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Annotation of /pkg/ChangeLog

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11 :     the C code depending on a slot structure that's no longer valid.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

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