SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1232 - (view) (download)

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