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Annotation of /pkg/ChangeLog

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36 :     the C code depending on a slot structure that's no longer valid.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

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