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Annotation of /pkg/ChangeLog

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Revision 1398 - (view) (download)

1 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
2 :    
3 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
4 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
5 :     and qr.fitted.
6 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
7 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
8 :    
9 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
10 :    
11 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
12 :     the base version has no "..." argument.
13 :    
14 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
15 :    
16 :     * R/Matrix.R: define and
17 :     * NAMESPACE: export as.numeric() and as.logical() methods.
18 :     Let's hope these do not badly slow down something...
19 :     Finally export the zapsmall() method.
20 :    
21 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
22 :    
23 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
24 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
25 :     * src/dtCMatrix.c :Remove code that is no longer used
26 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
27 :    
28 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
29 :    
30 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
31 :     Csparse_to_logical and Csparse_symmetric_to_general.
32 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
33 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
34 : bates 1373
35 :     2006-08-14 Douglas Bates <bates@R-project.org>
36 :    
37 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
38 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
39 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
40 :     possible.
41 :    
42 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
43 :    
44 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
45 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
46 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
47 :     generalize conversions between TsparseMatrix, CsparseMatrix,
48 :     denseMatrix and matrix. Preserve triangularity property and
49 :     propagate Dimnames in the easy cases.
50 :    
51 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
52 :    
53 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
54 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
55 :     before S4SXP but for the wrong reasons.
56 :    
57 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
58 :    
59 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
60 :     Later modified to return the upper triangle only.
61 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
62 : maechler 1389
63 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
64 :    
65 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
66 :     R-level conversion to a sparse symmetric class.
67 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
68 :     Remove conversion to sparse symmetric classes (now done in C code).
69 :    
70 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
73 :     * man/band.Rd: adapt the \dontshow{} unit test.
74 :    
75 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
76 :    
77 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
78 :    
79 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
80 :    
81 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
82 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
83 :    
84 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
85 :     * R/Tsparse.R (tril, triu, band): methods
86 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
87 :     * man/band.Rd: ditto
88 : maechler 1349
89 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
90 :    
91 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
92 :     to be up-to-date automatically.
93 :    
94 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
95 :    
96 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
97 :    
98 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
99 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
100 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
101 :     such that the S4 objects are always created by the current version
102 :     of R and 'Matrix' class definitions.
103 :    
104 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
105 :    
106 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
107 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
108 : bates 1342 boundary and test cases.
109 :    
110 :     * src/lmer.c (mer_postVar): Modified to return the variances that
111 :     are marginal to the fixed effects, not conditional on them (which
112 :     is what the bVar slot contents represent).
113 :    
114 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
115 :    
116 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
117 :     function which calls the C function mer_hat_trace2.
118 : maechler 1346
119 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
120 :     producing a caterpillar plot.
121 : bates 1338
122 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
123 :    
124 :     * NAMESPACE: change "correlation" to "corMatrix"
125 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
126 : bates 1352 * R/dpoMatrix.R: ditto
127 :     * R/lmer.R: ditto
128 : maechler 1335
129 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
130 :    
131 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
132 :     RZXinv slot's contents into a separate internal function that can
133 :     be used in mer_hat_trace.
134 :    
135 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
136 :    
137 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
138 :     via new smart
139 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
140 :     utility functions.
141 :    
142 :    
143 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
144 :    
145 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
146 :     matrices when appropriate; band() even symmetric ones.
147 :     (replCmat): extend to potentially all "CsparseMatrix"
148 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
149 :     allow subassignment for special sparse matrices.
150 :    
151 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
152 :    
153 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
154 :     argument; in glmer_*(): print only if(verbose).
155 :    
156 :     speed-optimize a few places by moving REAL(.) out of loops.
157 :    
158 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
159 :    
160 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
161 :    
162 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
163 :     since that wrongly triggers also for M[ logi , ]
164 :    
165 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
166 :     a symmetric matrix that results in a non-symmetric one.
167 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
168 :    
169 :     * R/dMatrix.R: make round(M) work as round(M, 0)
170 :    
171 :     * R/dgTMatrix.R (image): coordinate system and axis now use
172 :     1-based indices, not 0-based ones.
173 :    
174 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
175 :     * tests/indexing.R: test it.
176 :    
177 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
178 :     * man/isSymmetric-methods.Rd: and document it.
179 :    
180 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
181 :     * man/SparseM-conv.Rd: docu them
182 :    
183 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
184 :     for 'SparseM' conversions
185 :    
186 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
187 :    
188 :     * R/Matrix.R (head): added head() and tail() methods.
189 :    
190 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
191 :    
192 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
193 :    
194 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
195 :    
196 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
197 :     add check for correct printing of symmetric sparse matrices.
198 :    
199 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
200 :     for sparse symmetric matrices.
201 :    
202 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
203 :     diagonal twice.
204 :    
205 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
206 :    
207 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
208 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
209 : bates 1316
210 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
211 :    
212 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
213 :    
214 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
215 :    
216 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
217 :    
218 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
219 :     * R/lgCMatrix.R (diag): for new method
220 :    
221 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
222 :     ==> construction of illegal "*gTMatrix" via new() should
223 :     now be much less easy:
224 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
225 :    
226 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
227 :     directly.
228 :     * man/Matrix.Rd: documents it.
229 :    
230 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
231 :    
232 :     * src/pedigree.c (pedigree_inbreeding): Correction in
233 :     initialization. This function is not currently being used and is
234 :     not fully tested.
235 :    
236 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
237 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
238 :     objects. Modified validity check on pedigree objects to account
239 :     for nonparallel patterns of missingness of parents.
240 : bates 1311
241 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
242 :     class.
243 : maechler 1315
244 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
245 :    
246 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
247 :    
248 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
249 :    
250 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
251 :    
252 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
253 :     the output from mcmcsamp.
254 :    
255 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
256 :    
257 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
258 :     of the hat matrix.
259 : bates 1298
260 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
261 :    
262 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
263 :     classes.
264 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
265 : maechler 1295
266 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
267 :    
268 :     * R/dgTMatrix.R (colSums): etc. All four of
269 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
270 :     all "Matrices".
271 :    
272 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
273 :    
274 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
275 :     background grid to the qqmath plot of ranef.lmer.
276 :    
277 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
278 : bates 1284
279 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
280 :     grouping factors to be specified in the formula as (1|foo/bar).
281 :    
282 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
283 :    
284 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
285 :     !is.language to resolve the bug reported by Jacob Wegelin.
286 :    
287 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
288 :     code to evaluate inbreeding coefficients without calculating T,
289 :     based on code in Sargolzaei and Iwaisaki's paper.
290 :    
291 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
292 :    
293 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
294 :     generic and mer methods for isNested and denomDF. This denomDF was
295 :     an attempt to emulate that in lme but I don't think that makes
296 :     sense. Use the trace of the hat matrix instead.
297 :    
298 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
299 :    
300 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
301 :     the C code depending on a slot structure that's no longer valid.
302 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
303 : maechler 1271
304 :    
305 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
306 :    
307 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
308 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
309 :     and added a general band extractor.
310 :    
311 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
312 :    
313 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
314 :     allowable range with NAs. Added a corresponding check in the
315 :     validity check for the pedigree class.
316 :    
317 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
318 :     crossprod methods now inherits from symmetricMatrix.
319 :    
320 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
321 :    
322 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
323 :     generics lowerTriMatrix and upperTriMatrix along with methods for
324 :     the Csparse virtual class. Also added a C function Csparse_band
325 :     that implements these methods by calling cholmod_band.
326 :    
327 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
328 :    
329 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
330 :     erased when it was NULL. This led to invalid subselections!
331 :    
332 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
333 :    
334 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
335 :     in method for "t" so as not to lose the unit diagonal property.
336 :    
337 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
338 :    
339 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
340 :     and methods. This is now an option to the ranef method for the
341 :     mer class.
342 :    
343 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
344 :     compressed column-oriented matrix. Minor formatting cleanup.
345 :    
346 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
347 :     objects.
348 :    
349 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
350 :    
351 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
352 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
353 :    
354 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
355 :    
356 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
357 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
358 :    
359 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
360 :     for the dtCMatrix class.
361 : maechler 1253
362 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
363 :    
364 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
365 :     and methods for it.
366 :    
367 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
368 :    
369 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
370 :     arguments, such that M %*% 1:6 now works
371 :     * Tests/matprod.R: test the above
372 :    
373 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
374 : bates 1243
375 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
376 :     the ranef.lmer class.
377 :    
378 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
379 :     methods to extract the posterior variances from the bVar slot.
380 :    
381 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
382 :    
383 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
384 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
385 :    
386 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
387 :     * tests/simple: (extended)
388 :    
389 :     * R/sparseMatrix.R (isTriangular): now using much improved
390 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
391 :    
392 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
393 :    
394 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
395 :     (problem report from Franklin Parlamis). This should be done
396 : maechler 1238 generally.
397 : bates 1236
398 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
399 :    
400 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
401 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
402 :     update the plot methods.
403 :    
404 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
405 :    
406 :     * R/lmer.R (resid and ranef methods): Added methods for the
407 :     "residuals" and "resid" generic but only for linear mixed model
408 :     fits. Changed the ranef method to return a list of data frames so
409 :     that the plot methods now work.
410 :    
411 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
412 :    
413 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
414 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
415 :    
416 :     * DESCRIPTION (Date): New release
417 :    
418 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
419 :    
420 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
421 :    
422 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
423 :     * man/KNex.Rd: and other help files
424 :     * tests/*.R: several ones needed adaption
425 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
426 : maechler 1228
427 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
430 :    
431 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
432 :    
433 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
434 :    
435 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
436 :    
437 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
438 :    
439 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
440 :    
441 :     * R/dMatrix.R: enable things like M [ M < 10 ]
442 :     * R/dgeMatrix.R: implement it
443 :    
444 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
445 :    
446 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
447 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
448 :     * R/lmer.R (show): now works with summary()
449 :    
450 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
451 :    
452 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
453 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
454 :     support the above
455 :    
456 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
457 :    
458 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
459 :     Use glmFit$prior.weights for weights in a glmm.
460 :     Allow an option usePQL = FALSE to skip the PQL steps for the
461 :     Laplace method (and, in time, the AGQ method).
462 :    
463 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
464 :     into a separate function internal_mer_Xfactor to be able to call
465 :     it from internal_bhat.
466 :    
467 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
468 :    
469 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
470 :     testing; now again of all actual classes.
471 :    
472 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
473 :     use macros and define make_d_matrix_* and make_i_matrix_*
474 :     where _i_ is for the ldense routines:
475 :    
476 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
477 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
478 :    
479 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
480 :    
481 :    
482 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
483 :    
484 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
485 :     many different kinds of matrices.
486 :     * R/*.R: quite a few new methods were needed for R CMD check with
487 :     new Matrix(). Very good for users playing around.
488 :    
489 :    
490 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * src/dgeMatrix.c (dMatrix_validate): new
493 :     * src/Mutils.c (dense_nonpacked_validate): new
494 :    
495 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
496 :    
497 :    
498 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
499 :    
500 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
501 :    
502 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
503 : bates 1119
504 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
505 :    
506 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
507 :     segfault in cases with multiple non-nested grouping factors.
508 :    
509 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
510 :    
511 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
512 :     (Depends): also on 'utils'
513 :    
514 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
515 :     * R/diagMatrix.R (Diagonal): constructor and methods for
516 :     diagonal matrices
517 :    
518 :     * R/ltTMatrix.R: new "minimal methods"
519 :    
520 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
521 :    
522 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
523 :     all methods (and help files).
524 :    
525 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
526 :    
527 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
528 :     for case (dimn. op no_dimn.)
529 :    
530 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
531 :    
532 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
533 : maechler 1084
534 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
535 :    
536 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
537 :     by Julian Faraway.
538 :    
539 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * R/Auxiliaries.R (try_as): new utility
542 :     * R/sparseMatrix.R: use try_as() in coercion to original class
543 :    
544 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
545 :    
546 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
547 :    
548 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
549 :    
550 :     * R/Auxiliaries.R (dimNamesCheck): added
551 :    
552 :     * R/Matrix.R (as.array), (as.vector): new
553 :    
554 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
555 :    
556 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
557 : maechler 956 default.
558 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
559 :     "pMatrix" now contains "sparseMatrix"
560 : maechler 954
561 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
562 :    
563 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
564 :    
565 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
566 :    
567 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
568 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
569 :    
570 :     * R/dspMatrix.R: typo in "t" method
571 :    
572 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
573 :    
574 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
575 :     * R/Tsparse.R: instead of R/gTMatrix.R
576 :     * R/Csparse.R: new
577 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
578 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
579 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
580 :     via cholmod
581 :    
582 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
583 :    
584 :     * R/Auxiliaries.R (non0ind): new function using new C code
585 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
586 :    
587 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
588 :    
589 :     * src/chm_common.h: header file required by all C sources that
590 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
591 : bates 917 called 'c' whose address is passed as the last argument to
592 :     (virtually) every CHOLMOD function.
593 :    
594 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
595 :    
596 :     * src/init.c: initialize and finalize the cholmod_common structure.
597 :    
598 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
599 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
600 :    
601 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
602 :    
603 :     * inst/test-tools.R: new file collecting the utility functions used
604 :     in ./tests/*.R
605 :    
606 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
607 :     * R/Matrix.R (cbind2): methods for NULL and missing
608 :    
609 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
610 :    
611 :     * R/AllClass.R: new "index" class for "[" and "[<-":
612 :     First cut at "symmetricMatrix" and "triangularMatrix"
613 :     * R/gTMatrix.R (.ind.prep): new function;
614 : maechler 1174 Logical and character indexing now work too.
615 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
616 :     * tests/indexing.R: new, including *.Rout.save
617 :     * tests/dgTMatrix.R: new
618 :    
619 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
620 :    
621 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
622 :     indicator pos not being updated. Also enforced upper triangular
623 :     for symmetric case. Need to coerce edges component of elements of
624 :     edge list - grr! (Why don't they define their classes cleanly?)
625 :    
626 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
627 :    
628 :     * R/Matrix.R: added first "[<-" methods; not yet functional
629 : bates 1352 * R/denseMatrix.R: ditto
630 : maechler 871 * man/Subassign-methods.Rd: new help file for these
631 :    
632 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
633 :    
634 :     * DESCRIPTION (Version): 0.98-6
635 :    
636 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
637 :     matrices.
638 :    
639 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
640 :    
641 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
642 :     as( <logical>, "matrix")
643 :    
644 :     * R/pMatrix.R: coercion to "lgTMatrix"
645 :    
646 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
647 :     * man/gTMatrix-class.Rd:
648 :     * General slight re-organization of where "[" methods are defined.
649 :     more to come.
650 :    
651 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
652 : maechler 868
653 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
654 : maechler 871
655 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
656 :     * .....
657 :    
658 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
659 :    
660 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
661 :     or glmer objects.
662 :    
663 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
664 :    
665 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
666 :    
667 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
668 :    
669 :     * R/HBMM.R: finish re-writing R-only code.
670 :    
671 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
672 :    
673 :     * man/externalFormats.Rd: move documentation for writeHB and
674 :     writeMM here.
675 :    
676 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
677 :     (suggested by Paul Roecker).
678 :    
679 :     * tests/validObj.R (assertError): Comment out test that is failing
680 :     after recent changes in r-devel.
681 :    
682 : maechler 860
683 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
684 :    
685 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
686 :     * man/denseMatrix-class.Rd
687 :     * NAMESPACE: export it, and also export
688 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
689 :    
690 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
691 :    
692 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
693 :    
694 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
695 :     matrix_solve code (which was really, really wrong).
696 :    
697 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
698 : maechler 834
699 :     * DESCRIPTION (Version): 0.98-2
700 :    
701 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
702 :    
703 :     * R/lmer.R (abbrvNms): new
704 :     * R/lmer.R (mcmcsamp): allow transformed parameters
705 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
706 :     for the Harwell-Boeing and the MatrixMarket formats.
707 : maechler 834
708 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
709 :    
710 :     * man/dtrMatrix-class.Rd: add examples
711 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
712 : maechler 834
713 :     * TODO: note the dtpMatrix (docu) bug
714 :    
715 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
716 :     in order to ensure that new as.matrix() is used by old functions,
717 :     e.g., svd(), qr(), eigen(), dist(),..;
718 :     apply(), also matplot() or pairs().
719 :    
720 :    
721 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
722 :    
723 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
724 :     add comments about 'control' / lmerControl() arguments
725 :    
726 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
727 : bates 820
728 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
729 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
730 : bates 820
731 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
732 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
733 :    
734 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
735 :     .Call calls that were producing spurious output.
736 :    
737 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
738 : bates 801
739 :     * R/lmer.R (lmer): stored updated variance component estimates in
740 :     mer object for the generalized model. (Bug reported by Renaud
741 :     Lancelot).
742 :    
743 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
744 : bates 794
745 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
746 :     unidimensional case.
747 :    
748 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
749 : maechler 791
750 :     * DESCRIPTION (Version): 0.96-1
751 :    
752 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
753 : maechler 791
754 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
755 : bates 763
756 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
757 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
758 :    
759 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
760 : bates 763
761 :     * src/Makefile.win: Forgot to update this when Makefile changed.
762 :    
763 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
764 : bates 726
765 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
766 :     bug reported by Kurt Hornik and Michael Hahsler.
767 :    
768 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
769 : bates 725
770 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
771 :     logical sparse matrices. These will also be used in the symbolic
772 :     analysis for lmer objects.
773 :    
774 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
775 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
776 : maechler 791
777 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
778 : bates 714
779 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
780 :     colMeans, colSums, rowMeans and rowSums.
781 :    
782 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
783 : bates 692
784 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
785 :     multiplication operation.
786 :    
787 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
788 :     to dgetrs.
789 :    
790 :     * src/init.c: Fix cut-and-paste error in definition of
791 :     dgeMatrix_matrix_solve
792 :    
793 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
794 :    
795 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
796 : bates 692
797 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
798 :    
799 :     * DESCRIPTION: Eliminate import of stats.
800 :    
801 : maechler 791
802 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
803 : bates 692
804 :     * R/AllClass.R : add logical sparse matrix classes
805 :    
806 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
807 :    
808 :     * R/dgTMatrix.R: add "[" method for triplet matrices
809 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
810 :    
811 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
812 : maechler 687
813 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
814 :    
815 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
816 :     * R/sparseMatrix.R: %*%, crossprod()
817 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
818 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
819 :     * src/lmer.c (lmer_fitted): fix thinko
820 :    
821 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
822 :    
823 :     * R/AllClass.R: add two virtual sparse classes ``on top''
824 :    
825 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
826 :    
827 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
828 :     correspondingly fix examples and tests/ since new()
829 :     doesn't work for virtual classes.
830 :    
831 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
832 :    
833 :     * R/Matrix.R (as.matrix): method and one for unname()
834 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
835 :     also run for R 2.1.0; using as.matrix()
836 :    
837 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
838 : maechler 658
839 :     * R/pMatrix.R: "pMatrix" class added
840 :     * ....
841 :    
842 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
843 : bates 645
844 :     * R/dtpMatrix.R: Add unpack method and an example.
845 :    
846 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
847 :     of general symmetric matrices and associated S4 methods.
848 :    
849 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
850 :     +
851 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
852 :    
853 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
854 :     crossprod() and "%*%" methods added; tests, too.
855 :     * tests/matprod.R: new, for testing these
856 :    
857 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
858 : bates 599
859 :     * src/lmer.c (lmer_fitted): Added.
860 :    
861 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
862 : bates 596
863 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
864 :    
865 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
866 : bates 582
867 :     * src/*.c,po/,inst/po: Internationalization and localization of
868 :     the package.
869 :    
870 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
871 :     R_ldl.c file.
872 :    
873 :     * src/flame.[ch]: Removed these source files.
874 : maechler 658
875 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
876 :    
877 :     * src/LU.[ch],src/init.c: absorb in factorizations
878 :    
879 :     * src/Mutils.h: prepare for internationalization
880 :    
881 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
882 :     this file
883 :    
884 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
885 :    
886 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
887 :    
888 :     * R/dtrMatrix.R: fix t() method
889 :    
890 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
891 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
892 : maechler 578 * tests/group-methods.R : and test them.
893 :    
894 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
895 :     border case
896 :    
897 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
898 :    
899 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
900 : maechler 578
901 :     * src/dgBCMatrix.c:
902 :     * src/lmer.c: many changes
903 :     * ...
904 :    
905 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
906 :    
907 :     * R/Matrix.R: add more sophisticated show() method.
908 :    
909 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
910 :    
911 :     * */* : almost complete reorganization of classes.
912 :    
913 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
914 : bates 460
915 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
916 :     for the geMatrix class.
917 :    
918 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
919 : bates 460
920 :     * src/Makefile (clean): Remove *.a and *.so
921 :    
922 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
923 :    
924 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
925 : bates 460
926 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
927 : bates 460 had an effect in cases with more than 2 grouping factors.
928 :    
929 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
930 : bates 415
931 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
932 :    
933 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
934 : bates 410
935 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
936 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
937 :    
938 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
939 : bates 392
940 :     * R/sscMatrix.R: Add determinant methods
941 :    
942 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
943 :     for tripletMatrix to matrix.
944 :    
945 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
946 : bates 388
947 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
948 :     no longer used.
949 :    
950 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
951 :     with dynamic allocation of scratch arrays.
952 :    
953 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
954 :     for multivariate random effects with multiple grouping factors.
955 :     Fixes part but not all of #15.
956 :    
957 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
958 : bates 375
959 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
960 :     scalar grouping factors corrected.
961 :    
962 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
963 : bates 375
964 :     * src/bCrosstab.c: remove diag_update which is no longer used
965 :    
966 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
967 : bates 350
968 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
969 :     .h file can be included.
970 :    
971 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
972 : bates 342
973 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
974 : bates 342 Complete allocation of slots in NEW_OBJECT.
975 :    
976 :     * src/Mutils.h: Moved list of symbols to an include file
977 :    
978 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
979 : bates 342
980 :     * src/geMutils.c (Matrix_init): remove unused function
981 :    
982 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
983 : bates 342
984 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
985 :    
986 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
987 : bates 327
988 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
989 :    
990 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
991 : bates 303
992 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
993 :    
994 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
995 : bates 296
996 :     * src/init.c: Created R_init_Matrix and added registration of C
997 :     routines.
998 :    
999 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1000 : bates 283
1001 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1002 :    
1003 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1004 : bates 229
1005 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1006 :    
1007 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1008 :    
1009 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1010 :    
1011 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1012 :    
1013 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1014 :     ssclme_update_mm
1015 :    
1016 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1017 :    
1018 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1019 :     in the order of unconstrained and constrained parameters.
1020 :     (ssclme_gradient): Added the gradients (not yet correct for
1021 :     multidimensional, unconstrained case).
1022 :    
1023 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1024 :    
1025 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1026 :    
1027 :     * src/Makefile.win: Remove unneeded ranlib call
1028 :    
1029 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1030 :    
1031 :     * DESCRIPTION (Version): New release
1032 :    
1033 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1034 :    
1035 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1036 :    
1037 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1038 : maechler 658 function, not the version from umfpack. There were problems with
1039 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1040 :     only one umfpack routine being used so I moved it here.
1041 :    
1042 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1043 :    
1044 :     * src/ssclme.c (ssclme_variances): New function.
1045 :    
1046 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1047 :    
1048 :     * src/ssclme.c (ssclme_fitted): Added function.
1049 :    
1050 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1051 :    
1052 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1053 :     store the dimnames in the XtX and bVar slots
1054 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1055 :     components and the returned value from ssclme_ranef.
1056 :    
1057 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1058 :    
1059 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1060 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1061 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1062 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1063 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1064 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1065 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1066 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1067 :     Moved the pdMat classes from the lme4 package.
1068 :    
1069 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1070 :    
1071 :     * man/ssclme-class.Rd: Update definition and documentation of the
1072 :     ssclme class to include the DIsqrt slot.
1073 :    
1074 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1075 :     (much faster using dsyrk, a level 3 BLAS routine).
1076 :    
1077 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1078 :    
1079 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1080 :    
1081 :     * tests/ssclme.R: Modify the test to account for the permutation
1082 :     of the levels of the grouping factors.
1083 :    
1084 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1085 :    
1086 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1087 :     directly into the ssclme class definition.
1088 :    
1089 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1090 :    
1091 :     * DESCRIPTION (Date): New release
1092 :    
1093 :     * man/ssclme-class.Rd: new file.
1094 :    
1095 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1096 :     works and it's fast!
1097 :    
1098 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1099 :    
1100 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1101 :    
1102 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1103 :    
1104 :     * DESCRIPTION (Date): New release
1105 :    
1106 :     * NAMESPACE: Don't export ssclme.
1107 :    
1108 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1109 :     school data.
1110 :    
1111 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1112 :    
1113 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1114 :     keep track of the fixed-effects and the response. Counts also
1115 :     gets an extra element, which is always one.
1116 :    
1117 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1118 :    
1119 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1120 :    
1121 :     * src/cscMatrix.c (csc_transpose): new function
1122 :    
1123 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1124 :     (csc_components_transpose): new function
1125 :    
1126 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1127 :    
1128 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1129 :     triplets
1130 :    
1131 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1132 :    
1133 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1134 :    
1135 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1136 :     and all other .h files in src.
1137 :    
1138 :     * src/Makefile.win: This and other Makefile.win files contributed
1139 :     by Brian Ripley.
1140 :    
1141 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1142 :    
1143 :     * R/syMatrix.R: Added methods for "%*%".
1144 :    
1145 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1146 :     poMatrix object.
1147 :    
1148 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1149 :    
1150 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1151 :    
1152 :     2004-01-25 Douglas Bates <bates@bates2_home>
1153 :    
1154 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1155 :    
1156 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1157 :     of nrow.
1158 :    
1159 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1160 :    
1161 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1162 :     subdirectories.
1163 :    
1164 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1165 :    
1166 :     * src/taucs.h: Accidently referred to global header files
1167 :     instead of local files.
1168 :    
1169 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1170 :    
1171 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1172 :     and methods and replaced all classes with S4 classes.
1173 :    
1174 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1175 :    
1176 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1177 :    
1178 :     * src/R_LapackPP.cc: Change method of calculating determinants
1179 :    
1180 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1181 :    
1182 :     * DESCRIPTION (Version): removed empty data directory as requested
1183 :     by CRAN maintainers. Changed version number and date.
1184 :    
1185 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1186 :    
1187 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1188 :     under Windows.
1189 :    
1190 :     * Added configure.win and src/Makevars.win as requested by Brian
1191 :     Ripley.
1192 :    
1193 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1194 :    
1195 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1196 :     Hornik.
1197 :    
1198 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1199 :    
1200 :     * configure.ac: Replaced configure.in with configure.ac
1201 :     contributed by Kurt Hornik.
1202 :    
1203 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1204 :     version for R-1.5.0
1205 :    
1206 : maechler 512
1207 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1208 :    
1209 :     * man/eigen.Rd: Removed the .Alias in the example

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