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1 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * DESCRIPTION (Version): 0.995-14 for CRAN
4 :    
5 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
6 :    
7 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
8 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
9 :    
10 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
11 :     * R/Tsparse.R (tril, triu, band): methods
12 :     * R/dgRMatrix.R (tril, ...): dito
13 :     * man/band.Rd: dito
14 :    
15 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
16 :    
17 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
18 :     to be up-to-date automatically.
19 :    
20 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
21 :    
22 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
23 :    
24 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
25 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
26 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
27 :     such that the S4 objects are always created by the current version
28 :     of R and 'Matrix' class definitions.
29 :    
30 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
31 :    
32 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
33 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
34 : bates 1342 boundary and test cases.
35 :    
36 :     * src/lmer.c (mer_postVar): Modified to return the variances that
37 :     are marginal to the fixed effects, not conditional on them (which
38 :     is what the bVar slot contents represent).
39 :    
40 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
41 :    
42 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
43 :     function which calls the C function mer_hat_trace2.
44 : maechler 1346
45 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
46 :     producing a caterpillar plot.
47 : bates 1338
48 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
49 :    
50 :     * NAMESPACE: change "correlation" to "corMatrix"
51 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
52 :     * R/dpoMatrix.R: dito
53 :     * R/lmer.R: dito
54 :    
55 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
56 :    
57 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
58 :     RZXinv slot's contents into a separate internal function that can
59 :     be used in mer_hat_trace.
60 :    
61 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
62 :    
63 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
64 :     via new smart
65 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
66 :     utility functions.
67 :    
68 :    
69 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
70 :    
71 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
72 :     matrices when appropriate; band() even symmetric ones.
73 :     (replCmat): extend to potentially all "CsparseMatrix"
74 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
75 :     allow subassignment for special sparse matrices.
76 :    
77 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
78 :    
79 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
80 :     argument; in glmer_*(): print only if(verbose).
81 :    
82 :     speed-optimize a few places by moving REAL(.) out of loops.
83 :    
84 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
85 :    
86 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
87 :    
88 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
89 :     since that wrongly triggers also for M[ logi , ]
90 :    
91 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
92 :     a symmetric matrix that results in a non-symmetric one.
93 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
94 :    
95 :     * R/dMatrix.R: make round(M) work as round(M, 0)
96 :    
97 :     * R/dgTMatrix.R (image): coordinate system and axis now use
98 :     1-based indices, not 0-based ones.
99 :    
100 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
101 :     * tests/indexing.R: test it.
102 :    
103 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
104 :     * man/isSymmetric-methods.Rd: and document it.
105 :    
106 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
107 :     * man/SparseM-conv.Rd: docu them
108 :    
109 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
110 :     for 'SparseM' conversions
111 :    
112 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
113 :    
114 :     * R/Matrix.R (head): added head() and tail() methods.
115 :    
116 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
117 :    
118 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
119 :    
120 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
121 :    
122 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
123 :     add check for correct printing of symmetric sparse matrices.
124 :    
125 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
126 :     for sparse symmetric matrices.
127 :    
128 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
129 :     diagonal twice.
130 :    
131 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
132 :    
133 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
134 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
135 : bates 1316
136 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
137 :    
138 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
139 :    
140 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
141 :    
142 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
145 :     * R/lgCMatrix.R (diag): for new method
146 :    
147 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
148 :     ==> construction of illegal "*gTMatrix" via new() should
149 :     now be much less easy:
150 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
151 :    
152 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
153 :     directly.
154 :     * man/Matrix.Rd: documents it.
155 :    
156 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
157 :    
158 :     * src/pedigree.c (pedigree_inbreeding): Correction in
159 :     initialization. This function is not currently being used and is
160 :     not fully tested.
161 :    
162 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
163 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
164 :     objects. Modified validity check on pedigree objects to account
165 :     for nonparallel patterns of missingness of parents.
166 : bates 1311
167 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
168 :     class.
169 : maechler 1315
170 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
173 :    
174 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
175 :    
176 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
177 :    
178 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
179 :     the output from mcmcsamp.
180 :    
181 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
182 :    
183 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
184 :     of the hat matrix.
185 : bates 1298
186 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
187 :    
188 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
189 :     classes.
190 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
191 : maechler 1295
192 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
193 :    
194 :     * R/dgTMatrix.R (colSums): etc. All four of
195 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
196 :     all "Matrices".
197 :    
198 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
199 :    
200 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
201 :     background grid to the qqmath plot of ranef.lmer.
202 :    
203 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
204 : bates 1284
205 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
206 :     grouping factors to be specified in the formula as (1|foo/bar).
207 :    
208 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
209 :    
210 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
211 :     !is.language to resolve the bug reported by Jacob Wegelin.
212 :    
213 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
214 :     code to evaluate inbreeding coefficients without calculating T,
215 :     based on code in Sargolzaei and Iwaisaki's paper.
216 :    
217 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
218 :    
219 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
220 :     generic and mer methods for isNested and denomDF. This denomDF was
221 :     an attempt to emulate that in lme but I don't think that makes
222 :     sense. Use the trace of the hat matrix instead.
223 :    
224 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
225 :    
226 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
227 :     the C code depending on a slot structure that's no longer valid.
228 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
229 :    
230 :    
231 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
232 :    
233 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
234 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
235 :     and added a general band extractor.
236 :    
237 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
238 :    
239 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
240 :     allowable range with NAs. Added a corresponding check in the
241 :     validity check for the pedigree class.
242 :    
243 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
244 :     crossprod methods now inherits from symmetricMatrix.
245 :    
246 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
247 :    
248 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
249 :     generics lowerTriMatrix and upperTriMatrix along with methods for
250 :     the Csparse virtual class. Also added a C function Csparse_band
251 :     that implements these methods by calling cholmod_band.
252 :    
253 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
254 :    
255 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
256 :     erased when it was NULL. This led to invalid subselections!
257 :    
258 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
261 :     in method for "t" so as not to lose the unit diagonal property.
262 :    
263 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
264 :    
265 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
266 :     and methods. This is now an option to the ranef method for the
267 :     mer class.
268 :    
269 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
270 :     compressed column-oriented matrix. Minor formatting cleanup.
271 :    
272 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
273 :     objects.
274 :    
275 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
276 :    
277 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
278 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
279 :    
280 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
281 :    
282 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
283 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
284 :    
285 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
286 :     for the dtCMatrix class.
287 : maechler 1253
288 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
289 :    
290 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
291 :     and methods for it.
292 :    
293 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
294 :    
295 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
296 :     arguments, such that M %*% 1:6 now works
297 :     * Tests/matprod.R: test the above
298 :    
299 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
300 : bates 1243
301 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
302 :     the ranef.lmer class.
303 :    
304 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
305 :     methods to extract the posterior variances from the bVar slot.
306 :    
307 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
308 :    
309 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
310 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
311 :    
312 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
313 :     * tests/simple: (extended)
314 :    
315 :     * R/sparseMatrix.R (isTriangular): now using much improved
316 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
317 :    
318 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
319 :    
320 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
321 :     (problem report from Franklin Parlamis). This should be done
322 : maechler 1238 generally.
323 : bates 1236
324 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
325 :    
326 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
327 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
328 :     update the plot methods.
329 :    
330 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
331 :    
332 :     * R/lmer.R (resid and ranef methods): Added methods for the
333 :     "residuals" and "resid" generic but only for linear mixed model
334 :     fits. Changed the ranef method to return a list of data frames so
335 :     that the plot methods now work.
336 :    
337 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
338 :    
339 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
340 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
341 :    
342 :     * DESCRIPTION (Date): New release
343 :    
344 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
345 :    
346 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
347 :    
348 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
349 :     * man/KNex.Rd: and other help files
350 :     * tests/*.R: several ones needed adaption
351 :     * inst/doc/Comparisons.Rnw: dito
352 :    
353 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
354 :    
355 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
356 :    
357 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
358 :    
359 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
360 :    
361 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
362 :    
363 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
364 :    
365 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
366 :    
367 :     * R/dMatrix.R: enable things like M [ M < 10 ]
368 :     * R/dgeMatrix.R: implement it
369 :    
370 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
371 :    
372 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
373 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
374 :     * R/lmer.R (show): now works with summary()
375 :    
376 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
377 :    
378 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
379 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
380 :     support the above
381 :    
382 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
383 :    
384 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
385 :     Use glmFit$prior.weights for weights in a glmm.
386 :     Allow an option usePQL = FALSE to skip the PQL steps for the
387 :     Laplace method (and, in time, the AGQ method).
388 :    
389 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
390 :     into a separate function internal_mer_Xfactor to be able to call
391 :     it from internal_bhat.
392 :    
393 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
394 :    
395 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
396 :     testing; now again of all actual classes.
397 :    
398 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
399 :     use macros and define make_d_matrix_* and make_i_matrix_*
400 :     where _i_ is for the ldense routines:
401 :    
402 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
403 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
404 :    
405 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
406 :    
407 :    
408 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
409 :    
410 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
411 :     many different kinds of matrices.
412 :     * R/*.R: quite a few new methods were needed for R CMD check with
413 :     new Matrix(). Very good for users playing around.
414 :    
415 :    
416 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
417 :    
418 :     * src/dgeMatrix.c (dMatrix_validate): new
419 :     * src/Mutils.c (dense_nonpacked_validate): new
420 :    
421 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
422 :    
423 :    
424 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
425 :    
426 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
427 :    
428 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
429 : bates 1119
430 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
431 :    
432 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
433 :     segfault in cases with multiple non-nested grouping factors.
434 :    
435 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
436 :    
437 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
438 :     (Depends): also on 'utils'
439 :    
440 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
441 :     * R/diagMatrix.R (Diagonal): constructor and methods for
442 :     diagonal matrices
443 :    
444 :     * R/ltTMatrix.R: new "minimal methods"
445 :    
446 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
447 :    
448 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
449 :     all methods (and help files).
450 :    
451 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
454 :     for case (dimn. op no_dimn.)
455 :    
456 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
457 :    
458 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
459 : maechler 1084
460 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
461 :    
462 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
463 :     by Julian Faraway.
464 :    
465 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
466 :    
467 :     * R/Auxiliaries.R (try_as): new utility
468 :     * R/sparseMatrix.R: use try_as() in coercion to original class
469 :    
470 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
471 :    
472 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
473 :    
474 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 :     * R/Auxiliaries.R (dimNamesCheck): added
477 :    
478 :     * R/Matrix.R (as.array), (as.vector): new
479 :    
480 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
481 :    
482 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
483 : maechler 956 default.
484 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
485 :     "pMatrix" now contains "sparseMatrix"
486 : maechler 954
487 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
488 :    
489 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
490 :    
491 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
492 :    
493 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
494 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
495 :    
496 :     * R/dspMatrix.R: typo in "t" method
497 :    
498 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
499 :    
500 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
501 :     * R/Tsparse.R: instead of R/gTMatrix.R
502 :     * R/Csparse.R: new
503 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
504 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
505 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
506 :     via cholmod
507 :    
508 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
509 :    
510 :     * R/Auxiliaries.R (non0ind): new function using new C code
511 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
512 :    
513 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
514 :    
515 :     * src/chm_common.h: header file required by all C sources that
516 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
517 : bates 917 called 'c' whose address is passed as the last argument to
518 :     (virtually) every CHOLMOD function.
519 :    
520 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
521 :    
522 :     * src/init.c: initialize and finalize the cholmod_common structure.
523 :    
524 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
525 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
526 :    
527 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 :     * inst/test-tools.R: new file collecting the utility functions used
530 :     in ./tests/*.R
531 :    
532 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
533 :     * R/Matrix.R (cbind2): methods for NULL and missing
534 :    
535 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
536 :    
537 :     * R/AllClass.R: new "index" class for "[" and "[<-":
538 :     First cut at "symmetricMatrix" and "triangularMatrix"
539 :     * R/gTMatrix.R (.ind.prep): new function;
540 : maechler 1174 Logical and character indexing now work too.
541 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
542 :     * tests/indexing.R: new, including *.Rout.save
543 :     * tests/dgTMatrix.R: new
544 :    
545 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
546 :    
547 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
548 :     indicator pos not being updated. Also enforced upper triangular
549 :     for symmetric case. Need to coerce edges component of elements of
550 :     edge list - grr! (Why don't they define their classes cleanly?)
551 :    
552 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
553 :    
554 :     * R/Matrix.R: added first "[<-" methods; not yet functional
555 :     * R/denseMatrix.R: dito
556 :     * man/Subassign-methods.Rd: new help file for these
557 :    
558 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
559 :    
560 :     * DESCRIPTION (Version): 0.98-6
561 :    
562 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
563 :     matrices.
564 :    
565 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
566 :    
567 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
568 :     as( <logical>, "matrix")
569 :    
570 :     * R/pMatrix.R: coercion to "lgTMatrix"
571 :    
572 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
573 :     * man/gTMatrix-class.Rd:
574 :     * General slight re-organization of where "[" methods are defined.
575 :     more to come.
576 :    
577 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
578 : maechler 868
579 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
580 : maechler 871
581 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
582 :     * .....
583 :    
584 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
585 :    
586 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
587 :     or glmer objects.
588 :    
589 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
590 :    
591 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
592 :    
593 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
594 :    
595 :     * R/HBMM.R: finish re-writing R-only code.
596 :    
597 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
598 :    
599 :     * man/externalFormats.Rd: move documentation for writeHB and
600 :     writeMM here.
601 :    
602 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
603 :     (suggested by Paul Roecker).
604 :    
605 :     * tests/validObj.R (assertError): Comment out test that is failing
606 :     after recent changes in r-devel.
607 :    
608 : maechler 860
609 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
610 :    
611 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
612 :     * man/denseMatrix-class.Rd
613 :     * NAMESPACE: export it, and also export
614 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
615 :    
616 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
617 :    
618 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
619 :    
620 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
621 :     matrix_solve code (which was really, really wrong).
622 :    
623 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
624 : maechler 834
625 :     * DESCRIPTION (Version): 0.98-2
626 :    
627 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
628 :    
629 :     * R/lmer.R (abbrvNms): new
630 :     * R/lmer.R (mcmcsamp): allow transformed parameters
631 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
632 :     for the Harwell-Boeing and the MatrixMarket formats.
633 : maechler 834
634 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
635 :    
636 :     * man/dtrMatrix-class.Rd: add examples
637 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
638 : maechler 834
639 :     * TODO: note the dtpMatrix (docu) bug
640 :    
641 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
642 :     in order to ensure that new as.matrix() is used by old functions,
643 :     e.g., svd(), qr(), eigen(), dist(),..;
644 :     apply(), also matplot() or pairs().
645 :    
646 :    
647 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
648 :    
649 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
650 :     add comments about 'control' / lmerControl() arguments
651 :    
652 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
653 : bates 820
654 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
655 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
656 : bates 820
657 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
658 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
659 :    
660 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
661 :     .Call calls that were producing spurious output.
662 :    
663 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
664 : bates 801
665 :     * R/lmer.R (lmer): stored updated variance component estimates in
666 :     mer object for the generalized model. (Bug reported by Renaud
667 :     Lancelot).
668 :    
669 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
670 : bates 794
671 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
672 :     unidimensional case.
673 :    
674 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
675 : maechler 791
676 :     * DESCRIPTION (Version): 0.96-1
677 :    
678 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
679 : maechler 791
680 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
681 : bates 763
682 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
683 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
684 :    
685 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
686 : bates 763
687 :     * src/Makefile.win: Forgot to update this when Makefile changed.
688 :    
689 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
690 : bates 726
691 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
692 :     bug reported by Kurt Hornik and Michael Hahsler.
693 :    
694 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
695 : bates 725
696 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
697 :     logical sparse matrices. These will also be used in the symbolic
698 :     analysis for lmer objects.
699 :    
700 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
701 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
702 : maechler 791
703 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
704 : bates 714
705 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
706 :     colMeans, colSums, rowMeans and rowSums.
707 :    
708 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
709 : bates 692
710 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
711 :     multiplication operation.
712 :    
713 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
714 :     to dgetrs.
715 :    
716 :     * src/init.c: Fix cut-and-paste error in definition of
717 :     dgeMatrix_matrix_solve
718 :    
719 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
720 :    
721 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
722 : bates 692
723 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
724 :    
725 :     * DESCRIPTION: Eliminate import of stats.
726 :    
727 : maechler 791
728 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
729 : bates 692
730 :     * R/AllClass.R : add logical sparse matrix classes
731 :    
732 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
733 :    
734 :     * R/dgTMatrix.R: add "[" method for triplet matrices
735 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
736 :    
737 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
738 : maechler 687
739 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
740 :    
741 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
742 :     * R/sparseMatrix.R: %*%, crossprod()
743 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
744 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
745 :     * src/lmer.c (lmer_fitted): fix thinko
746 :    
747 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
748 :    
749 :     * R/AllClass.R: add two virtual sparse classes ``on top''
750 :    
751 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
752 :    
753 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
754 :     correspondingly fix examples and tests/ since new()
755 :     doesn't work for virtual classes.
756 :    
757 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
758 :    
759 :     * R/Matrix.R (as.matrix): method and one for unname()
760 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
761 :     also run for R 2.1.0; using as.matrix()
762 :    
763 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
764 : maechler 658
765 :     * R/pMatrix.R: "pMatrix" class added
766 :     * ....
767 :    
768 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
769 : bates 645
770 :     * R/dtpMatrix.R: Add unpack method and an example.
771 :    
772 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
773 :     of general symmetric matrices and associated S4 methods.
774 :    
775 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
776 :     +
777 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
778 :    
779 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
780 :     crossprod() and "%*%" methods added; tests, too.
781 :     * tests/matprod.R: new, for testing these
782 :    
783 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
784 : bates 599
785 :     * src/lmer.c (lmer_fitted): Added.
786 :    
787 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
788 : bates 596
789 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
790 :    
791 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
792 : bates 582
793 :     * src/*.c,po/,inst/po: Internationalization and localization of
794 :     the package.
795 :    
796 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
797 :     R_ldl.c file.
798 :    
799 :     * src/flame.[ch]: Removed these source files.
800 : maechler 658
801 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
802 :    
803 :     * src/LU.[ch],src/init.c: absorb in factorizations
804 :    
805 :     * src/Mutils.h: prepare for internationalization
806 :    
807 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
808 :     this file
809 :    
810 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
811 :    
812 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
813 :    
814 :     * R/dtrMatrix.R: fix t() method
815 :    
816 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
817 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
818 : maechler 578 * tests/group-methods.R : and test them.
819 :    
820 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
821 :     border case
822 :    
823 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
824 :    
825 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
826 : maechler 578
827 :     * src/dgBCMatrix.c:
828 :     * src/lmer.c: many changes
829 :     * ...
830 :    
831 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
832 :    
833 :     * R/Matrix.R: add more sophisticated show() method.
834 :    
835 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
836 :    
837 :     * */* : almost complete reorganization of classes.
838 :    
839 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
840 : bates 460
841 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
842 :     for the geMatrix class.
843 :    
844 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
845 : bates 460
846 :     * src/Makefile (clean): Remove *.a and *.so
847 :    
848 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
849 :    
850 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
851 : bates 460
852 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
853 : bates 460 had an effect in cases with more than 2 grouping factors.
854 :    
855 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
856 : bates 415
857 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
858 :    
859 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
860 : bates 410
861 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
862 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
863 :    
864 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
865 : bates 392
866 :     * R/sscMatrix.R: Add determinant methods
867 :    
868 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
869 :     for tripletMatrix to matrix.
870 :    
871 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
872 : bates 388
873 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
874 :     no longer used.
875 :    
876 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
877 :     with dynamic allocation of scratch arrays.
878 :    
879 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
880 :     for multivariate random effects with multiple grouping factors.
881 :     Fixes part but not all of #15.
882 :    
883 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
884 : bates 375
885 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
886 :     scalar grouping factors corrected.
887 :    
888 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
889 : bates 375
890 :     * src/bCrosstab.c: remove diag_update which is no longer used
891 :    
892 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
893 : bates 350
894 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
895 :     .h file can be included.
896 :    
897 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
898 : bates 342
899 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
900 : bates 342 Complete allocation of slots in NEW_OBJECT.
901 :    
902 :     * src/Mutils.h: Moved list of symbols to an include file
903 :    
904 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
905 : bates 342
906 :     * src/geMutils.c (Matrix_init): remove unused function
907 :    
908 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
909 : bates 342
910 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
911 :    
912 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
913 : bates 327
914 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
915 :    
916 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
917 : bates 303
918 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
919 :    
920 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
921 : bates 296
922 :     * src/init.c: Created R_init_Matrix and added registration of C
923 :     routines.
924 :    
925 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
926 : bates 283
927 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
928 :    
929 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
930 : bates 229
931 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
932 :    
933 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
934 :    
935 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
936 :    
937 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
938 :    
939 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
940 :     ssclme_update_mm
941 :    
942 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
943 :    
944 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
945 :     in the order of unconstrained and constrained parameters.
946 :     (ssclme_gradient): Added the gradients (not yet correct for
947 :     multidimensional, unconstrained case).
948 :    
949 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
950 :    
951 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
952 :    
953 :     * src/Makefile.win: Remove unneeded ranlib call
954 :    
955 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
956 :    
957 :     * DESCRIPTION (Version): New release
958 :    
959 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
960 :    
961 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
962 :    
963 :     * src/triplet_to_col.c: Create triplet_to_col as a native
964 : maechler 658 function, not the version from umfpack. There were problems with
965 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
966 :     only one umfpack routine being used so I moved it here.
967 :    
968 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
969 :    
970 :     * src/ssclme.c (ssclme_variances): New function.
971 :    
972 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
973 :    
974 :     * src/ssclme.c (ssclme_fitted): Added function.
975 :    
976 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
977 :    
978 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
979 :     store the dimnames in the XtX and bVar slots
980 :     (ssclme_update_mm): Change the dimensions of the bVar slot
981 :     components and the returned value from ssclme_ranef.
982 :    
983 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
984 :    
985 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
986 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
987 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
988 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
989 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
990 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
991 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
992 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
993 :     Moved the pdMat classes from the lme4 package.
994 :    
995 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
996 :    
997 :     * man/ssclme-class.Rd: Update definition and documentation of the
998 :     ssclme class to include the DIsqrt slot.
999 :    
1000 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1001 :     (much faster using dsyrk, a level 3 BLAS routine).
1002 :    
1003 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1004 :    
1005 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1006 :    
1007 :     * tests/ssclme.R: Modify the test to account for the permutation
1008 :     of the levels of the grouping factors.
1009 :    
1010 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1011 :    
1012 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1013 :     directly into the ssclme class definition.
1014 :    
1015 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1016 :    
1017 :     * DESCRIPTION (Date): New release
1018 :    
1019 :     * man/ssclme-class.Rd: new file.
1020 :    
1021 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1022 :     works and it's fast!
1023 :    
1024 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1025 :    
1026 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1027 :    
1028 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1029 :    
1030 :     * DESCRIPTION (Date): New release
1031 :    
1032 :     * NAMESPACE: Don't export ssclme.
1033 :    
1034 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1035 :     school data.
1036 :    
1037 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1038 :    
1039 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1040 :     keep track of the fixed-effects and the response. Counts also
1041 :     gets an extra element, which is always one.
1042 :    
1043 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1044 :    
1045 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1046 :    
1047 :     * src/cscMatrix.c (csc_transpose): new function
1048 :    
1049 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1050 :     (csc_components_transpose): new function
1051 :    
1052 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1053 :    
1054 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1055 :     triplets
1056 :    
1057 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1058 :    
1059 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1060 :    
1061 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1062 :     and all other .h files in src.
1063 :    
1064 :     * src/Makefile.win: This and other Makefile.win files contributed
1065 :     by Brian Ripley.
1066 :    
1067 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1068 :    
1069 :     * R/syMatrix.R: Added methods for "%*%".
1070 :    
1071 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1072 :     poMatrix object.
1073 :    
1074 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1075 :    
1076 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1077 :    
1078 :     2004-01-25 Douglas Bates <bates@bates2_home>
1079 :    
1080 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1081 :    
1082 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1083 :     of nrow.
1084 :    
1085 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1086 :    
1087 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1088 :     subdirectories.
1089 :    
1090 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1091 :    
1092 :     * src/taucs.h: Accidently referred to global header files
1093 :     instead of local files.
1094 :    
1095 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1096 :    
1097 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1098 :     and methods and replaced all classes with S4 classes.
1099 :    
1100 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1101 :    
1102 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1103 :    
1104 :     * src/R_LapackPP.cc: Change method of calculating determinants
1105 :    
1106 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1107 :    
1108 :     * DESCRIPTION (Version): removed empty data directory as requested
1109 :     by CRAN maintainers. Changed version number and date.
1110 :    
1111 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1112 :    
1113 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1114 :     under Windows.
1115 :    
1116 :     * Added configure.win and src/Makevars.win as requested by Brian
1117 :     Ripley.
1118 :    
1119 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1120 :    
1121 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1122 :     Hornik.
1123 :    
1124 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1125 :    
1126 :     * configure.ac: Replaced configure.in with configure.ac
1127 :     contributed by Kurt Hornik.
1128 :    
1129 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1130 :     version for R-1.5.0
1131 :    
1132 : maechler 512
1133 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1134 :    
1135 :     * man/eigen.Rd: Removed the .Alias in the example

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