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Annotation of /pkg/ChangeLog

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

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