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Annotation of /pkg/ChangeLog

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Revision 1298 - (view) (download)

1 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
2 :    
3 :     * R/lmer.R (simulestimate): added
4 :    
5 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
6 :    
7 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
8 :     classes.
9 :    
10 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
11 :    
12 :     * R/dgTMatrix.R (colSums): etc. All four of
13 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
14 :     all "Matrices".
15 :    
16 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
17 :    
18 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
19 :     background grid to the qqmath plot of ranef.lmer.
20 :    
21 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
22 : bates 1284
23 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
24 :     grouping factors to be specified in the formula as (1|foo/bar).
25 :    
26 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
27 :    
28 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
29 :     !is.language to resolve the bug reported by Jacob Wegelin.
30 :    
31 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
32 :     code to evaluate inbreeding coefficients without calculating T,
33 :     based on code in Sargolzaei and Iwaisaki's paper.
34 :    
35 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
36 :    
37 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
38 :     generic and mer methods for isNested and denomDF. This denomDF was
39 :     an attempt to emulate that in lme but I don't think that makes
40 :     sense. Use the trace of the hat matrix instead.
41 :    
42 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
43 :    
44 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
45 :     the C code depending on a slot structure that's no longer valid.
46 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
47 :    
48 :    
49 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
50 :    
51 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
52 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
53 :     and added a general band extractor.
54 :    
55 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
56 :    
57 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
58 :     allowable range with NAs. Added a corresponding check in the
59 :     validity check for the pedigree class.
60 :    
61 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
62 :     crossprod methods now inherits from symmetricMatrix.
63 :    
64 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
65 :    
66 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
67 :     generics lowerTriMatrix and upperTriMatrix along with methods for
68 :     the Csparse virtual class. Also added a C function Csparse_band
69 :     that implements these methods by calling cholmod_band.
70 :    
71 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
72 :    
73 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
74 :     erased when it was NULL. This led to invalid subselections!
75 :    
76 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
77 :    
78 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
79 :     in method for "t" so as not to lose the unit diagonal property.
80 :    
81 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
82 :    
83 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
84 :     and methods. This is now an option to the ranef method for the
85 :     mer class.
86 :    
87 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
88 :     compressed column-oriented matrix. Minor formatting cleanup.
89 :    
90 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
91 :     objects.
92 :    
93 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
94 :    
95 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
96 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
97 :    
98 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
99 :    
100 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
101 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
102 :    
103 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
104 :     for the dtCMatrix class.
105 : maechler 1253
106 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
107 :    
108 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
109 :     and methods for it.
110 :    
111 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
112 :    
113 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
114 :     arguments, such that M %*% 1:6 now works
115 :     * Tests/matprod.R: test the above
116 :    
117 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
118 : bates 1243
119 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
120 :     the ranef.lmer class.
121 :    
122 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
123 :     methods to extract the posterior variances from the bVar slot.
124 :    
125 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
126 :    
127 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
128 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
129 :    
130 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
131 :     * tests/simple: (extended)
132 :    
133 :     * R/sparseMatrix.R (isTriangular): now using much improved
134 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
135 :    
136 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
137 :    
138 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
139 :     (problem report from Franklin Parlamis). This should be done
140 : maechler 1238 generally.
141 : bates 1236
142 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
143 :    
144 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
145 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
146 :     update the plot methods.
147 :    
148 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
149 :    
150 :     * R/lmer.R (resid and ranef methods): Added methods for the
151 :     "residuals" and "resid" generic but only for linear mixed model
152 :     fits. Changed the ranef method to return a list of data frames so
153 :     that the plot methods now work.
154 :    
155 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
156 :    
157 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
158 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
159 :    
160 :     * DESCRIPTION (Date): New release
161 :    
162 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
163 :    
164 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
165 :    
166 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
167 :     * man/KNex.Rd: and other help files
168 :     * tests/*.R: several ones needed adaption
169 :     * inst/doc/Comparisons.Rnw: dito
170 :    
171 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
172 :    
173 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
174 :    
175 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
176 :    
177 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
178 :    
179 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
180 :    
181 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
182 :    
183 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
184 :    
185 :     * R/dMatrix.R: enable things like M [ M < 10 ]
186 :     * R/dgeMatrix.R: implement it
187 :    
188 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
189 :    
190 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
191 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
192 :     * R/lmer.R (show): now works with summary()
193 :    
194 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
195 :    
196 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
197 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
198 :     support the above
199 :    
200 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
201 :    
202 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
203 :     Use glmFit$prior.weights for weights in a glmm.
204 :     Allow an option usePQL = FALSE to skip the PQL steps for the
205 :     Laplace method (and, in time, the AGQ method).
206 :    
207 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
208 :     into a separate function internal_mer_Xfactor to be able to call
209 :     it from internal_bhat.
210 :    
211 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
212 :    
213 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
214 :     testing; now again of all actual classes.
215 :    
216 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
217 :     use macros and define make_d_matrix_* and make_i_matrix_*
218 :     where _i_ is for the ldense routines:
219 :    
220 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
221 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
222 :    
223 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
224 :    
225 :    
226 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
227 :    
228 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
229 :     many different kinds of matrices.
230 :     * R/*.R: quite a few new methods were needed for R CMD check with
231 :     new Matrix(). Very good for users playing around.
232 :    
233 :    
234 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
235 :    
236 :     * src/dgeMatrix.c (dMatrix_validate): new
237 :     * src/Mutils.c (dense_nonpacked_validate): new
238 :    
239 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
240 :    
241 :    
242 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
243 :    
244 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
245 :    
246 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
247 : bates 1119
248 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
249 :    
250 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
251 :     segfault in cases with multiple non-nested grouping factors.
252 :    
253 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
254 :    
255 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
256 :     (Depends): also on 'utils'
257 :    
258 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
259 :     * R/diagMatrix.R (Diagonal): constructor and methods for
260 :     diagonal matrices
261 :    
262 :     * R/ltTMatrix.R: new "minimal methods"
263 :    
264 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
265 :    
266 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
267 :     all methods (and help files).
268 :    
269 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
270 :    
271 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
272 :     for case (dimn. op no_dimn.)
273 :    
274 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
275 :    
276 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
277 : maechler 1084
278 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
279 :    
280 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
281 :     by Julian Faraway.
282 :    
283 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
284 :    
285 :     * R/Auxiliaries.R (try_as): new utility
286 :     * R/sparseMatrix.R: use try_as() in coercion to original class
287 :    
288 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
289 :    
290 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
291 :    
292 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
293 :    
294 :     * R/Auxiliaries.R (dimNamesCheck): added
295 :    
296 :     * R/Matrix.R (as.array), (as.vector): new
297 :    
298 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
299 :    
300 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
301 : maechler 956 default.
302 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
303 :     "pMatrix" now contains "sparseMatrix"
304 : maechler 954
305 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
308 :    
309 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
310 :    
311 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
312 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
313 :    
314 :     * R/dspMatrix.R: typo in "t" method
315 :    
316 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
317 :    
318 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
319 :     * R/Tsparse.R: instead of R/gTMatrix.R
320 :     * R/Csparse.R: new
321 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
322 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
323 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
324 :     via cholmod
325 :    
326 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
327 :    
328 :     * R/Auxiliaries.R (non0ind): new function using new C code
329 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
330 :    
331 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
332 :    
333 :     * src/chm_common.h: header file required by all C sources that
334 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
335 : bates 917 called 'c' whose address is passed as the last argument to
336 :     (virtually) every CHOLMOD function.
337 :    
338 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
339 :    
340 :     * src/init.c: initialize and finalize the cholmod_common structure.
341 :    
342 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
343 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
344 :    
345 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
346 :    
347 :     * inst/test-tools.R: new file collecting the utility functions used
348 :     in ./tests/*.R
349 :    
350 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
351 :     * R/Matrix.R (cbind2): methods for NULL and missing
352 :    
353 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
354 :    
355 :     * R/AllClass.R: new "index" class for "[" and "[<-":
356 :     First cut at "symmetricMatrix" and "triangularMatrix"
357 :     * R/gTMatrix.R (.ind.prep): new function;
358 : maechler 1174 Logical and character indexing now work too.
359 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
360 :     * tests/indexing.R: new, including *.Rout.save
361 :     * tests/dgTMatrix.R: new
362 :    
363 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
364 :    
365 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
366 :     indicator pos not being updated. Also enforced upper triangular
367 :     for symmetric case. Need to coerce edges component of elements of
368 :     edge list - grr! (Why don't they define their classes cleanly?)
369 :    
370 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
371 :    
372 :     * R/Matrix.R: added first "[<-" methods; not yet functional
373 :     * R/denseMatrix.R: dito
374 :     * man/Subassign-methods.Rd: new help file for these
375 :    
376 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
377 :    
378 :     * DESCRIPTION (Version): 0.98-6
379 :    
380 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
381 :     matrices.
382 :    
383 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
384 :    
385 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
386 :     as( <logical>, "matrix")
387 :    
388 :     * R/pMatrix.R: coercion to "lgTMatrix"
389 :    
390 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
391 :     * man/gTMatrix-class.Rd:
392 :     * General slight re-organization of where "[" methods are defined.
393 :     more to come.
394 :    
395 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
396 : maechler 868
397 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
398 : maechler 871
399 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
400 :     * .....
401 :    
402 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
403 :    
404 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
405 :     or glmer objects.
406 :    
407 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
408 :    
409 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
410 :    
411 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
412 :    
413 :     * R/HBMM.R: finish re-writing R-only code.
414 :    
415 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
416 :    
417 :     * man/externalFormats.Rd: move documentation for writeHB and
418 :     writeMM here.
419 :    
420 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
421 :     (suggested by Paul Roecker).
422 :    
423 :     * tests/validObj.R (assertError): Comment out test that is failing
424 :     after recent changes in r-devel.
425 :    
426 : maechler 860
427 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
430 :     * man/denseMatrix-class.Rd
431 :     * NAMESPACE: export it, and also export
432 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
433 :    
434 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
435 :    
436 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
437 :    
438 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
439 :     matrix_solve code (which was really, really wrong).
440 :    
441 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
442 : maechler 834
443 :     * DESCRIPTION (Version): 0.98-2
444 :    
445 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
446 :    
447 :     * R/lmer.R (abbrvNms): new
448 :     * R/lmer.R (mcmcsamp): allow transformed parameters
449 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
450 :     for the Harwell-Boeing and the MatrixMarket formats.
451 : maechler 834
452 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
453 :    
454 :     * man/dtrMatrix-class.Rd: add examples
455 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
456 : maechler 834
457 :     * TODO: note the dtpMatrix (docu) bug
458 :    
459 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
460 :     in order to ensure that new as.matrix() is used by old functions,
461 :     e.g., svd(), qr(), eigen(), dist(),..;
462 :     apply(), also matplot() or pairs().
463 :    
464 :    
465 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
466 :    
467 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
468 :     add comments about 'control' / lmerControl() arguments
469 :    
470 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
471 : bates 820
472 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
473 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
474 : bates 820
475 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
476 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
477 :    
478 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
479 :     .Call calls that were producing spurious output.
480 :    
481 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
482 : bates 801
483 :     * R/lmer.R (lmer): stored updated variance component estimates in
484 :     mer object for the generalized model. (Bug reported by Renaud
485 :     Lancelot).
486 :    
487 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
488 : bates 794
489 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
490 :     unidimensional case.
491 :    
492 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
493 : maechler 791
494 :     * DESCRIPTION (Version): 0.96-1
495 :    
496 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
497 : maechler 791
498 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
499 : bates 763
500 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
501 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
502 :    
503 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
504 : bates 763
505 :     * src/Makefile.win: Forgot to update this when Makefile changed.
506 :    
507 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
508 : bates 726
509 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
510 :     bug reported by Kurt Hornik and Michael Hahsler.
511 :    
512 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
513 : bates 725
514 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
515 :     logical sparse matrices. These will also be used in the symbolic
516 :     analysis for lmer objects.
517 :    
518 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
519 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
520 : maechler 791
521 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
522 : bates 714
523 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
524 :     colMeans, colSums, rowMeans and rowSums.
525 :    
526 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
527 : bates 692
528 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
529 :     multiplication operation.
530 :    
531 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
532 :     to dgetrs.
533 :    
534 :     * src/init.c: Fix cut-and-paste error in definition of
535 :     dgeMatrix_matrix_solve
536 :    
537 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
538 :    
539 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
540 : bates 692
541 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
542 :    
543 :     * DESCRIPTION: Eliminate import of stats.
544 :    
545 : maechler 791
546 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
547 : bates 692
548 :     * R/AllClass.R : add logical sparse matrix classes
549 :    
550 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
551 :    
552 :     * R/dgTMatrix.R: add "[" method for triplet matrices
553 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
554 :    
555 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
556 : maechler 687
557 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
558 :    
559 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
560 :     * R/sparseMatrix.R: %*%, crossprod()
561 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
562 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
563 :     * src/lmer.c (lmer_fitted): fix thinko
564 :    
565 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
566 :    
567 :     * R/AllClass.R: add two virtual sparse classes ``on top''
568 :    
569 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
570 :    
571 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
572 :     correspondingly fix examples and tests/ since new()
573 :     doesn't work for virtual classes.
574 :    
575 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
576 :    
577 :     * R/Matrix.R (as.matrix): method and one for unname()
578 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
579 :     also run for R 2.1.0; using as.matrix()
580 :    
581 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
582 : maechler 658
583 :     * R/pMatrix.R: "pMatrix" class added
584 :     * ....
585 :    
586 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
587 : bates 645
588 :     * R/dtpMatrix.R: Add unpack method and an example.
589 :    
590 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
591 :     of general symmetric matrices and associated S4 methods.
592 :    
593 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
594 :     +
595 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
596 :    
597 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
598 :     crossprod() and "%*%" methods added; tests, too.
599 :     * tests/matprod.R: new, for testing these
600 :    
601 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
602 : bates 599
603 :     * src/lmer.c (lmer_fitted): Added.
604 :    
605 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
606 : bates 596
607 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
608 :    
609 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
610 : bates 582
611 :     * src/*.c,po/,inst/po: Internationalization and localization of
612 :     the package.
613 :    
614 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
615 :     R_ldl.c file.
616 :    
617 :     * src/flame.[ch]: Removed these source files.
618 : maechler 658
619 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
620 :    
621 :     * src/LU.[ch],src/init.c: absorb in factorizations
622 :    
623 :     * src/Mutils.h: prepare for internationalization
624 :    
625 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
626 :     this file
627 :    
628 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
629 :    
630 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
631 :    
632 :     * R/dtrMatrix.R: fix t() method
633 :    
634 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
635 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
636 : maechler 578 * tests/group-methods.R : and test them.
637 :    
638 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
639 :     border case
640 :    
641 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
642 :    
643 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
644 : maechler 578
645 :     * src/dgBCMatrix.c:
646 :     * src/lmer.c: many changes
647 :     * ...
648 :    
649 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
650 :    
651 :     * R/Matrix.R: add more sophisticated show() method.
652 :    
653 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
654 :    
655 :     * */* : almost complete reorganization of classes.
656 :    
657 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
658 : bates 460
659 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
660 :     for the geMatrix class.
661 :    
662 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
663 : bates 460
664 :     * src/Makefile (clean): Remove *.a and *.so
665 :    
666 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
667 :    
668 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
669 : bates 460
670 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
671 : bates 460 had an effect in cases with more than 2 grouping factors.
672 :    
673 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
674 : bates 415
675 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
676 :    
677 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
678 : bates 410
679 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
680 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
681 :    
682 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
683 : bates 392
684 :     * R/sscMatrix.R: Add determinant methods
685 :    
686 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
687 :     for tripletMatrix to matrix.
688 :    
689 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
690 : bates 388
691 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
692 :     no longer used.
693 :    
694 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
695 :     with dynamic allocation of scratch arrays.
696 :    
697 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
698 :     for multivariate random effects with multiple grouping factors.
699 :     Fixes part but not all of #15.
700 :    
701 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
702 : bates 375
703 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
704 :     scalar grouping factors corrected.
705 :    
706 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
707 : bates 375
708 :     * src/bCrosstab.c: remove diag_update which is no longer used
709 :    
710 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
711 : bates 350
712 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
713 :     .h file can be included.
714 :    
715 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
716 : bates 342
717 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
718 : bates 342 Complete allocation of slots in NEW_OBJECT.
719 :    
720 :     * src/Mutils.h: Moved list of symbols to an include file
721 :    
722 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
723 : bates 342
724 :     * src/geMutils.c (Matrix_init): remove unused function
725 :    
726 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
727 : bates 342
728 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
729 :    
730 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
731 : bates 327
732 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
733 :    
734 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
735 : bates 303
736 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
737 :    
738 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
739 : bates 296
740 :     * src/init.c: Created R_init_Matrix and added registration of C
741 :     routines.
742 :    
743 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
744 : bates 283
745 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
746 :    
747 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
748 : bates 229
749 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
750 :    
751 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
752 :    
753 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
754 :    
755 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
756 :    
757 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
758 :     ssclme_update_mm
759 :    
760 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
761 :    
762 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
763 :     in the order of unconstrained and constrained parameters.
764 :     (ssclme_gradient): Added the gradients (not yet correct for
765 :     multidimensional, unconstrained case).
766 :    
767 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
768 :    
769 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
770 :    
771 :     * src/Makefile.win: Remove unneeded ranlib call
772 :    
773 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
774 :    
775 :     * DESCRIPTION (Version): New release
776 :    
777 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
778 :    
779 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
780 :    
781 :     * src/triplet_to_col.c: Create triplet_to_col as a native
782 : maechler 658 function, not the version from umfpack. There were problems with
783 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
784 :     only one umfpack routine being used so I moved it here.
785 :    
786 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
787 :    
788 :     * src/ssclme.c (ssclme_variances): New function.
789 :    
790 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
791 :    
792 :     * src/ssclme.c (ssclme_fitted): Added function.
793 :    
794 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
795 :    
796 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
797 :     store the dimnames in the XtX and bVar slots
798 :     (ssclme_update_mm): Change the dimensions of the bVar slot
799 :     components and the returned value from ssclme_ranef.
800 :    
801 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
802 :    
803 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
804 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
805 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
806 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
807 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
808 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
809 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
810 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
811 :     Moved the pdMat classes from the lme4 package.
812 :    
813 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
814 :    
815 :     * man/ssclme-class.Rd: Update definition and documentation of the
816 :     ssclme class to include the DIsqrt slot.
817 :    
818 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
819 :     (much faster using dsyrk, a level 3 BLAS routine).
820 :    
821 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
822 :    
823 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
824 :    
825 :     * tests/ssclme.R: Modify the test to account for the permutation
826 :     of the levels of the grouping factors.
827 :    
828 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
829 :    
830 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
831 :     directly into the ssclme class definition.
832 :    
833 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
834 :    
835 :     * DESCRIPTION (Date): New release
836 :    
837 :     * man/ssclme-class.Rd: new file.
838 :    
839 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
840 :     works and it's fast!
841 :    
842 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
843 :    
844 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
845 :    
846 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
847 :    
848 :     * DESCRIPTION (Date): New release
849 :    
850 :     * NAMESPACE: Don't export ssclme.
851 :    
852 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
853 :     school data.
854 :    
855 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
856 :    
857 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
858 :     keep track of the fixed-effects and the response. Counts also
859 :     gets an extra element, which is always one.
860 :    
861 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
862 :    
863 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
864 :    
865 :     * src/cscMatrix.c (csc_transpose): new function
866 :    
867 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
868 :     (csc_components_transpose): new function
869 :    
870 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
871 :    
872 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
873 :     triplets
874 :    
875 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
876 :    
877 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
878 :    
879 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
880 :     and all other .h files in src.
881 :    
882 :     * src/Makefile.win: This and other Makefile.win files contributed
883 :     by Brian Ripley.
884 :    
885 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
886 :    
887 :     * R/syMatrix.R: Added methods for "%*%".
888 :    
889 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
890 :     poMatrix object.
891 :    
892 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
893 :    
894 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
895 :    
896 :     2004-01-25 Douglas Bates <bates@bates2_home>
897 :    
898 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
899 :    
900 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
901 :     of nrow.
902 :    
903 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
904 :    
905 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
906 :     subdirectories.
907 :    
908 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
909 :    
910 :     * src/taucs.h: Accidently referred to global header files
911 :     instead of local files.
912 :    
913 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
914 :    
915 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
916 :     and methods and replaced all classes with S4 classes.
917 :    
918 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
919 :    
920 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
921 :    
922 :     * src/R_LapackPP.cc: Change method of calculating determinants
923 :    
924 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
925 :    
926 :     * DESCRIPTION (Version): removed empty data directory as requested
927 :     by CRAN maintainers. Changed version number and date.
928 :    
929 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
930 :    
931 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
932 :     under Windows.
933 :    
934 :     * Added configure.win and src/Makevars.win as requested by Brian
935 :     Ripley.
936 :    
937 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
938 :    
939 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
940 :     Hornik.
941 :    
942 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
943 :    
944 :     * configure.ac: Replaced configure.in with configure.ac
945 :     contributed by Kurt Hornik.
946 :    
947 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
948 :     version for R-1.5.0
949 :    
950 : maechler 512
951 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
952 :    
953 :     * man/eigen.Rd: Removed the .Alias in the example

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