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Annotation of /pkg/ChangeLog

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1 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
4 :     R-level conversion to a sparse symmetric class.
5 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
6 :     Remove conversion to sparse symmetric classes (now done in C code).
7 :    
8 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
9 :    
10 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
11 :     * man/band.Rd: adapt the \dontshow{} unit test.
12 :    
13 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
14 :    
15 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
16 :    
17 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
18 :    
19 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
20 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
21 :    
22 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
23 :     * R/Tsparse.R (tril, triu, band): methods
24 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
25 :     * man/band.Rd: ditto
26 : maechler 1349
27 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
30 :     to be up-to-date automatically.
31 :    
32 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
33 :    
34 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
35 :    
36 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
37 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
38 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
39 :     such that the S4 objects are always created by the current version
40 :     of R and 'Matrix' class definitions.
41 :    
42 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
43 :    
44 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
45 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
46 : bates 1342 boundary and test cases.
47 :    
48 :     * src/lmer.c (mer_postVar): Modified to return the variances that
49 :     are marginal to the fixed effects, not conditional on them (which
50 :     is what the bVar slot contents represent).
51 :    
52 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
53 :    
54 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
55 :     function which calls the C function mer_hat_trace2.
56 : maechler 1346
57 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
58 :     producing a caterpillar plot.
59 : bates 1338
60 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
61 :    
62 :     * NAMESPACE: change "correlation" to "corMatrix"
63 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
64 : bates 1352 * R/dpoMatrix.R: ditto
65 :     * R/lmer.R: ditto
66 : maechler 1335
67 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
68 :    
69 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
70 :     RZXinv slot's contents into a separate internal function that can
71 :     be used in mer_hat_trace.
72 :    
73 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
74 :    
75 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
76 :     via new smart
77 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
78 :     utility functions.
79 :    
80 :    
81 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
82 :    
83 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
84 :     matrices when appropriate; band() even symmetric ones.
85 :     (replCmat): extend to potentially all "CsparseMatrix"
86 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
87 :     allow subassignment for special sparse matrices.
88 :    
89 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
90 :    
91 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
92 :     argument; in glmer_*(): print only if(verbose).
93 :    
94 :     speed-optimize a few places by moving REAL(.) out of loops.
95 :    
96 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
97 :    
98 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
99 :    
100 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
101 :     since that wrongly triggers also for M[ logi , ]
102 :    
103 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
104 :     a symmetric matrix that results in a non-symmetric one.
105 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
106 :    
107 :     * R/dMatrix.R: make round(M) work as round(M, 0)
108 :    
109 :     * R/dgTMatrix.R (image): coordinate system and axis now use
110 :     1-based indices, not 0-based ones.
111 :    
112 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
113 :     * tests/indexing.R: test it.
114 :    
115 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
116 :     * man/isSymmetric-methods.Rd: and document it.
117 :    
118 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
119 :     * man/SparseM-conv.Rd: docu them
120 :    
121 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
122 :     for 'SparseM' conversions
123 :    
124 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
125 :    
126 :     * R/Matrix.R (head): added head() and tail() methods.
127 :    
128 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
129 :    
130 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
131 :    
132 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
133 :    
134 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
135 :     add check for correct printing of symmetric sparse matrices.
136 :    
137 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
138 :     for sparse symmetric matrices.
139 :    
140 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
141 :     diagonal twice.
142 :    
143 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
144 :    
145 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
146 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
147 : bates 1316
148 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
149 :    
150 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
151 :    
152 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
153 :    
154 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
155 :    
156 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
157 :     * R/lgCMatrix.R (diag): for new method
158 :    
159 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
160 :     ==> construction of illegal "*gTMatrix" via new() should
161 :     now be much less easy:
162 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
163 :    
164 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
165 :     directly.
166 :     * man/Matrix.Rd: documents it.
167 :    
168 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
169 :    
170 :     * src/pedigree.c (pedigree_inbreeding): Correction in
171 :     initialization. This function is not currently being used and is
172 :     not fully tested.
173 :    
174 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
175 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
176 :     objects. Modified validity check on pedigree objects to account
177 :     for nonparallel patterns of missingness of parents.
178 : bates 1311
179 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
180 :     class.
181 : maechler 1315
182 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
183 :    
184 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
185 :    
186 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
187 :    
188 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
189 :    
190 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
191 :     the output from mcmcsamp.
192 :    
193 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
194 :    
195 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
196 :     of the hat matrix.
197 : bates 1298
198 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
199 :    
200 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
201 :     classes.
202 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
203 : maechler 1295
204 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
205 :    
206 :     * R/dgTMatrix.R (colSums): etc. All four of
207 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
208 :     all "Matrices".
209 :    
210 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
211 :    
212 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
213 :     background grid to the qqmath plot of ranef.lmer.
214 :    
215 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
216 : bates 1284
217 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
218 :     grouping factors to be specified in the formula as (1|foo/bar).
219 :    
220 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
221 :    
222 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
223 :     !is.language to resolve the bug reported by Jacob Wegelin.
224 :    
225 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
226 :     code to evaluate inbreeding coefficients without calculating T,
227 :     based on code in Sargolzaei and Iwaisaki's paper.
228 :    
229 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
230 :    
231 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
232 :     generic and mer methods for isNested and denomDF. This denomDF was
233 :     an attempt to emulate that in lme but I don't think that makes
234 :     sense. Use the trace of the hat matrix instead.
235 :    
236 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
237 :    
238 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
239 :     the C code depending on a slot structure that's no longer valid.
240 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
241 : maechler 1271
242 :    
243 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
244 :    
245 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
246 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
247 :     and added a general band extractor.
248 :    
249 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
250 :    
251 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
252 :     allowable range with NAs. Added a corresponding check in the
253 :     validity check for the pedigree class.
254 :    
255 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
256 :     crossprod methods now inherits from symmetricMatrix.
257 :    
258 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
261 :     generics lowerTriMatrix and upperTriMatrix along with methods for
262 :     the Csparse virtual class. Also added a C function Csparse_band
263 :     that implements these methods by calling cholmod_band.
264 :    
265 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
266 :    
267 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
268 :     erased when it was NULL. This led to invalid subselections!
269 :    
270 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
271 :    
272 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
273 :     in method for "t" so as not to lose the unit diagonal property.
274 :    
275 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
276 :    
277 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
278 :     and methods. This is now an option to the ranef method for the
279 :     mer class.
280 :    
281 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
282 :     compressed column-oriented matrix. Minor formatting cleanup.
283 :    
284 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
285 :     objects.
286 :    
287 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
288 :    
289 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
290 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
291 :    
292 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
293 :    
294 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
295 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
296 :    
297 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
298 :     for the dtCMatrix class.
299 : maechler 1253
300 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
301 :    
302 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
303 :     and methods for it.
304 :    
305 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
308 :     arguments, such that M %*% 1:6 now works
309 :     * Tests/matprod.R: test the above
310 :    
311 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
312 : bates 1243
313 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
314 :     the ranef.lmer class.
315 :    
316 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
317 :     methods to extract the posterior variances from the bVar slot.
318 :    
319 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
320 :    
321 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
322 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
323 :    
324 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
325 :     * tests/simple: (extended)
326 :    
327 :     * R/sparseMatrix.R (isTriangular): now using much improved
328 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
329 :    
330 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
331 :    
332 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
333 :     (problem report from Franklin Parlamis). This should be done
334 : maechler 1238 generally.
335 : bates 1236
336 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
337 :    
338 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
339 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
340 :     update the plot methods.
341 :    
342 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
343 :    
344 :     * R/lmer.R (resid and ranef methods): Added methods for the
345 :     "residuals" and "resid" generic but only for linear mixed model
346 :     fits. Changed the ranef method to return a list of data frames so
347 :     that the plot methods now work.
348 :    
349 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
350 :    
351 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
352 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
353 :    
354 :     * DESCRIPTION (Date): New release
355 :    
356 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
359 :    
360 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
361 :     * man/KNex.Rd: and other help files
362 :     * tests/*.R: several ones needed adaption
363 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
364 : maechler 1228
365 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
366 :    
367 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
368 :    
369 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
370 :    
371 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
372 :    
373 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
374 :    
375 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
376 :    
377 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
378 :    
379 :     * R/dMatrix.R: enable things like M [ M < 10 ]
380 :     * R/dgeMatrix.R: implement it
381 :    
382 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
383 :    
384 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
385 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
386 :     * R/lmer.R (show): now works with summary()
387 :    
388 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
389 :    
390 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
391 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
392 :     support the above
393 :    
394 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
395 :    
396 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
397 :     Use glmFit$prior.weights for weights in a glmm.
398 :     Allow an option usePQL = FALSE to skip the PQL steps for the
399 :     Laplace method (and, in time, the AGQ method).
400 :    
401 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
402 :     into a separate function internal_mer_Xfactor to be able to call
403 :     it from internal_bhat.
404 :    
405 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
406 :    
407 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
408 :     testing; now again of all actual classes.
409 :    
410 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
411 :     use macros and define make_d_matrix_* and make_i_matrix_*
412 :     where _i_ is for the ldense routines:
413 :    
414 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
415 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
416 :    
417 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
418 :    
419 :    
420 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
421 :    
422 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
423 :     many different kinds of matrices.
424 :     * R/*.R: quite a few new methods were needed for R CMD check with
425 :     new Matrix(). Very good for users playing around.
426 :    
427 :    
428 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
429 :    
430 :     * src/dgeMatrix.c (dMatrix_validate): new
431 :     * src/Mutils.c (dense_nonpacked_validate): new
432 :    
433 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
434 :    
435 :    
436 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
437 :    
438 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
439 :    
440 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
441 : bates 1119
442 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
443 :    
444 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
445 :     segfault in cases with multiple non-nested grouping factors.
446 :    
447 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
448 :    
449 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
450 :     (Depends): also on 'utils'
451 :    
452 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
453 :     * R/diagMatrix.R (Diagonal): constructor and methods for
454 :     diagonal matrices
455 :    
456 :     * R/ltTMatrix.R: new "minimal methods"
457 :    
458 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
459 :    
460 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
461 :     all methods (and help files).
462 :    
463 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
464 :    
465 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
466 :     for case (dimn. op no_dimn.)
467 :    
468 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
469 :    
470 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
471 : maechler 1084
472 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
473 :    
474 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
475 :     by Julian Faraway.
476 :    
477 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
478 :    
479 :     * R/Auxiliaries.R (try_as): new utility
480 :     * R/sparseMatrix.R: use try_as() in coercion to original class
481 :    
482 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
483 :    
484 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
485 :    
486 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
487 :    
488 :     * R/Auxiliaries.R (dimNamesCheck): added
489 :    
490 :     * R/Matrix.R (as.array), (as.vector): new
491 :    
492 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
493 :    
494 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
495 : maechler 956 default.
496 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
497 :     "pMatrix" now contains "sparseMatrix"
498 : maechler 954
499 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
500 :    
501 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
502 :    
503 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
504 :    
505 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
506 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
507 :    
508 :     * R/dspMatrix.R: typo in "t" method
509 :    
510 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
511 :    
512 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
513 :     * R/Tsparse.R: instead of R/gTMatrix.R
514 :     * R/Csparse.R: new
515 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
516 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
517 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
518 :     via cholmod
519 :    
520 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
521 :    
522 :     * R/Auxiliaries.R (non0ind): new function using new C code
523 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
524 :    
525 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
526 :    
527 :     * src/chm_common.h: header file required by all C sources that
528 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
529 : bates 917 called 'c' whose address is passed as the last argument to
530 :     (virtually) every CHOLMOD function.
531 :    
532 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
533 :    
534 :     * src/init.c: initialize and finalize the cholmod_common structure.
535 :    
536 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
537 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
538 :    
539 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * inst/test-tools.R: new file collecting the utility functions used
542 :     in ./tests/*.R
543 :    
544 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
545 :     * R/Matrix.R (cbind2): methods for NULL and missing
546 :    
547 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
548 :    
549 :     * R/AllClass.R: new "index" class for "[" and "[<-":
550 :     First cut at "symmetricMatrix" and "triangularMatrix"
551 :     * R/gTMatrix.R (.ind.prep): new function;
552 : maechler 1174 Logical and character indexing now work too.
553 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
554 :     * tests/indexing.R: new, including *.Rout.save
555 :     * tests/dgTMatrix.R: new
556 :    
557 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
558 :    
559 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
560 :     indicator pos not being updated. Also enforced upper triangular
561 :     for symmetric case. Need to coerce edges component of elements of
562 :     edge list - grr! (Why don't they define their classes cleanly?)
563 :    
564 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
565 :    
566 :     * R/Matrix.R: added first "[<-" methods; not yet functional
567 : bates 1352 * R/denseMatrix.R: ditto
568 : maechler 871 * man/Subassign-methods.Rd: new help file for these
569 :    
570 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
571 :    
572 :     * DESCRIPTION (Version): 0.98-6
573 :    
574 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
575 :     matrices.
576 :    
577 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
578 :    
579 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
580 :     as( <logical>, "matrix")
581 :    
582 :     * R/pMatrix.R: coercion to "lgTMatrix"
583 :    
584 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
585 :     * man/gTMatrix-class.Rd:
586 :     * General slight re-organization of where "[" methods are defined.
587 :     more to come.
588 :    
589 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
590 : maechler 868
591 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
592 : maechler 871
593 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
594 :     * .....
595 :    
596 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
597 :    
598 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
599 :     or glmer objects.
600 :    
601 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
602 :    
603 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
604 :    
605 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
606 :    
607 :     * R/HBMM.R: finish re-writing R-only code.
608 :    
609 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
610 :    
611 :     * man/externalFormats.Rd: move documentation for writeHB and
612 :     writeMM here.
613 :    
614 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
615 :     (suggested by Paul Roecker).
616 :    
617 :     * tests/validObj.R (assertError): Comment out test that is failing
618 :     after recent changes in r-devel.
619 :    
620 : maechler 860
621 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
622 :    
623 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
624 :     * man/denseMatrix-class.Rd
625 :     * NAMESPACE: export it, and also export
626 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
627 :    
628 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
629 :    
630 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
631 :    
632 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
633 :     matrix_solve code (which was really, really wrong).
634 :    
635 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
636 : maechler 834
637 :     * DESCRIPTION (Version): 0.98-2
638 :    
639 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
640 :    
641 :     * R/lmer.R (abbrvNms): new
642 :     * R/lmer.R (mcmcsamp): allow transformed parameters
643 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
644 :     for the Harwell-Boeing and the MatrixMarket formats.
645 : maechler 834
646 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
647 :    
648 :     * man/dtrMatrix-class.Rd: add examples
649 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
650 : maechler 834
651 :     * TODO: note the dtpMatrix (docu) bug
652 :    
653 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
654 :     in order to ensure that new as.matrix() is used by old functions,
655 :     e.g., svd(), qr(), eigen(), dist(),..;
656 :     apply(), also matplot() or pairs().
657 :    
658 :    
659 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
660 :    
661 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
662 :     add comments about 'control' / lmerControl() arguments
663 :    
664 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
665 : bates 820
666 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
667 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
668 : bates 820
669 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
670 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
671 :    
672 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
673 :     .Call calls that were producing spurious output.
674 :    
675 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
676 : bates 801
677 :     * R/lmer.R (lmer): stored updated variance component estimates in
678 :     mer object for the generalized model. (Bug reported by Renaud
679 :     Lancelot).
680 :    
681 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
682 : bates 794
683 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
684 :     unidimensional case.
685 :    
686 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
687 : maechler 791
688 :     * DESCRIPTION (Version): 0.96-1
689 :    
690 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
691 : maechler 791
692 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
693 : bates 763
694 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
695 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
696 :    
697 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
698 : bates 763
699 :     * src/Makefile.win: Forgot to update this when Makefile changed.
700 :    
701 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
702 : bates 726
703 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
704 :     bug reported by Kurt Hornik and Michael Hahsler.
705 :    
706 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
707 : bates 725
708 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
709 :     logical sparse matrices. These will also be used in the symbolic
710 :     analysis for lmer objects.
711 :    
712 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
713 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
714 : maechler 791
715 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
716 : bates 714
717 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
718 :     colMeans, colSums, rowMeans and rowSums.
719 :    
720 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
721 : bates 692
722 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
723 :     multiplication operation.
724 :    
725 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
726 :     to dgetrs.
727 :    
728 :     * src/init.c: Fix cut-and-paste error in definition of
729 :     dgeMatrix_matrix_solve
730 :    
731 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
732 :    
733 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
734 : bates 692
735 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
736 :    
737 :     * DESCRIPTION: Eliminate import of stats.
738 :    
739 : maechler 791
740 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
741 : bates 692
742 :     * R/AllClass.R : add logical sparse matrix classes
743 :    
744 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
745 :    
746 :     * R/dgTMatrix.R: add "[" method for triplet matrices
747 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
748 :    
749 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
750 : maechler 687
751 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
752 :    
753 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
754 :     * R/sparseMatrix.R: %*%, crossprod()
755 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
756 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
757 :     * src/lmer.c (lmer_fitted): fix thinko
758 :    
759 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
760 :    
761 :     * R/AllClass.R: add two virtual sparse classes ``on top''
762 :    
763 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
764 :    
765 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
766 :     correspondingly fix examples and tests/ since new()
767 :     doesn't work for virtual classes.
768 :    
769 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
770 :    
771 :     * R/Matrix.R (as.matrix): method and one for unname()
772 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
773 :     also run for R 2.1.0; using as.matrix()
774 :    
775 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
776 : maechler 658
777 :     * R/pMatrix.R: "pMatrix" class added
778 :     * ....
779 :    
780 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
781 : bates 645
782 :     * R/dtpMatrix.R: Add unpack method and an example.
783 :    
784 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
785 :     of general symmetric matrices and associated S4 methods.
786 :    
787 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
788 :     +
789 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
790 :    
791 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
792 :     crossprod() and "%*%" methods added; tests, too.
793 :     * tests/matprod.R: new, for testing these
794 :    
795 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
796 : bates 599
797 :     * src/lmer.c (lmer_fitted): Added.
798 :    
799 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
800 : bates 596
801 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
802 :    
803 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
804 : bates 582
805 :     * src/*.c,po/,inst/po: Internationalization and localization of
806 :     the package.
807 :    
808 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
809 :     R_ldl.c file.
810 :    
811 :     * src/flame.[ch]: Removed these source files.
812 : maechler 658
813 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
814 :    
815 :     * src/LU.[ch],src/init.c: absorb in factorizations
816 :    
817 :     * src/Mutils.h: prepare for internationalization
818 :    
819 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
820 :     this file
821 :    
822 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
823 :    
824 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
825 :    
826 :     * R/dtrMatrix.R: fix t() method
827 :    
828 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
829 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
830 : maechler 578 * tests/group-methods.R : and test them.
831 :    
832 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
833 :     border case
834 :    
835 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
836 :    
837 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
838 : maechler 578
839 :     * src/dgBCMatrix.c:
840 :     * src/lmer.c: many changes
841 :     * ...
842 :    
843 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
844 :    
845 :     * R/Matrix.R: add more sophisticated show() method.
846 :    
847 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
848 :    
849 :     * */* : almost complete reorganization of classes.
850 :    
851 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
852 : bates 460
853 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
854 :     for the geMatrix class.
855 :    
856 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
857 : bates 460
858 :     * src/Makefile (clean): Remove *.a and *.so
859 :    
860 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
861 :    
862 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
863 : bates 460
864 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
865 : bates 460 had an effect in cases with more than 2 grouping factors.
866 :    
867 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
868 : bates 415
869 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
870 :    
871 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
872 : bates 410
873 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
874 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
875 :    
876 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
877 : bates 392
878 :     * R/sscMatrix.R: Add determinant methods
879 :    
880 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
881 :     for tripletMatrix to matrix.
882 :    
883 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
884 : bates 388
885 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
886 :     no longer used.
887 :    
888 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
889 :     with dynamic allocation of scratch arrays.
890 :    
891 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
892 :     for multivariate random effects with multiple grouping factors.
893 :     Fixes part but not all of #15.
894 :    
895 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
896 : bates 375
897 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
898 :     scalar grouping factors corrected.
899 :    
900 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
901 : bates 375
902 :     * src/bCrosstab.c: remove diag_update which is no longer used
903 :    
904 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
905 : bates 350
906 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
907 :     .h file can be included.
908 :    
909 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
910 : bates 342
911 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
912 : bates 342 Complete allocation of slots in NEW_OBJECT.
913 :    
914 :     * src/Mutils.h: Moved list of symbols to an include file
915 :    
916 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
917 : bates 342
918 :     * src/geMutils.c (Matrix_init): remove unused function
919 :    
920 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
921 : bates 342
922 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
923 :    
924 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
925 : bates 327
926 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
927 :    
928 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
929 : bates 303
930 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
931 :    
932 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
933 : bates 296
934 :     * src/init.c: Created R_init_Matrix and added registration of C
935 :     routines.
936 :    
937 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
938 : bates 283
939 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
940 :    
941 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
942 : bates 229
943 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
944 :    
945 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
946 :    
947 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
948 :    
949 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
950 :    
951 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
952 :     ssclme_update_mm
953 :    
954 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
955 :    
956 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
957 :     in the order of unconstrained and constrained parameters.
958 :     (ssclme_gradient): Added the gradients (not yet correct for
959 :     multidimensional, unconstrained case).
960 :    
961 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
962 :    
963 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
964 :    
965 :     * src/Makefile.win: Remove unneeded ranlib call
966 :    
967 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
968 :    
969 :     * DESCRIPTION (Version): New release
970 :    
971 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
972 :    
973 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
974 :    
975 :     * src/triplet_to_col.c: Create triplet_to_col as a native
976 : maechler 658 function, not the version from umfpack. There were problems with
977 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
978 :     only one umfpack routine being used so I moved it here.
979 :    
980 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
981 :    
982 :     * src/ssclme.c (ssclme_variances): New function.
983 :    
984 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
985 :    
986 :     * src/ssclme.c (ssclme_fitted): Added function.
987 :    
988 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
989 :    
990 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
991 :     store the dimnames in the XtX and bVar slots
992 :     (ssclme_update_mm): Change the dimensions of the bVar slot
993 :     components and the returned value from ssclme_ranef.
994 :    
995 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
996 :    
997 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
998 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
999 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1000 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1001 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1002 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1003 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1004 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1005 :     Moved the pdMat classes from the lme4 package.
1006 :    
1007 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1008 :    
1009 :     * man/ssclme-class.Rd: Update definition and documentation of the
1010 :     ssclme class to include the DIsqrt slot.
1011 :    
1012 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1013 :     (much faster using dsyrk, a level 3 BLAS routine).
1014 :    
1015 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1016 :    
1017 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1018 :    
1019 :     * tests/ssclme.R: Modify the test to account for the permutation
1020 :     of the levels of the grouping factors.
1021 :    
1022 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1023 :    
1024 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1025 :     directly into the ssclme class definition.
1026 :    
1027 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1028 :    
1029 :     * DESCRIPTION (Date): New release
1030 :    
1031 :     * man/ssclme-class.Rd: new file.
1032 :    
1033 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1034 :     works and it's fast!
1035 :    
1036 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1037 :    
1038 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1039 :    
1040 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1041 :    
1042 :     * DESCRIPTION (Date): New release
1043 :    
1044 :     * NAMESPACE: Don't export ssclme.
1045 :    
1046 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1047 :     school data.
1048 :    
1049 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1050 :    
1051 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1052 :     keep track of the fixed-effects and the response. Counts also
1053 :     gets an extra element, which is always one.
1054 :    
1055 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1056 :    
1057 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1058 :    
1059 :     * src/cscMatrix.c (csc_transpose): new function
1060 :    
1061 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1062 :     (csc_components_transpose): new function
1063 :    
1064 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1065 :    
1066 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1067 :     triplets
1068 :    
1069 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1070 :    
1071 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1072 :    
1073 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1074 :     and all other .h files in src.
1075 :    
1076 :     * src/Makefile.win: This and other Makefile.win files contributed
1077 :     by Brian Ripley.
1078 :    
1079 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1080 :    
1081 :     * R/syMatrix.R: Added methods for "%*%".
1082 :    
1083 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1084 :     poMatrix object.
1085 :    
1086 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1087 :    
1088 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1089 :    
1090 :     2004-01-25 Douglas Bates <bates@bates2_home>
1091 :    
1092 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1093 :    
1094 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1095 :     of nrow.
1096 :    
1097 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1098 :    
1099 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1100 :     subdirectories.
1101 :    
1102 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1103 :    
1104 :     * src/taucs.h: Accidently referred to global header files
1105 :     instead of local files.
1106 :    
1107 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1108 :    
1109 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1110 :     and methods and replaced all classes with S4 classes.
1111 :    
1112 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1113 :    
1114 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1115 :    
1116 :     * src/R_LapackPP.cc: Change method of calculating determinants
1117 :    
1118 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1119 :    
1120 :     * DESCRIPTION (Version): removed empty data directory as requested
1121 :     by CRAN maintainers. Changed version number and date.
1122 :    
1123 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1124 :    
1125 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1126 :     under Windows.
1127 :    
1128 :     * Added configure.win and src/Makevars.win as requested by Brian
1129 :     Ripley.
1130 :    
1131 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1132 :    
1133 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1134 :     Hornik.
1135 :    
1136 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1137 :    
1138 :     * configure.ac: Replaced configure.in with configure.ac
1139 :     contributed by Kurt Hornik.
1140 :    
1141 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1142 :     version for R-1.5.0
1143 :    
1144 : maechler 512
1145 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1146 :    
1147 :     * man/eigen.Rd: Removed the .Alias in the example

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