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

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