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Revision 1267 - (view) (download)

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

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