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Annotation of /pkg/ChangeLog

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Revision 1268 - (view) (download)

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

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