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Annotation of /pkg/ChangeLog

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1 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
4 :    
5 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
6 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
7 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
8 :     such that the S4 objects are always created by the current version
9 :     of R and 'Matrix' class definitions.
10 :    
11 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
12 :    
13 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
14 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
15 : bates 1342 boundary and test cases.
16 :    
17 :     * src/lmer.c (mer_postVar): Modified to return the variances that
18 :     are marginal to the fixed effects, not conditional on them (which
19 :     is what the bVar slot contents represent).
20 :    
21 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
22 :    
23 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
24 :     function which calls the C function mer_hat_trace2.
25 : maechler 1346
26 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
27 :     producing a caterpillar plot.
28 : bates 1338
29 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
30 :    
31 :     * NAMESPACE: change "correlation" to "corMatrix"
32 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
33 :     * R/dpoMatrix.R: dito
34 :     * R/lmer.R: dito
35 :    
36 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
37 :    
38 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
39 :     RZXinv slot's contents into a separate internal function that can
40 :     be used in mer_hat_trace.
41 :    
42 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
43 :    
44 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
45 :     via new smart
46 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
47 :     utility functions.
48 :    
49 :    
50 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
51 :    
52 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
53 :     matrices when appropriate; band() even symmetric ones.
54 :     (replCmat): extend to potentially all "CsparseMatrix"
55 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
56 :     allow subassignment for special sparse matrices.
57 :    
58 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
59 :    
60 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
61 :     argument; in glmer_*(): print only if(verbose).
62 :    
63 :     speed-optimize a few places by moving REAL(.) out of loops.
64 :    
65 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
66 :    
67 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
68 :    
69 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
70 :     since that wrongly triggers also for M[ logi , ]
71 :    
72 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
73 :     a symmetric matrix that results in a non-symmetric one.
74 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
75 :    
76 :     * R/dMatrix.R: make round(M) work as round(M, 0)
77 :    
78 :     * R/dgTMatrix.R (image): coordinate system and axis now use
79 :     1-based indices, not 0-based ones.
80 :    
81 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
82 :     * tests/indexing.R: test it.
83 :    
84 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
85 :     * man/isSymmetric-methods.Rd: and document it.
86 :    
87 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
88 :     * man/SparseM-conv.Rd: docu them
89 :    
90 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
91 :     for 'SparseM' conversions
92 :    
93 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
94 :    
95 :     * R/Matrix.R (head): added head() and tail() methods.
96 :    
97 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
98 :    
99 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
100 :    
101 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
104 :     add check for correct printing of symmetric sparse matrices.
105 :    
106 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
107 :     for sparse symmetric matrices.
108 :    
109 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
110 :     diagonal twice.
111 :    
112 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
113 :    
114 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
115 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
116 : bates 1316
117 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
118 :    
119 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
120 :    
121 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
122 :    
123 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
124 :    
125 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
126 :     * R/lgCMatrix.R (diag): for new method
127 :    
128 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
129 :     ==> construction of illegal "*gTMatrix" via new() should
130 :     now be much less easy:
131 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
132 :    
133 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
134 :     directly.
135 :     * man/Matrix.Rd: documents it.
136 :    
137 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
138 :    
139 :     * src/pedigree.c (pedigree_inbreeding): Correction in
140 :     initialization. This function is not currently being used and is
141 :     not fully tested.
142 :    
143 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
144 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
145 :     objects. Modified validity check on pedigree objects to account
146 :     for nonparallel patterns of missingness of parents.
147 : bates 1311
148 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
149 :     class.
150 : maechler 1315
151 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
154 :    
155 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
156 :    
157 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
158 :    
159 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
160 :     the output from mcmcsamp.
161 :    
162 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
163 :    
164 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
165 :     of the hat matrix.
166 : bates 1298
167 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
168 :    
169 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
170 :     classes.
171 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
172 : maechler 1295
173 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
174 :    
175 :     * R/dgTMatrix.R (colSums): etc. All four of
176 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
177 :     all "Matrices".
178 :    
179 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
180 :    
181 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
182 :     background grid to the qqmath plot of ranef.lmer.
183 :    
184 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
185 : bates 1284
186 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
187 :     grouping factors to be specified in the formula as (1|foo/bar).
188 :    
189 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
190 :    
191 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
192 :     !is.language to resolve the bug reported by Jacob Wegelin.
193 :    
194 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
195 :     code to evaluate inbreeding coefficients without calculating T,
196 :     based on code in Sargolzaei and Iwaisaki's paper.
197 :    
198 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
199 :    
200 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
201 :     generic and mer methods for isNested and denomDF. This denomDF was
202 :     an attempt to emulate that in lme but I don't think that makes
203 :     sense. Use the trace of the hat matrix instead.
204 :    
205 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
206 :    
207 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
208 :     the C code depending on a slot structure that's no longer valid.
209 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
210 :    
211 :    
212 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
213 :    
214 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
215 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
216 :     and added a general band extractor.
217 :    
218 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
219 :    
220 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
221 :     allowable range with NAs. Added a corresponding check in the
222 :     validity check for the pedigree class.
223 :    
224 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
225 :     crossprod methods now inherits from symmetricMatrix.
226 :    
227 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
228 :    
229 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
230 :     generics lowerTriMatrix and upperTriMatrix along with methods for
231 :     the Csparse virtual class. Also added a C function Csparse_band
232 :     that implements these methods by calling cholmod_band.
233 :    
234 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
235 :    
236 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
237 :     erased when it was NULL. This led to invalid subselections!
238 :    
239 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
240 :    
241 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
242 :     in method for "t" so as not to lose the unit diagonal property.
243 :    
244 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
245 :    
246 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
247 :     and methods. This is now an option to the ranef method for the
248 :     mer class.
249 :    
250 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
251 :     compressed column-oriented matrix. Minor formatting cleanup.
252 :    
253 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
254 :     objects.
255 :    
256 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
257 :    
258 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
259 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
260 :    
261 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
262 :    
263 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
264 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
265 :    
266 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
267 :     for the dtCMatrix class.
268 : maechler 1253
269 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
270 :    
271 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
272 :     and methods for it.
273 :    
274 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
277 :     arguments, such that M %*% 1:6 now works
278 :     * Tests/matprod.R: test the above
279 :    
280 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
281 : bates 1243
282 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
283 :     the ranef.lmer class.
284 :    
285 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
286 :     methods to extract the posterior variances from the bVar slot.
287 :    
288 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
289 :    
290 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
291 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
292 :    
293 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
294 :     * tests/simple: (extended)
295 :    
296 :     * R/sparseMatrix.R (isTriangular): now using much improved
297 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
298 :    
299 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
300 :    
301 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
302 :     (problem report from Franklin Parlamis). This should be done
303 : maechler 1238 generally.
304 : bates 1236
305 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
306 :    
307 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
308 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
309 :     update the plot methods.
310 :    
311 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
312 :    
313 :     * R/lmer.R (resid and ranef methods): Added methods for the
314 :     "residuals" and "resid" generic but only for linear mixed model
315 :     fits. Changed the ranef method to return a list of data frames so
316 :     that the plot methods now work.
317 :    
318 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
319 :    
320 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
321 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
322 :    
323 :     * DESCRIPTION (Date): New release
324 :    
325 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
326 :    
327 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
328 :    
329 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
330 :     * man/KNex.Rd: and other help files
331 :     * tests/*.R: several ones needed adaption
332 :     * inst/doc/Comparisons.Rnw: dito
333 :    
334 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
335 :    
336 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
337 :    
338 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
339 :    
340 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
341 :    
342 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
343 :    
344 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
345 :    
346 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
347 :    
348 :     * R/dMatrix.R: enable things like M [ M < 10 ]
349 :     * R/dgeMatrix.R: implement it
350 :    
351 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
352 :    
353 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
354 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
355 :     * R/lmer.R (show): now works with summary()
356 :    
357 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
358 :    
359 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
360 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
361 :     support the above
362 :    
363 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
364 :    
365 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
366 :     Use glmFit$prior.weights for weights in a glmm.
367 :     Allow an option usePQL = FALSE to skip the PQL steps for the
368 :     Laplace method (and, in time, the AGQ method).
369 :    
370 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
371 :     into a separate function internal_mer_Xfactor to be able to call
372 :     it from internal_bhat.
373 :    
374 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
375 :    
376 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
377 :     testing; now again of all actual classes.
378 :    
379 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
380 :     use macros and define make_d_matrix_* and make_i_matrix_*
381 :     where _i_ is for the ldense routines:
382 :    
383 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
384 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
385 :    
386 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
387 :    
388 :    
389 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
390 :    
391 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
392 :     many different kinds of matrices.
393 :     * R/*.R: quite a few new methods were needed for R CMD check with
394 :     new Matrix(). Very good for users playing around.
395 :    
396 :    
397 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
398 :    
399 :     * src/dgeMatrix.c (dMatrix_validate): new
400 :     * src/Mutils.c (dense_nonpacked_validate): new
401 :    
402 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
403 :    
404 :    
405 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
406 :    
407 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
408 :    
409 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
410 : bates 1119
411 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
412 :    
413 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
414 :     segfault in cases with multiple non-nested grouping factors.
415 :    
416 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
417 :    
418 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
419 :     (Depends): also on 'utils'
420 :    
421 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
422 :     * R/diagMatrix.R (Diagonal): constructor and methods for
423 :     diagonal matrices
424 :    
425 :     * R/ltTMatrix.R: new "minimal methods"
426 :    
427 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
430 :     all methods (and help files).
431 :    
432 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
433 :    
434 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
435 :     for case (dimn. op no_dimn.)
436 :    
437 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
438 :    
439 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
440 : maechler 1084
441 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
442 :    
443 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
444 :     by Julian Faraway.
445 :    
446 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
447 :    
448 :     * R/Auxiliaries.R (try_as): new utility
449 :     * R/sparseMatrix.R: use try_as() in coercion to original class
450 :    
451 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
454 :    
455 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
456 :    
457 :     * R/Auxiliaries.R (dimNamesCheck): added
458 :    
459 :     * R/Matrix.R (as.array), (as.vector): new
460 :    
461 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
462 :    
463 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
464 : maechler 956 default.
465 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
466 :     "pMatrix" now contains "sparseMatrix"
467 : maechler 954
468 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
469 :    
470 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
471 :    
472 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
473 :    
474 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
475 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
476 :    
477 :     * R/dspMatrix.R: typo in "t" method
478 :    
479 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
480 :    
481 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
482 :     * R/Tsparse.R: instead of R/gTMatrix.R
483 :     * R/Csparse.R: new
484 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
485 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
486 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
487 :     via cholmod
488 :    
489 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
490 :    
491 :     * R/Auxiliaries.R (non0ind): new function using new C code
492 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
493 :    
494 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
495 :    
496 :     * src/chm_common.h: header file required by all C sources that
497 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
498 : bates 917 called 'c' whose address is passed as the last argument to
499 :     (virtually) every CHOLMOD function.
500 :    
501 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
502 :    
503 :     * src/init.c: initialize and finalize the cholmod_common structure.
504 :    
505 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
506 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
507 :    
508 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
509 :    
510 :     * inst/test-tools.R: new file collecting the utility functions used
511 :     in ./tests/*.R
512 :    
513 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
514 :     * R/Matrix.R (cbind2): methods for NULL and missing
515 :    
516 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
517 :    
518 :     * R/AllClass.R: new "index" class for "[" and "[<-":
519 :     First cut at "symmetricMatrix" and "triangularMatrix"
520 :     * R/gTMatrix.R (.ind.prep): new function;
521 : maechler 1174 Logical and character indexing now work too.
522 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
523 :     * tests/indexing.R: new, including *.Rout.save
524 :     * tests/dgTMatrix.R: new
525 :    
526 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
527 :    
528 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
529 :     indicator pos not being updated. Also enforced upper triangular
530 :     for symmetric case. Need to coerce edges component of elements of
531 :     edge list - grr! (Why don't they define their classes cleanly?)
532 :    
533 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
534 :    
535 :     * R/Matrix.R: added first "[<-" methods; not yet functional
536 :     * R/denseMatrix.R: dito
537 :     * man/Subassign-methods.Rd: new help file for these
538 :    
539 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * DESCRIPTION (Version): 0.98-6
542 :    
543 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
544 :     matrices.
545 :    
546 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
547 :    
548 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
549 :     as( <logical>, "matrix")
550 :    
551 :     * R/pMatrix.R: coercion to "lgTMatrix"
552 :    
553 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
554 :     * man/gTMatrix-class.Rd:
555 :     * General slight re-organization of where "[" methods are defined.
556 :     more to come.
557 :    
558 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
559 : maechler 868
560 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
561 : maechler 871
562 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
563 :     * .....
564 :    
565 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
566 :    
567 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
568 :     or glmer objects.
569 :    
570 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
571 :    
572 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
573 :    
574 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
575 :    
576 :     * R/HBMM.R: finish re-writing R-only code.
577 :    
578 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
579 :    
580 :     * man/externalFormats.Rd: move documentation for writeHB and
581 :     writeMM here.
582 :    
583 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
584 :     (suggested by Paul Roecker).
585 :    
586 :     * tests/validObj.R (assertError): Comment out test that is failing
587 :     after recent changes in r-devel.
588 :    
589 : maechler 860
590 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
591 :    
592 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
593 :     * man/denseMatrix-class.Rd
594 :     * NAMESPACE: export it, and also export
595 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
596 :    
597 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
598 :    
599 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
600 :    
601 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
602 :     matrix_solve code (which was really, really wrong).
603 :    
604 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
605 : maechler 834
606 :     * DESCRIPTION (Version): 0.98-2
607 :    
608 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
609 :    
610 :     * R/lmer.R (abbrvNms): new
611 :     * R/lmer.R (mcmcsamp): allow transformed parameters
612 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
613 :     for the Harwell-Boeing and the MatrixMarket formats.
614 : maechler 834
615 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
616 :    
617 :     * man/dtrMatrix-class.Rd: add examples
618 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
619 : maechler 834
620 :     * TODO: note the dtpMatrix (docu) bug
621 :    
622 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
623 :     in order to ensure that new as.matrix() is used by old functions,
624 :     e.g., svd(), qr(), eigen(), dist(),..;
625 :     apply(), also matplot() or pairs().
626 :    
627 :    
628 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
629 :    
630 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
631 :     add comments about 'control' / lmerControl() arguments
632 :    
633 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
634 : bates 820
635 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
636 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
637 : bates 820
638 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
639 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
640 :    
641 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
642 :     .Call calls that were producing spurious output.
643 :    
644 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
645 : bates 801
646 :     * R/lmer.R (lmer): stored updated variance component estimates in
647 :     mer object for the generalized model. (Bug reported by Renaud
648 :     Lancelot).
649 :    
650 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
651 : bates 794
652 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
653 :     unidimensional case.
654 :    
655 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
656 : maechler 791
657 :     * DESCRIPTION (Version): 0.96-1
658 :    
659 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
660 : maechler 791
661 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
662 : bates 763
663 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
664 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
665 :    
666 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
667 : bates 763
668 :     * src/Makefile.win: Forgot to update this when Makefile changed.
669 :    
670 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
671 : bates 726
672 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
673 :     bug reported by Kurt Hornik and Michael Hahsler.
674 :    
675 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
676 : bates 725
677 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
678 :     logical sparse matrices. These will also be used in the symbolic
679 :     analysis for lmer objects.
680 :    
681 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
682 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
683 : maechler 791
684 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
685 : bates 714
686 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
687 :     colMeans, colSums, rowMeans and rowSums.
688 :    
689 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
690 : bates 692
691 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
692 :     multiplication operation.
693 :    
694 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
695 :     to dgetrs.
696 :    
697 :     * src/init.c: Fix cut-and-paste error in definition of
698 :     dgeMatrix_matrix_solve
699 :    
700 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
701 :    
702 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
703 : bates 692
704 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
705 :    
706 :     * DESCRIPTION: Eliminate import of stats.
707 :    
708 : maechler 791
709 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
710 : bates 692
711 :     * R/AllClass.R : add logical sparse matrix classes
712 :    
713 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
714 :    
715 :     * R/dgTMatrix.R: add "[" method for triplet matrices
716 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
717 :    
718 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
719 : maechler 687
720 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
721 :    
722 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
723 :     * R/sparseMatrix.R: %*%, crossprod()
724 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
725 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
726 :     * src/lmer.c (lmer_fitted): fix thinko
727 :    
728 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
729 :    
730 :     * R/AllClass.R: add two virtual sparse classes ``on top''
731 :    
732 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
733 :    
734 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
735 :     correspondingly fix examples and tests/ since new()
736 :     doesn't work for virtual classes.
737 :    
738 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
739 :    
740 :     * R/Matrix.R (as.matrix): method and one for unname()
741 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
742 :     also run for R 2.1.0; using as.matrix()
743 :    
744 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
745 : maechler 658
746 :     * R/pMatrix.R: "pMatrix" class added
747 :     * ....
748 :    
749 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
750 : bates 645
751 :     * R/dtpMatrix.R: Add unpack method and an example.
752 :    
753 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
754 :     of general symmetric matrices and associated S4 methods.
755 :    
756 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
757 :     +
758 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
759 :    
760 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
761 :     crossprod() and "%*%" methods added; tests, too.
762 :     * tests/matprod.R: new, for testing these
763 :    
764 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
765 : bates 599
766 :     * src/lmer.c (lmer_fitted): Added.
767 :    
768 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
769 : bates 596
770 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
771 :    
772 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
773 : bates 582
774 :     * src/*.c,po/,inst/po: Internationalization and localization of
775 :     the package.
776 :    
777 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
778 :     R_ldl.c file.
779 :    
780 :     * src/flame.[ch]: Removed these source files.
781 : maechler 658
782 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
783 :    
784 :     * src/LU.[ch],src/init.c: absorb in factorizations
785 :    
786 :     * src/Mutils.h: prepare for internationalization
787 :    
788 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
789 :     this file
790 :    
791 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
792 :    
793 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
794 :    
795 :     * R/dtrMatrix.R: fix t() method
796 :    
797 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
798 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
799 : maechler 578 * tests/group-methods.R : and test them.
800 :    
801 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
802 :     border case
803 :    
804 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
805 :    
806 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
807 : maechler 578
808 :     * src/dgBCMatrix.c:
809 :     * src/lmer.c: many changes
810 :     * ...
811 :    
812 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
813 :    
814 :     * R/Matrix.R: add more sophisticated show() method.
815 :    
816 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
817 :    
818 :     * */* : almost complete reorganization of classes.
819 :    
820 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
821 : bates 460
822 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
823 :     for the geMatrix class.
824 :    
825 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
826 : bates 460
827 :     * src/Makefile (clean): Remove *.a and *.so
828 :    
829 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
830 :    
831 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
832 : bates 460
833 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
834 : bates 460 had an effect in cases with more than 2 grouping factors.
835 :    
836 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
837 : bates 415
838 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
839 :    
840 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
841 : bates 410
842 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
843 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
844 :    
845 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
846 : bates 392
847 :     * R/sscMatrix.R: Add determinant methods
848 :    
849 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
850 :     for tripletMatrix to matrix.
851 :    
852 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
853 : bates 388
854 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
855 :     no longer used.
856 :    
857 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
858 :     with dynamic allocation of scratch arrays.
859 :    
860 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
861 :     for multivariate random effects with multiple grouping factors.
862 :     Fixes part but not all of #15.
863 :    
864 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
865 : bates 375
866 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
867 :     scalar grouping factors corrected.
868 :    
869 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
870 : bates 375
871 :     * src/bCrosstab.c: remove diag_update which is no longer used
872 :    
873 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
874 : bates 350
875 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
876 :     .h file can be included.
877 :    
878 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
879 : bates 342
880 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
881 : bates 342 Complete allocation of slots in NEW_OBJECT.
882 :    
883 :     * src/Mutils.h: Moved list of symbols to an include file
884 :    
885 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
886 : bates 342
887 :     * src/geMutils.c (Matrix_init): remove unused function
888 :    
889 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
890 : bates 342
891 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
892 :    
893 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
894 : bates 327
895 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
896 :    
897 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
898 : bates 303
899 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
900 :    
901 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
902 : bates 296
903 :     * src/init.c: Created R_init_Matrix and added registration of C
904 :     routines.
905 :    
906 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
907 : bates 283
908 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
909 :    
910 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
911 : bates 229
912 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
913 :    
914 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
915 :    
916 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
917 :    
918 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
919 :    
920 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
921 :     ssclme_update_mm
922 :    
923 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
924 :    
925 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
926 :     in the order of unconstrained and constrained parameters.
927 :     (ssclme_gradient): Added the gradients (not yet correct for
928 :     multidimensional, unconstrained case).
929 :    
930 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
931 :    
932 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
933 :    
934 :     * src/Makefile.win: Remove unneeded ranlib call
935 :    
936 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
937 :    
938 :     * DESCRIPTION (Version): New release
939 :    
940 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
941 :    
942 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
943 :    
944 :     * src/triplet_to_col.c: Create triplet_to_col as a native
945 : maechler 658 function, not the version from umfpack. There were problems with
946 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
947 :     only one umfpack routine being used so I moved it here.
948 :    
949 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
950 :    
951 :     * src/ssclme.c (ssclme_variances): New function.
952 :    
953 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
954 :    
955 :     * src/ssclme.c (ssclme_fitted): Added function.
956 :    
957 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
958 :    
959 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
960 :     store the dimnames in the XtX and bVar slots
961 :     (ssclme_update_mm): Change the dimensions of the bVar slot
962 :     components and the returned value from ssclme_ranef.
963 :    
964 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
965 :    
966 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
967 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
968 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
969 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
970 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
971 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
972 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
973 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
974 :     Moved the pdMat classes from the lme4 package.
975 :    
976 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
977 :    
978 :     * man/ssclme-class.Rd: Update definition and documentation of the
979 :     ssclme class to include the DIsqrt slot.
980 :    
981 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
982 :     (much faster using dsyrk, a level 3 BLAS routine).
983 :    
984 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
985 :    
986 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
987 :    
988 :     * tests/ssclme.R: Modify the test to account for the permutation
989 :     of the levels of the grouping factors.
990 :    
991 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
992 :    
993 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
994 :     directly into the ssclme class definition.
995 :    
996 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
997 :    
998 :     * DESCRIPTION (Date): New release
999 :    
1000 :     * man/ssclme-class.Rd: new file.
1001 :    
1002 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1003 :     works and it's fast!
1004 :    
1005 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1006 :    
1007 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1008 :    
1009 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1010 :    
1011 :     * DESCRIPTION (Date): New release
1012 :    
1013 :     * NAMESPACE: Don't export ssclme.
1014 :    
1015 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1016 :     school data.
1017 :    
1018 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1019 :    
1020 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1021 :     keep track of the fixed-effects and the response. Counts also
1022 :     gets an extra element, which is always one.
1023 :    
1024 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1025 :    
1026 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1027 :    
1028 :     * src/cscMatrix.c (csc_transpose): new function
1029 :    
1030 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1031 :     (csc_components_transpose): new function
1032 :    
1033 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1034 :    
1035 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1036 :     triplets
1037 :    
1038 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1039 :    
1040 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1041 :    
1042 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1043 :     and all other .h files in src.
1044 :    
1045 :     * src/Makefile.win: This and other Makefile.win files contributed
1046 :     by Brian Ripley.
1047 :    
1048 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1049 :    
1050 :     * R/syMatrix.R: Added methods for "%*%".
1051 :    
1052 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1053 :     poMatrix object.
1054 :    
1055 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1056 :    
1057 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1058 :    
1059 :     2004-01-25 Douglas Bates <bates@bates2_home>
1060 :    
1061 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1062 :    
1063 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1064 :     of nrow.
1065 :    
1066 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1067 :    
1068 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1069 :     subdirectories.
1070 :    
1071 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1072 :    
1073 :     * src/taucs.h: Accidently referred to global header files
1074 :     instead of local files.
1075 :    
1076 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1077 :    
1078 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1079 :     and methods and replaced all classes with S4 classes.
1080 :    
1081 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1082 :    
1083 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1084 :    
1085 :     * src/R_LapackPP.cc: Change method of calculating determinants
1086 :    
1087 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1088 :    
1089 :     * DESCRIPTION (Version): removed empty data directory as requested
1090 :     by CRAN maintainers. Changed version number and date.
1091 :    
1092 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1093 :    
1094 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1095 :     under Windows.
1096 :    
1097 :     * Added configure.win and src/Makevars.win as requested by Brian
1098 :     Ripley.
1099 :    
1100 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1101 :    
1102 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1103 :     Hornik.
1104 :    
1105 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1106 :    
1107 :     * configure.ac: Replaced configure.in with configure.ac
1108 :     contributed by Kurt Hornik.
1109 :    
1110 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1111 :     version for R-1.5.0
1112 :    
1113 : maechler 512
1114 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1115 :    
1116 :     * man/eigen.Rd: Removed the .Alias in the example

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