "%*%" methods added; tests, too.
524 :     * tests/matprod.R: new, for testing these
525 :    
526 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
527 : bates 599
528 :     * src/lmer.c (lmer_fitted): Added.
529 :    
530 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
531 : bates 596
532 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
533 :    
534 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
535 : bates 582
536 :     * src/*.c,po/,inst/po: Internationalization and localization of
537 :     the package.
538 :    
539 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
540 :     R_ldl.c file.
541 :    
542 :     * src/flame.[ch]: Removed these source files.
543 : maechler 658
544 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
545 :    
546 :     * src/LU.[ch],src/init.c: absorb in factorizations
547 :    
548 :     * src/Mutils.h: prepare for internationalization
549 :    
550 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
551 :     this file
552 :    
553 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
554 :    
555 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
556 :    
557 :     * R/dtrMatrix.R: fix t() method
558 :    
559 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
560 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
561 : maechler 578 * tests/group-methods.R : and test them.
562 :    
563 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
564 :     border case
565 :    
566 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
567 :    
568 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
569 : maechler 578
570 :     * src/dgBCMatrix.c:
571 :     * src/lmer.c: many changes
572 :     * ...
573 :    
574 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
575 :    
576 :     * R/Matrix.R: add more sophisticated show() method.
577 :    
578 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
579 :    
580 :     * */* : almost complete reorganization of classes.
581 :    
582 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
583 : bates 460
584 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
585 :     for the geMatrix class.
586 :    
587 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
588 : bates 460
589 :     * src/Makefile (clean): Remove *.a and *.so
590 :    
591 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
592 :    
593 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
594 : bates 460
595 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
596 : bates 460 had an effect in cases with more than 2 grouping factors.
597 :    
598 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
599 : bates 415
600 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
601 :    
602 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
603 : bates 410
604 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
605 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
606 :    
607 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
608 : bates 392
609 :     * R/sscMatrix.R: Add determinant methods
610 :    
611 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
612 :     for tripletMatrix to matrix.
613 :    
614 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
615 : bates 388
616 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
617 :     no longer used.
618 :    
619 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
620 :     with dynamic allocation of scratch arrays.
621 :    
622 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
623 :     for multivariate random effects with multiple grouping factors.
624 :     Fixes part but not all of #15.
625 :    
626 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
627 : bates 375
628 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
629 :     scalar grouping factors corrected.
630 :    
631 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
632 : bates 375
633 :     * src/bCrosstab.c: remove diag_update which is no longer used
634 :    
635 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
636 : bates 350
637 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
638 :     .h file can be included.
639 :    
640 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
641 : bates 342
642 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
643 : bates 342 Complete allocation of slots in NEW_OBJECT.
644 :    
645 :     * src/Mutils.h: Moved list of symbols to an include file
646 :    
647 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
648 : bates 342
649 :     * src/geMutils.c (Matrix_init): remove unused function
650 :    
651 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
652 : bates 342
653 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
654 :    
655 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
656 : bates 327
657 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
658 :    
659 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
660 : bates 303
661 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
662 :    
663 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
664 : bates 296
665 :     * src/init.c: Created R_init_Matrix and added registration of C
666 :     routines.
667 :    
668 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
669 : bates 283
670 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
671 :    
672 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
673 : bates 229
674 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
675 :    
676 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
677 :    
678 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
679 :    
680 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
681 :    
682 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
683 :     ssclme_update_mm
684 :    
685 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
686 :    
687 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
688 :     in the order of unconstrained and constrained parameters.
689 :     (ssclme_gradient): Added the gradients (not yet correct for
690 :     multidimensional, unconstrained case).
691 :    
692 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
693 :    
694 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
695 :    
696 :     * src/Makefile.win: Remove unneeded ranlib call
697 :    
698 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
699 :    
700 :     * DESCRIPTION (Version): New release
701 :    
702 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
703 :    
704 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
705 :    
706 :     * src/triplet_to_col.c: Create triplet_to_col as a native
707 : maechler 658 function, not the version from umfpack. There were problems with
708 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
709 :     only one umfpack routine being used so I moved it here.
710 :    
711 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
712 :    
713 :     * src/ssclme.c (ssclme_variances): New function.
714 :    
715 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
716 :    
717 :     * src/ssclme.c (ssclme_fitted): Added function.
718 :    
719 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
720 :    
721 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
722 :     store the dimnames in the XtX and bVar slots
723 :     (ssclme_update_mm): Change the dimensions of the bVar slot
724 :     components and the returned value from ssclme_ranef.
725 :    
726 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
727 :    
728 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
729 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
730 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
731 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
732 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
733 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
734 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
735 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
736 :     Moved the pdMat classes from the lme4 package.
737 :    
738 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
739 :    
740 :     * man/ssclme-class.Rd: Update definition and documentation of the
741 :     ssclme class to include the DIsqrt slot.
742 :    
743 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
744 :     (much faster using dsyrk, a level 3 BLAS routine).
745 :    
746 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
747 :    
748 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
749 :    
750 :     * tests/ssclme.R: Modify the test to account for the permutation
751 :     of the levels of the grouping factors.
752 :    
753 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
754 :    
755 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
756 :     directly into the ssclme class definition.
757 :    
758 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
759 :    
760 :     * DESCRIPTION (Date): New release
761 :    
762 :     * man/ssclme-class.Rd: new file.
763 :    
764 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
765 :     works and it's fast!
766 :    
767 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
768 :    
769 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
770 :    
771 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
772 :    
773 :     * DESCRIPTION (Date): New release
774 :    
775 :     * NAMESPACE: Don't export ssclme.
776 :    
777 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
778 :     school data.
779 :    
780 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
781 :    
782 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
783 :     keep track of the fixed-effects and the response. Counts also
784 :     gets an extra element, which is always one.
785 :    
786 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
787 :    
788 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
789 :    
790 :     * src/cscMatrix.c (csc_transpose): new function
791 :    
792 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
793 :     (csc_components_transpose): new function
794 :    
795 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
796 :    
797 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
798 :     triplets
799 :    
800 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
801 :    
802 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
803 :    
804 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
805 :     and all other .h files in src.
806 :    
807 :     * src/Makefile.win: This and other Makefile.win files contributed
808 :     by Brian Ripley.
809 :    
810 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
811 :    
812 :     * R/syMatrix.R: Added methods for "%*%".
813 :    
814 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
815 :     poMatrix object.
816 :    
817 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
818 :    
819 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
820 :    
821 :     2004-01-25 Douglas Bates <bates@bates2_home>
822 :    
823 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
824 :    
825 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
826 :     of nrow.
827 :    
828 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
829 :    
830 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
831 :     subdirectories.
832 :    
833 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
834 :    
835 :     * src/taucs.h: Accidently referred to global header files
836 :     instead of local files.
837 :    
838 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
839 :    
840 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
841 :     and methods and replaced all classes with S4 classes.
842 :    
843 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
844 :    
845 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
846 :    
847 :     * src/R_LapackPP.cc: Change method of calculating determinants
848 :    
849 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
850 :    
851 :     * DESCRIPTION (Version): removed empty data directory as requested
852 :     by CRAN maintainers. Changed version number and date.
853 :    
854 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
855 :    
856 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
857 :     under Windows.
858 :    
859 :     * Added configure.win and src/Makevars.win as requested by Brian
860 :     Ripley.
861 :    
862 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
863 :    
864 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
865 :     Hornik.
866 :    
867 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
868 :    
869 :     * configure.ac: Replaced configure.in with configure.ac
870 :     contributed by Kurt Hornik.
871 :    
872 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
873 :     version for R-1.5.0
874 :    
875 : maechler 512
876 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
877 :    
878 :     * man/eigen.Rd: Removed the .Alias in the example

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge