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Annotation of /pkg/ChangeLog

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1 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
4 :     via new smart
5 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
6 :     utility functions.
7 :    
8 :    
9 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
10 :    
11 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
12 :     matrices when appropriate; band() even symmetric ones.
13 :     (replCmat): extend to potentially all "CsparseMatrix"
14 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
15 :     allow subassignment for special sparse matrices.
16 :    
17 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
18 :    
19 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
20 :     argument; in glmer_*(): print only if(verbose).
21 :    
22 :     speed-optimize a few places by moving REAL(.) out of loops.
23 :    
24 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
25 :    
26 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
27 :    
28 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
29 :     since that wrongly triggers also for M[ logi , ]
30 :    
31 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
32 :     a symmetric matrix that results in a non-symmetric one.
33 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
34 :    
35 :     * R/dMatrix.R: make round(M) work as round(M, 0)
36 :    
37 :     * R/dgTMatrix.R (image): coordinate system and axis now use
38 :     1-based indices, not 0-based ones.
39 :    
40 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
41 :     * tests/indexing.R: test it.
42 :    
43 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
44 :     * man/isSymmetric-methods.Rd: and document it.
45 :    
46 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
47 :     * man/SparseM-conv.Rd: docu them
48 :    
49 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
50 :     for 'SparseM' conversions
51 :    
52 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
53 :    
54 :     * R/Matrix.R (head): added head() and tail() methods.
55 :    
56 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
57 :    
58 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
59 :    
60 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
61 :    
62 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
63 :     add check for correct printing of symmetric sparse matrices.
64 :    
65 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
66 :     for sparse symmetric matrices.
67 :    
68 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
69 :     diagonal twice.
70 :    
71 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
72 :    
73 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
74 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
75 : bates 1316
76 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
77 :    
78 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
79 :    
80 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
81 :    
82 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
85 :     * R/lgCMatrix.R (diag): for new method
86 :    
87 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
88 :     ==> construction of illegal "*gTMatrix" via new() should
89 :     now be much less easy:
90 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
91 :    
92 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
93 :     directly.
94 :     * man/Matrix.Rd: documents it.
95 :    
96 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
97 :    
98 :     * src/pedigree.c (pedigree_inbreeding): Correction in
99 :     initialization. This function is not currently being used and is
100 :     not fully tested.
101 :    
102 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
103 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
104 :     objects. Modified validity check on pedigree objects to account
105 :     for nonparallel patterns of missingness of parents.
106 : bates 1311
107 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
108 :     class.
109 : maechler 1315
110 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
111 :    
112 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
113 :    
114 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
115 :    
116 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
117 :    
118 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
119 :     the output from mcmcsamp.
120 :    
121 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
122 :    
123 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
124 :     of the hat matrix.
125 : bates 1298
126 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
127 :    
128 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
129 :     classes.
130 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
131 : maechler 1295
132 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
133 :    
134 :     * R/dgTMatrix.R (colSums): etc. All four of
135 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
136 :     all "Matrices".
137 :    
138 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
139 :    
140 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
141 :     background grid to the qqmath plot of ranef.lmer.
142 :    
143 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
144 : bates 1284
145 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
146 :     grouping factors to be specified in the formula as (1|foo/bar).
147 :    
148 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
149 :    
150 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
151 :     !is.language to resolve the bug reported by Jacob Wegelin.
152 :    
153 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
154 :     code to evaluate inbreeding coefficients without calculating T,
155 :     based on code in Sargolzaei and Iwaisaki's paper.
156 :    
157 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
158 :    
159 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
160 :     generic and mer methods for isNested and denomDF. This denomDF was
161 :     an attempt to emulate that in lme but I don't think that makes
162 :     sense. Use the trace of the hat matrix instead.
163 :    
164 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
165 :    
166 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
167 :     the C code depending on a slot structure that's no longer valid.
168 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
169 :    
170 :    
171 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
172 :    
173 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
174 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
175 :     and added a general band extractor.
176 :    
177 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
178 :    
179 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
180 :     allowable range with NAs. Added a corresponding check in the
181 :     validity check for the pedigree class.
182 :    
183 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
184 :     crossprod methods now inherits from symmetricMatrix.
185 :    
186 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
187 :    
188 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
189 :     generics lowerTriMatrix and upperTriMatrix along with methods for
190 :     the Csparse virtual class. Also added a C function Csparse_band
191 :     that implements these methods by calling cholmod_band.
192 :    
193 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
194 :    
195 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
196 :     erased when it was NULL. This led to invalid subselections!
197 :    
198 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
199 :    
200 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
201 :     in method for "t" so as not to lose the unit diagonal property.
202 :    
203 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
204 :    
205 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
206 :     and methods. This is now an option to the ranef method for the
207 :     mer class.
208 :    
209 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
210 :     compressed column-oriented matrix. Minor formatting cleanup.
211 :    
212 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
213 :     objects.
214 :    
215 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
216 :    
217 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
218 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
219 :    
220 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
221 :    
222 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
223 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
224 :    
225 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
226 :     for the dtCMatrix class.
227 : maechler 1253
228 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
229 :    
230 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
231 :     and methods for it.
232 :    
233 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
234 :    
235 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
236 :     arguments, such that M %*% 1:6 now works
237 :     * Tests/matprod.R: test the above
238 :    
239 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
240 : bates 1243
241 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
242 :     the ranef.lmer class.
243 :    
244 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
245 :     methods to extract the posterior variances from the bVar slot.
246 :    
247 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
248 :    
249 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
250 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
251 :    
252 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
253 :     * tests/simple: (extended)
254 :    
255 :     * R/sparseMatrix.R (isTriangular): now using much improved
256 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
257 :    
258 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
261 :     (problem report from Franklin Parlamis). This should be done
262 : maechler 1238 generally.
263 : bates 1236
264 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
265 :    
266 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
267 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
268 :     update the plot methods.
269 :    
270 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
271 :    
272 :     * R/lmer.R (resid and ranef methods): Added methods for the
273 :     "residuals" and "resid" generic but only for linear mixed model
274 :     fits. Changed the ranef method to return a list of data frames so
275 :     that the plot methods now work.
276 :    
277 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
278 :    
279 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
280 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
281 :    
282 :     * DESCRIPTION (Date): New release
283 :    
284 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
285 :    
286 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
287 :    
288 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
289 :     * man/KNex.Rd: and other help files
290 :     * tests/*.R: several ones needed adaption
291 :     * inst/doc/Comparisons.Rnw: dito
292 :    
293 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
294 :    
295 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
296 :    
297 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
298 :    
299 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
300 :    
301 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
302 :    
303 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
304 :    
305 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * R/dMatrix.R: enable things like M [ M < 10 ]
308 :     * R/dgeMatrix.R: implement it
309 :    
310 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
311 :    
312 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
313 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
314 :     * R/lmer.R (show): now works with summary()
315 :    
316 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
317 :    
318 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
319 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
320 :     support the above
321 :    
322 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
323 :    
324 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
325 :     Use glmFit$prior.weights for weights in a glmm.
326 :     Allow an option usePQL = FALSE to skip the PQL steps for the
327 :     Laplace method (and, in time, the AGQ method).
328 :    
329 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
330 :     into a separate function internal_mer_Xfactor to be able to call
331 :     it from internal_bhat.
332 :    
333 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
334 :    
335 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
336 :     testing; now again of all actual classes.
337 :    
338 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
339 :     use macros and define make_d_matrix_* and make_i_matrix_*
340 :     where _i_ is for the ldense routines:
341 :    
342 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
343 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
344 :    
345 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
346 :    
347 :    
348 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
349 :    
350 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
351 :     many different kinds of matrices.
352 :     * R/*.R: quite a few new methods were needed for R CMD check with
353 :     new Matrix(). Very good for users playing around.
354 :    
355 :    
356 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * src/dgeMatrix.c (dMatrix_validate): new
359 :     * src/Mutils.c (dense_nonpacked_validate): new
360 :    
361 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
362 :    
363 :    
364 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
365 :    
366 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
367 :    
368 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
369 : bates 1119
370 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
371 :    
372 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
373 :     segfault in cases with multiple non-nested grouping factors.
374 :    
375 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
376 :    
377 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
378 :     (Depends): also on 'utils'
379 :    
380 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
381 :     * R/diagMatrix.R (Diagonal): constructor and methods for
382 :     diagonal matrices
383 :    
384 :     * R/ltTMatrix.R: new "minimal methods"
385 :    
386 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
387 :    
388 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
389 :     all methods (and help files).
390 :    
391 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
392 :    
393 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
394 :     for case (dimn. op no_dimn.)
395 :    
396 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
397 :    
398 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
399 : maechler 1084
400 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
401 :    
402 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
403 :     by Julian Faraway.
404 :    
405 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
406 :    
407 :     * R/Auxiliaries.R (try_as): new utility
408 :     * R/sparseMatrix.R: use try_as() in coercion to original class
409 :    
410 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
411 :    
412 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
413 :    
414 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
415 :    
416 :     * R/Auxiliaries.R (dimNamesCheck): added
417 :    
418 :     * R/Matrix.R (as.array), (as.vector): new
419 :    
420 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
421 :    
422 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
423 : maechler 956 default.
424 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
425 :     "pMatrix" now contains "sparseMatrix"
426 : maechler 954
427 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
430 :    
431 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
432 :    
433 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
434 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
435 :    
436 :     * R/dspMatrix.R: typo in "t" method
437 :    
438 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
439 :    
440 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
441 :     * R/Tsparse.R: instead of R/gTMatrix.R
442 :     * R/Csparse.R: new
443 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
444 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
445 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
446 :     via cholmod
447 :    
448 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
449 :    
450 :     * R/Auxiliaries.R (non0ind): new function using new C code
451 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
452 :    
453 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
454 :    
455 :     * src/chm_common.h: header file required by all C sources that
456 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
457 : bates 917 called 'c' whose address is passed as the last argument to
458 :     (virtually) every CHOLMOD function.
459 :    
460 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
461 :    
462 :     * src/init.c: initialize and finalize the cholmod_common structure.
463 :    
464 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
465 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
466 :    
467 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
468 :    
469 :     * inst/test-tools.R: new file collecting the utility functions used
470 :     in ./tests/*.R
471 :    
472 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
473 :     * R/Matrix.R (cbind2): methods for NULL and missing
474 :    
475 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
476 :    
477 :     * R/AllClass.R: new "index" class for "[" and "[<-":
478 :     First cut at "symmetricMatrix" and "triangularMatrix"
479 :     * R/gTMatrix.R (.ind.prep): new function;
480 : maechler 1174 Logical and character indexing now work too.
481 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
482 :     * tests/indexing.R: new, including *.Rout.save
483 :     * tests/dgTMatrix.R: new
484 :    
485 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
486 :    
487 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
488 :     indicator pos not being updated. Also enforced upper triangular
489 :     for symmetric case. Need to coerce edges component of elements of
490 :     edge list - grr! (Why don't they define their classes cleanly?)
491 :    
492 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
493 :    
494 :     * R/Matrix.R: added first "[<-" methods; not yet functional
495 :     * R/denseMatrix.R: dito
496 :     * man/Subassign-methods.Rd: new help file for these
497 :    
498 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
499 :    
500 :     * DESCRIPTION (Version): 0.98-6
501 :    
502 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
503 :     matrices.
504 :    
505 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
506 :    
507 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
508 :     as( <logical>, "matrix")
509 :    
510 :     * R/pMatrix.R: coercion to "lgTMatrix"
511 :    
512 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
513 :     * man/gTMatrix-class.Rd:
514 :     * General slight re-organization of where "[" methods are defined.
515 :     more to come.
516 :    
517 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
518 : maechler 868
519 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
520 : maechler 871
521 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
522 :     * .....
523 :    
524 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
525 :    
526 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
527 :     or glmer objects.
528 :    
529 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
530 :    
531 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
532 :    
533 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
534 :    
535 :     * R/HBMM.R: finish re-writing R-only code.
536 :    
537 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
538 :    
539 :     * man/externalFormats.Rd: move documentation for writeHB and
540 :     writeMM here.
541 :    
542 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
543 :     (suggested by Paul Roecker).
544 :    
545 :     * tests/validObj.R (assertError): Comment out test that is failing
546 :     after recent changes in r-devel.
547 :    
548 : maechler 860
549 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
550 :    
551 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
552 :     * man/denseMatrix-class.Rd
553 :     * NAMESPACE: export it, and also export
554 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
555 :    
556 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
557 :    
558 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
559 :    
560 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
561 :     matrix_solve code (which was really, really wrong).
562 :    
563 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
564 : maechler 834
565 :     * DESCRIPTION (Version): 0.98-2
566 :    
567 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
568 :    
569 :     * R/lmer.R (abbrvNms): new
570 :     * R/lmer.R (mcmcsamp): allow transformed parameters
571 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
572 :     for the Harwell-Boeing and the MatrixMarket formats.
573 : maechler 834
574 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
575 :    
576 :     * man/dtrMatrix-class.Rd: add examples
577 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
578 : maechler 834
579 :     * TODO: note the dtpMatrix (docu) bug
580 :    
581 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
582 :     in order to ensure that new as.matrix() is used by old functions,
583 :     e.g., svd(), qr(), eigen(), dist(),..;
584 :     apply(), also matplot() or pairs().
585 :    
586 :    
587 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
588 :    
589 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
590 :     add comments about 'control' / lmerControl() arguments
591 :    
592 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
593 : bates 820
594 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
595 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
596 : bates 820
597 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
598 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
599 :    
600 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
601 :     .Call calls that were producing spurious output.
602 :    
603 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
604 : bates 801
605 :     * R/lmer.R (lmer): stored updated variance component estimates in
606 :     mer object for the generalized model. (Bug reported by Renaud
607 :     Lancelot).
608 :    
609 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
610 : bates 794
611 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
612 :     unidimensional case.
613 :    
614 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
615 : maechler 791
616 :     * DESCRIPTION (Version): 0.96-1
617 :    
618 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
619 : maechler 791
620 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
621 : bates 763
622 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
623 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
624 :    
625 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
626 : bates 763
627 :     * src/Makefile.win: Forgot to update this when Makefile changed.
628 :    
629 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
630 : bates 726
631 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
632 :     bug reported by Kurt Hornik and Michael Hahsler.
633 :    
634 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
635 : bates 725
636 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
637 :     logical sparse matrices. These will also be used in the symbolic
638 :     analysis for lmer objects.
639 :    
640 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
641 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
642 : maechler 791
643 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
644 : bates 714
645 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
646 :     colMeans, colSums, rowMeans and rowSums.
647 :    
648 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
649 : bates 692
650 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
651 :     multiplication operation.
652 :    
653 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
654 :     to dgetrs.
655 :    
656 :     * src/init.c: Fix cut-and-paste error in definition of
657 :     dgeMatrix_matrix_solve
658 :    
659 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
660 :    
661 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
662 : bates 692
663 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
664 :    
665 :     * DESCRIPTION: Eliminate import of stats.
666 :    
667 : maechler 791
668 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
669 : bates 692
670 :     * R/AllClass.R : add logical sparse matrix classes
671 :    
672 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
673 :    
674 :     * R/dgTMatrix.R: add "[" method for triplet matrices
675 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
676 :    
677 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
678 : maechler 687
679 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
680 :    
681 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
682 :     * R/sparseMatrix.R: %*%, crossprod()
683 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
684 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
685 :     * src/lmer.c (lmer_fitted): fix thinko
686 :    
687 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
688 :    
689 :     * R/AllClass.R: add two virtual sparse classes ``on top''
690 :    
691 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
692 :    
693 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
694 :     correspondingly fix examples and tests/ since new()
695 :     doesn't work for virtual classes.
696 :    
697 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
698 :    
699 :     * R/Matrix.R (as.matrix): method and one for unname()
700 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
701 :     also run for R 2.1.0; using as.matrix()
702 :    
703 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
704 : maechler 658
705 :     * R/pMatrix.R: "pMatrix" class added
706 :     * ....
707 :    
708 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
709 : bates 645
710 :     * R/dtpMatrix.R: Add unpack method and an example.
711 :    
712 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
713 :     of general symmetric matrices and associated S4 methods.
714 :    
715 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
716 :     +
717 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
718 :    
719 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
720 :     crossprod() and "%*%" methods added; tests, too.
721 :     * tests/matprod.R: new, for testing these
722 :    
723 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
724 : bates 599
725 :     * src/lmer.c (lmer_fitted): Added.
726 :    
727 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
728 : bates 596
729 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
730 :    
731 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
732 : bates 582
733 :     * src/*.c,po/,inst/po: Internationalization and localization of
734 :     the package.
735 :    
736 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
737 :     R_ldl.c file.
738 :    
739 :     * src/flame.[ch]: Removed these source files.
740 : maechler 658
741 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
742 :    
743 :     * src/LU.[ch],src/init.c: absorb in factorizations
744 :    
745 :     * src/Mutils.h: prepare for internationalization
746 :    
747 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
748 :     this file
749 :    
750 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
751 :    
752 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
753 :    
754 :     * R/dtrMatrix.R: fix t() method
755 :    
756 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
757 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
758 : maechler 578 * tests/group-methods.R : and test them.
759 :    
760 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
761 :     border case
762 :    
763 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
764 :    
765 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
766 : maechler 578
767 :     * src/dgBCMatrix.c:
768 :     * src/lmer.c: many changes
769 :     * ...
770 :    
771 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
772 :    
773 :     * R/Matrix.R: add more sophisticated show() method.
774 :    
775 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
776 :    
777 :     * */* : almost complete reorganization of classes.
778 :    
779 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
780 : bates 460
781 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
782 :     for the geMatrix class.
783 :    
784 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
785 : bates 460
786 :     * src/Makefile (clean): Remove *.a and *.so
787 :    
788 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
789 :    
790 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
791 : bates 460
792 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
793 : bates 460 had an effect in cases with more than 2 grouping factors.
794 :    
795 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
796 : bates 415
797 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
798 :    
799 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
800 : bates 410
801 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
802 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
803 :    
804 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
805 : bates 392
806 :     * R/sscMatrix.R: Add determinant methods
807 :    
808 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
809 :     for tripletMatrix to matrix.
810 :    
811 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
812 : bates 388
813 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
814 :     no longer used.
815 :    
816 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
817 :     with dynamic allocation of scratch arrays.
818 :    
819 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
820 :     for multivariate random effects with multiple grouping factors.
821 :     Fixes part but not all of #15.
822 :    
823 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
824 : bates 375
825 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
826 :     scalar grouping factors corrected.
827 :    
828 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
829 : bates 375
830 :     * src/bCrosstab.c: remove diag_update which is no longer used
831 :    
832 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
833 : bates 350
834 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
835 :     .h file can be included.
836 :    
837 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
838 : bates 342
839 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
840 : bates 342 Complete allocation of slots in NEW_OBJECT.
841 :    
842 :     * src/Mutils.h: Moved list of symbols to an include file
843 :    
844 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
845 : bates 342
846 :     * src/geMutils.c (Matrix_init): remove unused function
847 :    
848 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
849 : bates 342
850 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
851 :    
852 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
853 : bates 327
854 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
855 :    
856 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
857 : bates 303
858 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
859 :    
860 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
861 : bates 296
862 :     * src/init.c: Created R_init_Matrix and added registration of C
863 :     routines.
864 :    
865 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
866 : bates 283
867 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
868 :    
869 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
870 : bates 229
871 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
872 :    
873 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
874 :    
875 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
876 :    
877 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
878 :    
879 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
880 :     ssclme_update_mm
881 :    
882 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
883 :    
884 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
885 :     in the order of unconstrained and constrained parameters.
886 :     (ssclme_gradient): Added the gradients (not yet correct for
887 :     multidimensional, unconstrained case).
888 :    
889 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
890 :    
891 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
892 :    
893 :     * src/Makefile.win: Remove unneeded ranlib call
894 :    
895 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
896 :    
897 :     * DESCRIPTION (Version): New release
898 :    
899 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
900 :    
901 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
902 :    
903 :     * src/triplet_to_col.c: Create triplet_to_col as a native
904 : maechler 658 function, not the version from umfpack. There were problems with
905 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
906 :     only one umfpack routine being used so I moved it here.
907 :    
908 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
909 :    
910 :     * src/ssclme.c (ssclme_variances): New function.
911 :    
912 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
913 :    
914 :     * src/ssclme.c (ssclme_fitted): Added function.
915 :    
916 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
917 :    
918 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
919 :     store the dimnames in the XtX and bVar slots
920 :     (ssclme_update_mm): Change the dimensions of the bVar slot
921 :     components and the returned value from ssclme_ranef.
922 :    
923 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
924 :    
925 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
926 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
927 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
928 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
929 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
930 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
931 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
932 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
933 :     Moved the pdMat classes from the lme4 package.
934 :    
935 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
936 :    
937 :     * man/ssclme-class.Rd: Update definition and documentation of the
938 :     ssclme class to include the DIsqrt slot.
939 :    
940 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
941 :     (much faster using dsyrk, a level 3 BLAS routine).
942 :    
943 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
944 :    
945 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
946 :    
947 :     * tests/ssclme.R: Modify the test to account for the permutation
948 :     of the levels of the grouping factors.
949 :    
950 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
951 :    
952 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
953 :     directly into the ssclme class definition.
954 :    
955 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
956 :    
957 :     * DESCRIPTION (Date): New release
958 :    
959 :     * man/ssclme-class.Rd: new file.
960 :    
961 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
962 :     works and it's fast!
963 :    
964 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
965 :    
966 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
967 :    
968 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
969 :    
970 :     * DESCRIPTION (Date): New release
971 :    
972 :     * NAMESPACE: Don't export ssclme.
973 :    
974 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
975 :     school data.
976 :    
977 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
978 :    
979 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
980 :     keep track of the fixed-effects and the response. Counts also
981 :     gets an extra element, which is always one.
982 :    
983 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
984 :    
985 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
986 :    
987 :     * src/cscMatrix.c (csc_transpose): new function
988 :    
989 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
990 :     (csc_components_transpose): new function
991 :    
992 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
993 :    
994 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
995 :     triplets
996 :    
997 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
998 :    
999 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1000 :    
1001 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1002 :     and all other .h files in src.
1003 :    
1004 :     * src/Makefile.win: This and other Makefile.win files contributed
1005 :     by Brian Ripley.
1006 :    
1007 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1008 :    
1009 :     * R/syMatrix.R: Added methods for "%*%".
1010 :    
1011 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1012 :     poMatrix object.
1013 :    
1014 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1015 :    
1016 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1017 :    
1018 :     2004-01-25 Douglas Bates <bates@bates2_home>
1019 :    
1020 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1021 :    
1022 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1023 :     of nrow.
1024 :    
1025 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1026 :    
1027 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1028 :     subdirectories.
1029 :    
1030 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1031 :    
1032 :     * src/taucs.h: Accidently referred to global header files
1033 :     instead of local files.
1034 :    
1035 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1036 :    
1037 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1038 :     and methods and replaced all classes with S4 classes.
1039 :    
1040 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1041 :    
1042 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1043 :    
1044 :     * src/R_LapackPP.cc: Change method of calculating determinants
1045 :    
1046 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1047 :    
1048 :     * DESCRIPTION (Version): removed empty data directory as requested
1049 :     by CRAN maintainers. Changed version number and date.
1050 :    
1051 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1052 :    
1053 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1054 :     under Windows.
1055 :    
1056 :     * Added configure.win and src/Makevars.win as requested by Brian
1057 :     Ripley.
1058 :    
1059 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1060 :    
1061 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1062 :     Hornik.
1063 :    
1064 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1065 :    
1066 :     * configure.ac: Replaced configure.in with configure.ac
1067 :     contributed by Kurt Hornik.
1068 :    
1069 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1070 :     version for R-1.5.0
1071 :    
1072 : maechler 512
1073 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1074 :    
1075 :     * man/eigen.Rd: Removed the .Alias in the example

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