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Annotation of /pkg/ChangeLog

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

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