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Annotation of /pkg/ChangeLog

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

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