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Annotation of /pkg/ChangeLog

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Revision 1265 - (view) (download)

1 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
2 :    
3 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
4 :     generics lowerTriMatrix and upperTriMatrix along with methods for
5 :     the Csparse virtual class. Also added a C function Csparse_band
6 :     that implements these methods by calling cholmod_band.
7 :    
8 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
9 :    
10 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
11 :     erased when it was NULL. This led to invalid subselections!
12 :    
13 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
14 :    
15 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
16 :     in method for "t" so as not to lose the unit diagonal property.
17 :    
18 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
19 :    
20 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
21 :     and methods. This is now an option to the ranef method for the
22 :     mer class.
23 :    
24 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
25 :     compressed column-oriented matrix. Minor formatting cleanup.
26 :    
27 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
28 :     objects.
29 :    
30 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
31 :    
32 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
33 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
34 :    
35 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
36 :    
37 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
38 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
39 :    
40 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
41 :     for the dtCMatrix class.
42 : maechler 1253
43 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
44 :    
45 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
46 :     and methods for it.
47 :    
48 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
49 :    
50 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
51 :     arguments, such that M %*% 1:6 now works
52 :     * Tests/matprod.R: test the above
53 :    
54 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
55 : bates 1243
56 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
57 :     the ranef.lmer class.
58 :    
59 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
60 :     methods to extract the posterior variances from the bVar slot.
61 :    
62 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
63 :    
64 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
65 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
66 :    
67 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
68 :     * tests/simple: (extended)
69 :    
70 :     * R/sparseMatrix.R (isTriangular): now using much improved
71 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
72 :    
73 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
74 :    
75 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
76 :     (problem report from Franklin Parlamis). This should be done
77 : maechler 1238 generally.
78 : bates 1236
79 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
80 :    
81 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
82 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
83 :     update the plot methods.
84 :    
85 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
86 :    
87 :     * R/lmer.R (resid and ranef methods): Added methods for the
88 :     "residuals" and "resid" generic but only for linear mixed model
89 :     fits. Changed the ranef method to return a list of data frames so
90 :     that the plot methods now work.
91 :    
92 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
93 :    
94 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
95 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
96 :    
97 :     * DESCRIPTION (Date): New release
98 :    
99 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
100 :    
101 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
102 :    
103 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
104 :     * man/KNex.Rd: and other help files
105 :     * tests/*.R: several ones needed adaption
106 :     * inst/doc/Comparisons.Rnw: dito
107 :    
108 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
111 :    
112 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
113 :    
114 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
115 :    
116 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
117 :    
118 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
119 :    
120 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
121 :    
122 :     * R/dMatrix.R: enable things like M [ M < 10 ]
123 :     * R/dgeMatrix.R: implement it
124 :    
125 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
126 :    
127 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
128 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
129 :     * R/lmer.R (show): now works with summary()
130 :    
131 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
132 :    
133 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
134 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
135 :     support the above
136 :    
137 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
138 :    
139 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
140 :     Use glmFit$prior.weights for weights in a glmm.
141 :     Allow an option usePQL = FALSE to skip the PQL steps for the
142 :     Laplace method (and, in time, the AGQ method).
143 :    
144 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
145 :     into a separate function internal_mer_Xfactor to be able to call
146 :     it from internal_bhat.
147 :    
148 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
149 :    
150 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
151 :     testing; now again of all actual classes.
152 :    
153 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
154 :     use macros and define make_d_matrix_* and make_i_matrix_*
155 :     where _i_ is for the ldense routines:
156 :    
157 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
158 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
159 :    
160 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
161 :    
162 :    
163 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
164 :    
165 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
166 :     many different kinds of matrices.
167 :     * R/*.R: quite a few new methods were needed for R CMD check with
168 :     new Matrix(). Very good for users playing around.
169 :    
170 :    
171 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
172 :    
173 :     * src/dgeMatrix.c (dMatrix_validate): new
174 :     * src/Mutils.c (dense_nonpacked_validate): new
175 :    
176 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
177 :    
178 :    
179 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
180 :    
181 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
182 :    
183 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
184 : bates 1119
185 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
186 :    
187 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
188 :     segfault in cases with multiple non-nested grouping factors.
189 :    
190 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
191 :    
192 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
193 :     (Depends): also on 'utils'
194 :    
195 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
196 :     * R/diagMatrix.R (Diagonal): constructor and methods for
197 :     diagonal matrices
198 :    
199 :     * R/ltTMatrix.R: new "minimal methods"
200 :    
201 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
202 :    
203 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
204 :     all methods (and help files).
205 :    
206 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
207 :    
208 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
209 :     for case (dimn. op no_dimn.)
210 :    
211 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
212 :    
213 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
214 : maechler 1084
215 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
216 :    
217 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
218 :     by Julian Faraway.
219 :    
220 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * R/Auxiliaries.R (try_as): new utility
223 :     * R/sparseMatrix.R: use try_as() in coercion to original class
224 :    
225 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
226 :    
227 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
228 :    
229 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
230 :    
231 :     * R/Auxiliaries.R (dimNamesCheck): added
232 :    
233 :     * R/Matrix.R (as.array), (as.vector): new
234 :    
235 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
236 :    
237 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
238 : maechler 956 default.
239 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
240 :     "pMatrix" now contains "sparseMatrix"
241 : maechler 954
242 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
243 :    
244 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
245 :    
246 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
247 :    
248 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
249 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
250 :    
251 :     * R/dspMatrix.R: typo in "t" method
252 :    
253 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
254 :    
255 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
256 :     * R/Tsparse.R: instead of R/gTMatrix.R
257 :     * R/Csparse.R: new
258 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
259 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
260 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
261 :     via cholmod
262 :    
263 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * R/Auxiliaries.R (non0ind): new function using new C code
266 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
267 :    
268 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
269 :    
270 :     * src/chm_common.h: header file required by all C sources that
271 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
272 : bates 917 called 'c' whose address is passed as the last argument to
273 :     (virtually) every CHOLMOD function.
274 :    
275 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
276 :    
277 :     * src/init.c: initialize and finalize the cholmod_common structure.
278 :    
279 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
280 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
281 :    
282 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
283 :    
284 :     * inst/test-tools.R: new file collecting the utility functions used
285 :     in ./tests/*.R
286 :    
287 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
288 :     * R/Matrix.R (cbind2): methods for NULL and missing
289 :    
290 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * R/AllClass.R: new "index" class for "[" and "[<-":
293 :     First cut at "symmetricMatrix" and "triangularMatrix"
294 :     * R/gTMatrix.R (.ind.prep): new function;
295 : maechler 1174 Logical and character indexing now work too.
296 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
297 :     * tests/indexing.R: new, including *.Rout.save
298 :     * tests/dgTMatrix.R: new
299 :    
300 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
301 :    
302 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
303 :     indicator pos not being updated. Also enforced upper triangular
304 :     for symmetric case. Need to coerce edges component of elements of
305 :     edge list - grr! (Why don't they define their classes cleanly?)
306 :    
307 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
308 :    
309 :     * R/Matrix.R: added first "[<-" methods; not yet functional
310 :     * R/denseMatrix.R: dito
311 :     * man/Subassign-methods.Rd: new help file for these
312 :    
313 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
314 :    
315 :     * DESCRIPTION (Version): 0.98-6
316 :    
317 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
318 :     matrices.
319 :    
320 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
321 :    
322 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
323 :     as( <logical>, "matrix")
324 :    
325 :     * R/pMatrix.R: coercion to "lgTMatrix"
326 :    
327 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
328 :     * man/gTMatrix-class.Rd:
329 :     * General slight re-organization of where "[" methods are defined.
330 :     more to come.
331 :    
332 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
333 : maechler 868
334 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
335 : maechler 871
336 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
337 :     * .....
338 :    
339 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
340 :    
341 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
342 :     or glmer objects.
343 :    
344 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
345 :    
346 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
347 :    
348 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
349 :    
350 :     * R/HBMM.R: finish re-writing R-only code.
351 :    
352 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
353 :    
354 :     * man/externalFormats.Rd: move documentation for writeHB and
355 :     writeMM here.
356 :    
357 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
358 :     (suggested by Paul Roecker).
359 :    
360 :     * tests/validObj.R (assertError): Comment out test that is failing
361 :     after recent changes in r-devel.
362 :    
363 : maechler 860
364 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
365 :    
366 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
367 :     * man/denseMatrix-class.Rd
368 :     * NAMESPACE: export it, and also export
369 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
370 :    
371 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
372 :    
373 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
374 :    
375 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
376 :     matrix_solve code (which was really, really wrong).
377 :    
378 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
379 : maechler 834
380 :     * DESCRIPTION (Version): 0.98-2
381 :    
382 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
383 :    
384 :     * R/lmer.R (abbrvNms): new
385 :     * R/lmer.R (mcmcsamp): allow transformed parameters
386 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
387 :     for the Harwell-Boeing and the MatrixMarket formats.
388 : maechler 834
389 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
390 :    
391 :     * man/dtrMatrix-class.Rd: add examples
392 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
393 : maechler 834
394 :     * TODO: note the dtpMatrix (docu) bug
395 :    
396 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
397 :     in order to ensure that new as.matrix() is used by old functions,
398 :     e.g., svd(), qr(), eigen(), dist(),..;
399 :     apply(), also matplot() or pairs().
400 :    
401 :    
402 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
403 :    
404 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
405 :     add comments about 'control' / lmerControl() arguments
406 :    
407 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
408 : bates 820
409 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
410 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
411 : bates 820
412 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
413 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
414 :    
415 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
416 :     .Call calls that were producing spurious output.
417 :    
418 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
419 : bates 801
420 :     * R/lmer.R (lmer): stored updated variance component estimates in
421 :     mer object for the generalized model. (Bug reported by Renaud
422 :     Lancelot).
423 :    
424 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
425 : bates 794
426 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
427 :     unidimensional case.
428 :    
429 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
430 : maechler 791
431 :     * DESCRIPTION (Version): 0.96-1
432 :    
433 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
434 : maechler 791
435 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
436 : bates 763
437 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
438 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
439 :    
440 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
441 : bates 763
442 :     * src/Makefile.win: Forgot to update this when Makefile changed.
443 :    
444 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
445 : bates 726
446 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
447 :     bug reported by Kurt Hornik and Michael Hahsler.
448 :    
449 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
450 : bates 725
451 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
452 :     logical sparse matrices. These will also be used in the symbolic
453 :     analysis for lmer objects.
454 :    
455 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
456 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
457 : maechler 791
458 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
459 : bates 714
460 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
461 :     colMeans, colSums, rowMeans and rowSums.
462 :    
463 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
464 : bates 692
465 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
466 :     multiplication operation.
467 :    
468 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
469 :     to dgetrs.
470 :    
471 :     * src/init.c: Fix cut-and-paste error in definition of
472 :     dgeMatrix_matrix_solve
473 :    
474 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
475 :    
476 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
477 : bates 692
478 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
479 :    
480 :     * DESCRIPTION: Eliminate import of stats.
481 :    
482 : maechler 791
483 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
484 : bates 692
485 :     * R/AllClass.R : add logical sparse matrix classes
486 :    
487 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
488 :    
489 :     * R/dgTMatrix.R: add "[" method for triplet matrices
490 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
491 :    
492 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
493 : maechler 687
494 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
495 :    
496 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
497 :     * R/sparseMatrix.R: %*%, crossprod()
498 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
499 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
500 :     * src/lmer.c (lmer_fitted): fix thinko
501 :    
502 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
503 :    
504 :     * R/AllClass.R: add two virtual sparse classes ``on top''
505 :    
506 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
507 :    
508 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
509 :     correspondingly fix examples and tests/ since new()
510 :     doesn't work for virtual classes.
511 :    
512 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
513 :    
514 :     * R/Matrix.R (as.matrix): method and one for unname()
515 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
516 :     also run for R 2.1.0; using as.matrix()
517 :    
518 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
519 : maechler 658
520 :     * R/pMatrix.R: "pMatrix" class added
521 :     * ....
522 :    
523 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
524 : bates 645
525 :     * R/dtpMatrix.R: Add unpack method and an example.
526 :    
527 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
528 :     of general symmetric matrices and associated S4 methods.
529 :    
530 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
531 :     +
532 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
533 :    
534 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
535 :     crossprod() and "%*%" methods added; tests, too.
536 :     * tests/matprod.R: new, for testing these
537 :    
538 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
539 : bates 599
540 :     * src/lmer.c (lmer_fitted): Added.
541 :    
542 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
543 : bates 596
544 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
545 :    
546 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
547 : bates 582
548 :     * src/*.c,po/,inst/po: Internationalization and localization of
549 :     the package.
550 :    
551 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
552 :     R_ldl.c file.
553 :    
554 :     * src/flame.[ch]: Removed these source files.
555 : maechler 658
556 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
557 :    
558 :     * src/LU.[ch],src/init.c: absorb in factorizations
559 :    
560 :     * src/Mutils.h: prepare for internationalization
561 :    
562 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
563 :     this file
564 :    
565 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
566 :    
567 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
568 :    
569 :     * R/dtrMatrix.R: fix t() method
570 :    
571 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
572 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
573 : maechler 578 * tests/group-methods.R : and test them.
574 :    
575 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
576 :     border case
577 :    
578 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
579 :    
580 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
581 : maechler 578
582 :     * src/dgBCMatrix.c:
583 :     * src/lmer.c: many changes
584 :     * ...
585 :    
586 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
587 :    
588 :     * R/Matrix.R: add more sophisticated show() method.
589 :    
590 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
591 :    
592 :     * */* : almost complete reorganization of classes.
593 :    
594 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
595 : bates 460
596 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
597 :     for the geMatrix class.
598 :    
599 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
600 : bates 460
601 :     * src/Makefile (clean): Remove *.a and *.so
602 :    
603 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
604 :    
605 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
606 : bates 460
607 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
608 : bates 460 had an effect in cases with more than 2 grouping factors.
609 :    
610 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
611 : bates 415
612 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
613 :    
614 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
615 : bates 410
616 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
617 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
618 :    
619 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
620 : bates 392
621 :     * R/sscMatrix.R: Add determinant methods
622 :    
623 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
624 :     for tripletMatrix to matrix.
625 :    
626 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
627 : bates 388
628 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
629 :     no longer used.
630 :    
631 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
632 :     with dynamic allocation of scratch arrays.
633 :    
634 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
635 :     for multivariate random effects with multiple grouping factors.
636 :     Fixes part but not all of #15.
637 :    
638 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
639 : bates 375
640 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
641 :     scalar grouping factors corrected.
642 :    
643 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
644 : bates 375
645 :     * src/bCrosstab.c: remove diag_update which is no longer used
646 :    
647 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
648 : bates 350
649 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
650 :     .h file can be included.
651 :    
652 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
653 : bates 342
654 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
655 : bates 342 Complete allocation of slots in NEW_OBJECT.
656 :    
657 :     * src/Mutils.h: Moved list of symbols to an include file
658 :    
659 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
660 : bates 342
661 :     * src/geMutils.c (Matrix_init): remove unused function
662 :    
663 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
664 : bates 342
665 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
666 :    
667 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
668 : bates 327
669 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
670 :    
671 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
672 : bates 303
673 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
674 :    
675 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
676 : bates 296
677 :     * src/init.c: Created R_init_Matrix and added registration of C
678 :     routines.
679 :    
680 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
681 : bates 283
682 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
683 :    
684 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
685 : bates 229
686 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
687 :    
688 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
691 :    
692 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
693 :    
694 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
695 :     ssclme_update_mm
696 :    
697 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
698 :    
699 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
700 :     in the order of unconstrained and constrained parameters.
701 :     (ssclme_gradient): Added the gradients (not yet correct for
702 :     multidimensional, unconstrained case).
703 :    
704 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
705 :    
706 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
707 :    
708 :     * src/Makefile.win: Remove unneeded ranlib call
709 :    
710 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
711 :    
712 :     * DESCRIPTION (Version): New release
713 :    
714 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
715 :    
716 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
717 :    
718 :     * src/triplet_to_col.c: Create triplet_to_col as a native
719 : maechler 658 function, not the version from umfpack. There were problems with
720 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
721 :     only one umfpack routine being used so I moved it here.
722 :    
723 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
724 :    
725 :     * src/ssclme.c (ssclme_variances): New function.
726 :    
727 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
728 :    
729 :     * src/ssclme.c (ssclme_fitted): Added function.
730 :    
731 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
732 :    
733 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
734 :     store the dimnames in the XtX and bVar slots
735 :     (ssclme_update_mm): Change the dimensions of the bVar slot
736 :     components and the returned value from ssclme_ranef.
737 :    
738 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
739 :    
740 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
741 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
742 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
743 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
744 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
745 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
746 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
747 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
748 :     Moved the pdMat classes from the lme4 package.
749 :    
750 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
751 :    
752 :     * man/ssclme-class.Rd: Update definition and documentation of the
753 :     ssclme class to include the DIsqrt slot.
754 :    
755 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
756 :     (much faster using dsyrk, a level 3 BLAS routine).
757 :    
758 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
759 :    
760 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
761 :    
762 :     * tests/ssclme.R: Modify the test to account for the permutation
763 :     of the levels of the grouping factors.
764 :    
765 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
766 :    
767 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
768 :     directly into the ssclme class definition.
769 :    
770 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
771 :    
772 :     * DESCRIPTION (Date): New release
773 :    
774 :     * man/ssclme-class.Rd: new file.
775 :    
776 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
777 :     works and it's fast!
778 :    
779 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
780 :    
781 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
782 :    
783 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
784 :    
785 :     * DESCRIPTION (Date): New release
786 :    
787 :     * NAMESPACE: Don't export ssclme.
788 :    
789 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
790 :     school data.
791 :    
792 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
793 :    
794 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
795 :     keep track of the fixed-effects and the response. Counts also
796 :     gets an extra element, which is always one.
797 :    
798 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
799 :    
800 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
801 :    
802 :     * src/cscMatrix.c (csc_transpose): new function
803 :    
804 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
805 :     (csc_components_transpose): new function
806 :    
807 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
808 :    
809 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
810 :     triplets
811 :    
812 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
813 :    
814 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
815 :    
816 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
817 :     and all other .h files in src.
818 :    
819 :     * src/Makefile.win: This and other Makefile.win files contributed
820 :     by Brian Ripley.
821 :    
822 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
823 :    
824 :     * R/syMatrix.R: Added methods for "%*%".
825 :    
826 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
827 :     poMatrix object.
828 :    
829 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
830 :    
831 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
832 :    
833 :     2004-01-25 Douglas Bates <bates@bates2_home>
834 :    
835 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
836 :    
837 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
838 :     of nrow.
839 :    
840 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
841 :    
842 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
843 :     subdirectories.
844 :    
845 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
846 :    
847 :     * src/taucs.h: Accidently referred to global header files
848 :     instead of local files.
849 :    
850 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
851 :    
852 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
853 :     and methods and replaced all classes with S4 classes.
854 :    
855 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
856 :    
857 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
858 :    
859 :     * src/R_LapackPP.cc: Change method of calculating determinants
860 :    
861 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
862 :    
863 :     * DESCRIPTION (Version): removed empty data directory as requested
864 :     by CRAN maintainers. Changed version number and date.
865 :    
866 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
867 :    
868 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
869 :     under Windows.
870 :    
871 :     * Added configure.win and src/Makevars.win as requested by Brian
872 :     Ripley.
873 :    
874 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
875 :    
876 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
877 :     Hornik.
878 :    
879 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
880 :    
881 :     * configure.ac: Replaced configure.in with configure.ac
882 :     contributed by Kurt Hornik.
883 :    
884 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
885 :     version for R-1.5.0
886 :    
887 : maechler 512
888 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
889 :    
890 :     * man/eigen.Rd: Removed the .Alias in the example

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