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Annotation of /pkg/ChangeLog

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1 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
4 :     the C code depending on a slot structure that's no longer valid.
5 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
6 :    
7 :    
8 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
9 :    
10 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
11 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
12 :     and added a general band extractor.
13 :    
14 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
15 :    
16 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
17 :     allowable range with NAs. Added a corresponding check in the
18 :     validity check for the pedigree class.
19 :    
20 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
21 :     crossprod methods now inherits from symmetricMatrix.
22 :    
23 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
24 :    
25 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
26 :     generics lowerTriMatrix and upperTriMatrix along with methods for
27 :     the Csparse virtual class. Also added a C function Csparse_band
28 :     that implements these methods by calling cholmod_band.
29 :    
30 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
31 :    
32 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
33 :     erased when it was NULL. This led to invalid subselections!
34 :    
35 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
36 :    
37 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
38 :     in method for "t" so as not to lose the unit diagonal property.
39 :    
40 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
41 :    
42 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
43 :     and methods. This is now an option to the ranef method for the
44 :     mer class.
45 :    
46 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
47 :     compressed column-oriented matrix. Minor formatting cleanup.
48 :    
49 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
50 :     objects.
51 :    
52 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
53 :    
54 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
55 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
56 :    
57 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
58 :    
59 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
60 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
61 :    
62 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
63 :     for the dtCMatrix class.
64 : maechler 1253
65 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
66 :    
67 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
68 :     and methods for it.
69 :    
70 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
73 :     arguments, such that M %*% 1:6 now works
74 :     * Tests/matprod.R: test the above
75 :    
76 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
77 : bates 1243
78 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
79 :     the ranef.lmer class.
80 :    
81 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
82 :     methods to extract the posterior variances from the bVar slot.
83 :    
84 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
85 :    
86 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
87 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
88 :    
89 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
90 :     * tests/simple: (extended)
91 :    
92 :     * R/sparseMatrix.R (isTriangular): now using much improved
93 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
94 :    
95 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
96 :    
97 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
98 :     (problem report from Franklin Parlamis). This should be done
99 : maechler 1238 generally.
100 : bates 1236
101 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
102 :    
103 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
104 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
105 :     update the plot methods.
106 :    
107 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
108 :    
109 :     * R/lmer.R (resid and ranef methods): Added methods for the
110 :     "residuals" and "resid" generic but only for linear mixed model
111 :     fits. Changed the ranef method to return a list of data frames so
112 :     that the plot methods now work.
113 :    
114 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
115 :    
116 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
117 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
118 :    
119 :     * DESCRIPTION (Date): New release
120 :    
121 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
122 :    
123 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
124 :    
125 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
126 :     * man/KNex.Rd: and other help files
127 :     * tests/*.R: several ones needed adaption
128 :     * inst/doc/Comparisons.Rnw: dito
129 :    
130 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
131 :    
132 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
133 :    
134 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
135 :    
136 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
137 :    
138 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
139 :    
140 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
141 :    
142 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * R/dMatrix.R: enable things like M [ M < 10 ]
145 :     * R/dgeMatrix.R: implement it
146 :    
147 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
150 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
151 :     * R/lmer.R (show): now works with summary()
152 :    
153 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
154 :    
155 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
156 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
157 :     support the above
158 :    
159 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
160 :    
161 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
162 :     Use glmFit$prior.weights for weights in a glmm.
163 :     Allow an option usePQL = FALSE to skip the PQL steps for the
164 :     Laplace method (and, in time, the AGQ method).
165 :    
166 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
167 :     into a separate function internal_mer_Xfactor to be able to call
168 :     it from internal_bhat.
169 :    
170 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
173 :     testing; now again of all actual classes.
174 :    
175 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
176 :     use macros and define make_d_matrix_* and make_i_matrix_*
177 :     where _i_ is for the ldense routines:
178 :    
179 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
180 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
181 :    
182 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
183 :    
184 :    
185 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
186 :    
187 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
188 :     many different kinds of matrices.
189 :     * R/*.R: quite a few new methods were needed for R CMD check with
190 :     new Matrix(). Very good for users playing around.
191 :    
192 :    
193 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
194 :    
195 :     * src/dgeMatrix.c (dMatrix_validate): new
196 :     * src/Mutils.c (dense_nonpacked_validate): new
197 :    
198 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
199 :    
200 :    
201 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
202 :    
203 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
204 :    
205 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
206 : bates 1119
207 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
208 :    
209 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
210 :     segfault in cases with multiple non-nested grouping factors.
211 :    
212 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
213 :    
214 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
215 :     (Depends): also on 'utils'
216 :    
217 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
218 :     * R/diagMatrix.R (Diagonal): constructor and methods for
219 :     diagonal matrices
220 :    
221 :     * R/ltTMatrix.R: new "minimal methods"
222 :    
223 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
224 :    
225 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
226 :     all methods (and help files).
227 :    
228 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
231 :     for case (dimn. op no_dimn.)
232 :    
233 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
234 :    
235 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
236 : maechler 1084
237 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
238 :    
239 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
240 :     by Julian Faraway.
241 :    
242 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
243 :    
244 :     * R/Auxiliaries.R (try_as): new utility
245 :     * R/sparseMatrix.R: use try_as() in coercion to original class
246 :    
247 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
248 :    
249 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
250 :    
251 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
252 :    
253 :     * R/Auxiliaries.R (dimNamesCheck): added
254 :    
255 :     * R/Matrix.R (as.array), (as.vector): new
256 :    
257 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
258 :    
259 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
260 : maechler 956 default.
261 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
262 :     "pMatrix" now contains "sparseMatrix"
263 : maechler 954
264 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
265 :    
266 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
267 :    
268 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
269 :    
270 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
271 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
272 :    
273 :     * R/dspMatrix.R: typo in "t" method
274 :    
275 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
276 :    
277 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
278 :     * R/Tsparse.R: instead of R/gTMatrix.R
279 :     * R/Csparse.R: new
280 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
281 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
282 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
283 :     via cholmod
284 :    
285 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * R/Auxiliaries.R (non0ind): new function using new C code
288 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
289 :    
290 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
291 :    
292 :     * src/chm_common.h: header file required by all C sources that
293 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
294 : bates 917 called 'c' whose address is passed as the last argument to
295 :     (virtually) every CHOLMOD function.
296 :    
297 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
298 :    
299 :     * src/init.c: initialize and finalize the cholmod_common structure.
300 :    
301 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
302 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
303 :    
304 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
305 :    
306 :     * inst/test-tools.R: new file collecting the utility functions used
307 :     in ./tests/*.R
308 :    
309 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
310 :     * R/Matrix.R (cbind2): methods for NULL and missing
311 :    
312 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
313 :    
314 :     * R/AllClass.R: new "index" class for "[" and "[<-":
315 :     First cut at "symmetricMatrix" and "triangularMatrix"
316 :     * R/gTMatrix.R (.ind.prep): new function;
317 : maechler 1174 Logical and character indexing now work too.
318 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
319 :     * tests/indexing.R: new, including *.Rout.save
320 :     * tests/dgTMatrix.R: new
321 :    
322 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
323 :    
324 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
325 :     indicator pos not being updated. Also enforced upper triangular
326 :     for symmetric case. Need to coerce edges component of elements of
327 :     edge list - grr! (Why don't they define their classes cleanly?)
328 :    
329 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
330 :    
331 :     * R/Matrix.R: added first "[<-" methods; not yet functional
332 :     * R/denseMatrix.R: dito
333 :     * man/Subassign-methods.Rd: new help file for these
334 :    
335 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
336 :    
337 :     * DESCRIPTION (Version): 0.98-6
338 :    
339 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
340 :     matrices.
341 :    
342 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
343 :    
344 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
345 :     as( <logical>, "matrix")
346 :    
347 :     * R/pMatrix.R: coercion to "lgTMatrix"
348 :    
349 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
350 :     * man/gTMatrix-class.Rd:
351 :     * General slight re-organization of where "[" methods are defined.
352 :     more to come.
353 :    
354 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
355 : maechler 868
356 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
357 : maechler 871
358 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
359 :     * .....
360 :    
361 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
362 :    
363 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
364 :     or glmer objects.
365 :    
366 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
369 :    
370 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
371 :    
372 :     * R/HBMM.R: finish re-writing R-only code.
373 :    
374 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
375 :    
376 :     * man/externalFormats.Rd: move documentation for writeHB and
377 :     writeMM here.
378 :    
379 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
380 :     (suggested by Paul Roecker).
381 :    
382 :     * tests/validObj.R (assertError): Comment out test that is failing
383 :     after recent changes in r-devel.
384 :    
385 : maechler 860
386 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
387 :    
388 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
389 :     * man/denseMatrix-class.Rd
390 :     * NAMESPACE: export it, and also export
391 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
392 :    
393 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
394 :    
395 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
396 :    
397 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
398 :     matrix_solve code (which was really, really wrong).
399 :    
400 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
401 : maechler 834
402 :     * DESCRIPTION (Version): 0.98-2
403 :    
404 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
405 :    
406 :     * R/lmer.R (abbrvNms): new
407 :     * R/lmer.R (mcmcsamp): allow transformed parameters
408 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
409 :     for the Harwell-Boeing and the MatrixMarket formats.
410 : maechler 834
411 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
412 :    
413 :     * man/dtrMatrix-class.Rd: add examples
414 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
415 : maechler 834
416 :     * TODO: note the dtpMatrix (docu) bug
417 :    
418 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
419 :     in order to ensure that new as.matrix() is used by old functions,
420 :     e.g., svd(), qr(), eigen(), dist(),..;
421 :     apply(), also matplot() or pairs().
422 :    
423 :    
424 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
425 :    
426 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
427 :     add comments about 'control' / lmerControl() arguments
428 :    
429 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
430 : bates 820
431 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
432 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
433 : bates 820
434 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
435 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
436 :    
437 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
438 :     .Call calls that were producing spurious output.
439 :    
440 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
441 : bates 801
442 :     * R/lmer.R (lmer): stored updated variance component estimates in
443 :     mer object for the generalized model. (Bug reported by Renaud
444 :     Lancelot).
445 :    
446 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
447 : bates 794
448 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
449 :     unidimensional case.
450 :    
451 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
452 : maechler 791
453 :     * DESCRIPTION (Version): 0.96-1
454 :    
455 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
456 : maechler 791
457 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
458 : bates 763
459 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
460 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
461 :    
462 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
463 : bates 763
464 :     * src/Makefile.win: Forgot to update this when Makefile changed.
465 :    
466 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
467 : bates 726
468 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
469 :     bug reported by Kurt Hornik and Michael Hahsler.
470 :    
471 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
472 : bates 725
473 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
474 :     logical sparse matrices. These will also be used in the symbolic
475 :     analysis for lmer objects.
476 :    
477 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
478 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
479 : maechler 791
480 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
481 : bates 714
482 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
483 :     colMeans, colSums, rowMeans and rowSums.
484 :    
485 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
486 : bates 692
487 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
488 :     multiplication operation.
489 :    
490 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
491 :     to dgetrs.
492 :    
493 :     * src/init.c: Fix cut-and-paste error in definition of
494 :     dgeMatrix_matrix_solve
495 :    
496 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
497 :    
498 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
499 : bates 692
500 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
501 :    
502 :     * DESCRIPTION: Eliminate import of stats.
503 :    
504 : maechler 791
505 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
506 : bates 692
507 :     * R/AllClass.R : add logical sparse matrix classes
508 :    
509 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
510 :    
511 :     * R/dgTMatrix.R: add "[" method for triplet matrices
512 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
513 :    
514 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
515 : maechler 687
516 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
517 :    
518 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
519 :     * R/sparseMatrix.R: %*%, crossprod()
520 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
521 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
522 :     * src/lmer.c (lmer_fitted): fix thinko
523 :    
524 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
525 :    
526 :     * R/AllClass.R: add two virtual sparse classes ``on top''
527 :    
528 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
529 :    
530 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
531 :     correspondingly fix examples and tests/ since new()
532 :     doesn't work for virtual classes.
533 :    
534 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
535 :    
536 :     * R/Matrix.R (as.matrix): method and one for unname()
537 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
538 :     also run for R 2.1.0; using as.matrix()
539 :    
540 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
541 : maechler 658
542 :     * R/pMatrix.R: "pMatrix" class added
543 :     * ....
544 :    
545 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
546 : bates 645
547 :     * R/dtpMatrix.R: Add unpack method and an example.
548 :    
549 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
550 :     of general symmetric matrices and associated S4 methods.
551 :    
552 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
553 :     +
554 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
555 :    
556 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
557 :     crossprod() and "%*%" methods added; tests, too.
558 :     * tests/matprod.R: new, for testing these
559 :    
560 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
561 : bates 599
562 :     * src/lmer.c (lmer_fitted): Added.
563 :    
564 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
565 : bates 596
566 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
567 :    
568 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
569 : bates 582
570 :     * src/*.c,po/,inst/po: Internationalization and localization of
571 :     the package.
572 :    
573 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
574 :     R_ldl.c file.
575 :    
576 :     * src/flame.[ch]: Removed these source files.
577 : maechler 658
578 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
579 :    
580 :     * src/LU.[ch],src/init.c: absorb in factorizations
581 :    
582 :     * src/Mutils.h: prepare for internationalization
583 :    
584 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
585 :     this file
586 :    
587 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
588 :    
589 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
590 :    
591 :     * R/dtrMatrix.R: fix t() method
592 :    
593 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
594 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
595 : maechler 578 * tests/group-methods.R : and test them.
596 :    
597 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
598 :     border case
599 :    
600 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
601 :    
602 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
603 : maechler 578
604 :     * src/dgBCMatrix.c:
605 :     * src/lmer.c: many changes
606 :     * ...
607 :    
608 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
609 :    
610 :     * R/Matrix.R: add more sophisticated show() method.
611 :    
612 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
613 :    
614 :     * */* : almost complete reorganization of classes.
615 :    
616 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
617 : bates 460
618 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
619 :     for the geMatrix class.
620 :    
621 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
622 : bates 460
623 :     * src/Makefile (clean): Remove *.a and *.so
624 :    
625 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
626 :    
627 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
628 : bates 460
629 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
630 : bates 460 had an effect in cases with more than 2 grouping factors.
631 :    
632 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
633 : bates 415
634 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
635 :    
636 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
637 : bates 410
638 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
639 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
640 :    
641 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
642 : bates 392
643 :     * R/sscMatrix.R: Add determinant methods
644 :    
645 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
646 :     for tripletMatrix to matrix.
647 :    
648 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
649 : bates 388
650 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
651 :     no longer used.
652 :    
653 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
654 :     with dynamic allocation of scratch arrays.
655 :    
656 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
657 :     for multivariate random effects with multiple grouping factors.
658 :     Fixes part but not all of #15.
659 :    
660 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
661 : bates 375
662 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
663 :     scalar grouping factors corrected.
664 :    
665 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
666 : bates 375
667 :     * src/bCrosstab.c: remove diag_update which is no longer used
668 :    
669 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
670 : bates 350
671 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
672 :     .h file can be included.
673 :    
674 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
675 : bates 342
676 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
677 : bates 342 Complete allocation of slots in NEW_OBJECT.
678 :    
679 :     * src/Mutils.h: Moved list of symbols to an include file
680 :    
681 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
682 : bates 342
683 :     * src/geMutils.c (Matrix_init): remove unused function
684 :    
685 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
686 : bates 342
687 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
688 :    
689 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
690 : bates 327
691 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
692 :    
693 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
694 : bates 303
695 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
696 :    
697 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
698 : bates 296
699 :     * src/init.c: Created R_init_Matrix and added registration of C
700 :     routines.
701 :    
702 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
703 : bates 283
704 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
705 :    
706 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
707 : bates 229
708 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
709 :    
710 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
711 :    
712 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
713 :    
714 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
715 :    
716 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
717 :     ssclme_update_mm
718 :    
719 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
720 :    
721 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
722 :     in the order of unconstrained and constrained parameters.
723 :     (ssclme_gradient): Added the gradients (not yet correct for
724 :     multidimensional, unconstrained case).
725 :    
726 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
727 :    
728 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
729 :    
730 :     * src/Makefile.win: Remove unneeded ranlib call
731 :    
732 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
733 :    
734 :     * DESCRIPTION (Version): New release
735 :    
736 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
737 :    
738 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
739 :    
740 :     * src/triplet_to_col.c: Create triplet_to_col as a native
741 : maechler 658 function, not the version from umfpack. There were problems with
742 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
743 :     only one umfpack routine being used so I moved it here.
744 :    
745 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
746 :    
747 :     * src/ssclme.c (ssclme_variances): New function.
748 :    
749 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
750 :    
751 :     * src/ssclme.c (ssclme_fitted): Added function.
752 :    
753 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
754 :    
755 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
756 :     store the dimnames in the XtX and bVar slots
757 :     (ssclme_update_mm): Change the dimensions of the bVar slot
758 :     components and the returned value from ssclme_ranef.
759 :    
760 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
761 :    
762 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
763 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
764 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
765 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
766 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
767 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
768 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
769 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
770 :     Moved the pdMat classes from the lme4 package.
771 :    
772 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
773 :    
774 :     * man/ssclme-class.Rd: Update definition and documentation of the
775 :     ssclme class to include the DIsqrt slot.
776 :    
777 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
778 :     (much faster using dsyrk, a level 3 BLAS routine).
779 :    
780 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
781 :    
782 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
783 :    
784 :     * tests/ssclme.R: Modify the test to account for the permutation
785 :     of the levels of the grouping factors.
786 :    
787 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
788 :    
789 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
790 :     directly into the ssclme class definition.
791 :    
792 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
793 :    
794 :     * DESCRIPTION (Date): New release
795 :    
796 :     * man/ssclme-class.Rd: new file.
797 :    
798 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
799 :     works and it's fast!
800 :    
801 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
802 :    
803 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
804 :    
805 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
806 :    
807 :     * DESCRIPTION (Date): New release
808 :    
809 :     * NAMESPACE: Don't export ssclme.
810 :    
811 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
812 :     school data.
813 :    
814 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
815 :    
816 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
817 :     keep track of the fixed-effects and the response. Counts also
818 :     gets an extra element, which is always one.
819 :    
820 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
821 :    
822 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
823 :    
824 :     * src/cscMatrix.c (csc_transpose): new function
825 :    
826 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
827 :     (csc_components_transpose): new function
828 :    
829 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
830 :    
831 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
832 :     triplets
833 :    
834 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
835 :    
836 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
837 :    
838 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
839 :     and all other .h files in src.
840 :    
841 :     * src/Makefile.win: This and other Makefile.win files contributed
842 :     by Brian Ripley.
843 :    
844 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
845 :    
846 :     * R/syMatrix.R: Added methods for "%*%".
847 :    
848 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
849 :     poMatrix object.
850 :    
851 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
852 :    
853 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
854 :    
855 :     2004-01-25 Douglas Bates <bates@bates2_home>
856 :    
857 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
858 :    
859 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
860 :     of nrow.
861 :    
862 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
863 :    
864 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
865 :     subdirectories.
866 :    
867 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
868 :    
869 :     * src/taucs.h: Accidently referred to global header files
870 :     instead of local files.
871 :    
872 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
873 :    
874 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
875 :     and methods and replaced all classes with S4 classes.
876 :    
877 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
878 :    
879 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
880 :    
881 :     * src/R_LapackPP.cc: Change method of calculating determinants
882 :    
883 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
884 :    
885 :     * DESCRIPTION (Version): removed empty data directory as requested
886 :     by CRAN maintainers. Changed version number and date.
887 :    
888 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
889 :    
890 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
891 :     under Windows.
892 :    
893 :     * Added configure.win and src/Makevars.win as requested by Brian
894 :     Ripley.
895 :    
896 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
897 :    
898 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
899 :     Hornik.
900 :    
901 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
902 :    
903 :     * configure.ac: Replaced configure.in with configure.ac
904 :     contributed by Kurt Hornik.
905 :    
906 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
907 :     version for R-1.5.0
908 :    
909 : maechler 512
910 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
911 :    
912 :     * man/eigen.Rd: Removed the .Alias in the example

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