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Annotation of /pkg/ChangeLog

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1 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
4 :     * tests/sparseQR.R: Added
5 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
6 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
7 :    
8 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
9 :    
10 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
11 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
12 :     and qr.fitted.
13 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
14 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
15 :    
16 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
17 :    
18 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
19 :     the base version has no "..." argument.
20 :    
21 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
22 :    
23 :     * R/Matrix.R: define and
24 :     * NAMESPACE: export as.numeric() and as.logical() methods.
25 :     Let's hope these do not badly slow down something...
26 :     Finally export the zapsmall() method.
27 :    
28 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
29 :    
30 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
31 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
32 :     * src/dtCMatrix.c :Remove code that is no longer used
33 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
34 :    
35 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
36 :    
37 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
38 :     Csparse_to_logical and Csparse_symmetric_to_general.
39 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
40 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
41 : bates 1373
42 :     2006-08-14 Douglas Bates <bates@R-project.org>
43 :    
44 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
45 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
46 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
47 :     possible.
48 :    
49 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
50 :    
51 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
52 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
53 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
54 :     generalize conversions between TsparseMatrix, CsparseMatrix,
55 :     denseMatrix and matrix. Preserve triangularity property and
56 :     propagate Dimnames in the easy cases.
57 :    
58 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
59 :    
60 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
61 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
62 :     before S4SXP but for the wrong reasons.
63 :    
64 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
65 :    
66 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
67 :     Later modified to return the upper triangle only.
68 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
69 : maechler 1389
70 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
71 :    
72 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
73 :     R-level conversion to a sparse symmetric class.
74 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
75 :     Remove conversion to sparse symmetric classes (now done in C code).
76 :    
77 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
78 :    
79 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
80 :     * man/band.Rd: adapt the \dontshow{} unit test.
81 :    
82 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
85 :    
86 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
87 :    
88 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
89 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
90 :    
91 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
92 :     * R/Tsparse.R (tril, triu, band): methods
93 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
94 :     * man/band.Rd: ditto
95 : maechler 1349
96 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
97 :    
98 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
99 :     to be up-to-date automatically.
100 :    
101 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
104 :    
105 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
106 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
107 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
108 :     such that the S4 objects are always created by the current version
109 :     of R and 'Matrix' class definitions.
110 :    
111 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
112 :    
113 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
114 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
115 : bates 1342 boundary and test cases.
116 :    
117 :     * src/lmer.c (mer_postVar): Modified to return the variances that
118 :     are marginal to the fixed effects, not conditional on them (which
119 :     is what the bVar slot contents represent).
120 :    
121 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
122 :    
123 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
124 :     function which calls the C function mer_hat_trace2.
125 : maechler 1346
126 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
127 :     producing a caterpillar plot.
128 : bates 1338
129 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * NAMESPACE: change "correlation" to "corMatrix"
132 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
133 : bates 1352 * R/dpoMatrix.R: ditto
134 :     * R/lmer.R: ditto
135 : maechler 1335
136 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
137 :    
138 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
139 :     RZXinv slot's contents into a separate internal function that can
140 :     be used in mer_hat_trace.
141 :    
142 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
145 :     via new smart
146 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
147 :     utility functions.
148 :    
149 :    
150 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
151 :    
152 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
153 :     matrices when appropriate; band() even symmetric ones.
154 :     (replCmat): extend to potentially all "CsparseMatrix"
155 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
156 :     allow subassignment for special sparse matrices.
157 :    
158 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
159 :    
160 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
161 :     argument; in glmer_*(): print only if(verbose).
162 :    
163 :     speed-optimize a few places by moving REAL(.) out of loops.
164 :    
165 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
166 :    
167 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
168 :    
169 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
170 :     since that wrongly triggers also for M[ logi , ]
171 :    
172 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
173 :     a symmetric matrix that results in a non-symmetric one.
174 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
175 :    
176 :     * R/dMatrix.R: make round(M) work as round(M, 0)
177 :    
178 :     * R/dgTMatrix.R (image): coordinate system and axis now use
179 :     1-based indices, not 0-based ones.
180 :    
181 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
182 :     * tests/indexing.R: test it.
183 :    
184 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
185 :     * man/isSymmetric-methods.Rd: and document it.
186 :    
187 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
188 :     * man/SparseM-conv.Rd: docu them
189 :    
190 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
191 :     for 'SparseM' conversions
192 :    
193 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
194 :    
195 :     * R/Matrix.R (head): added head() and tail() methods.
196 :    
197 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
200 :    
201 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
202 :    
203 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
204 :     add check for correct printing of symmetric sparse matrices.
205 :    
206 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
207 :     for sparse symmetric matrices.
208 :    
209 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
210 :     diagonal twice.
211 :    
212 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
213 :    
214 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
215 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
216 : bates 1316
217 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
218 :    
219 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
220 :    
221 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
222 :    
223 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
224 :    
225 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
226 :     * R/lgCMatrix.R (diag): for new method
227 :    
228 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
229 :     ==> construction of illegal "*gTMatrix" via new() should
230 :     now be much less easy:
231 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
232 :    
233 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
234 :     directly.
235 :     * man/Matrix.Rd: documents it.
236 :    
237 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
238 :    
239 :     * src/pedigree.c (pedigree_inbreeding): Correction in
240 :     initialization. This function is not currently being used and is
241 :     not fully tested.
242 :    
243 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
244 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
245 :     objects. Modified validity check on pedigree objects to account
246 :     for nonparallel patterns of missingness of parents.
247 : bates 1311
248 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
249 :     class.
250 : maechler 1315
251 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
252 :    
253 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
254 :    
255 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
256 :    
257 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
258 :    
259 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
260 :     the output from mcmcsamp.
261 :    
262 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
263 :    
264 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
265 :     of the hat matrix.
266 : bates 1298
267 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
268 :    
269 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
270 :     classes.
271 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
272 : maechler 1295
273 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
274 :    
275 :     * R/dgTMatrix.R (colSums): etc. All four of
276 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
277 :     all "Matrices".
278 :    
279 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
280 :    
281 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
282 :     background grid to the qqmath plot of ranef.lmer.
283 :    
284 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
285 : bates 1284
286 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
287 :     grouping factors to be specified in the formula as (1|foo/bar).
288 :    
289 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
290 :    
291 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
292 :     !is.language to resolve the bug reported by Jacob Wegelin.
293 :    
294 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
295 :     code to evaluate inbreeding coefficients without calculating T,
296 :     based on code in Sargolzaei and Iwaisaki's paper.
297 :    
298 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
299 :    
300 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
301 :     generic and mer methods for isNested and denomDF. This denomDF was
302 :     an attempt to emulate that in lme but I don't think that makes
303 :     sense. Use the trace of the hat matrix instead.
304 :    
305 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
308 :     the C code depending on a slot structure that's no longer valid.
309 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
310 : maechler 1271
311 :    
312 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
313 :    
314 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
315 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
316 :     and added a general band extractor.
317 :    
318 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
319 :    
320 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
321 :     allowable range with NAs. Added a corresponding check in the
322 :     validity check for the pedigree class.
323 :    
324 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
325 :     crossprod methods now inherits from symmetricMatrix.
326 :    
327 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
328 :    
329 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
330 :     generics lowerTriMatrix and upperTriMatrix along with methods for
331 :     the Csparse virtual class. Also added a C function Csparse_band
332 :     that implements these methods by calling cholmod_band.
333 :    
334 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
335 :    
336 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
337 :     erased when it was NULL. This led to invalid subselections!
338 :    
339 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
340 :    
341 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
342 :     in method for "t" so as not to lose the unit diagonal property.
343 :    
344 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
345 :    
346 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
347 :     and methods. This is now an option to the ranef method for the
348 :     mer class.
349 :    
350 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
351 :     compressed column-oriented matrix. Minor formatting cleanup.
352 :    
353 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
354 :     objects.
355 :    
356 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
359 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
360 :    
361 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
362 :    
363 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
364 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
365 :    
366 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
367 :     for the dtCMatrix class.
368 : maechler 1253
369 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
370 :    
371 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
372 :     and methods for it.
373 :    
374 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
375 :    
376 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
377 :     arguments, such that M %*% 1:6 now works
378 :     * Tests/matprod.R: test the above
379 :    
380 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
381 : bates 1243
382 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
383 :     the ranef.lmer class.
384 :    
385 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
386 :     methods to extract the posterior variances from the bVar slot.
387 :    
388 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
389 :    
390 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
391 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
392 :    
393 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
394 :     * tests/simple: (extended)
395 :    
396 :     * R/sparseMatrix.R (isTriangular): now using much improved
397 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
398 :    
399 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
400 :    
401 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
402 :     (problem report from Franklin Parlamis). This should be done
403 : maechler 1238 generally.
404 : bates 1236
405 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
406 :    
407 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
408 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
409 :     update the plot methods.
410 :    
411 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
412 :    
413 :     * R/lmer.R (resid and ranef methods): Added methods for the
414 :     "residuals" and "resid" generic but only for linear mixed model
415 :     fits. Changed the ranef method to return a list of data frames so
416 :     that the plot methods now work.
417 :    
418 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
419 :    
420 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
421 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
422 :    
423 :     * DESCRIPTION (Date): New release
424 :    
425 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
426 :    
427 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
428 :    
429 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
430 :     * man/KNex.Rd: and other help files
431 :     * tests/*.R: several ones needed adaption
432 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
433 : maechler 1228
434 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
435 :    
436 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
437 :    
438 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
439 :    
440 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
441 :    
442 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
443 :    
444 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
445 :    
446 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
447 :    
448 :     * R/dMatrix.R: enable things like M [ M < 10 ]
449 :     * R/dgeMatrix.R: implement it
450 :    
451 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
454 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
455 :     * R/lmer.R (show): now works with summary()
456 :    
457 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
460 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
461 :     support the above
462 :    
463 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
464 :    
465 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
466 :     Use glmFit$prior.weights for weights in a glmm.
467 :     Allow an option usePQL = FALSE to skip the PQL steps for the
468 :     Laplace method (and, in time, the AGQ method).
469 :    
470 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
471 :     into a separate function internal_mer_Xfactor to be able to call
472 :     it from internal_bhat.
473 :    
474 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
477 :     testing; now again of all actual classes.
478 :    
479 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
480 :     use macros and define make_d_matrix_* and make_i_matrix_*
481 :     where _i_ is for the ldense routines:
482 :    
483 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
484 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
485 :    
486 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
487 :    
488 :    
489 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
490 :    
491 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
492 :     many different kinds of matrices.
493 :     * R/*.R: quite a few new methods were needed for R CMD check with
494 :     new Matrix(). Very good for users playing around.
495 :    
496 :    
497 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
498 :    
499 :     * src/dgeMatrix.c (dMatrix_validate): new
500 :     * src/Mutils.c (dense_nonpacked_validate): new
501 :    
502 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
503 :    
504 :    
505 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
506 :    
507 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
508 :    
509 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
510 : bates 1119
511 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
512 :    
513 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
514 :     segfault in cases with multiple non-nested grouping factors.
515 :    
516 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
517 :    
518 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
519 :     (Depends): also on 'utils'
520 :    
521 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
522 :     * R/diagMatrix.R (Diagonal): constructor and methods for
523 :     diagonal matrices
524 :    
525 :     * R/ltTMatrix.R: new "minimal methods"
526 :    
527 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
530 :     all methods (and help files).
531 :    
532 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
533 :    
534 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
535 :     for case (dimn. op no_dimn.)
536 :    
537 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
538 :    
539 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
540 : maechler 1084
541 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
542 :    
543 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
544 :     by Julian Faraway.
545 :    
546 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
547 :    
548 :     * R/Auxiliaries.R (try_as): new utility
549 :     * R/sparseMatrix.R: use try_as() in coercion to original class
550 :    
551 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
552 :    
553 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
554 :    
555 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
556 :    
557 :     * R/Auxiliaries.R (dimNamesCheck): added
558 :    
559 :     * R/Matrix.R (as.array), (as.vector): new
560 :    
561 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
562 :    
563 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
564 : maechler 956 default.
565 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
566 :     "pMatrix" now contains "sparseMatrix"
567 : maechler 954
568 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
569 :    
570 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
571 :    
572 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
573 :    
574 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
575 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
576 :    
577 :     * R/dspMatrix.R: typo in "t" method
578 :    
579 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
580 :    
581 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
582 :     * R/Tsparse.R: instead of R/gTMatrix.R
583 :     * R/Csparse.R: new
584 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
585 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
586 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
587 :     via cholmod
588 :    
589 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
590 :    
591 :     * R/Auxiliaries.R (non0ind): new function using new C code
592 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
593 :    
594 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
595 :    
596 :     * src/chm_common.h: header file required by all C sources that
597 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
598 : bates 917 called 'c' whose address is passed as the last argument to
599 :     (virtually) every CHOLMOD function.
600 :    
601 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
602 :    
603 :     * src/init.c: initialize and finalize the cholmod_common structure.
604 :    
605 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
606 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
607 :    
608 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
609 :    
610 :     * inst/test-tools.R: new file collecting the utility functions used
611 :     in ./tests/*.R
612 :    
613 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
614 :     * R/Matrix.R (cbind2): methods for NULL and missing
615 :    
616 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
617 :    
618 :     * R/AllClass.R: new "index" class for "[" and "[<-":
619 :     First cut at "symmetricMatrix" and "triangularMatrix"
620 :     * R/gTMatrix.R (.ind.prep): new function;
621 : maechler 1174 Logical and character indexing now work too.
622 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
623 :     * tests/indexing.R: new, including *.Rout.save
624 :     * tests/dgTMatrix.R: new
625 :    
626 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
627 :    
628 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
629 :     indicator pos not being updated. Also enforced upper triangular
630 :     for symmetric case. Need to coerce edges component of elements of
631 :     edge list - grr! (Why don't they define their classes cleanly?)
632 :    
633 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
634 :    
635 :     * R/Matrix.R: added first "[<-" methods; not yet functional
636 : bates 1352 * R/denseMatrix.R: ditto
637 : maechler 871 * man/Subassign-methods.Rd: new help file for these
638 :    
639 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
640 :    
641 :     * DESCRIPTION (Version): 0.98-6
642 :    
643 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
644 :     matrices.
645 :    
646 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
647 :    
648 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
649 :     as( <logical>, "matrix")
650 :    
651 :     * R/pMatrix.R: coercion to "lgTMatrix"
652 :    
653 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
654 :     * man/gTMatrix-class.Rd:
655 :     * General slight re-organization of where "[" methods are defined.
656 :     more to come.
657 :    
658 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
659 : maechler 868
660 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
661 : maechler 871
662 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
663 :     * .....
664 :    
665 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
666 :    
667 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
668 :     or glmer objects.
669 :    
670 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
671 :    
672 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
673 :    
674 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
675 :    
676 :     * R/HBMM.R: finish re-writing R-only code.
677 :    
678 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
679 :    
680 :     * man/externalFormats.Rd: move documentation for writeHB and
681 :     writeMM here.
682 :    
683 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
684 :     (suggested by Paul Roecker).
685 :    
686 :     * tests/validObj.R (assertError): Comment out test that is failing
687 :     after recent changes in r-devel.
688 :    
689 : maechler 860
690 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
691 :    
692 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
693 :     * man/denseMatrix-class.Rd
694 :     * NAMESPACE: export it, and also export
695 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
696 :    
697 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
698 :    
699 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
700 :    
701 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
702 :     matrix_solve code (which was really, really wrong).
703 :    
704 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
705 : maechler 834
706 :     * DESCRIPTION (Version): 0.98-2
707 :    
708 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
709 :    
710 :     * R/lmer.R (abbrvNms): new
711 :     * R/lmer.R (mcmcsamp): allow transformed parameters
712 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
713 :     for the Harwell-Boeing and the MatrixMarket formats.
714 : maechler 834
715 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
716 :    
717 :     * man/dtrMatrix-class.Rd: add examples
718 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
719 : maechler 834
720 :     * TODO: note the dtpMatrix (docu) bug
721 :    
722 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
723 :     in order to ensure that new as.matrix() is used by old functions,
724 :     e.g., svd(), qr(), eigen(), dist(),..;
725 :     apply(), also matplot() or pairs().
726 :    
727 :    
728 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
729 :    
730 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
731 :     add comments about 'control' / lmerControl() arguments
732 :    
733 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
734 : bates 820
735 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
736 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
737 : bates 820
738 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
739 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
740 :    
741 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
742 :     .Call calls that were producing spurious output.
743 :    
744 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
745 : bates 801
746 :     * R/lmer.R (lmer): stored updated variance component estimates in
747 :     mer object for the generalized model. (Bug reported by Renaud
748 :     Lancelot).
749 :    
750 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
751 : bates 794
752 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
753 :     unidimensional case.
754 :    
755 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
756 : maechler 791
757 :     * DESCRIPTION (Version): 0.96-1
758 :    
759 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
760 : maechler 791
761 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
762 : bates 763
763 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
764 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
765 :    
766 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
767 : bates 763
768 :     * src/Makefile.win: Forgot to update this when Makefile changed.
769 :    
770 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
771 : bates 726
772 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
773 :     bug reported by Kurt Hornik and Michael Hahsler.
774 :    
775 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
776 : bates 725
777 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
778 :     logical sparse matrices. These will also be used in the symbolic
779 :     analysis for lmer objects.
780 :    
781 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
782 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
783 : maechler 791
784 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
785 : bates 714
786 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
787 :     colMeans, colSums, rowMeans and rowSums.
788 :    
789 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
790 : bates 692
791 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
792 :     multiplication operation.
793 :    
794 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
795 :     to dgetrs.
796 :    
797 :     * src/init.c: Fix cut-and-paste error in definition of
798 :     dgeMatrix_matrix_solve
799 :    
800 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
801 :    
802 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
803 : bates 692
804 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
805 :    
806 :     * DESCRIPTION: Eliminate import of stats.
807 :    
808 : maechler 791
809 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
810 : bates 692
811 :     * R/AllClass.R : add logical sparse matrix classes
812 :    
813 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
814 :    
815 :     * R/dgTMatrix.R: add "[" method for triplet matrices
816 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
817 :    
818 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
819 : maechler 687
820 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
821 :    
822 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
823 :     * R/sparseMatrix.R: %*%, crossprod()
824 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
825 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
826 :     * src/lmer.c (lmer_fitted): fix thinko
827 :    
828 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
829 :    
830 :     * R/AllClass.R: add two virtual sparse classes ``on top''
831 :    
832 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
833 :    
834 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
835 :     correspondingly fix examples and tests/ since new()
836 :     doesn't work for virtual classes.
837 :    
838 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
839 :    
840 :     * R/Matrix.R (as.matrix): method and one for unname()
841 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
842 :     also run for R 2.1.0; using as.matrix()
843 :    
844 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
845 : maechler 658
846 :     * R/pMatrix.R: "pMatrix" class added
847 :     * ....
848 :    
849 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
850 : bates 645
851 :     * R/dtpMatrix.R: Add unpack method and an example.
852 :    
853 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
854 :     of general symmetric matrices and associated S4 methods.
855 :    
856 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
857 :     +
858 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
859 :    
860 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
861 :     crossprod() and "%*%" methods added; tests, too.
862 :     * tests/matprod.R: new, for testing these
863 :    
864 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
865 : bates 599
866 :     * src/lmer.c (lmer_fitted): Added.
867 :    
868 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
869 : bates 596
870 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
871 :    
872 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
873 : bates 582
874 :     * src/*.c,po/,inst/po: Internationalization and localization of
875 :     the package.
876 :    
877 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
878 :     R_ldl.c file.
879 :    
880 :     * src/flame.[ch]: Removed these source files.
881 : maechler 658
882 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
883 :    
884 :     * src/LU.[ch],src/init.c: absorb in factorizations
885 :    
886 :     * src/Mutils.h: prepare for internationalization
887 :    
888 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
889 :     this file
890 :    
891 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
892 :    
893 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
894 :    
895 :     * R/dtrMatrix.R: fix t() method
896 :    
897 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
898 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
899 : maechler 578 * tests/group-methods.R : and test them.
900 :    
901 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
902 :     border case
903 :    
904 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
905 :    
906 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
907 : maechler 578
908 :     * src/dgBCMatrix.c:
909 :     * src/lmer.c: many changes
910 :     * ...
911 :    
912 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
913 :    
914 :     * R/Matrix.R: add more sophisticated show() method.
915 :    
916 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
917 :    
918 :     * */* : almost complete reorganization of classes.
919 :    
920 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
921 : bates 460
922 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
923 :     for the geMatrix class.
924 :    
925 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
926 : bates 460
927 :     * src/Makefile (clean): Remove *.a and *.so
928 :    
929 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
930 :    
931 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
932 : bates 460
933 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
934 : bates 460 had an effect in cases with more than 2 grouping factors.
935 :    
936 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
937 : bates 415
938 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
939 :    
940 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
941 : bates 410
942 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
943 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
944 :    
945 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
946 : bates 392
947 :     * R/sscMatrix.R: Add determinant methods
948 :    
949 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
950 :     for tripletMatrix to matrix.
951 :    
952 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
953 : bates 388
954 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
955 :     no longer used.
956 :    
957 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
958 :     with dynamic allocation of scratch arrays.
959 :    
960 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
961 :     for multivariate random effects with multiple grouping factors.
962 :     Fixes part but not all of #15.
963 :    
964 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
965 : bates 375
966 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
967 :     scalar grouping factors corrected.
968 :    
969 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
970 : bates 375
971 :     * src/bCrosstab.c: remove diag_update which is no longer used
972 :    
973 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
974 : bates 350
975 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
976 :     .h file can be included.
977 :    
978 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
979 : bates 342
980 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
981 : bates 342 Complete allocation of slots in NEW_OBJECT.
982 :    
983 :     * src/Mutils.h: Moved list of symbols to an include file
984 :    
985 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
986 : bates 342
987 :     * src/geMutils.c (Matrix_init): remove unused function
988 :    
989 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
990 : bates 342
991 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
992 :    
993 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
994 : bates 327
995 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
996 :    
997 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
998 : bates 303
999 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1000 :    
1001 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1002 : bates 296
1003 :     * src/init.c: Created R_init_Matrix and added registration of C
1004 :     routines.
1005 :    
1006 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1007 : bates 283
1008 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1009 :    
1010 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1011 : bates 229
1012 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1013 :    
1014 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1015 :    
1016 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1017 :    
1018 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1019 :    
1020 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1021 :     ssclme_update_mm
1022 :    
1023 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1024 :    
1025 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1026 :     in the order of unconstrained and constrained parameters.
1027 :     (ssclme_gradient): Added the gradients (not yet correct for
1028 :     multidimensional, unconstrained case).
1029 :    
1030 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1031 :    
1032 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1033 :    
1034 :     * src/Makefile.win: Remove unneeded ranlib call
1035 :    
1036 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1037 :    
1038 :     * DESCRIPTION (Version): New release
1039 :    
1040 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1041 :    
1042 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1043 :    
1044 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1045 : maechler 658 function, not the version from umfpack. There were problems with
1046 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1047 :     only one umfpack routine being used so I moved it here.
1048 :    
1049 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1050 :    
1051 :     * src/ssclme.c (ssclme_variances): New function.
1052 :    
1053 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1054 :    
1055 :     * src/ssclme.c (ssclme_fitted): Added function.
1056 :    
1057 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1058 :    
1059 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1060 :     store the dimnames in the XtX and bVar slots
1061 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1062 :     components and the returned value from ssclme_ranef.
1063 :    
1064 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1065 :    
1066 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1067 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1068 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1069 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1070 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1071 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1072 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1073 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1074 :     Moved the pdMat classes from the lme4 package.
1075 :    
1076 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1077 :    
1078 :     * man/ssclme-class.Rd: Update definition and documentation of the
1079 :     ssclme class to include the DIsqrt slot.
1080 :    
1081 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1082 :     (much faster using dsyrk, a level 3 BLAS routine).
1083 :    
1084 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1085 :    
1086 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1087 :    
1088 :     * tests/ssclme.R: Modify the test to account for the permutation
1089 :     of the levels of the grouping factors.
1090 :    
1091 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1092 :    
1093 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1094 :     directly into the ssclme class definition.
1095 :    
1096 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1097 :    
1098 :     * DESCRIPTION (Date): New release
1099 :    
1100 :     * man/ssclme-class.Rd: new file.
1101 :    
1102 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1103 :     works and it's fast!
1104 :    
1105 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1106 :    
1107 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1108 :    
1109 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1110 :    
1111 :     * DESCRIPTION (Date): New release
1112 :    
1113 :     * NAMESPACE: Don't export ssclme.
1114 :    
1115 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1116 :     school data.
1117 :    
1118 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1119 :    
1120 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1121 :     keep track of the fixed-effects and the response. Counts also
1122 :     gets an extra element, which is always one.
1123 :    
1124 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1125 :    
1126 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1127 :    
1128 :     * src/cscMatrix.c (csc_transpose): new function
1129 :    
1130 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1131 :     (csc_components_transpose): new function
1132 :    
1133 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1134 :    
1135 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1136 :     triplets
1137 :    
1138 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1139 :    
1140 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1141 :    
1142 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1143 :     and all other .h files in src.
1144 :    
1145 :     * src/Makefile.win: This and other Makefile.win files contributed
1146 :     by Brian Ripley.
1147 :    
1148 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1149 :    
1150 :     * R/syMatrix.R: Added methods for "%*%".
1151 :    
1152 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1153 :     poMatrix object.
1154 :    
1155 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1156 :    
1157 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1158 :    
1159 :     2004-01-25 Douglas Bates <bates@bates2_home>
1160 :    
1161 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1162 :    
1163 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1164 :     of nrow.
1165 :    
1166 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1167 :    
1168 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1169 :     subdirectories.
1170 :    
1171 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1172 :    
1173 :     * src/taucs.h: Accidently referred to global header files
1174 :     instead of local files.
1175 :    
1176 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1177 :    
1178 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1179 :     and methods and replaced all classes with S4 classes.
1180 :    
1181 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1182 :    
1183 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1184 :    
1185 :     * src/R_LapackPP.cc: Change method of calculating determinants
1186 :    
1187 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1188 :    
1189 :     * DESCRIPTION (Version): removed empty data directory as requested
1190 :     by CRAN maintainers. Changed version number and date.
1191 :    
1192 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1193 :    
1194 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1195 :     under Windows.
1196 :    
1197 :     * Added configure.win and src/Makevars.win as requested by Brian
1198 :     Ripley.
1199 :    
1200 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1201 :    
1202 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1203 :     Hornik.
1204 :    
1205 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1206 :    
1207 :     * configure.ac: Replaced configure.in with configure.ac
1208 :     contributed by Kurt Hornik.
1209 :    
1210 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1211 :     version for R-1.5.0
1212 :    
1213 : maechler 512
1214 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1215 :    
1216 :     * man/eigen.Rd: Removed the .Alias in the example

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