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Annotation of /pkg/ChangeLog

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1 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
2 :    
3 :     * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
4 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
5 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
6 :     possible.
7 :    
8 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
9 :    
10 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
11 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
12 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
13 :     generalize conversions between TsparseMatrix, CsparseMatrix,
14 :     denseMatrix and matrix. Preserve triangularity property and
15 :     propagate Dimnames in the easy cases.
16 :    
17 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
18 :    
19 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
20 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
21 :     before S4SXP but for the wrong reasons.
22 :    
23 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
24 :    
25 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
26 :     Later modified to return the upper triangle only.
27 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
28 :    
29 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
30 :    
31 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
32 :     R-level conversion to a sparse symmetric class.
33 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
34 :     Remove conversion to sparse symmetric classes (now done in C code).
35 :    
36 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
37 :    
38 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
39 :     * man/band.Rd: adapt the \dontshow{} unit test.
40 :    
41 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
42 :    
43 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
44 :    
45 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
46 :    
47 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
48 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
49 :    
50 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
51 :     * R/Tsparse.R (tril, triu, band): methods
52 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
53 :     * man/band.Rd: ditto
54 : maechler 1349
55 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
56 :    
57 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
58 :     to be up-to-date automatically.
59 :    
60 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
61 :    
62 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
63 :    
64 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
65 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
66 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
67 :     such that the S4 objects are always created by the current version
68 :     of R and 'Matrix' class definitions.
69 :    
70 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
71 :    
72 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
73 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
74 : bates 1342 boundary and test cases.
75 :    
76 :     * src/lmer.c (mer_postVar): Modified to return the variances that
77 :     are marginal to the fixed effects, not conditional on them (which
78 :     is what the bVar slot contents represent).
79 :    
80 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
81 :    
82 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
83 :     function which calls the C function mer_hat_trace2.
84 : maechler 1346
85 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
86 :     producing a caterpillar plot.
87 : bates 1338
88 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
89 :    
90 :     * NAMESPACE: change "correlation" to "corMatrix"
91 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
92 : bates 1352 * R/dpoMatrix.R: ditto
93 :     * R/lmer.R: ditto
94 : maechler 1335
95 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
96 :    
97 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
98 :     RZXinv slot's contents into a separate internal function that can
99 :     be used in mer_hat_trace.
100 :    
101 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
104 :     via new smart
105 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
106 :     utility functions.
107 :    
108 :    
109 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
110 :    
111 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
112 :     matrices when appropriate; band() even symmetric ones.
113 :     (replCmat): extend to potentially all "CsparseMatrix"
114 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
115 :     allow subassignment for special sparse matrices.
116 :    
117 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
118 :    
119 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
120 :     argument; in glmer_*(): print only if(verbose).
121 :    
122 :     speed-optimize a few places by moving REAL(.) out of loops.
123 :    
124 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
125 :    
126 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
127 :    
128 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
129 :     since that wrongly triggers also for M[ logi , ]
130 :    
131 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
132 :     a symmetric matrix that results in a non-symmetric one.
133 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
134 :    
135 :     * R/dMatrix.R: make round(M) work as round(M, 0)
136 :    
137 :     * R/dgTMatrix.R (image): coordinate system and axis now use
138 :     1-based indices, not 0-based ones.
139 :    
140 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
141 :     * tests/indexing.R: test it.
142 :    
143 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
144 :     * man/isSymmetric-methods.Rd: and document it.
145 :    
146 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
147 :     * man/SparseM-conv.Rd: docu them
148 :    
149 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
150 :     for 'SparseM' conversions
151 :    
152 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
153 :    
154 :     * R/Matrix.R (head): added head() and tail() methods.
155 :    
156 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
157 :    
158 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
159 :    
160 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
161 :    
162 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
163 :     add check for correct printing of symmetric sparse matrices.
164 :    
165 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
166 :     for sparse symmetric matrices.
167 :    
168 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
169 :     diagonal twice.
170 :    
171 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
172 :    
173 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
174 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
175 : bates 1316
176 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
177 :    
178 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
179 :    
180 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
181 :    
182 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
183 :    
184 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
185 :     * R/lgCMatrix.R (diag): for new method
186 :    
187 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
188 :     ==> construction of illegal "*gTMatrix" via new() should
189 :     now be much less easy:
190 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
191 :    
192 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
193 :     directly.
194 :     * man/Matrix.Rd: documents it.
195 :    
196 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
197 :    
198 :     * src/pedigree.c (pedigree_inbreeding): Correction in
199 :     initialization. This function is not currently being used and is
200 :     not fully tested.
201 :    
202 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
203 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
204 :     objects. Modified validity check on pedigree objects to account
205 :     for nonparallel patterns of missingness of parents.
206 : bates 1311
207 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
208 :     class.
209 : maechler 1315
210 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
211 :    
212 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
213 :    
214 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
215 :    
216 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
217 :    
218 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
219 :     the output from mcmcsamp.
220 :    
221 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
222 :    
223 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
224 :     of the hat matrix.
225 : bates 1298
226 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
227 :    
228 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
229 :     classes.
230 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
231 : maechler 1295
232 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
233 :    
234 :     * R/dgTMatrix.R (colSums): etc. All four of
235 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
236 :     all "Matrices".
237 :    
238 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
239 :    
240 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
241 :     background grid to the qqmath plot of ranef.lmer.
242 :    
243 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
244 : bates 1284
245 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
246 :     grouping factors to be specified in the formula as (1|foo/bar).
247 :    
248 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
249 :    
250 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
251 :     !is.language to resolve the bug reported by Jacob Wegelin.
252 :    
253 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
254 :     code to evaluate inbreeding coefficients without calculating T,
255 :     based on code in Sargolzaei and Iwaisaki's paper.
256 :    
257 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
258 :    
259 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
260 :     generic and mer methods for isNested and denomDF. This denomDF was
261 :     an attempt to emulate that in lme but I don't think that makes
262 :     sense. Use the trace of the hat matrix instead.
263 :    
264 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
265 :    
266 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
267 :     the C code depending on a slot structure that's no longer valid.
268 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
269 : maechler 1271
270 :    
271 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
272 :    
273 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
274 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
275 :     and added a general band extractor.
276 :    
277 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
278 :    
279 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
280 :     allowable range with NAs. Added a corresponding check in the
281 :     validity check for the pedigree class.
282 :    
283 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
284 :     crossprod methods now inherits from symmetricMatrix.
285 :    
286 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
287 :    
288 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
289 :     generics lowerTriMatrix and upperTriMatrix along with methods for
290 :     the Csparse virtual class. Also added a C function Csparse_band
291 :     that implements these methods by calling cholmod_band.
292 :    
293 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
294 :    
295 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
296 :     erased when it was NULL. This led to invalid subselections!
297 :    
298 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
299 :    
300 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
301 :     in method for "t" so as not to lose the unit diagonal property.
302 :    
303 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
304 :    
305 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
306 :     and methods. This is now an option to the ranef method for the
307 :     mer class.
308 :    
309 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
310 :     compressed column-oriented matrix. Minor formatting cleanup.
311 :    
312 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
313 :     objects.
314 :    
315 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
316 :    
317 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
318 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
319 :    
320 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
321 :    
322 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
323 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
324 :    
325 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
326 :     for the dtCMatrix class.
327 : maechler 1253
328 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
329 :    
330 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
331 :     and methods for it.
332 :    
333 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
334 :    
335 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
336 :     arguments, such that M %*% 1:6 now works
337 :     * Tests/matprod.R: test the above
338 :    
339 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
340 : bates 1243
341 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
342 :     the ranef.lmer class.
343 :    
344 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
345 :     methods to extract the posterior variances from the bVar slot.
346 :    
347 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
348 :    
349 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
350 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
351 :    
352 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
353 :     * tests/simple: (extended)
354 :    
355 :     * R/sparseMatrix.R (isTriangular): now using much improved
356 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
357 :    
358 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
359 :    
360 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
361 :     (problem report from Franklin Parlamis). This should be done
362 : maechler 1238 generally.
363 : bates 1236
364 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
365 :    
366 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
367 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
368 :     update the plot methods.
369 :    
370 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
371 :    
372 :     * R/lmer.R (resid and ranef methods): Added methods for the
373 :     "residuals" and "resid" generic but only for linear mixed model
374 :     fits. Changed the ranef method to return a list of data frames so
375 :     that the plot methods now work.
376 :    
377 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
378 :    
379 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
380 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
381 :    
382 :     * DESCRIPTION (Date): New release
383 :    
384 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
385 :    
386 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
387 :    
388 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
389 :     * man/KNex.Rd: and other help files
390 :     * tests/*.R: several ones needed adaption
391 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
392 : maechler 1228
393 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
394 :    
395 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
396 :    
397 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
398 :    
399 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
402 :    
403 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
404 :    
405 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
406 :    
407 :     * R/dMatrix.R: enable things like M [ M < 10 ]
408 :     * R/dgeMatrix.R: implement it
409 :    
410 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
411 :    
412 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
413 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
414 :     * R/lmer.R (show): now works with summary()
415 :    
416 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
417 :    
418 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
419 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
420 :     support the above
421 :    
422 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
423 :    
424 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
425 :     Use glmFit$prior.weights for weights in a glmm.
426 :     Allow an option usePQL = FALSE to skip the PQL steps for the
427 :     Laplace method (and, in time, the AGQ method).
428 :    
429 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
430 :     into a separate function internal_mer_Xfactor to be able to call
431 :     it from internal_bhat.
432 :    
433 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
434 :    
435 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
436 :     testing; now again of all actual classes.
437 :    
438 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
439 :     use macros and define make_d_matrix_* and make_i_matrix_*
440 :     where _i_ is for the ldense routines:
441 :    
442 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
443 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
444 :    
445 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
446 :    
447 :    
448 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
449 :    
450 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
451 :     many different kinds of matrices.
452 :     * R/*.R: quite a few new methods were needed for R CMD check with
453 :     new Matrix(). Very good for users playing around.
454 :    
455 :    
456 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
457 :    
458 :     * src/dgeMatrix.c (dMatrix_validate): new
459 :     * src/Mutils.c (dense_nonpacked_validate): new
460 :    
461 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
462 :    
463 :    
464 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
465 :    
466 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
467 :    
468 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
469 : bates 1119
470 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
471 :    
472 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
473 :     segfault in cases with multiple non-nested grouping factors.
474 :    
475 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
476 :    
477 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
478 :     (Depends): also on 'utils'
479 :    
480 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
481 :     * R/diagMatrix.R (Diagonal): constructor and methods for
482 :     diagonal matrices
483 :    
484 :     * R/ltTMatrix.R: new "minimal methods"
485 :    
486 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
487 :    
488 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
489 :     all methods (and help files).
490 :    
491 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
492 :    
493 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
494 :     for case (dimn. op no_dimn.)
495 :    
496 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
497 :    
498 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
499 : maechler 1084
500 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
501 :    
502 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
503 :     by Julian Faraway.
504 :    
505 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
506 :    
507 :     * R/Auxiliaries.R (try_as): new utility
508 :     * R/sparseMatrix.R: use try_as() in coercion to original class
509 :    
510 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
511 :    
512 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
513 :    
514 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
515 :    
516 :     * R/Auxiliaries.R (dimNamesCheck): added
517 :    
518 :     * R/Matrix.R (as.array), (as.vector): new
519 :    
520 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
521 :    
522 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
523 : maechler 956 default.
524 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
525 :     "pMatrix" now contains "sparseMatrix"
526 : maechler 954
527 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
530 :    
531 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
532 :    
533 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
534 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
535 :    
536 :     * R/dspMatrix.R: typo in "t" method
537 :    
538 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
539 :    
540 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
541 :     * R/Tsparse.R: instead of R/gTMatrix.R
542 :     * R/Csparse.R: new
543 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
544 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
545 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
546 :     via cholmod
547 :    
548 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
549 :    
550 :     * R/Auxiliaries.R (non0ind): new function using new C code
551 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
552 :    
553 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
554 :    
555 :     * src/chm_common.h: header file required by all C sources that
556 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
557 : bates 917 called 'c' whose address is passed as the last argument to
558 :     (virtually) every CHOLMOD function.
559 :    
560 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
561 :    
562 :     * src/init.c: initialize and finalize the cholmod_common structure.
563 :    
564 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
565 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
566 :    
567 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
568 :    
569 :     * inst/test-tools.R: new file collecting the utility functions used
570 :     in ./tests/*.R
571 :    
572 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
573 :     * R/Matrix.R (cbind2): methods for NULL and missing
574 :    
575 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
576 :    
577 :     * R/AllClass.R: new "index" class for "[" and "[<-":
578 :     First cut at "symmetricMatrix" and "triangularMatrix"
579 :     * R/gTMatrix.R (.ind.prep): new function;
580 : maechler 1174 Logical and character indexing now work too.
581 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
582 :     * tests/indexing.R: new, including *.Rout.save
583 :     * tests/dgTMatrix.R: new
584 :    
585 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
586 :    
587 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
588 :     indicator pos not being updated. Also enforced upper triangular
589 :     for symmetric case. Need to coerce edges component of elements of
590 :     edge list - grr! (Why don't they define their classes cleanly?)
591 :    
592 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
593 :    
594 :     * R/Matrix.R: added first "[<-" methods; not yet functional
595 : bates 1352 * R/denseMatrix.R: ditto
596 : maechler 871 * man/Subassign-methods.Rd: new help file for these
597 :    
598 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
599 :    
600 :     * DESCRIPTION (Version): 0.98-6
601 :    
602 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
603 :     matrices.
604 :    
605 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
606 :    
607 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
608 :     as( <logical>, "matrix")
609 :    
610 :     * R/pMatrix.R: coercion to "lgTMatrix"
611 :    
612 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
613 :     * man/gTMatrix-class.Rd:
614 :     * General slight re-organization of where "[" methods are defined.
615 :     more to come.
616 :    
617 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
618 : maechler 868
619 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
620 : maechler 871
621 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
622 :     * .....
623 :    
624 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
625 :    
626 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
627 :     or glmer objects.
628 :    
629 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
630 :    
631 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
632 :    
633 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
634 :    
635 :     * R/HBMM.R: finish re-writing R-only code.
636 :    
637 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
638 :    
639 :     * man/externalFormats.Rd: move documentation for writeHB and
640 :     writeMM here.
641 :    
642 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
643 :     (suggested by Paul Roecker).
644 :    
645 :     * tests/validObj.R (assertError): Comment out test that is failing
646 :     after recent changes in r-devel.
647 :    
648 : maechler 860
649 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
650 :    
651 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
652 :     * man/denseMatrix-class.Rd
653 :     * NAMESPACE: export it, and also export
654 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
655 :    
656 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
657 :    
658 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
659 :    
660 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
661 :     matrix_solve code (which was really, really wrong).
662 :    
663 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
664 : maechler 834
665 :     * DESCRIPTION (Version): 0.98-2
666 :    
667 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
668 :    
669 :     * R/lmer.R (abbrvNms): new
670 :     * R/lmer.R (mcmcsamp): allow transformed parameters
671 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
672 :     for the Harwell-Boeing and the MatrixMarket formats.
673 : maechler 834
674 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
675 :    
676 :     * man/dtrMatrix-class.Rd: add examples
677 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
678 : maechler 834
679 :     * TODO: note the dtpMatrix (docu) bug
680 :    
681 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
682 :     in order to ensure that new as.matrix() is used by old functions,
683 :     e.g., svd(), qr(), eigen(), dist(),..;
684 :     apply(), also matplot() or pairs().
685 :    
686 :    
687 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
688 :    
689 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
690 :     add comments about 'control' / lmerControl() arguments
691 :    
692 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
693 : bates 820
694 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
695 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
696 : bates 820
697 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
698 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
699 :    
700 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
701 :     .Call calls that were producing spurious output.
702 :    
703 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
704 : bates 801
705 :     * R/lmer.R (lmer): stored updated variance component estimates in
706 :     mer object for the generalized model. (Bug reported by Renaud
707 :     Lancelot).
708 :    
709 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
710 : bates 794
711 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
712 :     unidimensional case.
713 :    
714 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
715 : maechler 791
716 :     * DESCRIPTION (Version): 0.96-1
717 :    
718 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
719 : maechler 791
720 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
721 : bates 763
722 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
723 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
724 :    
725 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
726 : bates 763
727 :     * src/Makefile.win: Forgot to update this when Makefile changed.
728 :    
729 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
730 : bates 726
731 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
732 :     bug reported by Kurt Hornik and Michael Hahsler.
733 :    
734 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
735 : bates 725
736 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
737 :     logical sparse matrices. These will also be used in the symbolic
738 :     analysis for lmer objects.
739 :    
740 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
741 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
742 : maechler 791
743 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
744 : bates 714
745 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
746 :     colMeans, colSums, rowMeans and rowSums.
747 :    
748 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
749 : bates 692
750 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
751 :     multiplication operation.
752 :    
753 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
754 :     to dgetrs.
755 :    
756 :     * src/init.c: Fix cut-and-paste error in definition of
757 :     dgeMatrix_matrix_solve
758 :    
759 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
760 :    
761 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
762 : bates 692
763 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
764 :    
765 :     * DESCRIPTION: Eliminate import of stats.
766 :    
767 : maechler 791
768 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
769 : bates 692
770 :     * R/AllClass.R : add logical sparse matrix classes
771 :    
772 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
773 :    
774 :     * R/dgTMatrix.R: add "[" method for triplet matrices
775 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
776 :    
777 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
778 : maechler 687
779 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
780 :    
781 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
782 :     * R/sparseMatrix.R: %*%, crossprod()
783 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
784 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
785 :     * src/lmer.c (lmer_fitted): fix thinko
786 :    
787 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
788 :    
789 :     * R/AllClass.R: add two virtual sparse classes ``on top''
790 :    
791 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
792 :    
793 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
794 :     correspondingly fix examples and tests/ since new()
795 :     doesn't work for virtual classes.
796 :    
797 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
798 :    
799 :     * R/Matrix.R (as.matrix): method and one for unname()
800 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
801 :     also run for R 2.1.0; using as.matrix()
802 :    
803 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
804 : maechler 658
805 :     * R/pMatrix.R: "pMatrix" class added
806 :     * ....
807 :    
808 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
809 : bates 645
810 :     * R/dtpMatrix.R: Add unpack method and an example.
811 :    
812 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
813 :     of general symmetric matrices and associated S4 methods.
814 :    
815 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
816 :     +
817 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
818 :    
819 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
820 :     crossprod() and "%*%" methods added; tests, too.
821 :     * tests/matprod.R: new, for testing these
822 :    
823 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
824 : bates 599
825 :     * src/lmer.c (lmer_fitted): Added.
826 :    
827 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
828 : bates 596
829 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
830 :    
831 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
832 : bates 582
833 :     * src/*.c,po/,inst/po: Internationalization and localization of
834 :     the package.
835 :    
836 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
837 :     R_ldl.c file.
838 :    
839 :     * src/flame.[ch]: Removed these source files.
840 : maechler 658
841 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
842 :    
843 :     * src/LU.[ch],src/init.c: absorb in factorizations
844 :    
845 :     * src/Mutils.h: prepare for internationalization
846 :    
847 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
848 :     this file
849 :    
850 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
851 :    
852 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
853 :    
854 :     * R/dtrMatrix.R: fix t() method
855 :    
856 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
857 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
858 : maechler 578 * tests/group-methods.R : and test them.
859 :    
860 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
861 :     border case
862 :    
863 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
864 :    
865 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
866 : maechler 578
867 :     * src/dgBCMatrix.c:
868 :     * src/lmer.c: many changes
869 :     * ...
870 :    
871 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
872 :    
873 :     * R/Matrix.R: add more sophisticated show() method.
874 :    
875 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
876 :    
877 :     * */* : almost complete reorganization of classes.
878 :    
879 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
880 : bates 460
881 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
882 :     for the geMatrix class.
883 :    
884 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
885 : bates 460
886 :     * src/Makefile (clean): Remove *.a and *.so
887 :    
888 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
889 :    
890 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
891 : bates 460
892 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
893 : bates 460 had an effect in cases with more than 2 grouping factors.
894 :    
895 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
896 : bates 415
897 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
898 :    
899 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
900 : bates 410
901 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
902 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
903 :    
904 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
905 : bates 392
906 :     * R/sscMatrix.R: Add determinant methods
907 :    
908 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
909 :     for tripletMatrix to matrix.
910 :    
911 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
912 : bates 388
913 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
914 :     no longer used.
915 :    
916 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
917 :     with dynamic allocation of scratch arrays.
918 :    
919 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
920 :     for multivariate random effects with multiple grouping factors.
921 :     Fixes part but not all of #15.
922 :    
923 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
924 : bates 375
925 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
926 :     scalar grouping factors corrected.
927 :    
928 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
929 : bates 375
930 :     * src/bCrosstab.c: remove diag_update which is no longer used
931 :    
932 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
933 : bates 350
934 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
935 :     .h file can be included.
936 :    
937 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
938 : bates 342
939 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
940 : bates 342 Complete allocation of slots in NEW_OBJECT.
941 :    
942 :     * src/Mutils.h: Moved list of symbols to an include file
943 :    
944 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
945 : bates 342
946 :     * src/geMutils.c (Matrix_init): remove unused function
947 :    
948 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
949 : bates 342
950 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
951 :    
952 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
953 : bates 327
954 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
955 :    
956 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
957 : bates 303
958 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
959 :    
960 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
961 : bates 296
962 :     * src/init.c: Created R_init_Matrix and added registration of C
963 :     routines.
964 :    
965 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
966 : bates 283
967 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
968 :    
969 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
970 : bates 229
971 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
972 :    
973 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
974 :    
975 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
976 :    
977 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
978 :    
979 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
980 :     ssclme_update_mm
981 :    
982 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
983 :    
984 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
985 :     in the order of unconstrained and constrained parameters.
986 :     (ssclme_gradient): Added the gradients (not yet correct for
987 :     multidimensional, unconstrained case).
988 :    
989 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
990 :    
991 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
992 :    
993 :     * src/Makefile.win: Remove unneeded ranlib call
994 :    
995 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
996 :    
997 :     * DESCRIPTION (Version): New release
998 :    
999 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1000 :    
1001 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1002 :    
1003 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1004 : maechler 658 function, not the version from umfpack. There were problems with
1005 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1006 :     only one umfpack routine being used so I moved it here.
1007 :    
1008 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1009 :    
1010 :     * src/ssclme.c (ssclme_variances): New function.
1011 :    
1012 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1013 :    
1014 :     * src/ssclme.c (ssclme_fitted): Added function.
1015 :    
1016 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1017 :    
1018 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1019 :     store the dimnames in the XtX and bVar slots
1020 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1021 :     components and the returned value from ssclme_ranef.
1022 :    
1023 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1024 :    
1025 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1026 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1027 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1028 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1029 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1030 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1031 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1032 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1033 :     Moved the pdMat classes from the lme4 package.
1034 :    
1035 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1036 :    
1037 :     * man/ssclme-class.Rd: Update definition and documentation of the
1038 :     ssclme class to include the DIsqrt slot.
1039 :    
1040 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1041 :     (much faster using dsyrk, a level 3 BLAS routine).
1042 :    
1043 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1044 :    
1045 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1046 :    
1047 :     * tests/ssclme.R: Modify the test to account for the permutation
1048 :     of the levels of the grouping factors.
1049 :    
1050 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1051 :    
1052 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1053 :     directly into the ssclme class definition.
1054 :    
1055 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1056 :    
1057 :     * DESCRIPTION (Date): New release
1058 :    
1059 :     * man/ssclme-class.Rd: new file.
1060 :    
1061 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1062 :     works and it's fast!
1063 :    
1064 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1065 :    
1066 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1067 :    
1068 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1069 :    
1070 :     * DESCRIPTION (Date): New release
1071 :    
1072 :     * NAMESPACE: Don't export ssclme.
1073 :    
1074 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1075 :     school data.
1076 :    
1077 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1078 :    
1079 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1080 :     keep track of the fixed-effects and the response. Counts also
1081 :     gets an extra element, which is always one.
1082 :    
1083 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1084 :    
1085 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1086 :    
1087 :     * src/cscMatrix.c (csc_transpose): new function
1088 :    
1089 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1090 :     (csc_components_transpose): new function
1091 :    
1092 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1093 :    
1094 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1095 :     triplets
1096 :    
1097 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1098 :    
1099 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1100 :    
1101 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1102 :     and all other .h files in src.
1103 :    
1104 :     * src/Makefile.win: This and other Makefile.win files contributed
1105 :     by Brian Ripley.
1106 :    
1107 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1108 :    
1109 :     * R/syMatrix.R: Added methods for "%*%".
1110 :    
1111 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1112 :     poMatrix object.
1113 :    
1114 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1115 :    
1116 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1117 :    
1118 :     2004-01-25 Douglas Bates <bates@bates2_home>
1119 :    
1120 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1121 :    
1122 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1123 :     of nrow.
1124 :    
1125 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1126 :    
1127 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1128 :     subdirectories.
1129 :    
1130 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1131 :    
1132 :     * src/taucs.h: Accidently referred to global header files
1133 :     instead of local files.
1134 :    
1135 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1136 :    
1137 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1138 :     and methods and replaced all classes with S4 classes.
1139 :    
1140 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1141 :    
1142 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1143 :    
1144 :     * src/R_LapackPP.cc: Change method of calculating determinants
1145 :    
1146 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1147 :    
1148 :     * DESCRIPTION (Version): removed empty data directory as requested
1149 :     by CRAN maintainers. Changed version number and date.
1150 :    
1151 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1152 :    
1153 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1154 :     under Windows.
1155 :    
1156 :     * Added configure.win and src/Makevars.win as requested by Brian
1157 :     Ripley.
1158 :    
1159 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1160 :    
1161 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1162 :     Hornik.
1163 :    
1164 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1165 :    
1166 :     * configure.ac: Replaced configure.in with configure.ac
1167 :     contributed by Kurt Hornik.
1168 :    
1169 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1170 :     version for R-1.5.0
1171 :    
1172 : maechler 512
1173 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1174 :    
1175 :     * man/eigen.Rd: Removed the .Alias in the example

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