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Annotation of /pkg/ChangeLog

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1 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
4 :     since that wrongly triggers also for M[ logi , ]
5 :    
6 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
7 :     a symmetric matrix that results in a non-symmetric one.
8 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
9 :    
10 :     * R/dMatrix.R: make round(M) work as round(M, 0)
11 :    
12 :     * R/dgTMatrix.R (image): coordinate system and axis now use
13 :     1-based indices, not 0-based ones.
14 :    
15 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
16 :     * tests/indexing.R: test it.
17 :    
18 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
19 :     * man/isSymmetric-methods.Rd: and document it.
20 :    
21 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
22 :     * man/SparseM-conv.Rd: docu them
23 :    
24 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
25 :     for 'SparseM' conversions
26 :    
27 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
28 :    
29 :     * R/Matrix.R (head): added head() and tail() methods.
30 :    
31 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
32 :    
33 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
34 :    
35 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
36 :    
37 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
38 :     add check for correct printing of symmetric sparse matrices.
39 :    
40 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
41 :     for sparse symmetric matrices.
42 :    
43 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
44 :     diagonal twice.
45 :    
46 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
47 :    
48 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
49 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
50 : bates 1316
51 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
52 :    
53 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
54 :    
55 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
56 :    
57 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
58 :    
59 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
60 :     * R/lgCMatrix.R (diag): for new method
61 :    
62 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
63 :     ==> construction of illegal "*gTMatrix" via new() should
64 :     now be much less easy:
65 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
66 :    
67 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
68 :     directly.
69 :     * man/Matrix.Rd: documents it.
70 :    
71 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
72 :    
73 :     * src/pedigree.c (pedigree_inbreeding): Correction in
74 :     initialization. This function is not currently being used and is
75 :     not fully tested.
76 :    
77 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
78 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
79 :     objects. Modified validity check on pedigree objects to account
80 :     for nonparallel patterns of missingness of parents.
81 : bates 1311
82 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
83 :     class.
84 : maechler 1315
85 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
86 :    
87 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
88 :    
89 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
90 :    
91 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
92 :    
93 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
94 :     the output from mcmcsamp.
95 :    
96 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
97 :    
98 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
99 :     of the hat matrix.
100 : bates 1298
101 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
104 :     classes.
105 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
106 : maechler 1295
107 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
108 :    
109 :     * R/dgTMatrix.R (colSums): etc. All four of
110 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
111 :     all "Matrices".
112 :    
113 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
114 :    
115 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
116 :     background grid to the qqmath plot of ranef.lmer.
117 :    
118 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
119 : bates 1284
120 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
121 :     grouping factors to be specified in the formula as (1|foo/bar).
122 :    
123 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
124 :    
125 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
126 :     !is.language to resolve the bug reported by Jacob Wegelin.
127 :    
128 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
129 :     code to evaluate inbreeding coefficients without calculating T,
130 :     based on code in Sargolzaei and Iwaisaki's paper.
131 :    
132 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
133 :    
134 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
135 :     generic and mer methods for isNested and denomDF. This denomDF was
136 :     an attempt to emulate that in lme but I don't think that makes
137 :     sense. Use the trace of the hat matrix instead.
138 :    
139 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
140 :    
141 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
142 :     the C code depending on a slot structure that's no longer valid.
143 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
144 :    
145 :    
146 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
147 :    
148 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
149 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
150 :     and added a general band extractor.
151 :    
152 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
153 :    
154 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
155 :     allowable range with NAs. Added a corresponding check in the
156 :     validity check for the pedigree class.
157 :    
158 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
159 :     crossprod methods now inherits from symmetricMatrix.
160 :    
161 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
162 :    
163 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
164 :     generics lowerTriMatrix and upperTriMatrix along with methods for
165 :     the Csparse virtual class. Also added a C function Csparse_band
166 :     that implements these methods by calling cholmod_band.
167 :    
168 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
169 :    
170 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
171 :     erased when it was NULL. This led to invalid subselections!
172 :    
173 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
174 :    
175 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
176 :     in method for "t" so as not to lose the unit diagonal property.
177 :    
178 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
179 :    
180 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
181 :     and methods. This is now an option to the ranef method for the
182 :     mer class.
183 :    
184 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
185 :     compressed column-oriented matrix. Minor formatting cleanup.
186 :    
187 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
188 :     objects.
189 :    
190 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
191 :    
192 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
193 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
194 :    
195 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
196 :    
197 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
198 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
199 :    
200 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
201 :     for the dtCMatrix class.
202 : maechler 1253
203 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
204 :    
205 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
206 :     and methods for it.
207 :    
208 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
209 :    
210 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
211 :     arguments, such that M %*% 1:6 now works
212 :     * Tests/matprod.R: test the above
213 :    
214 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
215 : bates 1243
216 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
217 :     the ranef.lmer class.
218 :    
219 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
220 :     methods to extract the posterior variances from the bVar slot.
221 :    
222 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
223 :    
224 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
225 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
226 :    
227 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
228 :     * tests/simple: (extended)
229 :    
230 :     * R/sparseMatrix.R (isTriangular): now using much improved
231 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
232 :    
233 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
234 :    
235 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
236 :     (problem report from Franklin Parlamis). This should be done
237 : maechler 1238 generally.
238 : bates 1236
239 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
240 :    
241 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
242 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
243 :     update the plot methods.
244 :    
245 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
246 :    
247 :     * R/lmer.R (resid and ranef methods): Added methods for the
248 :     "residuals" and "resid" generic but only for linear mixed model
249 :     fits. Changed the ranef method to return a list of data frames so
250 :     that the plot methods now work.
251 :    
252 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
253 :    
254 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
255 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
256 :    
257 :     * DESCRIPTION (Date): New release
258 :    
259 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
260 :    
261 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
262 :    
263 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
264 :     * man/KNex.Rd: and other help files
265 :     * tests/*.R: several ones needed adaption
266 :     * inst/doc/Comparisons.Rnw: dito
267 :    
268 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
271 :    
272 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
273 :    
274 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
277 :    
278 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
279 :    
280 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
281 :    
282 :     * R/dMatrix.R: enable things like M [ M < 10 ]
283 :     * R/dgeMatrix.R: implement it
284 :    
285 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
288 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
289 :     * R/lmer.R (show): now works with summary()
290 :    
291 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
292 :    
293 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
294 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
295 :     support the above
296 :    
297 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
298 :    
299 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
300 :     Use glmFit$prior.weights for weights in a glmm.
301 :     Allow an option usePQL = FALSE to skip the PQL steps for the
302 :     Laplace method (and, in time, the AGQ method).
303 :    
304 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
305 :     into a separate function internal_mer_Xfactor to be able to call
306 :     it from internal_bhat.
307 :    
308 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
309 :    
310 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
311 :     testing; now again of all actual classes.
312 :    
313 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
314 :     use macros and define make_d_matrix_* and make_i_matrix_*
315 :     where _i_ is for the ldense routines:
316 :    
317 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
318 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
319 :    
320 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
321 :    
322 :    
323 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
324 :    
325 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
326 :     many different kinds of matrices.
327 :     * R/*.R: quite a few new methods were needed for R CMD check with
328 :     new Matrix(). Very good for users playing around.
329 :    
330 :    
331 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
332 :    
333 :     * src/dgeMatrix.c (dMatrix_validate): new
334 :     * src/Mutils.c (dense_nonpacked_validate): new
335 :    
336 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
337 :    
338 :    
339 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
340 :    
341 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
342 :    
343 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
344 : bates 1119
345 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
346 :    
347 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
348 :     segfault in cases with multiple non-nested grouping factors.
349 :    
350 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
351 :    
352 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
353 :     (Depends): also on 'utils'
354 :    
355 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
356 :     * R/diagMatrix.R (Diagonal): constructor and methods for
357 :     diagonal matrices
358 :    
359 :     * R/ltTMatrix.R: new "minimal methods"
360 :    
361 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
364 :     all methods (and help files).
365 :    
366 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
369 :     for case (dimn. op no_dimn.)
370 :    
371 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
372 :    
373 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
374 : maechler 1084
375 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
376 :    
377 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
378 :     by Julian Faraway.
379 :    
380 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
381 :    
382 :     * R/Auxiliaries.R (try_as): new utility
383 :     * R/sparseMatrix.R: use try_as() in coercion to original class
384 :    
385 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
386 :    
387 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
388 :    
389 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
390 :    
391 :     * R/Auxiliaries.R (dimNamesCheck): added
392 :    
393 :     * R/Matrix.R (as.array), (as.vector): new
394 :    
395 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
396 :    
397 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
398 : maechler 956 default.
399 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
400 :     "pMatrix" now contains "sparseMatrix"
401 : maechler 954
402 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
403 :    
404 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
405 :    
406 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
407 :    
408 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
409 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
410 :    
411 :     * R/dspMatrix.R: typo in "t" method
412 :    
413 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
414 :    
415 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
416 :     * R/Tsparse.R: instead of R/gTMatrix.R
417 :     * R/Csparse.R: new
418 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
419 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
420 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
421 :     via cholmod
422 :    
423 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
424 :    
425 :     * R/Auxiliaries.R (non0ind): new function using new C code
426 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
427 :    
428 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
429 :    
430 :     * src/chm_common.h: header file required by all C sources that
431 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
432 : bates 917 called 'c' whose address is passed as the last argument to
433 :     (virtually) every CHOLMOD function.
434 :    
435 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
436 :    
437 :     * src/init.c: initialize and finalize the cholmod_common structure.
438 :    
439 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
440 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
441 :    
442 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
443 :    
444 :     * inst/test-tools.R: new file collecting the utility functions used
445 :     in ./tests/*.R
446 :    
447 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
448 :     * R/Matrix.R (cbind2): methods for NULL and missing
449 :    
450 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
451 :    
452 :     * R/AllClass.R: new "index" class for "[" and "[<-":
453 :     First cut at "symmetricMatrix" and "triangularMatrix"
454 :     * R/gTMatrix.R (.ind.prep): new function;
455 : maechler 1174 Logical and character indexing now work too.
456 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
457 :     * tests/indexing.R: new, including *.Rout.save
458 :     * tests/dgTMatrix.R: new
459 :    
460 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
461 :    
462 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
463 :     indicator pos not being updated. Also enforced upper triangular
464 :     for symmetric case. Need to coerce edges component of elements of
465 :     edge list - grr! (Why don't they define their classes cleanly?)
466 :    
467 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
468 :    
469 :     * R/Matrix.R: added first "[<-" methods; not yet functional
470 :     * R/denseMatrix.R: dito
471 :     * man/Subassign-methods.Rd: new help file for these
472 :    
473 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
474 :    
475 :     * DESCRIPTION (Version): 0.98-6
476 :    
477 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
478 :     matrices.
479 :    
480 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
481 :    
482 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
483 :     as( <logical>, "matrix")
484 :    
485 :     * R/pMatrix.R: coercion to "lgTMatrix"
486 :    
487 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
488 :     * man/gTMatrix-class.Rd:
489 :     * General slight re-organization of where "[" methods are defined.
490 :     more to come.
491 :    
492 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
493 : maechler 868
494 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
495 : maechler 871
496 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
497 :     * .....
498 :    
499 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
500 :    
501 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
502 :     or glmer objects.
503 :    
504 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
505 :    
506 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
507 :    
508 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
509 :    
510 :     * R/HBMM.R: finish re-writing R-only code.
511 :    
512 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
513 :    
514 :     * man/externalFormats.Rd: move documentation for writeHB and
515 :     writeMM here.
516 :    
517 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
518 :     (suggested by Paul Roecker).
519 :    
520 :     * tests/validObj.R (assertError): Comment out test that is failing
521 :     after recent changes in r-devel.
522 :    
523 : maechler 860
524 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
525 :    
526 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
527 :     * man/denseMatrix-class.Rd
528 :     * NAMESPACE: export it, and also export
529 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
530 :    
531 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
532 :    
533 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
534 :    
535 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
536 :     matrix_solve code (which was really, really wrong).
537 :    
538 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
539 : maechler 834
540 :     * DESCRIPTION (Version): 0.98-2
541 :    
542 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
543 :    
544 :     * R/lmer.R (abbrvNms): new
545 :     * R/lmer.R (mcmcsamp): allow transformed parameters
546 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
547 :     for the Harwell-Boeing and the MatrixMarket formats.
548 : maechler 834
549 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
550 :    
551 :     * man/dtrMatrix-class.Rd: add examples
552 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
553 : maechler 834
554 :     * TODO: note the dtpMatrix (docu) bug
555 :    
556 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
557 :     in order to ensure that new as.matrix() is used by old functions,
558 :     e.g., svd(), qr(), eigen(), dist(),..;
559 :     apply(), also matplot() or pairs().
560 :    
561 :    
562 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
563 :    
564 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
565 :     add comments about 'control' / lmerControl() arguments
566 :    
567 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
568 : bates 820
569 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
570 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
571 : bates 820
572 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
573 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
574 :    
575 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
576 :     .Call calls that were producing spurious output.
577 :    
578 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
579 : bates 801
580 :     * R/lmer.R (lmer): stored updated variance component estimates in
581 :     mer object for the generalized model. (Bug reported by Renaud
582 :     Lancelot).
583 :    
584 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
585 : bates 794
586 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
587 :     unidimensional case.
588 :    
589 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
590 : maechler 791
591 :     * DESCRIPTION (Version): 0.96-1
592 :    
593 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
594 : maechler 791
595 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
596 : bates 763
597 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
598 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
599 :    
600 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
601 : bates 763
602 :     * src/Makefile.win: Forgot to update this when Makefile changed.
603 :    
604 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
605 : bates 726
606 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
607 :     bug reported by Kurt Hornik and Michael Hahsler.
608 :    
609 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
610 : bates 725
611 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
612 :     logical sparse matrices. These will also be used in the symbolic
613 :     analysis for lmer objects.
614 :    
615 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
616 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
617 : maechler 791
618 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
619 : bates 714
620 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
621 :     colMeans, colSums, rowMeans and rowSums.
622 :    
623 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
624 : bates 692
625 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
626 :     multiplication operation.
627 :    
628 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
629 :     to dgetrs.
630 :    
631 :     * src/init.c: Fix cut-and-paste error in definition of
632 :     dgeMatrix_matrix_solve
633 :    
634 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
635 :    
636 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
637 : bates 692
638 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
639 :    
640 :     * DESCRIPTION: Eliminate import of stats.
641 :    
642 : maechler 791
643 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
644 : bates 692
645 :     * R/AllClass.R : add logical sparse matrix classes
646 :    
647 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
648 :    
649 :     * R/dgTMatrix.R: add "[" method for triplet matrices
650 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
651 :    
652 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
653 : maechler 687
654 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
655 :    
656 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
657 :     * R/sparseMatrix.R: %*%, crossprod()
658 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
659 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
660 :     * src/lmer.c (lmer_fitted): fix thinko
661 :    
662 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
663 :    
664 :     * R/AllClass.R: add two virtual sparse classes ``on top''
665 :    
666 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
667 :    
668 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
669 :     correspondingly fix examples and tests/ since new()
670 :     doesn't work for virtual classes.
671 :    
672 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
673 :    
674 :     * R/Matrix.R (as.matrix): method and one for unname()
675 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
676 :     also run for R 2.1.0; using as.matrix()
677 :    
678 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
679 : maechler 658
680 :     * R/pMatrix.R: "pMatrix" class added
681 :     * ....
682 :    
683 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
684 : bates 645
685 :     * R/dtpMatrix.R: Add unpack method and an example.
686 :    
687 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
688 :     of general symmetric matrices and associated S4 methods.
689 :    
690 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
691 :     +
692 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
693 :    
694 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
695 :     crossprod() and "%*%" methods added; tests, too.
696 :     * tests/matprod.R: new, for testing these
697 :    
698 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
699 : bates 599
700 :     * src/lmer.c (lmer_fitted): Added.
701 :    
702 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
703 : bates 596
704 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
705 :    
706 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
707 : bates 582
708 :     * src/*.c,po/,inst/po: Internationalization and localization of
709 :     the package.
710 :    
711 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
712 :     R_ldl.c file.
713 :    
714 :     * src/flame.[ch]: Removed these source files.
715 : maechler 658
716 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
717 :    
718 :     * src/LU.[ch],src/init.c: absorb in factorizations
719 :    
720 :     * src/Mutils.h: prepare for internationalization
721 :    
722 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
723 :     this file
724 :    
725 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
726 :    
727 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
728 :    
729 :     * R/dtrMatrix.R: fix t() method
730 :    
731 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
732 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
733 : maechler 578 * tests/group-methods.R : and test them.
734 :    
735 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
736 :     border case
737 :    
738 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
739 :    
740 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
741 : maechler 578
742 :     * src/dgBCMatrix.c:
743 :     * src/lmer.c: many changes
744 :     * ...
745 :    
746 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
747 :    
748 :     * R/Matrix.R: add more sophisticated show() method.
749 :    
750 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
751 :    
752 :     * */* : almost complete reorganization of classes.
753 :    
754 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
755 : bates 460
756 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
757 :     for the geMatrix class.
758 :    
759 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
760 : bates 460
761 :     * src/Makefile (clean): Remove *.a and *.so
762 :    
763 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
764 :    
765 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
766 : bates 460
767 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
768 : bates 460 had an effect in cases with more than 2 grouping factors.
769 :    
770 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
771 : bates 415
772 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
773 :    
774 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
775 : bates 410
776 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
777 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
778 :    
779 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
780 : bates 392
781 :     * R/sscMatrix.R: Add determinant methods
782 :    
783 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
784 :     for tripletMatrix to matrix.
785 :    
786 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
787 : bates 388
788 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
789 :     no longer used.
790 :    
791 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
792 :     with dynamic allocation of scratch arrays.
793 :    
794 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
795 :     for multivariate random effects with multiple grouping factors.
796 :     Fixes part but not all of #15.
797 :    
798 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
799 : bates 375
800 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
801 :     scalar grouping factors corrected.
802 :    
803 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
804 : bates 375
805 :     * src/bCrosstab.c: remove diag_update which is no longer used
806 :    
807 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
808 : bates 350
809 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
810 :     .h file can be included.
811 :    
812 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
813 : bates 342
814 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
815 : bates 342 Complete allocation of slots in NEW_OBJECT.
816 :    
817 :     * src/Mutils.h: Moved list of symbols to an include file
818 :    
819 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
820 : bates 342
821 :     * src/geMutils.c (Matrix_init): remove unused function
822 :    
823 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
824 : bates 342
825 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
826 :    
827 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
828 : bates 327
829 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
830 :    
831 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
832 : bates 303
833 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
834 :    
835 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
836 : bates 296
837 :     * src/init.c: Created R_init_Matrix and added registration of C
838 :     routines.
839 :    
840 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
841 : bates 283
842 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
843 :    
844 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
845 : bates 229
846 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
847 :    
848 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
849 :    
850 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
851 :    
852 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
853 :    
854 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
855 :     ssclme_update_mm
856 :    
857 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
858 :    
859 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
860 :     in the order of unconstrained and constrained parameters.
861 :     (ssclme_gradient): Added the gradients (not yet correct for
862 :     multidimensional, unconstrained case).
863 :    
864 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
865 :    
866 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
867 :    
868 :     * src/Makefile.win: Remove unneeded ranlib call
869 :    
870 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
871 :    
872 :     * DESCRIPTION (Version): New release
873 :    
874 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
875 :    
876 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
877 :    
878 :     * src/triplet_to_col.c: Create triplet_to_col as a native
879 : maechler 658 function, not the version from umfpack. There were problems with
880 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
881 :     only one umfpack routine being used so I moved it here.
882 :    
883 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
884 :    
885 :     * src/ssclme.c (ssclme_variances): New function.
886 :    
887 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
888 :    
889 :     * src/ssclme.c (ssclme_fitted): Added function.
890 :    
891 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
892 :    
893 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
894 :     store the dimnames in the XtX and bVar slots
895 :     (ssclme_update_mm): Change the dimensions of the bVar slot
896 :     components and the returned value from ssclme_ranef.
897 :    
898 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
899 :    
900 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
901 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
902 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
903 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
904 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
905 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
906 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
907 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
908 :     Moved the pdMat classes from the lme4 package.
909 :    
910 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
911 :    
912 :     * man/ssclme-class.Rd: Update definition and documentation of the
913 :     ssclme class to include the DIsqrt slot.
914 :    
915 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
916 :     (much faster using dsyrk, a level 3 BLAS routine).
917 :    
918 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
919 :    
920 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
921 :    
922 :     * tests/ssclme.R: Modify the test to account for the permutation
923 :     of the levels of the grouping factors.
924 :    
925 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
926 :    
927 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
928 :     directly into the ssclme class definition.
929 :    
930 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
931 :    
932 :     * DESCRIPTION (Date): New release
933 :    
934 :     * man/ssclme-class.Rd: new file.
935 :    
936 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
937 :     works and it's fast!
938 :    
939 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
940 :    
941 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
942 :    
943 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
944 :    
945 :     * DESCRIPTION (Date): New release
946 :    
947 :     * NAMESPACE: Don't export ssclme.
948 :    
949 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
950 :     school data.
951 :    
952 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
953 :    
954 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
955 :     keep track of the fixed-effects and the response. Counts also
956 :     gets an extra element, which is always one.
957 :    
958 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
959 :    
960 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
961 :    
962 :     * src/cscMatrix.c (csc_transpose): new function
963 :    
964 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
965 :     (csc_components_transpose): new function
966 :    
967 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
968 :    
969 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
970 :     triplets
971 :    
972 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
973 :    
974 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
975 :    
976 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
977 :     and all other .h files in src.
978 :    
979 :     * src/Makefile.win: This and other Makefile.win files contributed
980 :     by Brian Ripley.
981 :    
982 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
983 :    
984 :     * R/syMatrix.R: Added methods for "%*%".
985 :    
986 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
987 :     poMatrix object.
988 :    
989 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
990 :    
991 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
992 :    
993 :     2004-01-25 Douglas Bates <bates@bates2_home>
994 :    
995 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
996 :    
997 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
998 :     of nrow.
999 :    
1000 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1001 :    
1002 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1003 :     subdirectories.
1004 :    
1005 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1006 :    
1007 :     * src/taucs.h: Accidently referred to global header files
1008 :     instead of local files.
1009 :    
1010 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1011 :    
1012 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1013 :     and methods and replaced all classes with S4 classes.
1014 :    
1015 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1016 :    
1017 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1018 :    
1019 :     * src/R_LapackPP.cc: Change method of calculating determinants
1020 :    
1021 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1022 :    
1023 :     * DESCRIPTION (Version): removed empty data directory as requested
1024 :     by CRAN maintainers. Changed version number and date.
1025 :    
1026 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1027 :    
1028 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1029 :     under Windows.
1030 :    
1031 :     * Added configure.win and src/Makevars.win as requested by Brian
1032 :     Ripley.
1033 :    
1034 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1035 :    
1036 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1037 :     Hornik.
1038 :    
1039 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1040 :    
1041 :     * configure.ac: Replaced configure.in with configure.ac
1042 :     contributed by Kurt Hornik.
1043 :    
1044 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1045 :     version for R-1.5.0
1046 :    
1047 : maechler 512
1048 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1049 :    
1050 :     * man/eigen.Rd: Removed the .Alias in the example

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