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Annotation of /pkg/ChangeLog

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1 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
4 :     * man/band.Rd: adapt the \dontshow{} unit test.
5 :    
6 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
9 :    
10 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
11 :    
12 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
13 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
14 :    
15 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
16 :     * R/Tsparse.R (tril, triu, band): methods
17 :     * R/dgRMatrix.R (tril, ...): dito
18 :     * man/band.Rd: dito
19 :    
20 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
21 :    
22 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
23 :     to be up-to-date automatically.
24 :    
25 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
26 :    
27 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
28 :    
29 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
30 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
31 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
32 :     such that the S4 objects are always created by the current version
33 :     of R and 'Matrix' class definitions.
34 :    
35 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
36 :    
37 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
38 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
39 : bates 1342 boundary and test cases.
40 :    
41 :     * src/lmer.c (mer_postVar): Modified to return the variances that
42 :     are marginal to the fixed effects, not conditional on them (which
43 :     is what the bVar slot contents represent).
44 :    
45 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
46 :    
47 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
48 :     function which calls the C function mer_hat_trace2.
49 : maechler 1346
50 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
51 :     producing a caterpillar plot.
52 : bates 1338
53 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
54 :    
55 :     * NAMESPACE: change "correlation" to "corMatrix"
56 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
57 :     * R/dpoMatrix.R: dito
58 :     * R/lmer.R: dito
59 :    
60 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
61 :    
62 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
63 :     RZXinv slot's contents into a separate internal function that can
64 :     be used in mer_hat_trace.
65 :    
66 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
67 :    
68 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
69 :     via new smart
70 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
71 :     utility functions.
72 :    
73 :    
74 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
75 :    
76 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
77 :     matrices when appropriate; band() even symmetric ones.
78 :     (replCmat): extend to potentially all "CsparseMatrix"
79 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
80 :     allow subassignment for special sparse matrices.
81 :    
82 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
83 :    
84 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
85 :     argument; in glmer_*(): print only if(verbose).
86 :    
87 :     speed-optimize a few places by moving REAL(.) out of loops.
88 :    
89 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
90 :    
91 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
92 :    
93 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
94 :     since that wrongly triggers also for M[ logi , ]
95 :    
96 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
97 :     a symmetric matrix that results in a non-symmetric one.
98 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
99 :    
100 :     * R/dMatrix.R: make round(M) work as round(M, 0)
101 :    
102 :     * R/dgTMatrix.R (image): coordinate system and axis now use
103 :     1-based indices, not 0-based ones.
104 :    
105 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
106 :     * tests/indexing.R: test it.
107 :    
108 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
109 :     * man/isSymmetric-methods.Rd: and document it.
110 :    
111 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
112 :     * man/SparseM-conv.Rd: docu them
113 :    
114 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
115 :     for 'SparseM' conversions
116 :    
117 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
118 :    
119 :     * R/Matrix.R (head): added head() and tail() methods.
120 :    
121 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
122 :    
123 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
124 :    
125 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
126 :    
127 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
128 :     add check for correct printing of symmetric sparse matrices.
129 :    
130 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
131 :     for sparse symmetric matrices.
132 :    
133 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
134 :     diagonal twice.
135 :    
136 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
137 :    
138 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
139 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
140 : bates 1316
141 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
142 :    
143 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
144 :    
145 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
146 :    
147 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
150 :     * R/lgCMatrix.R (diag): for new method
151 :    
152 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
153 :     ==> construction of illegal "*gTMatrix" via new() should
154 :     now be much less easy:
155 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
156 :    
157 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
158 :     directly.
159 :     * man/Matrix.Rd: documents it.
160 :    
161 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
162 :    
163 :     * src/pedigree.c (pedigree_inbreeding): Correction in
164 :     initialization. This function is not currently being used and is
165 :     not fully tested.
166 :    
167 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
168 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
169 :     objects. Modified validity check on pedigree objects to account
170 :     for nonparallel patterns of missingness of parents.
171 : bates 1311
172 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
173 :     class.
174 : maechler 1315
175 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
176 :    
177 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
178 :    
179 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
180 :    
181 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
182 :    
183 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
184 :     the output from mcmcsamp.
185 :    
186 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
187 :    
188 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
189 :     of the hat matrix.
190 : bates 1298
191 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
192 :    
193 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
194 :     classes.
195 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
196 : maechler 1295
197 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * R/dgTMatrix.R (colSums): etc. All four of
200 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
201 :     all "Matrices".
202 :    
203 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
204 :    
205 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
206 :     background grid to the qqmath plot of ranef.lmer.
207 :    
208 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
209 : bates 1284
210 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
211 :     grouping factors to be specified in the formula as (1|foo/bar).
212 :    
213 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
214 :    
215 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
216 :     !is.language to resolve the bug reported by Jacob Wegelin.
217 :    
218 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
219 :     code to evaluate inbreeding coefficients without calculating T,
220 :     based on code in Sargolzaei and Iwaisaki's paper.
221 :    
222 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
223 :    
224 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
225 :     generic and mer methods for isNested and denomDF. This denomDF was
226 :     an attempt to emulate that in lme but I don't think that makes
227 :     sense. Use the trace of the hat matrix instead.
228 :    
229 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
230 :    
231 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
232 :     the C code depending on a slot structure that's no longer valid.
233 :     * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
234 :    
235 :    
236 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
237 :    
238 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
239 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
240 :     and added a general band extractor.
241 :    
242 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
243 :    
244 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
245 :     allowable range with NAs. Added a corresponding check in the
246 :     validity check for the pedigree class.
247 :    
248 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
249 :     crossprod methods now inherits from symmetricMatrix.
250 :    
251 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
252 :    
253 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
254 :     generics lowerTriMatrix and upperTriMatrix along with methods for
255 :     the Csparse virtual class. Also added a C function Csparse_band
256 :     that implements these methods by calling cholmod_band.
257 :    
258 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
259 :    
260 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
261 :     erased when it was NULL. This led to invalid subselections!
262 :    
263 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
264 :    
265 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
266 :     in method for "t" so as not to lose the unit diagonal property.
267 :    
268 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
269 :    
270 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
271 :     and methods. This is now an option to the ranef method for the
272 :     mer class.
273 :    
274 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
275 :     compressed column-oriented matrix. Minor formatting cleanup.
276 :    
277 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
278 :     objects.
279 :    
280 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
281 :    
282 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
283 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
284 :    
285 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
286 :    
287 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
288 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
289 :    
290 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
291 :     for the dtCMatrix class.
292 : maechler 1253
293 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
294 :    
295 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
296 :     and methods for it.
297 :    
298 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
299 :    
300 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
301 :     arguments, such that M %*% 1:6 now works
302 :     * Tests/matprod.R: test the above
303 :    
304 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
305 : bates 1243
306 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
307 :     the ranef.lmer class.
308 :    
309 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
310 :     methods to extract the posterior variances from the bVar slot.
311 :    
312 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
313 :    
314 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
315 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
316 :    
317 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
318 :     * tests/simple: (extended)
319 :    
320 :     * R/sparseMatrix.R (isTriangular): now using much improved
321 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
322 :    
323 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
324 :    
325 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
326 :     (problem report from Franklin Parlamis). This should be done
327 : maechler 1238 generally.
328 : bates 1236
329 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
330 :    
331 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
332 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
333 :     update the plot methods.
334 :    
335 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
336 :    
337 :     * R/lmer.R (resid and ranef methods): Added methods for the
338 :     "residuals" and "resid" generic but only for linear mixed model
339 :     fits. Changed the ranef method to return a list of data frames so
340 :     that the plot methods now work.
341 :    
342 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
343 :    
344 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
345 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
346 :    
347 :     * DESCRIPTION (Date): New release
348 :    
349 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
350 :    
351 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
352 :    
353 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
354 :     * man/KNex.Rd: and other help files
355 :     * tests/*.R: several ones needed adaption
356 :     * inst/doc/Comparisons.Rnw: dito
357 :    
358 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
359 :    
360 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
361 :    
362 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
363 :    
364 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
365 :    
366 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
367 :    
368 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
369 :    
370 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
371 :    
372 :     * R/dMatrix.R: enable things like M [ M < 10 ]
373 :     * R/dgeMatrix.R: implement it
374 :    
375 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
376 :    
377 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
378 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
379 :     * R/lmer.R (show): now works with summary()
380 :    
381 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
382 :    
383 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
384 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
385 :     support the above
386 :    
387 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
388 :    
389 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
390 :     Use glmFit$prior.weights for weights in a glmm.
391 :     Allow an option usePQL = FALSE to skip the PQL steps for the
392 :     Laplace method (and, in time, the AGQ method).
393 :    
394 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
395 :     into a separate function internal_mer_Xfactor to be able to call
396 :     it from internal_bhat.
397 :    
398 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
399 :    
400 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
401 :     testing; now again of all actual classes.
402 :    
403 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
404 :     use macros and define make_d_matrix_* and make_i_matrix_*
405 :     where _i_ is for the ldense routines:
406 :    
407 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
408 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
409 :    
410 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
411 :    
412 :    
413 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
414 :    
415 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
416 :     many different kinds of matrices.
417 :     * R/*.R: quite a few new methods were needed for R CMD check with
418 :     new Matrix(). Very good for users playing around.
419 :    
420 :    
421 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
422 :    
423 :     * src/dgeMatrix.c (dMatrix_validate): new
424 :     * src/Mutils.c (dense_nonpacked_validate): new
425 :    
426 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
427 :    
428 :    
429 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
430 :    
431 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
432 :    
433 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
434 : bates 1119
435 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
436 :    
437 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
438 :     segfault in cases with multiple non-nested grouping factors.
439 :    
440 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
441 :    
442 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
443 :     (Depends): also on 'utils'
444 :    
445 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
446 :     * R/diagMatrix.R (Diagonal): constructor and methods for
447 :     diagonal matrices
448 :    
449 :     * R/ltTMatrix.R: new "minimal methods"
450 :    
451 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
454 :     all methods (and help files).
455 :    
456 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
457 :    
458 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
459 :     for case (dimn. op no_dimn.)
460 :    
461 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
462 :    
463 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
464 : maechler 1084
465 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
466 :    
467 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
468 :     by Julian Faraway.
469 :    
470 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
471 :    
472 :     * R/Auxiliaries.R (try_as): new utility
473 :     * R/sparseMatrix.R: use try_as() in coercion to original class
474 :    
475 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
476 :    
477 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
478 :    
479 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
480 :    
481 :     * R/Auxiliaries.R (dimNamesCheck): added
482 :    
483 :     * R/Matrix.R (as.array), (as.vector): new
484 :    
485 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
486 :    
487 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
488 : maechler 956 default.
489 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
490 :     "pMatrix" now contains "sparseMatrix"
491 : maechler 954
492 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
493 :    
494 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
495 :    
496 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
497 :    
498 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
499 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
500 :    
501 :     * R/dspMatrix.R: typo in "t" method
502 :    
503 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
504 :    
505 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
506 :     * R/Tsparse.R: instead of R/gTMatrix.R
507 :     * R/Csparse.R: new
508 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
509 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
510 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
511 :     via cholmod
512 :    
513 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
514 :    
515 :     * R/Auxiliaries.R (non0ind): new function using new C code
516 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
517 :    
518 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
519 :    
520 :     * src/chm_common.h: header file required by all C sources that
521 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
522 : bates 917 called 'c' whose address is passed as the last argument to
523 :     (virtually) every CHOLMOD function.
524 :    
525 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
526 :    
527 :     * src/init.c: initialize and finalize the cholmod_common structure.
528 :    
529 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
530 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
531 :    
532 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
533 :    
534 :     * inst/test-tools.R: new file collecting the utility functions used
535 :     in ./tests/*.R
536 :    
537 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
538 :     * R/Matrix.R (cbind2): methods for NULL and missing
539 :    
540 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
541 :    
542 :     * R/AllClass.R: new "index" class for "[" and "[<-":
543 :     First cut at "symmetricMatrix" and "triangularMatrix"
544 :     * R/gTMatrix.R (.ind.prep): new function;
545 : maechler 1174 Logical and character indexing now work too.
546 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
547 :     * tests/indexing.R: new, including *.Rout.save
548 :     * tests/dgTMatrix.R: new
549 :    
550 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
551 :    
552 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
553 :     indicator pos not being updated. Also enforced upper triangular
554 :     for symmetric case. Need to coerce edges component of elements of
555 :     edge list - grr! (Why don't they define their classes cleanly?)
556 :    
557 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
558 :    
559 :     * R/Matrix.R: added first "[<-" methods; not yet functional
560 :     * R/denseMatrix.R: dito
561 :     * man/Subassign-methods.Rd: new help file for these
562 :    
563 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
564 :    
565 :     * DESCRIPTION (Version): 0.98-6
566 :    
567 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
568 :     matrices.
569 :    
570 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
571 :    
572 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
573 :     as( <logical>, "matrix")
574 :    
575 :     * R/pMatrix.R: coercion to "lgTMatrix"
576 :    
577 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
578 :     * man/gTMatrix-class.Rd:
579 :     * General slight re-organization of where "[" methods are defined.
580 :     more to come.
581 :    
582 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
583 : maechler 868
584 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
585 : maechler 871
586 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
587 :     * .....
588 :    
589 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
590 :    
591 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
592 :     or glmer objects.
593 :    
594 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
595 :    
596 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
597 :    
598 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
599 :    
600 :     * R/HBMM.R: finish re-writing R-only code.
601 :    
602 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
603 :    
604 :     * man/externalFormats.Rd: move documentation for writeHB and
605 :     writeMM here.
606 :    
607 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
608 :     (suggested by Paul Roecker).
609 :    
610 :     * tests/validObj.R (assertError): Comment out test that is failing
611 :     after recent changes in r-devel.
612 :    
613 : maechler 860
614 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
615 :    
616 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
617 :     * man/denseMatrix-class.Rd
618 :     * NAMESPACE: export it, and also export
619 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
620 :    
621 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
622 :    
623 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
624 :    
625 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
626 :     matrix_solve code (which was really, really wrong).
627 :    
628 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
629 : maechler 834
630 :     * DESCRIPTION (Version): 0.98-2
631 :    
632 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
633 :    
634 :     * R/lmer.R (abbrvNms): new
635 :     * R/lmer.R (mcmcsamp): allow transformed parameters
636 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
637 :     for the Harwell-Boeing and the MatrixMarket formats.
638 : maechler 834
639 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
640 :    
641 :     * man/dtrMatrix-class.Rd: add examples
642 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
643 : maechler 834
644 :     * TODO: note the dtpMatrix (docu) bug
645 :    
646 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
647 :     in order to ensure that new as.matrix() is used by old functions,
648 :     e.g., svd(), qr(), eigen(), dist(),..;
649 :     apply(), also matplot() or pairs().
650 :    
651 :    
652 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
653 :    
654 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
655 :     add comments about 'control' / lmerControl() arguments
656 :    
657 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
658 : bates 820
659 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
660 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
661 : bates 820
662 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
663 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
664 :    
665 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
666 :     .Call calls that were producing spurious output.
667 :    
668 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
669 : bates 801
670 :     * R/lmer.R (lmer): stored updated variance component estimates in
671 :     mer object for the generalized model. (Bug reported by Renaud
672 :     Lancelot).
673 :    
674 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
675 : bates 794
676 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
677 :     unidimensional case.
678 :    
679 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
680 : maechler 791
681 :     * DESCRIPTION (Version): 0.96-1
682 :    
683 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
684 : maechler 791
685 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
686 : bates 763
687 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
688 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
689 :    
690 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
691 : bates 763
692 :     * src/Makefile.win: Forgot to update this when Makefile changed.
693 :    
694 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
695 : bates 726
696 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
697 :     bug reported by Kurt Hornik and Michael Hahsler.
698 :    
699 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
700 : bates 725
701 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
702 :     logical sparse matrices. These will also be used in the symbolic
703 :     analysis for lmer objects.
704 :    
705 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
706 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
707 : maechler 791
708 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
709 : bates 714
710 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
711 :     colMeans, colSums, rowMeans and rowSums.
712 :    
713 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
714 : bates 692
715 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
716 :     multiplication operation.
717 :    
718 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
719 :     to dgetrs.
720 :    
721 :     * src/init.c: Fix cut-and-paste error in definition of
722 :     dgeMatrix_matrix_solve
723 :    
724 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
725 :    
726 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
727 : bates 692
728 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
729 :    
730 :     * DESCRIPTION: Eliminate import of stats.
731 :    
732 : maechler 791
733 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
734 : bates 692
735 :     * R/AllClass.R : add logical sparse matrix classes
736 :    
737 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
738 :    
739 :     * R/dgTMatrix.R: add "[" method for triplet matrices
740 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
741 :    
742 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
743 : maechler 687
744 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
745 :    
746 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
747 :     * R/sparseMatrix.R: %*%, crossprod()
748 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
749 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
750 :     * src/lmer.c (lmer_fitted): fix thinko
751 :    
752 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
753 :    
754 :     * R/AllClass.R: add two virtual sparse classes ``on top''
755 :    
756 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
757 :    
758 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
759 :     correspondingly fix examples and tests/ since new()
760 :     doesn't work for virtual classes.
761 :    
762 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
763 :    
764 :     * R/Matrix.R (as.matrix): method and one for unname()
765 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
766 :     also run for R 2.1.0; using as.matrix()
767 :    
768 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
769 : maechler 658
770 :     * R/pMatrix.R: "pMatrix" class added
771 :     * ....
772 :    
773 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
774 : bates 645
775 :     * R/dtpMatrix.R: Add unpack method and an example.
776 :    
777 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
778 :     of general symmetric matrices and associated S4 methods.
779 :    
780 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
781 :     +
782 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
783 :    
784 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
785 :     crossprod() and "%*%" methods added; tests, too.
786 :     * tests/matprod.R: new, for testing these
787 :    
788 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
789 : bates 599
790 :     * src/lmer.c (lmer_fitted): Added.
791 :    
792 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
793 : bates 596
794 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
795 :    
796 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
797 : bates 582
798 :     * src/*.c,po/,inst/po: Internationalization and localization of
799 :     the package.
800 :    
801 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
802 :     R_ldl.c file.
803 :    
804 :     * src/flame.[ch]: Removed these source files.
805 : maechler 658
806 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
807 :    
808 :     * src/LU.[ch],src/init.c: absorb in factorizations
809 :    
810 :     * src/Mutils.h: prepare for internationalization
811 :    
812 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
813 :     this file
814 :    
815 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
816 :    
817 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
818 :    
819 :     * R/dtrMatrix.R: fix t() method
820 :    
821 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
822 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
823 : maechler 578 * tests/group-methods.R : and test them.
824 :    
825 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
826 :     border case
827 :    
828 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
829 :    
830 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
831 : maechler 578
832 :     * src/dgBCMatrix.c:
833 :     * src/lmer.c: many changes
834 :     * ...
835 :    
836 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
837 :    
838 :     * R/Matrix.R: add more sophisticated show() method.
839 :    
840 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
841 :    
842 :     * */* : almost complete reorganization of classes.
843 :    
844 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
845 : bates 460
846 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
847 :     for the geMatrix class.
848 :    
849 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
850 : bates 460
851 :     * src/Makefile (clean): Remove *.a and *.so
852 :    
853 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
854 :    
855 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
856 : bates 460
857 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
858 : bates 460 had an effect in cases with more than 2 grouping factors.
859 :    
860 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
861 : bates 415
862 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
863 :    
864 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
865 : bates 410
866 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
867 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
868 :    
869 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
870 : bates 392
871 :     * R/sscMatrix.R: Add determinant methods
872 :    
873 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
874 :     for tripletMatrix to matrix.
875 :    
876 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
877 : bates 388
878 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
879 :     no longer used.
880 :    
881 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
882 :     with dynamic allocation of scratch arrays.
883 :    
884 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
885 :     for multivariate random effects with multiple grouping factors.
886 :     Fixes part but not all of #15.
887 :    
888 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
889 : bates 375
890 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
891 :     scalar grouping factors corrected.
892 :    
893 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
894 : bates 375
895 :     * src/bCrosstab.c: remove diag_update which is no longer used
896 :    
897 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
898 : bates 350
899 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
900 :     .h file can be included.
901 :    
902 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
903 : bates 342
904 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
905 : bates 342 Complete allocation of slots in NEW_OBJECT.
906 :    
907 :     * src/Mutils.h: Moved list of symbols to an include file
908 :    
909 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
910 : bates 342
911 :     * src/geMutils.c (Matrix_init): remove unused function
912 :    
913 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
914 : bates 342
915 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
916 :    
917 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
918 : bates 327
919 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
920 :    
921 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
922 : bates 303
923 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
924 :    
925 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
926 : bates 296
927 :     * src/init.c: Created R_init_Matrix and added registration of C
928 :     routines.
929 :    
930 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
931 : bates 283
932 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
933 :    
934 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
935 : bates 229
936 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
937 :    
938 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
939 :    
940 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
941 :    
942 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
943 :    
944 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
945 :     ssclme_update_mm
946 :    
947 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
948 :    
949 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
950 :     in the order of unconstrained and constrained parameters.
951 :     (ssclme_gradient): Added the gradients (not yet correct for
952 :     multidimensional, unconstrained case).
953 :    
954 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
955 :    
956 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
957 :    
958 :     * src/Makefile.win: Remove unneeded ranlib call
959 :    
960 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
961 :    
962 :     * DESCRIPTION (Version): New release
963 :    
964 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
965 :    
966 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
967 :    
968 :     * src/triplet_to_col.c: Create triplet_to_col as a native
969 : maechler 658 function, not the version from umfpack. There were problems with
970 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
971 :     only one umfpack routine being used so I moved it here.
972 :    
973 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
974 :    
975 :     * src/ssclme.c (ssclme_variances): New function.
976 :    
977 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
978 :    
979 :     * src/ssclme.c (ssclme_fitted): Added function.
980 :    
981 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
982 :    
983 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
984 :     store the dimnames in the XtX and bVar slots
985 :     (ssclme_update_mm): Change the dimensions of the bVar slot
986 :     components and the returned value from ssclme_ranef.
987 :    
988 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
989 :    
990 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
991 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
992 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
993 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
994 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
995 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
996 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
997 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
998 :     Moved the pdMat classes from the lme4 package.
999 :    
1000 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1001 :    
1002 :     * man/ssclme-class.Rd: Update definition and documentation of the
1003 :     ssclme class to include the DIsqrt slot.
1004 :    
1005 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1006 :     (much faster using dsyrk, a level 3 BLAS routine).
1007 :    
1008 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1009 :    
1010 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1011 :    
1012 :     * tests/ssclme.R: Modify the test to account for the permutation
1013 :     of the levels of the grouping factors.
1014 :    
1015 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1016 :    
1017 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1018 :     directly into the ssclme class definition.
1019 :    
1020 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1021 :    
1022 :     * DESCRIPTION (Date): New release
1023 :    
1024 :     * man/ssclme-class.Rd: new file.
1025 :    
1026 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1027 :     works and it's fast!
1028 :    
1029 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1030 :    
1031 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1032 :    
1033 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1034 :    
1035 :     * DESCRIPTION (Date): New release
1036 :    
1037 :     * NAMESPACE: Don't export ssclme.
1038 :    
1039 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1040 :     school data.
1041 :    
1042 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1043 :    
1044 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1045 :     keep track of the fixed-effects and the response. Counts also
1046 :     gets an extra element, which is always one.
1047 :    
1048 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1049 :    
1050 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1051 :    
1052 :     * src/cscMatrix.c (csc_transpose): new function
1053 :    
1054 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1055 :     (csc_components_transpose): new function
1056 :    
1057 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1058 :    
1059 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1060 :     triplets
1061 :    
1062 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1063 :    
1064 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1065 :    
1066 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1067 :     and all other .h files in src.
1068 :    
1069 :     * src/Makefile.win: This and other Makefile.win files contributed
1070 :     by Brian Ripley.
1071 :    
1072 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1073 :    
1074 :     * R/syMatrix.R: Added methods for "%*%".
1075 :    
1076 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1077 :     poMatrix object.
1078 :    
1079 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1080 :    
1081 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1082 :    
1083 :     2004-01-25 Douglas Bates <bates@bates2_home>
1084 :    
1085 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1086 :    
1087 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1088 :     of nrow.
1089 :    
1090 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1091 :    
1092 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1093 :     subdirectories.
1094 :    
1095 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1096 :    
1097 :     * src/taucs.h: Accidently referred to global header files
1098 :     instead of local files.
1099 :    
1100 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1101 :    
1102 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1103 :     and methods and replaced all classes with S4 classes.
1104 :    
1105 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1106 :    
1107 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1108 :    
1109 :     * src/R_LapackPP.cc: Change method of calculating determinants
1110 :    
1111 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1112 :    
1113 :     * DESCRIPTION (Version): removed empty data directory as requested
1114 :     by CRAN maintainers. Changed version number and date.
1115 :    
1116 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1117 :    
1118 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1119 :     under Windows.
1120 :    
1121 :     * Added configure.win and src/Makevars.win as requested by Brian
1122 :     Ripley.
1123 :    
1124 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1125 :    
1126 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1127 :     Hornik.
1128 :    
1129 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1130 :    
1131 :     * configure.ac: Replaced configure.in with configure.ac
1132 :     contributed by Kurt Hornik.
1133 :    
1134 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1135 :     version for R-1.5.0
1136 :    
1137 : maechler 512
1138 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1139 :    
1140 :     * man/eigen.Rd: Removed the .Alias in the example

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