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Annotation of /pkg/ChangeLog

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1 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/pedigree.c (pedigree_inbreeding): Correction in
4 :     initialization. This function is not currently being used and is
5 :     not fully tested.
6 :    
7 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
8 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
9 :     objects. Modified validity check on pedigree objects to account
10 :     for nonparallel patterns of missingness of parents.
11 : bates 1311
12 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
13 :    
14 :     * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
15 :     the output from mcmcsamp.
16 :    
17 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
18 :    
19 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
20 :     of the hat matrix.
21 : bates 1298
22 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
23 :    
24 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
25 :     classes.
26 :    
27 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * R/dgTMatrix.R (colSums): etc. All four of
30 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
31 :     all "Matrices".
32 :    
33 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
34 :    
35 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
36 :     background grid to the qqmath plot of ranef.lmer.
37 :    
38 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
39 : bates 1284
40 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
41 :     grouping factors to be specified in the formula as (1|foo/bar).
42 :    
43 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
44 :    
45 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
46 :     !is.language to resolve the bug reported by Jacob Wegelin.
47 :    
48 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
49 :     code to evaluate inbreeding coefficients without calculating T,
50 :     based on code in Sargolzaei and Iwaisaki's paper.
51 :    
52 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
53 :    
54 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
55 :     generic and mer methods for isNested and denomDF. This denomDF was
56 :     an attempt to emulate that in lme but I don't think that makes
57 :     sense. Use the trace of the hat matrix instead.
58 :    
59 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
60 :    
61 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
62 :     the C code depending on a slot structure that's no longer valid.
63 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
64 :    
65 :    
66 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
67 :    
68 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
69 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
70 :     and added a general band extractor.
71 :    
72 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
73 :    
74 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
75 :     allowable range with NAs. Added a corresponding check in the
76 :     validity check for the pedigree class.
77 :    
78 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
79 :     crossprod methods now inherits from symmetricMatrix.
80 :    
81 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
82 :    
83 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
84 :     generics lowerTriMatrix and upperTriMatrix along with methods for
85 :     the Csparse virtual class. Also added a C function Csparse_band
86 :     that implements these methods by calling cholmod_band.
87 :    
88 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
89 :    
90 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
91 :     erased when it was NULL. This led to invalid subselections!
92 :    
93 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
94 :    
95 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
96 :     in method for "t" so as not to lose the unit diagonal property.
97 :    
98 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
99 :    
100 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
101 :     and methods. This is now an option to the ranef method for the
102 :     mer class.
103 :    
104 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
105 :     compressed column-oriented matrix. Minor formatting cleanup.
106 :    
107 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
108 :     objects.
109 :    
110 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
111 :    
112 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
113 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
114 :    
115 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
116 :    
117 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
118 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
119 :    
120 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
121 :     for the dtCMatrix class.
122 : maechler 1253
123 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
124 :    
125 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
126 :     and methods for it.
127 :    
128 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
129 :    
130 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
131 :     arguments, such that M %*% 1:6 now works
132 :     * Tests/matprod.R: test the above
133 :    
134 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
135 : bates 1243
136 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
137 :     the ranef.lmer class.
138 :    
139 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
140 :     methods to extract the posterior variances from the bVar slot.
141 :    
142 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
145 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
146 :    
147 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
148 :     * tests/simple: (extended)
149 :    
150 :     * R/sparseMatrix.R (isTriangular): now using much improved
151 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
152 :    
153 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
154 :    
155 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
156 :     (problem report from Franklin Parlamis). This should be done
157 : maechler 1238 generally.
158 : bates 1236
159 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
160 :    
161 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
162 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
163 :     update the plot methods.
164 :    
165 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
166 :    
167 :     * R/lmer.R (resid and ranef methods): Added methods for the
168 :     "residuals" and "resid" generic but only for linear mixed model
169 :     fits. Changed the ranef method to return a list of data frames so
170 :     that the plot methods now work.
171 :    
172 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
173 :    
174 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
175 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
176 :    
177 :     * DESCRIPTION (Date): New release
178 :    
179 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
180 :    
181 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
182 :    
183 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
184 :     * man/KNex.Rd: and other help files
185 :     * tests/*.R: several ones needed adaption
186 :     * inst/doc/Comparisons.Rnw: dito
187 :    
188 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
189 :    
190 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
191 :    
192 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
193 :    
194 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
195 :    
196 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
197 :    
198 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
199 :    
200 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
201 :    
202 :     * R/dMatrix.R: enable things like M [ M < 10 ]
203 :     * R/dgeMatrix.R: implement it
204 :    
205 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
206 :    
207 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
208 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
209 :     * R/lmer.R (show): now works with summary()
210 :    
211 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
212 :    
213 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
214 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
215 :     support the above
216 :    
217 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
218 :    
219 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
220 :     Use glmFit$prior.weights for weights in a glmm.
221 :     Allow an option usePQL = FALSE to skip the PQL steps for the
222 :     Laplace method (and, in time, the AGQ method).
223 :    
224 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
225 :     into a separate function internal_mer_Xfactor to be able to call
226 :     it from internal_bhat.
227 :    
228 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
231 :     testing; now again of all actual classes.
232 :    
233 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
234 :     use macros and define make_d_matrix_* and make_i_matrix_*
235 :     where _i_ is for the ldense routines:
236 :    
237 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
238 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
239 :    
240 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
241 :    
242 :    
243 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
244 :    
245 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
246 :     many different kinds of matrices.
247 :     * R/*.R: quite a few new methods were needed for R CMD check with
248 :     new Matrix(). Very good for users playing around.
249 :    
250 :    
251 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
252 :    
253 :     * src/dgeMatrix.c (dMatrix_validate): new
254 :     * src/Mutils.c (dense_nonpacked_validate): new
255 :    
256 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
257 :    
258 :    
259 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
260 :    
261 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
262 :    
263 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
264 : bates 1119
265 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
266 :    
267 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
268 :     segfault in cases with multiple non-nested grouping factors.
269 :    
270 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
271 :    
272 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
273 :     (Depends): also on 'utils'
274 :    
275 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
276 :     * R/diagMatrix.R (Diagonal): constructor and methods for
277 :     diagonal matrices
278 :    
279 :     * R/ltTMatrix.R: new "minimal methods"
280 :    
281 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
282 :    
283 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
284 :     all methods (and help files).
285 :    
286 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
287 :    
288 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
289 :     for case (dimn. op no_dimn.)
290 :    
291 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
292 :    
293 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
294 : maechler 1084
295 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
296 :    
297 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
298 :     by Julian Faraway.
299 :    
300 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
301 :    
302 :     * R/Auxiliaries.R (try_as): new utility
303 :     * R/sparseMatrix.R: use try_as() in coercion to original class
304 :    
305 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
308 :    
309 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
310 :    
311 :     * R/Auxiliaries.R (dimNamesCheck): added
312 :    
313 :     * R/Matrix.R (as.array), (as.vector): new
314 :    
315 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
316 :    
317 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
318 : maechler 956 default.
319 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
320 :     "pMatrix" now contains "sparseMatrix"
321 : maechler 954
322 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
325 :    
326 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
327 :    
328 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
329 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
330 :    
331 :     * R/dspMatrix.R: typo in "t" method
332 :    
333 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
334 :    
335 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
336 :     * R/Tsparse.R: instead of R/gTMatrix.R
337 :     * R/Csparse.R: new
338 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
339 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
340 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
341 :     via cholmod
342 :    
343 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
344 :    
345 :     * R/Auxiliaries.R (non0ind): new function using new C code
346 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
347 :    
348 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
349 :    
350 :     * src/chm_common.h: header file required by all C sources that
351 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
352 : bates 917 called 'c' whose address is passed as the last argument to
353 :     (virtually) every CHOLMOD function.
354 :    
355 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
356 :    
357 :     * src/init.c: initialize and finalize the cholmod_common structure.
358 :    
359 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
360 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
361 :    
362 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
363 :    
364 :     * inst/test-tools.R: new file collecting the utility functions used
365 :     in ./tests/*.R
366 :    
367 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
368 :     * R/Matrix.R (cbind2): methods for NULL and missing
369 :    
370 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
371 :    
372 :     * R/AllClass.R: new "index" class for "[" and "[<-":
373 :     First cut at "symmetricMatrix" and "triangularMatrix"
374 :     * R/gTMatrix.R (.ind.prep): new function;
375 : maechler 1174 Logical and character indexing now work too.
376 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
377 :     * tests/indexing.R: new, including *.Rout.save
378 :     * tests/dgTMatrix.R: new
379 :    
380 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
381 :    
382 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
383 :     indicator pos not being updated. Also enforced upper triangular
384 :     for symmetric case. Need to coerce edges component of elements of
385 :     edge list - grr! (Why don't they define their classes cleanly?)
386 :    
387 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
388 :    
389 :     * R/Matrix.R: added first "[<-" methods; not yet functional
390 :     * R/denseMatrix.R: dito
391 :     * man/Subassign-methods.Rd: new help file for these
392 :    
393 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
394 :    
395 :     * DESCRIPTION (Version): 0.98-6
396 :    
397 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
398 :     matrices.
399 :    
400 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
401 :    
402 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
403 :     as( <logical>, "matrix")
404 :    
405 :     * R/pMatrix.R: coercion to "lgTMatrix"
406 :    
407 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
408 :     * man/gTMatrix-class.Rd:
409 :     * General slight re-organization of where "[" methods are defined.
410 :     more to come.
411 :    
412 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
413 : maechler 868
414 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
415 : maechler 871
416 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
417 :     * .....
418 :    
419 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
420 :    
421 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
422 :     or glmer objects.
423 :    
424 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
425 :    
426 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
427 :    
428 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
429 :    
430 :     * R/HBMM.R: finish re-writing R-only code.
431 :    
432 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
433 :    
434 :     * man/externalFormats.Rd: move documentation for writeHB and
435 :     writeMM here.
436 :    
437 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
438 :     (suggested by Paul Roecker).
439 :    
440 :     * tests/validObj.R (assertError): Comment out test that is failing
441 :     after recent changes in r-devel.
442 :    
443 : maechler 860
444 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
445 :    
446 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
447 :     * man/denseMatrix-class.Rd
448 :     * NAMESPACE: export it, and also export
449 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
450 :    
451 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
452 :    
453 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
454 :    
455 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
456 :     matrix_solve code (which was really, really wrong).
457 :    
458 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
459 : maechler 834
460 :     * DESCRIPTION (Version): 0.98-2
461 :    
462 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
463 :    
464 :     * R/lmer.R (abbrvNms): new
465 :     * R/lmer.R (mcmcsamp): allow transformed parameters
466 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
467 :     for the Harwell-Boeing and the MatrixMarket formats.
468 : maechler 834
469 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
470 :    
471 :     * man/dtrMatrix-class.Rd: add examples
472 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
473 : maechler 834
474 :     * TODO: note the dtpMatrix (docu) bug
475 :    
476 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
477 :     in order to ensure that new as.matrix() is used by old functions,
478 :     e.g., svd(), qr(), eigen(), dist(),..;
479 :     apply(), also matplot() or pairs().
480 :    
481 :    
482 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
483 :    
484 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
485 :     add comments about 'control' / lmerControl() arguments
486 :    
487 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
488 : bates 820
489 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
490 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
491 : bates 820
492 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
493 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
494 :    
495 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
496 :     .Call calls that were producing spurious output.
497 :    
498 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
499 : bates 801
500 :     * R/lmer.R (lmer): stored updated variance component estimates in
501 :     mer object for the generalized model. (Bug reported by Renaud
502 :     Lancelot).
503 :    
504 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
505 : bates 794
506 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
507 :     unidimensional case.
508 :    
509 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
510 : maechler 791
511 :     * DESCRIPTION (Version): 0.96-1
512 :    
513 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
514 : maechler 791
515 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
516 : bates 763
517 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
518 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
519 :    
520 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
521 : bates 763
522 :     * src/Makefile.win: Forgot to update this when Makefile changed.
523 :    
524 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
525 : bates 726
526 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
527 :     bug reported by Kurt Hornik and Michael Hahsler.
528 :    
529 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
530 : bates 725
531 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
532 :     logical sparse matrices. These will also be used in the symbolic
533 :     analysis for lmer objects.
534 :    
535 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
536 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
537 : maechler 791
538 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
539 : bates 714
540 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
541 :     colMeans, colSums, rowMeans and rowSums.
542 :    
543 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
544 : bates 692
545 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
546 :     multiplication operation.
547 :    
548 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
549 :     to dgetrs.
550 :    
551 :     * src/init.c: Fix cut-and-paste error in definition of
552 :     dgeMatrix_matrix_solve
553 :    
554 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
555 :    
556 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
557 : bates 692
558 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
559 :    
560 :     * DESCRIPTION: Eliminate import of stats.
561 :    
562 : maechler 791
563 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
564 : bates 692
565 :     * R/AllClass.R : add logical sparse matrix classes
566 :    
567 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
568 :    
569 :     * R/dgTMatrix.R: add "[" method for triplet matrices
570 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
571 :    
572 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
573 : maechler 687
574 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
575 :    
576 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
577 :     * R/sparseMatrix.R: %*%, crossprod()
578 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
579 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
580 :     * src/lmer.c (lmer_fitted): fix thinko
581 :    
582 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
583 :    
584 :     * R/AllClass.R: add two virtual sparse classes ``on top''
585 :    
586 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
587 :    
588 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
589 :     correspondingly fix examples and tests/ since new()
590 :     doesn't work for virtual classes.
591 :    
592 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
593 :    
594 :     * R/Matrix.R (as.matrix): method and one for unname()
595 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
596 :     also run for R 2.1.0; using as.matrix()
597 :    
598 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
599 : maechler 658
600 :     * R/pMatrix.R: "pMatrix" class added
601 :     * ....
602 :    
603 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
604 : bates 645
605 :     * R/dtpMatrix.R: Add unpack method and an example.
606 :    
607 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
608 :     of general symmetric matrices and associated S4 methods.
609 :    
610 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
611 :     +
612 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
613 :    
614 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
615 :     crossprod() and "%*%" methods added; tests, too.
616 :     * tests/matprod.R: new, for testing these
617 :    
618 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
619 : bates 599
620 :     * src/lmer.c (lmer_fitted): Added.
621 :    
622 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
623 : bates 596
624 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
625 :    
626 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
627 : bates 582
628 :     * src/*.c,po/,inst/po: Internationalization and localization of
629 :     the package.
630 :    
631 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
632 :     R_ldl.c file.
633 :    
634 :     * src/flame.[ch]: Removed these source files.
635 : maechler 658
636 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
637 :    
638 :     * src/LU.[ch],src/init.c: absorb in factorizations
639 :    
640 :     * src/Mutils.h: prepare for internationalization
641 :    
642 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
643 :     this file
644 :    
645 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
646 :    
647 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
648 :    
649 :     * R/dtrMatrix.R: fix t() method
650 :    
651 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
652 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
653 : maechler 578 * tests/group-methods.R : and test them.
654 :    
655 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
656 :     border case
657 :    
658 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
659 :    
660 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
661 : maechler 578
662 :     * src/dgBCMatrix.c:
663 :     * src/lmer.c: many changes
664 :     * ...
665 :    
666 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
667 :    
668 :     * R/Matrix.R: add more sophisticated show() method.
669 :    
670 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
671 :    
672 :     * */* : almost complete reorganization of classes.
673 :    
674 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
675 : bates 460
676 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
677 :     for the geMatrix class.
678 :    
679 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
680 : bates 460
681 :     * src/Makefile (clean): Remove *.a and *.so
682 :    
683 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
684 :    
685 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
686 : bates 460
687 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
688 : bates 460 had an effect in cases with more than 2 grouping factors.
689 :    
690 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
691 : bates 415
692 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
693 :    
694 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
695 : bates 410
696 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
697 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
698 :    
699 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
700 : bates 392
701 :     * R/sscMatrix.R: Add determinant methods
702 :    
703 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
704 :     for tripletMatrix to matrix.
705 :    
706 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
707 : bates 388
708 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
709 :     no longer used.
710 :    
711 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
712 :     with dynamic allocation of scratch arrays.
713 :    
714 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
715 :     for multivariate random effects with multiple grouping factors.
716 :     Fixes part but not all of #15.
717 :    
718 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
719 : bates 375
720 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
721 :     scalar grouping factors corrected.
722 :    
723 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
724 : bates 375
725 :     * src/bCrosstab.c: remove diag_update which is no longer used
726 :    
727 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
728 : bates 350
729 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
730 :     .h file can be included.
731 :    
732 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
733 : bates 342
734 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
735 : bates 342 Complete allocation of slots in NEW_OBJECT.
736 :    
737 :     * src/Mutils.h: Moved list of symbols to an include file
738 :    
739 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
740 : bates 342
741 :     * src/geMutils.c (Matrix_init): remove unused function
742 :    
743 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
744 : bates 342
745 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
746 :    
747 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
748 : bates 327
749 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
750 :    
751 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
752 : bates 303
753 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
754 :    
755 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
756 : bates 296
757 :     * src/init.c: Created R_init_Matrix and added registration of C
758 :     routines.
759 :    
760 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
761 : bates 283
762 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
763 :    
764 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
765 : bates 229
766 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
767 :    
768 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
769 :    
770 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
771 :    
772 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
773 :    
774 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
775 :     ssclme_update_mm
776 :    
777 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
778 :    
779 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
780 :     in the order of unconstrained and constrained parameters.
781 :     (ssclme_gradient): Added the gradients (not yet correct for
782 :     multidimensional, unconstrained case).
783 :    
784 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
785 :    
786 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
787 :    
788 :     * src/Makefile.win: Remove unneeded ranlib call
789 :    
790 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
791 :    
792 :     * DESCRIPTION (Version): New release
793 :    
794 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
795 :    
796 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
797 :    
798 :     * src/triplet_to_col.c: Create triplet_to_col as a native
799 : maechler 658 function, not the version from umfpack. There were problems with
800 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
801 :     only one umfpack routine being used so I moved it here.
802 :    
803 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
804 :    
805 :     * src/ssclme.c (ssclme_variances): New function.
806 :    
807 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
808 :    
809 :     * src/ssclme.c (ssclme_fitted): Added function.
810 :    
811 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
812 :    
813 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
814 :     store the dimnames in the XtX and bVar slots
815 :     (ssclme_update_mm): Change the dimensions of the bVar slot
816 :     components and the returned value from ssclme_ranef.
817 :    
818 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
819 :    
820 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
821 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
822 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
823 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
824 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
825 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
826 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
827 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
828 :     Moved the pdMat classes from the lme4 package.
829 :    
830 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
831 :    
832 :     * man/ssclme-class.Rd: Update definition and documentation of the
833 :     ssclme class to include the DIsqrt slot.
834 :    
835 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
836 :     (much faster using dsyrk, a level 3 BLAS routine).
837 :    
838 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
839 :    
840 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
841 :    
842 :     * tests/ssclme.R: Modify the test to account for the permutation
843 :     of the levels of the grouping factors.
844 :    
845 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
846 :    
847 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
848 :     directly into the ssclme class definition.
849 :    
850 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
851 :    
852 :     * DESCRIPTION (Date): New release
853 :    
854 :     * man/ssclme-class.Rd: new file.
855 :    
856 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
857 :     works and it's fast!
858 :    
859 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
860 :    
861 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
862 :    
863 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
864 :    
865 :     * DESCRIPTION (Date): New release
866 :    
867 :     * NAMESPACE: Don't export ssclme.
868 :    
869 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
870 :     school data.
871 :    
872 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
873 :    
874 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
875 :     keep track of the fixed-effects and the response. Counts also
876 :     gets an extra element, which is always one.
877 :    
878 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
879 :    
880 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
881 :    
882 :     * src/cscMatrix.c (csc_transpose): new function
883 :    
884 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
885 :     (csc_components_transpose): new function
886 :    
887 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
888 :    
889 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
890 :     triplets
891 :    
892 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
893 :    
894 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
895 :    
896 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
897 :     and all other .h files in src.
898 :    
899 :     * src/Makefile.win: This and other Makefile.win files contributed
900 :     by Brian Ripley.
901 :    
902 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
903 :    
904 :     * R/syMatrix.R: Added methods for "%*%".
905 :    
906 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
907 :     poMatrix object.
908 :    
909 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
910 :    
911 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
912 :    
913 :     2004-01-25 Douglas Bates <bates@bates2_home>
914 :    
915 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
916 :    
917 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
918 :     of nrow.
919 :    
920 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
921 :    
922 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
923 :     subdirectories.
924 :    
925 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
926 :    
927 :     * src/taucs.h: Accidently referred to global header files
928 :     instead of local files.
929 :    
930 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
931 :    
932 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
933 :     and methods and replaced all classes with S4 classes.
934 :    
935 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
936 :    
937 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
938 :    
939 :     * src/R_LapackPP.cc: Change method of calculating determinants
940 :    
941 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
942 :    
943 :     * DESCRIPTION (Version): removed empty data directory as requested
944 :     by CRAN maintainers. Changed version number and date.
945 :    
946 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
947 :    
948 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
949 :     under Windows.
950 :    
951 :     * Added configure.win and src/Makevars.win as requested by Brian
952 :     Ripley.
953 :    
954 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
955 :    
956 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
957 :     Hornik.
958 :    
959 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
960 :    
961 :     * configure.ac: Replaced configure.in with configure.ac
962 :     contributed by Kurt Hornik.
963 :    
964 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
965 :     version for R-1.5.0
966 :    
967 : maechler 512
968 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
969 :    
970 :     * man/eigen.Rd: Removed the .Alias in the example

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