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Annotation of /pkg/ChangeLog

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1 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
2 :    
3 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
4 :     background grid to the qqmath plot of ranef.lmer.
5 :    
6 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
7 : bates 1284
8 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
9 :     grouping factors to be specified in the formula as (1|foo/bar).
10 :    
11 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
12 :    
13 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
14 :     !is.language to resolve the bug reported by Jacob Wegelin.
15 :    
16 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
17 :     code to evaluate inbreeding coefficients without calculating T,
18 :     based on code in Sargolzaei and Iwaisaki's paper.
19 :    
20 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
21 :    
22 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
23 :     generic and mer methods for isNested and denomDF. This denomDF was
24 :     an attempt to emulate that in lme but I don't think that makes
25 :     sense. Use the trace of the hat matrix instead.
26 :    
27 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
30 :     the C code depending on a slot structure that's no longer valid.
31 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
32 :    
33 :    
34 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
35 :    
36 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
37 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
38 :     and added a general band extractor.
39 :    
40 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
41 :    
42 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
43 :     allowable range with NAs. Added a corresponding check in the
44 :     validity check for the pedigree class.
45 :    
46 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
47 :     crossprod methods now inherits from symmetricMatrix.
48 :    
49 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
50 :    
51 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
52 :     generics lowerTriMatrix and upperTriMatrix along with methods for
53 :     the Csparse virtual class. Also added a C function Csparse_band
54 :     that implements these methods by calling cholmod_band.
55 :    
56 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
57 :    
58 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
59 :     erased when it was NULL. This led to invalid subselections!
60 :    
61 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
62 :    
63 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
64 :     in method for "t" so as not to lose the unit diagonal property.
65 :    
66 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
67 :    
68 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
69 :     and methods. This is now an option to the ranef method for the
70 :     mer class.
71 :    
72 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
73 :     compressed column-oriented matrix. Minor formatting cleanup.
74 :    
75 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
76 :     objects.
77 :    
78 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
79 :    
80 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
81 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
82 :    
83 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
84 :    
85 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
86 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
87 :    
88 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
89 :     for the dtCMatrix class.
90 : maechler 1253
91 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
92 :    
93 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
94 :     and methods for it.
95 :    
96 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
97 :    
98 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
99 :     arguments, such that M %*% 1:6 now works
100 :     * Tests/matprod.R: test the above
101 :    
102 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
103 : bates 1243
104 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
105 :     the ranef.lmer class.
106 :    
107 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
108 :     methods to extract the posterior variances from the bVar slot.
109 :    
110 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
111 :    
112 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
113 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
114 :    
115 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
116 :     * tests/simple: (extended)
117 :    
118 :     * R/sparseMatrix.R (isTriangular): now using much improved
119 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
120 :    
121 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
122 :    
123 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
124 :     (problem report from Franklin Parlamis). This should be done
125 : maechler 1238 generally.
126 : bates 1236
127 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
128 :    
129 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
130 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
131 :     update the plot methods.
132 :    
133 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
134 :    
135 :     * R/lmer.R (resid and ranef methods): Added methods for the
136 :     "residuals" and "resid" generic but only for linear mixed model
137 :     fits. Changed the ranef method to return a list of data frames so
138 :     that the plot methods now work.
139 :    
140 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
141 :    
142 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
143 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
144 :    
145 :     * DESCRIPTION (Date): New release
146 :    
147 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
150 :    
151 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
152 :     * man/KNex.Rd: and other help files
153 :     * tests/*.R: several ones needed adaption
154 :     * inst/doc/Comparisons.Rnw: dito
155 :    
156 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
157 :    
158 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
159 :    
160 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
161 :    
162 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
163 :    
164 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
165 :    
166 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
167 :    
168 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
169 :    
170 :     * R/dMatrix.R: enable things like M [ M < 10 ]
171 :     * R/dgeMatrix.R: implement it
172 :    
173 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
174 :    
175 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
176 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
177 :     * R/lmer.R (show): now works with summary()
178 :    
179 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
180 :    
181 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
182 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
183 :     support the above
184 :    
185 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
186 :    
187 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
188 :     Use glmFit$prior.weights for weights in a glmm.
189 :     Allow an option usePQL = FALSE to skip the PQL steps for the
190 :     Laplace method (and, in time, the AGQ method).
191 :    
192 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
193 :     into a separate function internal_mer_Xfactor to be able to call
194 :     it from internal_bhat.
195 :    
196 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
197 :    
198 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
199 :     testing; now again of all actual classes.
200 :    
201 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
202 :     use macros and define make_d_matrix_* and make_i_matrix_*
203 :     where _i_ is for the ldense routines:
204 :    
205 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
206 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
207 :    
208 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
209 :    
210 :    
211 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
212 :    
213 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
214 :     many different kinds of matrices.
215 :     * R/*.R: quite a few new methods were needed for R CMD check with
216 :     new Matrix(). Very good for users playing around.
217 :    
218 :    
219 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
220 :    
221 :     * src/dgeMatrix.c (dMatrix_validate): new
222 :     * src/Mutils.c (dense_nonpacked_validate): new
223 :    
224 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
225 :    
226 :    
227 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
228 :    
229 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
230 :    
231 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
232 : bates 1119
233 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
234 :    
235 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
236 :     segfault in cases with multiple non-nested grouping factors.
237 :    
238 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
239 :    
240 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
241 :     (Depends): also on 'utils'
242 :    
243 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
244 :     * R/diagMatrix.R (Diagonal): constructor and methods for
245 :     diagonal matrices
246 :    
247 :     * R/ltTMatrix.R: new "minimal methods"
248 :    
249 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
250 :    
251 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
252 :     all methods (and help files).
253 :    
254 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
255 :    
256 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
257 :     for case (dimn. op no_dimn.)
258 :    
259 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
260 :    
261 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
262 : maechler 1084
263 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
264 :    
265 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
266 :     by Julian Faraway.
267 :    
268 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * R/Auxiliaries.R (try_as): new utility
271 :     * R/sparseMatrix.R: use try_as() in coercion to original class
272 :    
273 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
274 :    
275 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
276 :    
277 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
278 :    
279 :     * R/Auxiliaries.R (dimNamesCheck): added
280 :    
281 :     * R/Matrix.R (as.array), (as.vector): new
282 :    
283 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
284 :    
285 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
286 : maechler 956 default.
287 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
288 :     "pMatrix" now contains "sparseMatrix"
289 : maechler 954
290 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
293 :    
294 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
295 :    
296 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
297 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
298 :    
299 :     * R/dspMatrix.R: typo in "t" method
300 :    
301 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
302 :    
303 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
304 :     * R/Tsparse.R: instead of R/gTMatrix.R
305 :     * R/Csparse.R: new
306 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
307 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
308 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
309 :     via cholmod
310 :    
311 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
312 :    
313 :     * R/Auxiliaries.R (non0ind): new function using new C code
314 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
315 :    
316 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
317 :    
318 :     * src/chm_common.h: header file required by all C sources that
319 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
320 : bates 917 called 'c' whose address is passed as the last argument to
321 :     (virtually) every CHOLMOD function.
322 :    
323 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
324 :    
325 :     * src/init.c: initialize and finalize the cholmod_common structure.
326 :    
327 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
328 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
329 :    
330 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
331 :    
332 :     * inst/test-tools.R: new file collecting the utility functions used
333 :     in ./tests/*.R
334 :    
335 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
336 :     * R/Matrix.R (cbind2): methods for NULL and missing
337 :    
338 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
339 :    
340 :     * R/AllClass.R: new "index" class for "[" and "[<-":
341 :     First cut at "symmetricMatrix" and "triangularMatrix"
342 :     * R/gTMatrix.R (.ind.prep): new function;
343 : maechler 1174 Logical and character indexing now work too.
344 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
345 :     * tests/indexing.R: new, including *.Rout.save
346 :     * tests/dgTMatrix.R: new
347 :    
348 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
349 :    
350 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
351 :     indicator pos not being updated. Also enforced upper triangular
352 :     for symmetric case. Need to coerce edges component of elements of
353 :     edge list - grr! (Why don't they define their classes cleanly?)
354 :    
355 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
356 :    
357 :     * R/Matrix.R: added first "[<-" methods; not yet functional
358 :     * R/denseMatrix.R: dito
359 :     * man/Subassign-methods.Rd: new help file for these
360 :    
361 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * DESCRIPTION (Version): 0.98-6
364 :    
365 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
366 :     matrices.
367 :    
368 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
369 :    
370 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
371 :     as( <logical>, "matrix")
372 :    
373 :     * R/pMatrix.R: coercion to "lgTMatrix"
374 :    
375 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
376 :     * man/gTMatrix-class.Rd:
377 :     * General slight re-organization of where "[" methods are defined.
378 :     more to come.
379 :    
380 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
381 : maechler 868
382 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
383 : maechler 871
384 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
385 :     * .....
386 :    
387 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
388 :    
389 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
390 :     or glmer objects.
391 :    
392 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
393 :    
394 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
395 :    
396 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
397 :    
398 :     * R/HBMM.R: finish re-writing R-only code.
399 :    
400 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
401 :    
402 :     * man/externalFormats.Rd: move documentation for writeHB and
403 :     writeMM here.
404 :    
405 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
406 :     (suggested by Paul Roecker).
407 :    
408 :     * tests/validObj.R (assertError): Comment out test that is failing
409 :     after recent changes in r-devel.
410 :    
411 : maechler 860
412 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
413 :    
414 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
415 :     * man/denseMatrix-class.Rd
416 :     * NAMESPACE: export it, and also export
417 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
418 :    
419 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
420 :    
421 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
422 :    
423 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
424 :     matrix_solve code (which was really, really wrong).
425 :    
426 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
427 : maechler 834
428 :     * DESCRIPTION (Version): 0.98-2
429 :    
430 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
431 :    
432 :     * R/lmer.R (abbrvNms): new
433 :     * R/lmer.R (mcmcsamp): allow transformed parameters
434 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
435 :     for the Harwell-Boeing and the MatrixMarket formats.
436 : maechler 834
437 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
438 :    
439 :     * man/dtrMatrix-class.Rd: add examples
440 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
441 : maechler 834
442 :     * TODO: note the dtpMatrix (docu) bug
443 :    
444 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
445 :     in order to ensure that new as.matrix() is used by old functions,
446 :     e.g., svd(), qr(), eigen(), dist(),..;
447 :     apply(), also matplot() or pairs().
448 :    
449 :    
450 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
451 :    
452 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
453 :     add comments about 'control' / lmerControl() arguments
454 :    
455 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
456 : bates 820
457 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
458 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
459 : bates 820
460 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
461 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
462 :    
463 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
464 :     .Call calls that were producing spurious output.
465 :    
466 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
467 : bates 801
468 :     * R/lmer.R (lmer): stored updated variance component estimates in
469 :     mer object for the generalized model. (Bug reported by Renaud
470 :     Lancelot).
471 :    
472 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
473 : bates 794
474 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
475 :     unidimensional case.
476 :    
477 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
478 : maechler 791
479 :     * DESCRIPTION (Version): 0.96-1
480 :    
481 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
482 : maechler 791
483 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
484 : bates 763
485 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
486 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
487 :    
488 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
489 : bates 763
490 :     * src/Makefile.win: Forgot to update this when Makefile changed.
491 :    
492 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
493 : bates 726
494 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
495 :     bug reported by Kurt Hornik and Michael Hahsler.
496 :    
497 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
498 : bates 725
499 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
500 :     logical sparse matrices. These will also be used in the symbolic
501 :     analysis for lmer objects.
502 :    
503 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
504 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
505 : maechler 791
506 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
507 : bates 714
508 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
509 :     colMeans, colSums, rowMeans and rowSums.
510 :    
511 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
512 : bates 692
513 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
514 :     multiplication operation.
515 :    
516 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
517 :     to dgetrs.
518 :    
519 :     * src/init.c: Fix cut-and-paste error in definition of
520 :     dgeMatrix_matrix_solve
521 :    
522 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
523 :    
524 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
525 : bates 692
526 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
527 :    
528 :     * DESCRIPTION: Eliminate import of stats.
529 :    
530 : maechler 791
531 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
532 : bates 692
533 :     * R/AllClass.R : add logical sparse matrix classes
534 :    
535 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
536 :    
537 :     * R/dgTMatrix.R: add "[" method for triplet matrices
538 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
539 :    
540 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
541 : maechler 687
542 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
543 :    
544 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
545 :     * R/sparseMatrix.R: %*%, crossprod()
546 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
547 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
548 :     * src/lmer.c (lmer_fitted): fix thinko
549 :    
550 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
551 :    
552 :     * R/AllClass.R: add two virtual sparse classes ``on top''
553 :    
554 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
555 :    
556 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
557 :     correspondingly fix examples and tests/ since new()
558 :     doesn't work for virtual classes.
559 :    
560 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
561 :    
562 :     * R/Matrix.R (as.matrix): method and one for unname()
563 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
564 :     also run for R 2.1.0; using as.matrix()
565 :    
566 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
567 : maechler 658
568 :     * R/pMatrix.R: "pMatrix" class added
569 :     * ....
570 :    
571 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
572 : bates 645
573 :     * R/dtpMatrix.R: Add unpack method and an example.
574 :    
575 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
576 :     of general symmetric matrices and associated S4 methods.
577 :    
578 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
579 :     +
580 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
581 :    
582 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
583 :     crossprod() and "%*%" methods added; tests, too.
584 :     * tests/matprod.R: new, for testing these
585 :    
586 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
587 : bates 599
588 :     * src/lmer.c (lmer_fitted): Added.
589 :    
590 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
591 : bates 596
592 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
593 :    
594 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
595 : bates 582
596 :     * src/*.c,po/,inst/po: Internationalization and localization of
597 :     the package.
598 :    
599 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
600 :     R_ldl.c file.
601 :    
602 :     * src/flame.[ch]: Removed these source files.
603 : maechler 658
604 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
605 :    
606 :     * src/LU.[ch],src/init.c: absorb in factorizations
607 :    
608 :     * src/Mutils.h: prepare for internationalization
609 :    
610 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
611 :     this file
612 :    
613 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
614 :    
615 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
616 :    
617 :     * R/dtrMatrix.R: fix t() method
618 :    
619 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
620 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
621 : maechler 578 * tests/group-methods.R : and test them.
622 :    
623 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
624 :     border case
625 :    
626 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
627 :    
628 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
629 : maechler 578
630 :     * src/dgBCMatrix.c:
631 :     * src/lmer.c: many changes
632 :     * ...
633 :    
634 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
635 :    
636 :     * R/Matrix.R: add more sophisticated show() method.
637 :    
638 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
639 :    
640 :     * */* : almost complete reorganization of classes.
641 :    
642 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
643 : bates 460
644 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
645 :     for the geMatrix class.
646 :    
647 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
648 : bates 460
649 :     * src/Makefile (clean): Remove *.a and *.so
650 :    
651 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
652 :    
653 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
654 : bates 460
655 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
656 : bates 460 had an effect in cases with more than 2 grouping factors.
657 :    
658 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
659 : bates 415
660 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
661 :    
662 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
663 : bates 410
664 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
665 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
666 :    
667 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
668 : bates 392
669 :     * R/sscMatrix.R: Add determinant methods
670 :    
671 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
672 :     for tripletMatrix to matrix.
673 :    
674 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
675 : bates 388
676 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
677 :     no longer used.
678 :    
679 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
680 :     with dynamic allocation of scratch arrays.
681 :    
682 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
683 :     for multivariate random effects with multiple grouping factors.
684 :     Fixes part but not all of #15.
685 :    
686 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
687 : bates 375
688 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
689 :     scalar grouping factors corrected.
690 :    
691 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
692 : bates 375
693 :     * src/bCrosstab.c: remove diag_update which is no longer used
694 :    
695 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
696 : bates 350
697 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
698 :     .h file can be included.
699 :    
700 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
701 : bates 342
702 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
703 : bates 342 Complete allocation of slots in NEW_OBJECT.
704 :    
705 :     * src/Mutils.h: Moved list of symbols to an include file
706 :    
707 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
708 : bates 342
709 :     * src/geMutils.c (Matrix_init): remove unused function
710 :    
711 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
712 : bates 342
713 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
714 :    
715 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
716 : bates 327
717 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
718 :    
719 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
720 : bates 303
721 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
722 :    
723 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
724 : bates 296
725 :     * src/init.c: Created R_init_Matrix and added registration of C
726 :     routines.
727 :    
728 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
729 : bates 283
730 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
731 :    
732 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
733 : bates 229
734 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
735 :    
736 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
737 :    
738 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
739 :    
740 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
741 :    
742 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
743 :     ssclme_update_mm
744 :    
745 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
746 :    
747 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
748 :     in the order of unconstrained and constrained parameters.
749 :     (ssclme_gradient): Added the gradients (not yet correct for
750 :     multidimensional, unconstrained case).
751 :    
752 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
753 :    
754 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
755 :    
756 :     * src/Makefile.win: Remove unneeded ranlib call
757 :    
758 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
759 :    
760 :     * DESCRIPTION (Version): New release
761 :    
762 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
763 :    
764 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
765 :    
766 :     * src/triplet_to_col.c: Create triplet_to_col as a native
767 : maechler 658 function, not the version from umfpack. There were problems with
768 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
769 :     only one umfpack routine being used so I moved it here.
770 :    
771 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
772 :    
773 :     * src/ssclme.c (ssclme_variances): New function.
774 :    
775 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
776 :    
777 :     * src/ssclme.c (ssclme_fitted): Added function.
778 :    
779 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
780 :    
781 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
782 :     store the dimnames in the XtX and bVar slots
783 :     (ssclme_update_mm): Change the dimensions of the bVar slot
784 :     components and the returned value from ssclme_ranef.
785 :    
786 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
787 :    
788 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
789 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
790 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
791 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
792 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
793 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
794 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
795 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
796 :     Moved the pdMat classes from the lme4 package.
797 :    
798 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
799 :    
800 :     * man/ssclme-class.Rd: Update definition and documentation of the
801 :     ssclme class to include the DIsqrt slot.
802 :    
803 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
804 :     (much faster using dsyrk, a level 3 BLAS routine).
805 :    
806 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
807 :    
808 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
809 :    
810 :     * tests/ssclme.R: Modify the test to account for the permutation
811 :     of the levels of the grouping factors.
812 :    
813 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
814 :    
815 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
816 :     directly into the ssclme class definition.
817 :    
818 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
819 :    
820 :     * DESCRIPTION (Date): New release
821 :    
822 :     * man/ssclme-class.Rd: new file.
823 :    
824 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
825 :     works and it's fast!
826 :    
827 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
828 :    
829 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
830 :    
831 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
832 :    
833 :     * DESCRIPTION (Date): New release
834 :    
835 :     * NAMESPACE: Don't export ssclme.
836 :    
837 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
838 :     school data.
839 :    
840 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
841 :    
842 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
843 :     keep track of the fixed-effects and the response. Counts also
844 :     gets an extra element, which is always one.
845 :    
846 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
847 :    
848 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
849 :    
850 :     * src/cscMatrix.c (csc_transpose): new function
851 :    
852 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
853 :     (csc_components_transpose): new function
854 :    
855 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
856 :    
857 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
858 :     triplets
859 :    
860 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
861 :    
862 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
863 :    
864 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
865 :     and all other .h files in src.
866 :    
867 :     * src/Makefile.win: This and other Makefile.win files contributed
868 :     by Brian Ripley.
869 :    
870 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
871 :    
872 :     * R/syMatrix.R: Added methods for "%*%".
873 :    
874 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
875 :     poMatrix object.
876 :    
877 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
878 :    
879 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
880 :    
881 :     2004-01-25 Douglas Bates <bates@bates2_home>
882 :    
883 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
884 :    
885 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
886 :     of nrow.
887 :    
888 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
889 :    
890 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
891 :     subdirectories.
892 :    
893 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
894 :    
895 :     * src/taucs.h: Accidently referred to global header files
896 :     instead of local files.
897 :    
898 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
899 :    
900 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
901 :     and methods and replaced all classes with S4 classes.
902 :    
903 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
904 :    
905 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
906 :    
907 :     * src/R_LapackPP.cc: Change method of calculating determinants
908 :    
909 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
910 :    
911 :     * DESCRIPTION (Version): removed empty data directory as requested
912 :     by CRAN maintainers. Changed version number and date.
913 :    
914 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
915 :    
916 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
917 :     under Windows.
918 :    
919 :     * Added configure.win and src/Makevars.win as requested by Brian
920 :     Ripley.
921 :    
922 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
923 :    
924 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
925 :     Hornik.
926 :    
927 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
928 :    
929 :     * configure.ac: Replaced configure.in with configure.ac
930 :     contributed by Kurt Hornik.
931 :    
932 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
933 :     version for R-1.5.0
934 :    
935 : maechler 512
936 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
937 :    
938 :     * man/eigen.Rd: Removed the .Alias in the example

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