SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1257 - (view) (download)

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