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Annotation of /pkg/ChangeLog

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Revision 1287 - (view) (download)

1 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
2 : bates 1284
3 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
4 :     grouping factors to be specified in the formula as (1|foo/bar).
5 :    
6 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
7 :    
8 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
9 :     !is.language to resolve the bug reported by Jacob Wegelin.
10 :    
11 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
12 :     code to evaluate inbreeding coefficients without calculating T,
13 :     based on code in Sargolzaei and Iwaisaki's paper.
14 :    
15 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
16 :    
17 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
18 :     generic and mer methods for isNested and denomDF. This denomDF was
19 :     an attempt to emulate that in lme but I don't think that makes
20 :     sense. Use the trace of the hat matrix instead.
21 :    
22 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
23 :    
24 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
25 :     the C code depending on a slot structure that's no longer valid.
26 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
27 :    
28 :    
29 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
30 :    
31 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
32 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
33 :     and added a general band extractor.
34 :    
35 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
36 :    
37 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
38 :     allowable range with NAs. Added a corresponding check in the
39 :     validity check for the pedigree class.
40 :    
41 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
42 :     crossprod methods now inherits from symmetricMatrix.
43 :    
44 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
45 :    
46 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
47 :     generics lowerTriMatrix and upperTriMatrix along with methods for
48 :     the Csparse virtual class. Also added a C function Csparse_band
49 :     that implements these methods by calling cholmod_band.
50 :    
51 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
52 :    
53 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
54 :     erased when it was NULL. This led to invalid subselections!
55 :    
56 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
57 :    
58 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
59 :     in method for "t" so as not to lose the unit diagonal property.
60 :    
61 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
62 :    
63 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
64 :     and methods. This is now an option to the ranef method for the
65 :     mer class.
66 :    
67 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
68 :     compressed column-oriented matrix. Minor formatting cleanup.
69 :    
70 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
71 :     objects.
72 :    
73 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
74 :    
75 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
76 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
77 :    
78 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
79 :    
80 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
81 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
82 :    
83 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
84 :     for the dtCMatrix class.
85 : maechler 1253
86 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
87 :    
88 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
89 :     and methods for it.
90 :    
91 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
92 :    
93 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
94 :     arguments, such that M %*% 1:6 now works
95 :     * Tests/matprod.R: test the above
96 :    
97 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
98 : bates 1243
99 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
100 :     the ranef.lmer class.
101 :    
102 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
103 :     methods to extract the posterior variances from the bVar slot.
104 :    
105 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
106 :    
107 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
108 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
109 :    
110 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
111 :     * tests/simple: (extended)
112 :    
113 :     * R/sparseMatrix.R (isTriangular): now using much improved
114 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
115 :    
116 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
117 :    
118 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
119 :     (problem report from Franklin Parlamis). This should be done
120 : maechler 1238 generally.
121 : bates 1236
122 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
123 :    
124 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
125 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
126 :     update the plot methods.
127 :    
128 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
129 :    
130 :     * R/lmer.R (resid and ranef methods): Added methods for the
131 :     "residuals" and "resid" generic but only for linear mixed model
132 :     fits. Changed the ranef method to return a list of data frames so
133 :     that the plot methods now work.
134 :    
135 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
136 :    
137 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
138 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
139 :    
140 :     * DESCRIPTION (Date): New release
141 :    
142 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
145 :    
146 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
147 :     * man/KNex.Rd: and other help files
148 :     * tests/*.R: several ones needed adaption
149 :     * inst/doc/Comparisons.Rnw: dito
150 :    
151 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
154 :    
155 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
156 :    
157 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
158 :    
159 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
160 :    
161 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
162 :    
163 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
164 :    
165 :     * R/dMatrix.R: enable things like M [ M < 10 ]
166 :     * R/dgeMatrix.R: implement it
167 :    
168 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
169 :    
170 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
171 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
172 :     * R/lmer.R (show): now works with summary()
173 :    
174 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
175 :    
176 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
177 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
178 :     support the above
179 :    
180 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
181 :    
182 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
183 :     Use glmFit$prior.weights for weights in a glmm.
184 :     Allow an option usePQL = FALSE to skip the PQL steps for the
185 :     Laplace method (and, in time, the AGQ method).
186 :    
187 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
188 :     into a separate function internal_mer_Xfactor to be able to call
189 :     it from internal_bhat.
190 :    
191 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
192 :    
193 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
194 :     testing; now again of all actual classes.
195 :    
196 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
197 :     use macros and define make_d_matrix_* and make_i_matrix_*
198 :     where _i_ is for the ldense routines:
199 :    
200 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
201 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
202 :    
203 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
204 :    
205 :    
206 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
207 :    
208 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
209 :     many different kinds of matrices.
210 :     * R/*.R: quite a few new methods were needed for R CMD check with
211 :     new Matrix(). Very good for users playing around.
212 :    
213 :    
214 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
215 :    
216 :     * src/dgeMatrix.c (dMatrix_validate): new
217 :     * src/Mutils.c (dense_nonpacked_validate): new
218 :    
219 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
220 :    
221 :    
222 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
223 :    
224 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
225 :    
226 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
227 : bates 1119
228 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
229 :    
230 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
231 :     segfault in cases with multiple non-nested grouping factors.
232 :    
233 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
234 :    
235 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
236 :     (Depends): also on 'utils'
237 :    
238 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
239 :     * R/diagMatrix.R (Diagonal): constructor and methods for
240 :     diagonal matrices
241 :    
242 :     * R/ltTMatrix.R: new "minimal methods"
243 :    
244 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
245 :    
246 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
247 :     all methods (and help files).
248 :    
249 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
250 :    
251 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
252 :     for case (dimn. op no_dimn.)
253 :    
254 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
255 :    
256 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
257 : maechler 1084
258 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
261 :     by Julian Faraway.
262 :    
263 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * R/Auxiliaries.R (try_as): new utility
266 :     * R/sparseMatrix.R: use try_as() in coercion to original class
267 :    
268 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
271 :    
272 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
273 :    
274 :     * R/Auxiliaries.R (dimNamesCheck): added
275 :    
276 :     * R/Matrix.R (as.array), (as.vector): new
277 :    
278 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
281 : maechler 956 default.
282 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
283 :     "pMatrix" now contains "sparseMatrix"
284 : maechler 954
285 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
288 :    
289 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
290 :    
291 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
292 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
293 :    
294 :     * R/dspMatrix.R: typo in "t" method
295 :    
296 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
297 :    
298 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
299 :     * R/Tsparse.R: instead of R/gTMatrix.R
300 :     * R/Csparse.R: new
301 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
302 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
303 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
304 :     via cholmod
305 :    
306 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
307 :    
308 :     * R/Auxiliaries.R (non0ind): new function using new C code
309 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
310 :    
311 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
312 :    
313 :     * src/chm_common.h: header file required by all C sources that
314 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
315 : bates 917 called 'c' whose address is passed as the last argument to
316 :     (virtually) every CHOLMOD function.
317 :    
318 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
319 :    
320 :     * src/init.c: initialize and finalize the cholmod_common structure.
321 :    
322 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
323 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
324 :    
325 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
326 :    
327 :     * inst/test-tools.R: new file collecting the utility functions used
328 :     in ./tests/*.R
329 :    
330 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
331 :     * R/Matrix.R (cbind2): methods for NULL and missing
332 :    
333 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
334 :    
335 :     * R/AllClass.R: new "index" class for "[" and "[<-":
336 :     First cut at "symmetricMatrix" and "triangularMatrix"
337 :     * R/gTMatrix.R (.ind.prep): new function;
338 : maechler 1174 Logical and character indexing now work too.
339 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
340 :     * tests/indexing.R: new, including *.Rout.save
341 :     * tests/dgTMatrix.R: new
342 :    
343 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
344 :    
345 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
346 :     indicator pos not being updated. Also enforced upper triangular
347 :     for symmetric case. Need to coerce edges component of elements of
348 :     edge list - grr! (Why don't they define their classes cleanly?)
349 :    
350 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
351 :    
352 :     * R/Matrix.R: added first "[<-" methods; not yet functional
353 :     * R/denseMatrix.R: dito
354 :     * man/Subassign-methods.Rd: new help file for these
355 :    
356 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * DESCRIPTION (Version): 0.98-6
359 :    
360 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
361 :     matrices.
362 :    
363 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
364 :    
365 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
366 :     as( <logical>, "matrix")
367 :    
368 :     * R/pMatrix.R: coercion to "lgTMatrix"
369 :    
370 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
371 :     * man/gTMatrix-class.Rd:
372 :     * General slight re-organization of where "[" methods are defined.
373 :     more to come.
374 :    
375 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
376 : maechler 868
377 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
378 : maechler 871
379 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
380 :     * .....
381 :    
382 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
383 :    
384 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
385 :     or glmer objects.
386 :    
387 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
388 :    
389 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
390 :    
391 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
392 :    
393 :     * R/HBMM.R: finish re-writing R-only code.
394 :    
395 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
396 :    
397 :     * man/externalFormats.Rd: move documentation for writeHB and
398 :     writeMM here.
399 :    
400 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
401 :     (suggested by Paul Roecker).
402 :    
403 :     * tests/validObj.R (assertError): Comment out test that is failing
404 :     after recent changes in r-devel.
405 :    
406 : maechler 860
407 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
408 :    
409 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
410 :     * man/denseMatrix-class.Rd
411 :     * NAMESPACE: export it, and also export
412 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
413 :    
414 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
415 :    
416 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
417 :    
418 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
419 :     matrix_solve code (which was really, really wrong).
420 :    
421 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
422 : maechler 834
423 :     * DESCRIPTION (Version): 0.98-2
424 :    
425 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
426 :    
427 :     * R/lmer.R (abbrvNms): new
428 :     * R/lmer.R (mcmcsamp): allow transformed parameters
429 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
430 :     for the Harwell-Boeing and the MatrixMarket formats.
431 : maechler 834
432 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
433 :    
434 :     * man/dtrMatrix-class.Rd: add examples
435 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
436 : maechler 834
437 :     * TODO: note the dtpMatrix (docu) bug
438 :    
439 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
440 :     in order to ensure that new as.matrix() is used by old functions,
441 :     e.g., svd(), qr(), eigen(), dist(),..;
442 :     apply(), also matplot() or pairs().
443 :    
444 :    
445 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
446 :    
447 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
448 :     add comments about 'control' / lmerControl() arguments
449 :    
450 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
451 : bates 820
452 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
453 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
454 : bates 820
455 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
456 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
457 :    
458 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
459 :     .Call calls that were producing spurious output.
460 :    
461 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
462 : bates 801
463 :     * R/lmer.R (lmer): stored updated variance component estimates in
464 :     mer object for the generalized model. (Bug reported by Renaud
465 :     Lancelot).
466 :    
467 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
468 : bates 794
469 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
470 :     unidimensional case.
471 :    
472 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
473 : maechler 791
474 :     * DESCRIPTION (Version): 0.96-1
475 :    
476 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
477 : maechler 791
478 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
479 : bates 763
480 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
481 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
482 :    
483 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
484 : bates 763
485 :     * src/Makefile.win: Forgot to update this when Makefile changed.
486 :    
487 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
488 : bates 726
489 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
490 :     bug reported by Kurt Hornik and Michael Hahsler.
491 :    
492 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
493 : bates 725
494 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
495 :     logical sparse matrices. These will also be used in the symbolic
496 :     analysis for lmer objects.
497 :    
498 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
499 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
500 : maechler 791
501 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
502 : bates 714
503 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
504 :     colMeans, colSums, rowMeans and rowSums.
505 :    
506 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
507 : bates 692
508 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
509 :     multiplication operation.
510 :    
511 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
512 :     to dgetrs.
513 :    
514 :     * src/init.c: Fix cut-and-paste error in definition of
515 :     dgeMatrix_matrix_solve
516 :    
517 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
518 :    
519 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
520 : bates 692
521 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
522 :    
523 :     * DESCRIPTION: Eliminate import of stats.
524 :    
525 : maechler 791
526 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
527 : bates 692
528 :     * R/AllClass.R : add logical sparse matrix classes
529 :    
530 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * R/dgTMatrix.R: add "[" method for triplet matrices
533 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
534 :    
535 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
536 : maechler 687
537 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
538 :    
539 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
540 :     * R/sparseMatrix.R: %*%, crossprod()
541 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
542 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
543 :     * src/lmer.c (lmer_fitted): fix thinko
544 :    
545 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
546 :    
547 :     * R/AllClass.R: add two virtual sparse classes ``on top''
548 :    
549 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
550 :    
551 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
552 :     correspondingly fix examples and tests/ since new()
553 :     doesn't work for virtual classes.
554 :    
555 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
556 :    
557 :     * R/Matrix.R (as.matrix): method and one for unname()
558 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
559 :     also run for R 2.1.0; using as.matrix()
560 :    
561 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
562 : maechler 658
563 :     * R/pMatrix.R: "pMatrix" class added
564 :     * ....
565 :    
566 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
567 : bates 645
568 :     * R/dtpMatrix.R: Add unpack method and an example.
569 :    
570 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
571 :     of general symmetric matrices and associated S4 methods.
572 :    
573 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
574 :     +
575 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
576 :    
577 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
578 :     crossprod() and "%*%" methods added; tests, too.
579 :     * tests/matprod.R: new, for testing these
580 :    
581 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
582 : bates 599
583 :     * src/lmer.c (lmer_fitted): Added.
584 :    
585 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
586 : bates 596
587 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
588 :    
589 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
590 : bates 582
591 :     * src/*.c,po/,inst/po: Internationalization and localization of
592 :     the package.
593 :    
594 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
595 :     R_ldl.c file.
596 :    
597 :     * src/flame.[ch]: Removed these source files.
598 : maechler 658
599 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
600 :    
601 :     * src/LU.[ch],src/init.c: absorb in factorizations
602 :    
603 :     * src/Mutils.h: prepare for internationalization
604 :    
605 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
606 :     this file
607 :    
608 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
609 :    
610 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
611 :    
612 :     * R/dtrMatrix.R: fix t() method
613 :    
614 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
615 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
616 : maechler 578 * tests/group-methods.R : and test them.
617 :    
618 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
619 :     border case
620 :    
621 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
622 :    
623 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
624 : maechler 578
625 :     * src/dgBCMatrix.c:
626 :     * src/lmer.c: many changes
627 :     * ...
628 :    
629 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
630 :    
631 :     * R/Matrix.R: add more sophisticated show() method.
632 :    
633 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
634 :    
635 :     * */* : almost complete reorganization of classes.
636 :    
637 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
638 : bates 460
639 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
640 :     for the geMatrix class.
641 :    
642 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
643 : bates 460
644 :     * src/Makefile (clean): Remove *.a and *.so
645 :    
646 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
647 :    
648 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
649 : bates 460
650 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
651 : bates 460 had an effect in cases with more than 2 grouping factors.
652 :    
653 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
654 : bates 415
655 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
656 :    
657 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
658 : bates 410
659 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
660 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
661 :    
662 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
663 : bates 392
664 :     * R/sscMatrix.R: Add determinant methods
665 :    
666 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
667 :     for tripletMatrix to matrix.
668 :    
669 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
670 : bates 388
671 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
672 :     no longer used.
673 :    
674 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
675 :     with dynamic allocation of scratch arrays.
676 :    
677 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
678 :     for multivariate random effects with multiple grouping factors.
679 :     Fixes part but not all of #15.
680 :    
681 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
682 : bates 375
683 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
684 :     scalar grouping factors corrected.
685 :    
686 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
687 : bates 375
688 :     * src/bCrosstab.c: remove diag_update which is no longer used
689 :    
690 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
691 : bates 350
692 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
693 :     .h file can be included.
694 :    
695 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
696 : bates 342
697 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
698 : bates 342 Complete allocation of slots in NEW_OBJECT.
699 :    
700 :     * src/Mutils.h: Moved list of symbols to an include file
701 :    
702 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
703 : bates 342
704 :     * src/geMutils.c (Matrix_init): remove unused function
705 :    
706 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
707 : bates 342
708 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
709 :    
710 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
711 : bates 327
712 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
713 :    
714 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
715 : bates 303
716 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
717 :    
718 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
719 : bates 296
720 :     * src/init.c: Created R_init_Matrix and added registration of C
721 :     routines.
722 :    
723 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
724 : bates 283
725 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
726 :    
727 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
728 : bates 229
729 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
730 :    
731 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
732 :    
733 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
734 :    
735 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
736 :    
737 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
738 :     ssclme_update_mm
739 :    
740 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
741 :    
742 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
743 :     in the order of unconstrained and constrained parameters.
744 :     (ssclme_gradient): Added the gradients (not yet correct for
745 :     multidimensional, unconstrained case).
746 :    
747 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
748 :    
749 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
750 :    
751 :     * src/Makefile.win: Remove unneeded ranlib call
752 :    
753 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
754 :    
755 :     * DESCRIPTION (Version): New release
756 :    
757 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
758 :    
759 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
760 :    
761 :     * src/triplet_to_col.c: Create triplet_to_col as a native
762 : maechler 658 function, not the version from umfpack. There were problems with
763 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
764 :     only one umfpack routine being used so I moved it here.
765 :    
766 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
767 :    
768 :     * src/ssclme.c (ssclme_variances): New function.
769 :    
770 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
771 :    
772 :     * src/ssclme.c (ssclme_fitted): Added function.
773 :    
774 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
775 :    
776 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
777 :     store the dimnames in the XtX and bVar slots
778 :     (ssclme_update_mm): Change the dimensions of the bVar slot
779 :     components and the returned value from ssclme_ranef.
780 :    
781 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
782 :    
783 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
784 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
785 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
786 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
787 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
788 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
789 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
790 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
791 :     Moved the pdMat classes from the lme4 package.
792 :    
793 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
794 :    
795 :     * man/ssclme-class.Rd: Update definition and documentation of the
796 :     ssclme class to include the DIsqrt slot.
797 :    
798 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
799 :     (much faster using dsyrk, a level 3 BLAS routine).
800 :    
801 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
802 :    
803 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
804 :    
805 :     * tests/ssclme.R: Modify the test to account for the permutation
806 :     of the levels of the grouping factors.
807 :    
808 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
809 :    
810 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
811 :     directly into the ssclme class definition.
812 :    
813 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
814 :    
815 :     * DESCRIPTION (Date): New release
816 :    
817 :     * man/ssclme-class.Rd: new file.
818 :    
819 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
820 :     works and it's fast!
821 :    
822 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
823 :    
824 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
825 :    
826 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
827 :    
828 :     * DESCRIPTION (Date): New release
829 :    
830 :     * NAMESPACE: Don't export ssclme.
831 :    
832 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
833 :     school data.
834 :    
835 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
836 :    
837 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
838 :     keep track of the fixed-effects and the response. Counts also
839 :     gets an extra element, which is always one.
840 :    
841 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
842 :    
843 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
844 :    
845 :     * src/cscMatrix.c (csc_transpose): new function
846 :    
847 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
848 :     (csc_components_transpose): new function
849 :    
850 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
851 :    
852 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
853 :     triplets
854 :    
855 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
856 :    
857 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
858 :    
859 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
860 :     and all other .h files in src.
861 :    
862 :     * src/Makefile.win: This and other Makefile.win files contributed
863 :     by Brian Ripley.
864 :    
865 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
866 :    
867 :     * R/syMatrix.R: Added methods for "%*%".
868 :    
869 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
870 :     poMatrix object.
871 :    
872 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
873 :    
874 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
875 :    
876 :     2004-01-25 Douglas Bates <bates@bates2_home>
877 :    
878 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
879 :    
880 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
881 :     of nrow.
882 :    
883 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
884 :    
885 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
886 :     subdirectories.
887 :    
888 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
889 :    
890 :     * src/taucs.h: Accidently referred to global header files
891 :     instead of local files.
892 :    
893 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
894 :    
895 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
896 :     and methods and replaced all classes with S4 classes.
897 :    
898 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
899 :    
900 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
901 :    
902 :     * src/R_LapackPP.cc: Change method of calculating determinants
903 :    
904 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
905 :    
906 :     * DESCRIPTION (Version): removed empty data directory as requested
907 :     by CRAN maintainers. Changed version number and date.
908 :    
909 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
910 :    
911 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
912 :     under Windows.
913 :    
914 :     * Added configure.win and src/Makevars.win as requested by Brian
915 :     Ripley.
916 :    
917 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
918 :    
919 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
920 :     Hornik.
921 :    
922 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
923 :    
924 :     * configure.ac: Replaced configure.in with configure.ac
925 :     contributed by Kurt Hornik.
926 :    
927 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
928 :     version for R-1.5.0
929 :    
930 : maechler 512
931 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
932 :    
933 :     * man/eigen.Rd: Removed the .Alias in the example

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