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Annotation of /pkg/ChangeLog

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

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